diff options
752 files changed, 10230 insertions, 18551 deletions
diff --git a/app-doc/gromacs-manual/ChangeLog b/app-doc/gromacs-manual/ChangeLog index db0912d58..b9f148f17 100644 --- a/app-doc/gromacs-manual/ChangeLog +++ b/app-doc/gromacs-manual/ChangeLog @@ -1,7 +1,17 @@ # ChangeLog for app-doc/gromacs-manual -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-manual-9999.ebuild: + Merged + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-manual-9999.ebuild: + Merged + + 25 Jun 2011; Christoph Junghans <ottxor@gentoo.org> + gromacs-manual-9999.ebuild: + migrate to git-2 + *gromacs-manual-9999 (26 Aug 2010) 26 Aug 2010; Christoph Junghans <kleiner_otti@gmx.de> diff --git a/app-doc/gromacs-manual/Manifest b/app-doc/gromacs-manual/Manifest index b36644647..768d401b7 100644 --- a/app-doc/gromacs-manual/Manifest +++ b/app-doc/gromacs-manual/Manifest @@ -1,17 +1,13 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 -EBUILD gromacs-manual-9999.ebuild 1164 RMD160 bf367bed939f5fee109781dee5db6642ddbc27db SHA1 b83ab80c568bc5bb7232bd21fa22e69602015aa5 SHA256 35ed9d0966a4273fdabf0ccb1a01fa0002aefca924a35ea54af795bb9ce9fec0 -MISC ChangeLog 279 RMD160 b790db407a33641064eeac7d30894f3398f31ed2 SHA1 85ff23743c7ea190900db5bd44b585507664c6cf SHA256 f977bc1ead52fce5bdf1c76fdd1dc965051d4e32eb6999ee3ed514550bbed043 -MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 +EBUILD gromacs-manual-9999.ebuild 1169 RMD160 0b3754c292104c1de63026d3a3aa74499f412adb SHA1 6f43ff72060eed4ef41f60df49e754abb912d86d SHA256 6f4b4761334a43297e7afb11510be82f6c4de37338a6ebe648354053c573e59a +MISC ChangeLog 553 RMD160 9e7e760c4f49b2b1d4a68cd9278e7c43dd087948 SHA1 e8b60767a7483e3da163e003ee34a42cdd379e9f SHA256 23aa1d6f8f1179dd732b537645778b21214f8fbcd79fcd8964b42286062e6854 +MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iQEcBAEBAgAGBQJNohTDAAoJEOeBhlrCAAWGTzoH/0EMOOmaVVqXT0mI4hTG6dKk -Tz9Vh7rNsHPChbLF5OlXXNrXkM92HwvAOTl7iTnp1hevLDm/D7bzaEYQ4zJEAAue -YxbD/5Do1JIrZ+WCbcgWSjMH9EX0uWtwi4eebXgkiT2l6U3D7UlwpOnVYhE1MT2c -AeXVFs4igX+1iW/nda/4yLsh3UeyBVy8zKQe04+16JCO9QaUT8c1l6kdkXxGwnch -n+5XW4Tt0OQ7JFy4IDQ41+V4JhoR+G+Ciu/48z/dqc4bOm85EL1cSNVb+DehUd+Y -v9XG0t99BbCQJolC0t7GBSJb2WcTnCgh4oLJiqVejNLTLpz8YrDWixmj5bnwqZI= -=lKq0 +iEYEAREIAAYFAk4GGJsACgkQgAnW8HDreRZkTwCfVhcxHDDiioFE1FlflkacpsNn +fvkAnRWvGIShj784zIcWRkicjZ2mwPmS +=3WPL -----END PGP SIGNATURE----- diff --git a/app-doc/gromacs-manual/gromacs-manual-9999.ebuild b/app-doc/gromacs-manual/gromacs-manual-9999.ebuild index c5a593a8a..c9f988336 100644 --- a/app-doc/gromacs-manual/gromacs-manual-9999.ebuild +++ b/app-doc/gromacs-manual/gromacs-manual-9999.ebuild @@ -2,12 +2,12 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="4" +EAPI=4 EGIT_REPO_URI="git://git.gromacs.org/manual" EGIT_BRANCH="master" -inherit cmake-utils git +inherit cmake-utils git-2 DESCRIPTION="Manual for gromacs" HOMEPAGE="http://www.gromacs.org/" @@ -18,11 +18,11 @@ SLOT="0" KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux" IUSE="" -DEPEND="=sci-chemistry/gromacs-${PV} +DEPEND=" + ~sci-chemistry/gromacs-${PV} dev-texlive/texlive-latex sys-apps/coreutils app-shells/tcsh" - RDEPEND="" src_prepare() { @@ -30,7 +30,8 @@ src_prepare() { progs=$(tr '\n' ' ' <${EROOT}usr/share/gromacs/programs.list) || die sed -i "s/^\(PROGRAMS\).*/\1='${progs}'/" mkman || die sed -i "s@^\(INSTALLED.*=\).*@\1${EROOT}usr/bin/g_options@" mkoptions || die - sed -e "s!\${GMXSRC}/admin/\(programs.txt\)!${EROOT}usr/share/gromacs/\1!" \ + sed \ + -e "s!\${GMXSRC}/admin/\(programs.txt\)!${EROOT}usr/share/gromacs/\1!" \ -e "s!\${GMXSRC}/share/html!${EROOT}usr/share/doc/gromacs-${PV}/html!" \ -e "s!\${GMXBIN}!${EROOT}usr/bin!" \ -e '/FATAL_ERROR.*GMX\(SRC\|BIN\)/s/^/#/' \ diff --git a/app-doc/gromacs-manual/metadata.xml b/app-doc/gromacs-manual/metadata.xml index 9ac9ffdb3..e42d0af60 100644 --- a/app-doc/gromacs-manual/metadata.xml +++ b/app-doc/gromacs-manual/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-chemistry</herd> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/app-portage/g-cran/ChangeLog b/app-portage/g-cran/ChangeLog index c89825fb3..f3e33ea1d 100644 --- a/app-portage/g-cran/ChangeLog +++ b/app-portage/g-cran/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for app-portage/g-cran -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> g-cran-9999.ebuild, + metadata.xml: + migrate from 'git' to 'git-2' + 15 Jul 2010; <auke@gentoo.org> g-cran-9999.ebuild: Keyword g-cran-9999 to ~x86 and ~amd64 diff --git a/app-portage/g-cran/Manifest b/app-portage/g-cran/Manifest index 2211405e1..fa8ecfb3a 100644 --- a/app-portage/g-cran/Manifest +++ b/app-portage/g-cran/Manifest @@ -1,3 +1,13 @@ -EBUILD g-cran-9999.ebuild 564 RMD160 f6c1ac3f4887bda5ff5fd38cacdcb01d019229a2 SHA1 6b80bf1c2763d0fda4a34d12111f879328ffe123 SHA256 988d569620ea51cee50010d59b46315e7e954ccb8ef03d5f832f325d4cfda4cc -MISC ChangeLog 514 RMD160 597a213848bb9047118233051b757a3d54b3f56f SHA1 033598ca1f0dbcd6ab0ea362055fa8a2fadd70ef SHA256 f6780a08f7e346b384348a75ec7b234cb743c9ad77ecf478a23c733782c97875 -MISC metadata.xml 356 RMD160 9c435d833896f82b17f06b65017865182401d0b0 SHA1 5681e4a19a82e7a48a465db1977b4735dddf799d SHA256 eec0c880a0450c381ca309a460da3cb7ed51b1887e06fb03e4f0bd73f9212f9d +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +EBUILD g-cran-9999.ebuild 566 RMD160 858168a0046ae0677e949d84bd2e63e775d31f5b SHA1 3c14d8239cb3edd53eca2511c11abb310f08fa58 SHA256 a26ab20d3e0090cd420d69ed3eb214804ad09f841bd63a48e23d138810b10ca3 +MISC ChangeLog 630 RMD160 3d05b6b8a31c955484313002aed5083999568e23 SHA1 e6fc33b2b498e26fbdde99108f31e992f59c7663 SHA256 e008568b75ce4b30ddd846eaf3985d0fb7c86c6ac5ea521c43991ec780dfc76b +MISC metadata.xml 358 RMD160 9c986cc6131f90cb348544c1cd32e867cc4d8247 SHA1 3be0736a7e1a470bf4970f691e7b9a8480f431dc SHA256 ec78fefe41faacca551b0f47a88f6639e66a8737921e39a2b28943536d51403e +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F6JcACgkQgAnW8HDreRYjYgCgnDvhovvm62hA4VcoQrF2jKjc +1FUAn3lJpN2qjKlgB+SkfK/lfkpdMDK4 +=wi4I +-----END PGP SIGNATURE----- diff --git a/app-portage/g-cran/g-cran-9999.ebuild b/app-portage/g-cran/g-cran-9999.ebuild index ca2395aa2..6635f0f57 100644 --- a/app-portage/g-cran/g-cran-9999.ebuild +++ b/app-portage/g-cran/g-cran-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -8,7 +8,7 @@ PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" RESTRICT_PYTHON_ABIS="3.*" -inherit distutils git +inherit distutils git-2 DESCRIPTION="CRAN-style packages installer helper for package managers" HOMEPAGE="http://git.overlays.gentoo.org/gitweb/?p=proj/g-cran.git;a=summary" diff --git a/app-portage/g-cran/metadata.xml b/app-portage/g-cran/metadata.xml index e79a1a6d3..4dd000045 100644 --- a/app-portage/g-cran/metadata.xml +++ b/app-portage/g-cran/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> G-CRAN helps package managers install R packages. It reads CRAN-style repositories and translates it into something most package managers can work with. diff --git a/app-text/dgs/ChangeLog b/app-text/dgs/ChangeLog index 45623d1fd..8c121ba2f 100644 --- a/app-text/dgs/ChangeLog +++ b/app-text/dgs/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for app-text/dgs -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/app-text/dgs/ChangeLog,v 1.30 2008/03/18 13:24:47 flameeyes Exp $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> dgs-0.5.10-r2.ebuild: + Sort inherit and/or USE + 23 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> dgs-0.5.10-r2.ebuild: Added note: upstream is dead diff --git a/app-text/dgs/Manifest b/app-text/dgs/Manifest index fb3ba9e04..e53116436 100644 --- a/app-text/dgs/Manifest +++ b/app-text/dgs/Manifest @@ -7,23 +7,13 @@ AUX dgs-0.5.10-gs-time_.h-gentoo.diff 415 RMD160 42b4b923d1ddc5bc301d7df0a5c75e0 AUX dgs-0.5.10-tcpd-gentoo.diff 939 RMD160 739b5d1954b5f95c8c38d0be3acf0f24a0d4bbd7 SHA1 4e528983004d09da387b17e607630b18d2868977 SHA256 82ef1fff0d799f398965047ff5556af7cac651317ede40e493fbd382aaf65185 AUX dgs-fix-as-needed.patch 519 RMD160 6b4d0d2b567b823580317ba582a8a5c7c6438401 SHA1 bdd91fe03f48a5840ea5d0794c6c37cf187b1665 SHA256 db0a15aa1a92e9b8f53072a480f42d7b6a366b73977314344f3f6246eb4b3516 DIST dgs-0.5.10.tar.gz 3572504 RMD160 4538e098ad4fab1ff4e1f483838fd3dd9515cd5c SHA1 94c35dbbf596dd35d47205cdde628457d95df084 SHA256 b01f21609241414fe92d8838e63150bfd7359d74ce05dfa38d2798e9d0f8a0ff -EBUILD dgs-0.5.10-r2.ebuild 1453 RMD160 5b8effc51723e933392775b5e3465e8dd6af6a90 SHA1 68b71604d724402dc8ba04ed5f4732cbca105d98 SHA256 91eaeaf246a06f909f8305d5019973c1c5dfcfc88f9229d9614a22644f8667f5 -MISC ChangeLog 2682 RMD160 b178b0caa53e11e24399b2540203063d84a0d1d6 SHA1 dd53592ccbc96a4e0a14dd37b90ee5c6d1a1132f SHA256 7836f41289bcff914905f8052fe7543456cf1ad99bb92583fb55d3faac94a9d1 +EBUILD dgs-0.5.10-r2.ebuild 1453 RMD160 7ebbdd9654c4d3b13be8a9be50aa8314fa3d3eca SHA1 db8a39efea46cb064a7e524af326a50c68a028d3 SHA256 b1f59fc2111bff17a1adeac0ec4a21fd078bb460aea7f0cc97c313683c871c87 +MISC ChangeLog 2778 RMD160 e69f3feb70adaae0c28a101f188a88f3b7cf1f16 SHA1 e27ffb6b00d65396d33f6688e6edc1500b7cc284 SHA256 4d3e1d48206ca57ee2082262bdb8f9f83f061e3fdd3d4566274665bdf856704a MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMIkzPAAoJENwGBM22xffegq8P/Rcb/2DCXVztfrTC+4tr+ULC -K4/jqg5NaCB1FrE3RIxdq4u004PKmCpc7o2FeyMC95io7CCLVaFn6Ci91oKwt4w7 -wLJgp9LrF30G3L1UdcEcYV0OUbeOxAn9Ld1HFWd15ZecxvjJWHVRao/ctmN+0L4K -SHheT18erNJ9SmICFQS4ZD+MLg/rosoMbwrZN6uYxOsjNJR1OJL9eLYwlKmAJvhd -GRcNq+F+mlg1xCiUPDla5HOwXdYvzdLCkpcA3ZUJSwFexdIkVFAFuUhF8lvaWgQa -mRLa3NB1X8uzrGJvrmjaoz4OiHofLc+rIMnMcGAFp+x6abzXDVpBx19W7UdbrIHn -Irc/G5pSyzKuYM1AhAAn/PcjL3eJKDMHslli4+VRUwFtvXjuFDn5fuyaEQZcB+SR -MmEMwUBBK3kzbOpi9YZOVhgB7p+0vStMJ8/sVpGh1N22Bm2d2Co0W1VAIThJasNl -8Q6miL2gh/DkRCvc9hsTF3e5YS89hEThCR7PLJxgHG01ixO1adezdU/RF2PCEGnb -LS56JuClJsijLeUYoYCWv5DzQ0ISZBQMyMbJp8njzlpA0FAoXWCj9HQztqp7sPoR -CDzo6+hs3Fe/mFcBWKzlewhiYvvdFgh+/P1VPZ98NaXtMR5UIYXSVj53bz0XU7C9 -yRw0507EKXxaz/EmBtkQ -=znet +iEYEARECAAYFAk4Efc8ACgkQgAnW8HDreRZPawCglxcy//i7QLxv/QszT1yOutj+ +fBoAn2RfVeLVkuJA4ivkVTv7OnsKWAD/ +=PmKw -----END PGP SIGNATURE----- diff --git a/app-text/dgs/dgs-0.5.10-r2.ebuild b/app-text/dgs/dgs-0.5.10-r2.ebuild index c9d923e88..f079fc4d9 100644 --- a/app-text/dgs/dgs-0.5.10-r2.ebuild +++ b/app-text/dgs/dgs-0.5.10-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/app-text/dgs/dgs-0.5.10-r1.ebuild,v 1.38 2008/03/18 13:24:47 flameeyes Exp $ @@ -8,7 +8,7 @@ EAPI=2 WANT_AUTOCONF="2.1" -inherit eutils autotools +inherit autotools eutils DESCRIPTION="A Ghostscript based Display Postscript (DPS) server" HOMEPAGE="http://www.gnustep.org/developers/DGS.html" diff --git a/app-vim/freefem++-syntax/ChangeLog b/app-vim/freefem++-syntax/ChangeLog index 5e30ba21f..03150fbc0 100644 --- a/app-vim/freefem++-syntax/ChangeLog +++ b/app-vim/freefem++-syntax/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for app-vim/freefem++-syntax -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + 23 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> freefem++-syntax-20081108-r1.ebuild: QA fixes diff --git a/app-vim/freefem++-syntax/Manifest b/app-vim/freefem++-syntax/Manifest index 1ac39e8a4..c6c44cbaa 100644 --- a/app-vim/freefem++-syntax/Manifest +++ b/app-vim/freefem++-syntax/Manifest @@ -3,22 +3,12 @@ Hash: SHA1 DIST freefem++-syntax-20081108.tar.gz 1108 RMD160 02c947dae0495de4b2ad1a49d7bdee8d2f4f21c0 SHA1 d0c718a41623d5b5897e97deed2acb5fa35b06a9 SHA256 1bad9e9150ca754695669dbc892c14a678062353a59ce648cc9a35650f014eff EBUILD freefem++-syntax-20081108-r1.ebuild 547 RMD160 43f1d75e2801de6d6557a4e25961f642a26e1dab SHA1 d1b68487f6dcd01abdb57dd4c7604d65d6e6656f SHA256 b7fde0b1f507bb1a0d1c50561b285a10ea5bcecdb5b8499a34909833f9912a16 -MISC ChangeLog 839 RMD160 85bd12f154d267569cb91851cbe7834964637977 SHA1 20cca2574d273723d8231a300f719c20d47c15b2 SHA256 f89747e9ccca306524982f07cd5cf4849cae9453cafdf19df5c02546c9662fd9 -MISC metadata.xml 294 RMD160 f0861f754064bfe5d6c1cb33cda3ec243bfa9770 SHA1 8d1e56c9fd1873f3800a816c320746bdc40d93d4 SHA256 9ae00119576875f3047da60f0502a37671d41a155bd152a204949836db51ef27 +MISC ChangeLog 936 RMD160 90b993746fbce21b6464f54c782a4cb338ce268a SHA1 da53232d619e77cfdf0edc342bfd2562bdf3f82a SHA256 c7d0eab694e73909717a425fe7a98649ab23de2b0221f914953b2b50a16252ca +MISC metadata.xml 298 RMD160 82724d2d1b72298c83a8f71bdba84914a90d378c SHA1 963ef7a56a9e3d304d4e617ce3b3d42095c0e677 SHA256 4218c0e1fc03bd83faa7347bb81d9c0501d0872376a457c80e1216b2a37ba7e7 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMIk13AAoJENwGBM22xffeIoEQAJ000WfJgStb+Q7GJEobHnDs -cNZu7tGR4ebd3vBYEv8oD5IQFUjoH59qgirkBwt7jjePjf4lCm6mNjUl1lt1lJJX -GvW83bhFzC+qltvPm7J/CQ19QKG3XPUG0Gv1MAQYlYs1PSRExcKFebWaU5h65+aj -Jzv1hv92NJ7pkf6vDRJ0eXM9mKaqrQBIXAlp75kQrBjEcIKEPY0vY+3evy/arh5x -hfUXK1bB+/ihaAe7pBSBH4Xb4w813ahBkWd8VbYtc/oRNTVZAKTl7Zm7r+vXQQz7 -432ZfKm/1NON+odg/4Z3fQ6zo103ts1u5MWNt28XB0neg/tGgW8D+6770cb8nLgO -uw64EPoWa0xcYKfI1lsFKTHkiK6czkSVXTgqjyRW0d9GA5ckfVJHjqJdfw1l8fbT -BVSYpk+IbP/8tEpho6Kpvz2hlsM6m5nJt46gZnqu49rJPD34P9nQ83TWEiOQ5oT0 -NU+CeTLmsQt2hn3lFZosvMhUXbdA0Ixi1S9CMFeLH98VUs4JRpaN9qtRkXvLpwuI -ZjGNY+bleX2J5L9QYK6w1P+L0JPlk9aeru1fOSbCyLE3YP1T5TD1Jb6gsqdFl6Bi -Y8zR/K/ogxQ1WcFWOUwrMobw5uBrpz87nWbk7HQdOMrlzueNhAI3j3twR0C7BRiM -L+f7WKxOAwVoaQZY4Dht -=MXHX +iEYEARECAAYFAk4FjooACgkQgAnW8HDreRa7eACfUfRDqIJHhbASyn/IDWP4OubM +DbEAn35gHjHaeQc6tga/Jho2YGxNnfJY +=TFBs -----END PGP SIGNATURE----- diff --git a/app-vim/freefem++-syntax/metadata.xml b/app-vim/freefem++-syntax/metadata.xml index af9a10c4e..2dbae84da 100644 --- a/app-vim/freefem++-syntax/metadata.xml +++ b/app-vim/freefem++-syntax/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>app-vim</herd> -<longdescription lang="en"> + <herd>no-herd</herd> + <longdescription lang="en"> VIM syntax plugin which provides syntax highlighting for the freefem++ script files. </longdescription> diff --git a/dev-cpp/growler-link/ChangeLog b/dev-cpp/growler-link/ChangeLog index c719e0bc9..a9c6f4299 100644 --- a/dev-cpp/growler-link/ChangeLog +++ b/dev-cpp/growler-link/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for dev-cpp/growler-link -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> growler-link-0.3.7.ebuild: + Sort inherit and/or USE + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> growler-link-0.3.7.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> growler-link-0.3.7.ebuild: + Added fortran-2.eclass support + 23 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> growler-link-0.3.7.ebuild: QA fixes diff --git a/dev-cpp/growler-link/Manifest b/dev-cpp/growler-link/Manifest index 8084b27e8..ce153229e 100644 --- a/dev-cpp/growler-link/Manifest +++ b/dev-cpp/growler-link/Manifest @@ -3,23 +3,13 @@ Hash: SHA1 AUX 0.3.7-gcc4.patch 746 RMD160 45ddd21f4a258a0d8561a6a23686c39a294613c2 SHA1 c23af38c7d74fca88916e4661791a0e3530cb771 SHA256 bcd19b7855eb0da6eec9e468c6172ff82db419208508e24268d1408d40729c65 DIST growler-link-0.3.7.tar.gz 548768 RMD160 38153300e2ea8375116804ffe3823e0fabd3a831 SHA1 9384b97e7d9010d4a85c8cfbc26f71f312520943 SHA256 eec2e6f91146bc68004114adc7ee00617eab4b459649029cfcdcfc4db3d17719 -EBUILD growler-link-0.3.7.ebuild 818 RMD160 d1c7bcd60e3f9bbafb92b29c439ef5274a432ea3 SHA1 92518ac1d947973bffab2955f134cd86be0def3d SHA256 cd8aa907e52df76adfe836bfeb5ac68576d961efa11c11c31eb647ee1e9695b0 -MISC ChangeLog 601 RMD160 cc3619f6ec31c6fc39805e2a900700587d5f6b96 SHA1 ea9462b2bbdd72fe1d29b36b115d46bad3869688 SHA256 851380c82083d0cd6f3410dfd50ce3f085e282da8cd7fa90eb347376d50f4d8f +EBUILD growler-link-0.3.7.ebuild 751 RMD160 c00d2e8fc74bba7a92b819effb953cc2d13dacff SHA1 bcd67a02123c736682eb6c4efaabb6dbcca41e9a SHA256 c503b16442f83f6779fb3a00f6592aea5a01db84bd5a12a16674e374c428783c +MISC ChangeLog 922 RMD160 5f48e661d05f2d66ab1e147380ae28c034e58081 SHA1 a2eba5c6cc9dbac05ce86451a1d837d48fd56db1 SHA256 2bc63bb17acc61f500123e0e078e8e112119db6b1b314dee869944038aa2de23 MISC metadata.xml 481 RMD160 be4b7a9b4472d0c3861813d9f8f3097a00e9577e SHA1 ea067e55e4948b6015acc9c08e3df412ea2c0b12 SHA256 79b99b68b79b06620061d066e89197fff4f24f8b6c8a559bca2d0b6c20752e24 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMIk6jAAoJENwGBM22xffeZR4P/iBdHm3aecLb7YYZTJqSysMJ -84KvjbP2dlkTI5mTOnrFQWmc8+ftKIg6Vk+k0vSgJ+nNEqFQZeLdNIQFRkLM2xkY -/Oaqk9WWGGOu68PH4o0jGCF+Pr46rAu9CU/DIXE7vOw97arGIw999x/a5wcnvoYf -ZxIbQRQPyE6D/7rTbEtUYgD5LPNAwrN5sqxjzm58BrKcPShkUaipYyCdKd6xwcjF -07p8ZbwKmufmLUmHUstdR6ezTW+OpGhjOgjoSdtaPwAX3O3GZjaZj0w2iibSRRB6 -Ey0eJWEq4s2pK8KddAsBTRHKk1F+NzMyL/ZXl7gGdiQRTUY4HMXy39/DMRTSDe7g -e8PoDSQ41gOJudTr4EIba4JtGnIMHxwTAVT/h6bTmCDpMRwN21gt6FDVVidcCo8S -BdzcJMF9+i2LCI6PT8Mi7+Upjtqc+EfI2O3UhLjZbFssfZG98vWF97cMrSfOl8BR -NB1KN0AaQvGs7mRbxvLZWUPJWsjhmb+QfgWWiCqAN3zG0LA/S34p6oFXSvrh2GMm -+fefF5nPWBHDY7uzFm9r26XBy4CeA6Rmi96bSGl7iMg8zpUMwdi3VqUw/PuNuNfJ -rluuRp/CRtydwS+8zjtU8HLPzhiW27KSr27m3c0k4bBFUHXWse/ah4dLhlSALnK9 -jZHOvzLexceRTtBMRq9b -=Ef4P +iEYEARECAAYFAk4EfjcACgkQgAnW8HDreRbhFQCeOS9DWr29E7PA/laS3gMZ31zr +GS0An3p3Gi4cMQ3Afbk3U5T5hFHKL2xZ +=1Kd2 -----END PGP SIGNATURE----- diff --git a/dev-cpp/growler-link/growler-link-0.3.7.ebuild b/dev-cpp/growler-link/growler-link-0.3.7.ebuild index aba9ccccd..fcca83ffb 100644 --- a/dev-cpp/growler-link/growler-link-0.3.7.ebuild +++ b/dev-cpp/growler-link/growler-link-0.3.7.ebuild @@ -1,25 +1,31 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=4 -inherit eutils +inherit eutils fortran-2 -DESCRIPTION="Growler-Link: the lowest-level Growler library." +DESCRIPTION="The lowest-level Growler library" HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/" SRC_URI="${HOMEPAGE}/downloads/growler-link-${PV}.tar.gz" SLOT="0" LICENSE="NOSA" KEYWORDS="~amd64 ~x86" -IUSE="doc tcpd static fortran" +IUSE="doc fortran static tcpd" -RDEPEND=">=dev-libs/boost-1.33.1 - tcpd? ( sys-apps/tcp-wrappers )" +RDEPEND=" + virtual/fortran + dev-libs/boost + tcpd? ( sys-apps/tcp-wrappers )" DEPEND="${RDEPEND} doc? ( app-doc/doxygen )" +pkg_setup() { + use fortran && fortran-2_pkg_setup +} + src_prepare() { epatch "${FILESDIR}"/${PV}-gcc4.patch } @@ -31,8 +37,3 @@ src_configure() { $(use_enable static) \ $(use_enable fortran) } - -src_install() { - emake DESTDIR="${D}" install || die "install failed" - dodoc README NEWS AUTHORS NOSA ChangeLog || die -} diff --git a/dev-java/jgraphx/ChangeLog b/dev-java/jgraphx/ChangeLog index db63fbc87..6cc153d72 100644 --- a/dev-java/jgraphx/ChangeLog +++ b/dev-java/jgraphx/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for dev-java/jgraphx -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*jgraphx-1.4.1.0 (30 Jun 2011) + + 30 Jun 2011; Guillaume Horel <guillaume.horel@gmail.com> + +jgraphx-1.4.1.0.ebuild: + Version 1.4.1.0 is specifically required by scilab + *jgraphx-1.4.1.2 (06 Oct 2010) 06 Oct 2010; Thomas Kahle <tom111@gmx.de> +jgraphx-1.4.1.2.ebuild: diff --git a/dev-java/jgraphx/jgraphx-1.4.1.0.ebuild b/dev-java/jgraphx/jgraphx-1.4.1.0.ebuild new file mode 100644 index 000000000..5813fb713 --- /dev/null +++ b/dev-java/jgraphx/jgraphx-1.4.1.0.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +JAVA_PKG_IUSE="doc source" +EAPI=2 +inherit java-pkg-2 java-ant-2 versionator + +MY_PV=$(replace_all_version_separators '_') + +DESCRIPTION="Open-source graph component for Java" +SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip\ + -> ${P}.zip" +HOMEPAGE="http://www.jgraph.com" +IUSE="doc examples source" +DEPEND=">=virtual/jdk-1.5 + app-arch/unzip" +RDEPEND=">=virtual/jre-1.5" +LICENSE="as-is" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}/${PN}" + +src_prepare() { + # don't do javadoc always + sed -i \ + -e 's/depends="doc"/depends="compile"/' \ + build.xml || die "sed failed" + rm -rf doc/api lib/jgraphx.jar || die +} + +EANT_BUILD_TARGET="build" +EANT_DOC_TARGET="doc" + +src_install() { + java-pkg_dojar lib/${PN}.jar + + use doc && java-pkg_dojavadoc docs/api + use source && java-pkg_dosrc src/org + use examples && java-pkg_doexamples examples +} diff --git a/dev-lang/aldor/ChangeLog b/dev-lang/aldor/ChangeLog deleted file mode 100644 index 5e3c7005c..000000000 --- a/dev-lang/aldor/ChangeLog +++ /dev/null @@ -1,22 +0,0 @@ -# ChangeLog for sci-mathematics/yorick -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*aldor-1.1.0 (09 Oct 2007) - - 09 Oct 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su> - +aldor-1.1.0.ebuild +files/aldor-1.1.0.patch - -aldor-1.0.3.ebuild -aldor-1.1.0_rc.ebuild: - The first opensource release! - -*aldor-1.1.0_rc (20 Apr 2007) - - 20 Apr 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su> - +aldor-1.1.0_rc.ebuild: - Version bump - -*aldor-1.0.3 (15 Feb 2007) - - 15 Feb 2007; Andrey Grozin <A.G.Grozin@inp.nsk.su> - +metadata.xml, +aldor-1.0.3.ebuild: - Initial import, bug 131590 diff --git a/dev-lang/aldor/Manifest b/dev-lang/aldor/Manifest deleted file mode 100644 index 30b3b1e69..000000000 --- a/dev-lang/aldor/Manifest +++ /dev/null @@ -1,9 +0,0 @@ -AUX aldor-1.1.0.patch 837 RMD160 e43ce6c6e17c43bc2a8223e85dcaed70c3a482fb SHA1 0daa89ff91aac843c95f864636534e9eb29f0014 SHA256 dee4048e8fc96d2a675bbedb17998210c4b1cb95035e0d4beaabd1af8038e7e0 -DIST aldor.el.nw 51482 RMD160 8b785abf23ea5cd1107d1a05b187723f81b04559 SHA1 628ff6f36d720e4a32d72125d3559e4da498f750 SHA256 c6c80e1fd32b36555fe3d90e9cadb48795907514129b6c23406f720db18bd43e -DIST aldorug.pdf.gz 767850 RMD160 7b2f9496b303caee0642ea74e58524699b122f19 SHA1 02e89472a34fe974900a529c644c093c55452793 SHA256 dec98eed7c9065c9233d2eb3e30e5dc98a2128709d541f7b626d086979b80c3a -DIST algebra.html.tar.gz 749742 RMD160 9b0d1d2a7d7cda047a911ee9d2f1a23d21ed6b76 SHA1 8cf0853897947b7f073ff62efda6b14ec8edf7f2 SHA256 b4e38a1d36e4f4661df0314da43aa09846e6c62156ac4243bcb051dcc829e33f -DIST libaldor.pdf.gz 434487 RMD160 c7d7130eca8d820a291786f11288deefbe1a672e SHA1 e231e2171b5906ba0812508d548c759f235625b5 SHA256 57371d1bd6031c350783e063533ba9ba1d82e681dca54fa3b4de42a339c9a668 -DIST tutorial.pdf.gz 164786 RMD160 1ceea46bd6a7b22003ff06842d656b0d57d011bf SHA1 62a4d224a60b6abc1fc8d49ac0f2a41860f001da SHA256 a0339b7c59632c8825e26603330b5a4010aeeb843ddad06c6b54d029519c7e65 -EBUILD aldor-1.1.0.ebuild 2172 RMD160 739e225b613bb15c37fb8563a8be1f3f5c38024a SHA1 abca520ba78b3c3598a570699f362eee28cc864a SHA256 dc91e28b137a6fef5c52d62f17f48562d909f679f6580e5f84b4f64467876277 -MISC ChangeLog 604 RMD160 0e82b957c36f50bc4f1ea826dc11b9507f9e3fc3 SHA1 3f1237a0ad448efa3d3324eaa19f1f1567732074 SHA256 c1874a2da1126c705e8a31098c6c7c12bec8c2f101bd35a353fafe770bc3db15 -MISC metadata.xml 811 RMD160 f7b329f9abd26f80f54235f2ad214bd4d8fd6d92 SHA1 e95d400caa56b900562d16d943ab8da837c281ed SHA256 005c18ae92ac4022daa3da7381a2eb712c28b6444f853c1a889cbc4750d8f9ef diff --git a/dev-lang/aldor/aldor-1.1.0.ebuild b/dev-lang/aldor/aldor-1.1.0.ebuild deleted file mode 100644 index ecadbc975..000000000 --- a/dev-lang/aldor/aldor-1.1.0.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# Copyright 1999-2008 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ -inherit subversion elisp-common - -DESCRIPTION="Aldor - programming language with a two-level type system" -HOMEPAGE="http://www.aldor.org/" -LICENSE="aldor-2" -SLOT="0" -KEYWORDS="~x86" -IUSE="doc emacs" -RDEPEND="emacs? ( virtual/emacs )" -DEPEND="${RDEPEND} - dev-util/byacc - emacs? ( app-text/noweb doc? ( virtual/tetex ) )" -ESVN_REPO_URI="https://aquarium.aldor.csd.uwo.ca/svn/trunk" -SRC_URI="doc? ( http://aldor.org/docs/aldorug.pdf.gz - http://aldor.org/docs/libaldor.pdf.gz - http://aldor.org/docs/tutorial.pdf.gz - ftp://ftp-sop.inria.fr/cafe/software/algebra/algebra.html.tar.gz ) - emacs? ( http://www.risc.uni-linz.ac.at/people/hemmecke/aldor/aldor.el.nw )" - -src_compile() { - if use emacs; then - einfo "The aldor emacs mode" - notangle "${DISTDIR}/aldor.el.nw" > aldor.el - notangle -Rinit.el "${DISTDIR}/aldor.el.nw" | \ - sed -e '1s/^.*$/;; aldor mode/' > 64aldor-gentoo.el - if use doc; then - einfo "Documentation for the aldor emacs mode" - noweave "${DISTDIR}/aldor.el.nw" > aldor-mode.tex - pdflatex aldor-mode.tex - pdflatex aldor-mode.tex - fi - fi - if use doc; then - einfo "Documentation" - cp "${DISTDIR}/aldorug.pdf.gz" . - cp "${DISTDIR}/libaldor.pdf.gz" . - cp "${DISTDIR}/tutorial.pdf.gz" . - gunzip aldorug.pdf.gz libaldor.pdf.gz tutorial.pdf.gz - tar xzf "${DISTDIR}/algebra.html.tar.gz" - fi - cd "${PN}" - einfo "Compiling aldor and its libraries" - epatch "${FILESDIR}/${P}.patch" - emake distrib -} - -src_install() { - cat > 64aldor <<EOF -ALDORROOT=/opt/${PN}/linux/${PV} -PATH=/opt/${PN}/linux/${PV}/bin -EOF - doenvd 64aldor - if use doc; then - einfo "Installing the aldor documentation" - insinto "/usr/share/doc/${P}" - doins *.pdf - doins -r algebra.html - fi - if use emacs; then - einfo "Installing the aldor emacs mode" - elisp-site-file-install aldor.el - elisp-site-file-install 64aldor-gentoo.el - fi - einfo "Installing aldor and its libraries" - cd "${PN}/install" - dodir /opt - cp -a "${PN}" "${D}opt/" -} - -pkg_postinst() { - use emacs && elisp-site-regen -} - -pkg_prerm() { - [ -f "${SITELISP}/site-gentoo.el" ] && elisp-site-regen -} diff --git a/dev-lang/aldor/files/aldor-1.1.0.patch b/dev-lang/aldor/files/aldor-1.1.0.patch deleted file mode 100644 index e1807e44e..000000000 --- a/dev-lang/aldor/files/aldor-1.1.0.patch +++ /dev/null @@ -1,23 +0,0 @@ ---- Makefile.globals.orig 2007-09-30 22:59:31.000000000 +0700 -+++ Makefile.globals 2007-09-30 22:57:27.000000000 +0700 -@@ -21,5 +21,5 @@ - # - SHELL=/bin/bash --ALDOR_PROJECT=d:\projects\aldor\aldorsvn -+ALDOR_PROJECT=$(S)/$(PN) - - # All these things under $(ALDOR_PROJECT) can actually be in unrelated places, -@@ -33,5 +33,5 @@ - # MACHINE should be one of: linux, win32gcc, win32msvc, sun4os55g64 - # or the machines listed in: $(ALDOR_PROJECT)/aldor/tools/unix/docc. --MACHINE=win32msvc -+MACHINE=linux - - # This varible sets the name of the libraries to be built -@@ -43,5 +43,5 @@ - # Note: the order in the list sets the order of building the libraries. - #LIBS_TO_BUILD=aldor axllib debuglib algebra --LIBS_TO_BUILD=aldor axllib -+LIBS_TO_BUILD=aldor axllib algebra - - # This is used to form the name of the tarball archive used for binary diff --git a/dev-lang/aldor/metadata.xml b/dev-lang/aldor/metadata.xml deleted file mode 100644 index 7b8af4e8c..000000000 --- a/dev-lang/aldor/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci</herd> -<maintainer> -<email>A.G.Grozin@inp.nsk.su</email> -<name>Andrey Grozin</name> -</maintainer> -<longdescription lang="en"> -From a technical point of perspective, Aldor is a type-complete, -strongly-typed, imperative programming language with a two-level -object model of categories and domains (similar to the concept of -interfaces and classes in Java). Types and functions are first class -entities allowing them to be constructed and manipulated within -Aldor programs just like any other value. Pervasive use of dependent -types allows static checking of dynamic objects and provides -object-oriented features such as parametric polymorphism. -</longdescription> -</pkgmetadata> diff --git a/dev-libs/libunzip/ChangeLog b/dev-libs/libunzip/ChangeLog index fe424aea6..486ff991d 100644 --- a/dev-libs/libunzip/ChangeLog +++ b/dev-libs/libunzip/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-libs/libunzip -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> libunzip-5.52.ebuild: + Sort inherit and/or USE + 23 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> libunzip-5.52.ebuild: QA fixes diff --git a/dev-libs/libunzip/Manifest b/dev-libs/libunzip/Manifest index 1809672e5..dbf33beb5 100644 --- a/dev-libs/libunzip/Manifest +++ b/dev-libs/libunzip/Manifest @@ -5,23 +5,13 @@ AUX libunzip-5.52-CVE-2008-0888.patch 1075 RMD160 03d5ec7845ae9347a197c7d1484bb2 AUX libunzip-5.52-Makefile.patch 1296 RMD160 e4d0c3bd9e865ff6701f4500725d69c43bab4de3 SHA1 bb7a4fe61c89ae6214e7d4bae495a52bc5ad2526 SHA256 17d857b746d4d699e7d816d240c2b211710ede7a8fac242b1574821ec5928fd5 AUX libunzip-5.52-no-exec-stack.patch 334 RMD160 81d73b5bb66fb54f8f71252c1fe6e2036d488de9 SHA1 0f318fecebd548e9feb2e93a32c56258d5c552b1 SHA256 8e165db2c138f9729020f3e60e9d8be58d504f4cf8eb7aae18b9432d2d751d4f DIST unzip552.tar.gz 1140291 RMD160 b749b0923bc4cceaa6f937aef688e9713a84328c SHA1 1831bd59b9e607a69052f83b263384895e2d4a19 SHA256 145d95e2ef1ef9add2e3c97d1340907e33ab8749eb1235372e7f0b7af600a8e9 -EBUILD libunzip-5.52.ebuild 1299 RMD160 6977af724484f9f60ca3fd421968e095ef936b5c SHA1 bad9ada0df6ed9442c61a0da08dadd52d7046cd9 SHA256 fb3e78c0c9db10b241efb53b61a2e46efa508d0f197624f10fd362ae8312e2ca -MISC ChangeLog 500 RMD160 1dec57e77dab11fcd79f067fc3aeaf3ac9d3ea3b SHA1 b367438425b5c884fcec3bacf503241d86ba6eb2 SHA256 f24c8abdcaaec1d392720187d8c4d7a631e4911ba5cd5ea5a9cd51b1119008da +EBUILD libunzip-5.52.ebuild 1299 RMD160 cd97810ad9536b647ffd19c0a9ba7af7fd07cfa8 SHA1 d4e3d89df0d3f8fb09fc1d68226bfbdf4126b0e1 SHA256 89bc89e68013fda4ce76c3f900290b5a430e06cee376d5a92229c3419ed7745d +MISC ChangeLog 596 RMD160 f53222765daa90812752fed5eaf9a16ae13b19ee SHA1 fcfae48192f71ceb5df05ce7f1ffc3abf39ad026 SHA256 51f2795473418b9f268f7061fbc7e8ad12004ac2ed131aaf2fdc02faa04b9555 MISC metadata.xml 164 RMD160 f43cbec30b7074319087c9acffdb9354b17b0db3 SHA1 9c213f5803676c56439df3716be07d6692588856 SHA256 f5f2891f2a4791cd31350bb2bb572131ad7235cd0eeb124c9912c187ac10ce92 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMIlJUAAoJENwGBM22xffe8MUP/1ckR8ieBLHDotG6RyRc0A8y -AJ9sNjZ8NLjvsTO1MDEV2IfL6lSMqhOxeUCSmAI19qFTfyXWmPqAViVcpPXEtdmm -JULvcUAIGveFnVGiQHHV/gWNTZyNCc5iS3X4B2yH+dun8FH7+Bhg8UMAOBPPjW05 -ilXPfacFlCprHsGvK4R4vjstLShWktW/lk1OK31UDNla+jkJOXQ2P0cfrayIcagO -lqK8Kvly0uyMEYjKq5n/dCbZjdUUkaJlP6BsAvnckAIhSu56AJNgzLNF5HPeicmq -4KAgsnowPyx+UeWwp1ipRxAnnP75eClKRRXa2a582+6iEv6KH9eDIa+MA4ZnobLj -OV/VEX4KvbtgpcZr7Tp4gZfo8R+DSYcQPM1eK+sLsb5TNzTHv4VyP61cHtvpRgOF -dO6jeECGGv49fVicpBPSjQPX1BAnwWHGEzBwSwGUAQXHGqbET2ekqnFgXwCQiEkH -woNJdfoHUtvRbS2HShCVopdOuv4NndpPEoXkX17YmFAkEJDGUXVMBi7vooElN/5u -WLNBS9DnZALExFKqrG1dRQpr5nd+3CZUWQWpCGK3vUHUhyzyipTYKCrKu7U4gOrx -X5bcFZ+JP3vhloxfbLm5QhHAgW9kHUmIwQdSzSi1viBZcki2Jejv6WB/xXcrVWuk -zroPB/2njO/ZGSob0yM7 -=AKqQ +iEYEARECAAYFAk4EfwUACgkQgAnW8HDreRbsAQCeMJtbvbP1SwH5QNQhEm9Iqprj +EpgAn1nMuZztuEMSoAY4b+75mUq33lsN +=X6ad -----END PGP SIGNATURE----- diff --git a/dev-libs/libunzip/libunzip-5.52.ebuild b/dev-libs/libunzip/libunzip-5.52.ebuild index 7aa8d11e5..d34950ff5 100644 --- a/dev-libs/libunzip/libunzip-5.52.ebuild +++ b/dev-libs/libunzip/libunzip-5.52.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI="2" -inherit eutils toolchain-funcs flag-o-matic +inherit eutils flag-o-matic toolchain-funcs MY_PN="${PN#lib}" diff --git a/dev-ml/ocamlgraph/ChangeLog b/dev-ml/ocamlgraph/ChangeLog index 614ac4897..666d4fd4d 100644 --- a/dev-ml/ocamlgraph/ChangeLog +++ b/dev-ml/ocamlgraph/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> ocamlgraph-1.7.ebuild: + Sort inherit and/or USE + 06 May 2011; J.-C. Demay <jcdemay@gmail.com> -ocamlgraph-1.6.ebuild, +ocamlgraph-1.7.ebuild: version bump diff --git a/dev-ml/ocamlgraph/Manifest b/dev-ml/ocamlgraph/Manifest index f65add3f5..838fb41ab 100644 --- a/dev-ml/ocamlgraph/Manifest +++ b/dev-ml/ocamlgraph/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX ocamlgraph-makefile.patch 1564 RMD160 f1a4949963658165492b67d456ff57b40af1608e SHA1 963e31c341579f9417eb46dd61a6851d7c27d3dd SHA256 c36612f740033a3d158f5d2a458697b1a41dacf2d1964484c1fd0c0f39fd276b DIST ocamlgraph-1.7.tar.gz 236906 RMD160 5006095e66f5f552b187a1b37b760dbaae88bd0e SHA1 fb15adbcdc5d258b733eec32a69f9db0c2f7581d SHA256 ec5e79a441ea575b50c9301824917e82738ed712a9e5bcf4aa6bea018eff60c6 -EBUILD ocamlgraph-1.7.ebuild 946 RMD160 ffc6d09472a06a1cd865774f76f7f2d12f91447d SHA1 8b24849145a9992fe2b01e7de4cb82b1bbe71a65 SHA256 3104cc843432da702894afbf1442365be3ab7da6893e4e35e64076474f17b37d -MISC ChangeLog 723 RMD160 b8622b05f277d617a8e9aa2d971c368afe5a4ae8 SHA1 81d2a7debf92a70fdd26521d8b33fb70c0f3da7d SHA256 d9fbce1b2d7dfb07e40f8fee0ad3ab9262e86c763b17b77e81e50363fc115106 +EBUILD ocamlgraph-1.7.ebuild 946 RMD160 9099cbe28ec43ac93867284cc0f41b626371e729 SHA1 4e2c003202aca2d63771e295a0723980c41d8d5f SHA256 c9b4f1f9bb65817d9e946ae1c5c2c5d129d87a14ed73d7743bfd9d829ec6631f +MISC ChangeLog 820 RMD160 4a3a571fcaa89d18eb07427ba30c339c60168771 SHA1 b395e312ae1bd1c0385d09d2396aee235937ebf0 SHA256 a900532779edacd3ef37637fd0922e677c7827cec5a28fec2b068fd97da98c2d MISC metadata.xml 1387 RMD160 8fc86d9fb0b1ae585c9ed9c8cca5a47416ea1a2c SHA1 654c9811c01e785f5a6c3ea31a5a15c0f90f3634 SHA256 2a242778c24a7fb97cce396194c7e5813d1cb9f9a12f3d00a1fc8bdfad988cbf +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EfxwACgkQgAnW8HDreRYgJACguE7X9LjDF29Y3MyOq2mnlLJ6 +TOYAn3AjEcO3ToZ5koukm+cSTVPj4y8w +=OqPu +-----END PGP SIGNATURE----- diff --git a/dev-ml/ocamlgraph/ocamlgraph-1.7.ebuild b/dev-ml/ocamlgraph/ocamlgraph-1.7.ebuild index 344e23a92..b880e944d 100644 --- a/dev-ml/ocamlgraph/ocamlgraph-1.7.ebuild +++ b/dev-ml/ocamlgraph/ocamlgraph-1.7.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI="2" -inherit eutils autotools +inherit autotools eutils DESCRIPTION="A graph library for Objective Caml" HOMEPAGE="http://ocamlgraph.lri.fr/" diff --git a/dev-perl/Lab-Tools/ChangeLog b/dev-perl/Lab-Tools/ChangeLog index 4fbc2544f..c7aabe19b 100644 --- a/dev-perl/Lab-Tools/ChangeLog +++ b/dev-perl/Lab-Tools/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-perl/Lab-Tools -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + *Lab-Tools-1.4 (22 Jun 2010) 22 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> diff --git a/dev-perl/Lab-Tools/Manifest b/dev-perl/Lab-Tools/Manifest index ad112e203..d4cde36fe 100644 --- a/dev-perl/Lab-Tools/Manifest +++ b/dev-perl/Lab-Tools/Manifest @@ -1,14 +1,14 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA512 +Hash: SHA1 DIST Lab-Tools-1.4.tar.gz 23609 RMD160 6da9f8c136f8201bdc02e79b4b6812662bb76ab1 SHA1 0818f60c346b0662fe2f357533a2d127eed65677 SHA256 eeff55177c951dc9805fcdef467bd5c35ed6b56ea1fae3e9493aee5c4ae7b290 EBUILD Lab-Tools-1.4.ebuild 582 RMD160 05f1c983ec8723c8699bf5b4de5ad3dcf1a3cc5e SHA1 bfbef4ec7c181bc2aae4f15765134dfd36935281 SHA256 4964fe6b6e54f3e213be4cfa32026b371e44480a3c813e60c263ac8bff13325d -MISC ChangeLog 270 RMD160 831ded807993e998d4b8f3e8a2b764a25a9c4d7a SHA1 d806c2bde5efd365d2ca5d6b55c04b44d0a9bbbb SHA256 bae6d6c82240df76fbf667f82bbb05fb7b03f7d984b0cc548e117dc63cacc933 -MISC metadata.xml 171 RMD160 ed284df01c230fc7990a6b5888b39166d23f29ba SHA1 f3d64a69044b710e23fb874b3ee4cd338858c8b4 SHA256 a7b30fbacd0e4c312c07a3efac112a3794c81d134442d8104325734d03425adf +MISC ChangeLog 367 RMD160 91f531194a3c02e3e9a30b212b0a93d10c305e20 SHA1 9ee88fececf6ef31732af5f95fe0bb4f6eb79773 SHA256 f84348b75b8e9d9d40a55d80eeb92d0d837e8a01ce1baa4a76ff7ab5eac183a4 +MISC metadata.xml 162 RMD160 5c824235f1e4a7c8ef787db43136f0285955ae3b SHA1 cf1542a31296264abe609cf1d52a803902a73dd1 SHA256 dd95a1972c8af554246b7010b2f0097c60c60b2152034bf74ccf842a48c7670f -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEAREKAAYFAkwg6KYACgkQL+gLs3iH94eUfgCfef6Z/pdAf1RYl4zctNOrNJgO -mpcAniUNMrT55HYuoH6QI1ul+h+Omhcb -=pRTq +iEYEARECAAYFAk4FkTYACgkQgAnW8HDreRYJJwCgwNz7sk/219k12ymdOgerzk7J +1hYAniXoXZdbbV3cc/LOsWCEi/EmSqIg +=G6Av -----END PGP SIGNATURE----- diff --git a/dev-perl/Lab-Tools/metadata.xml b/dev-perl/Lab-Tools/metadata.xml index 6f1d493c5..97577520b 100644 --- a/dev-perl/Lab-Tools/metadata.xml +++ b/dev-perl/Lab-Tools/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>maintainer-wanted</herd> + <herd>no-herd</herd> </pkgmetadata> diff --git a/dev-python/coords/ChangeLog b/dev-python/coords/ChangeLog index 407b4fcf5..d75b7cef3 100644 --- a/dev-python/coords/ChangeLog +++ b/dev-python/coords/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for dev-python/coords -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> coords-0.37.ebuild, + metadata.xml: + Fixed malformat CVS line in header + 17 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> coords-0.37.ebuild: Update HOMEPAGE diff --git a/dev-python/coords/Manifest b/dev-python/coords/Manifest index d3311e41c..ce65b9bef 100644 --- a/dev-python/coords/Manifest +++ b/dev-python/coords/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST coords-0.37.tar.gz 736179 RMD160 bb273716fd4bd3f5df7558f5cdb19dde732ee5c3 SHA1 8de4563e2d2b43d9c1b308f6dad0dd702e795a1a SHA256 67ce4316e37a75b83a459e1103b497149d4fec9388ac042f756338fff1fc22b3 -EBUILD coords-0.37.ebuild 732 RMD160 47ed82801c1e54e345569f91527cbe0c4bba64c8 SHA1 990ea06892abc56288bafa10bb52b06ff5fc4342 SHA256 dec8506cae9475b7c6a5da1a212c565236b32d16c86345e96aa5819bb9f9595f -MISC ChangeLog 452 RMD160 feb9c139f994b5f5d2c7316ba608fa0f534c69cc SHA1 a4b5581598bde4379ad11bc9cf35da7bf08a1dfe SHA256 2ef0866cdd059917470fb2594869853831a7c27b435b656e69cb6053281fd418 -MISC metadata.xml 312 RMD160 7e25d9a79b5ac6608509dd864444389325afb97c SHA1 354d91501ec2dbe63d85231f0863133697a0d752 SHA256 2e5632eaa0d493cbfaa1b36feea250483ae9ea51eb4607a89c50feb134e7a1e3 +EBUILD coords-0.37.ebuild 736 RMD160 6b013f0857597eba71c9e8f5a96549321d472e89 SHA1 57fc05af48e7787ee5470b69ff8ba455310bc6a0 SHA256 ecc134f372dfe23dd7ec8e0738a6e5a5ed4764064f4274ccce72935f866aac8d +MISC ChangeLog 573 RMD160 d76c93db183b59073ccd84ec73abf9bc80cf7605 SHA1 aebd16cdd6527c4d465aa500b7b575832f5a1719 SHA256 1917a3261622a39a0706a0013569ca5fc69bde77c1a3fbd5fdde9b3c0a4d9543 +MISC metadata.xml 314 RMD160 e5366240b8eecf07bbcbaaa0e3102a70a439ae6d SHA1 ecdd6ca0f44aee7f6df2102639692c8b6e61fb1e SHA256 b5eecff4fb2537a471c6aebc9a9a30f5abfa0c9e2a8b8f59e234331e183e00ee +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F6V0ACgkQgAnW8HDreRbTKQCgz1iCMZ57UDT1xQLK+xubDjLv +PZAAn3TlUTKlMvG1DY9kVCrumPmRuuOC +=WYdz +-----END PGP SIGNATURE----- diff --git a/dev-python/coords/coords-0.37.ebuild b/dev-python/coords/coords-0.37.ebuild index c1dd7fcbb..c9be8c7c8 100644 --- a/dev-python/coords/coords-0.37.ebuild +++ b/dev-python/coords/coords-0.37.ebuild @@ -1,16 +1,17 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header$ +# $Header: $ EAPI=3 PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.*" inherit distutils -DESCRIPTION="managing astronomical coordinate systems" -HOMEPAGE="https://trac6.assembla.com/astrolib/wiki http://www.scipy.org/AstroLib" +DESCRIPTION="Managing astronomical coordinate systems" +HOMEPAGE="https://trac6.assembla.com/astrolib/wiki/ http://www.scipy.org/AstroLib/" SRC_URI="http://stsdas.stsci.edu/astrolib/${P}.tar.gz" LICENSE="AURA" @@ -20,7 +21,6 @@ IUSE="" DEPEND="" RDEPEND="dev-python/numpy" -RESTRICT_PYTHON_ABIS="3.*" src_test() { testing() { diff --git a/dev-python/coords/metadata.xml b/dev-python/coords/metadata.xml index d5b2c7915..0cc1b5f15 100644 --- a/dev-python/coords/metadata.xml +++ b/dev-python/coords/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> coords is a part of Astrolib and provide a set of routines for managing astronomical coordinate systems </longdescription> diff --git a/dev-python/cvxopt/ChangeLog b/dev-python/cvxopt/ChangeLog index 21370e049..2d4bb92bc 100644 --- a/dev-python/cvxopt/ChangeLog +++ b/dev-python/cvxopt/ChangeLog @@ -2,6 +2,17 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> cvxopt-1.1.3.ebuild: + Sort inherit and/or USE + + 20 Jun 2011; François Bissey <francois.bissey@canterbury.ac.nz> + cvxopt-1.1.3.ebuild, +files/cvxopt-1.1.3-blas.patch, metadata.xml: + Add useflag description in metadata + + 20 Jun 2011; François Bissey <francois.bissey@canterbury.ac.nz> + cvxopt-1.1.3.ebuild, +files/cvxopt-1.1.3-blas.patch: + Make cvxopt use pkg-config for BLAS/LAPACK + 03 May 2011; Justin Lecher <jlec@gentoo.org> cvxopt-1.1.3.ebuild: Smaller reorganization of the ebuild diff --git a/dev-python/cvxopt/Manifest b/dev-python/cvxopt/Manifest index a931b4c5b..8044a7b2f 100644 --- a/dev-python/cvxopt/Manifest +++ b/dev-python/cvxopt/Manifest @@ -1,14 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 +AUX cvxopt-1.1.3-blas.patch 2833 RMD160 5c247a60c42a2b0507eed17410f7f9cff9b79464 SHA1 628b178c5f617217fcdac2f0e3f49cb5ab5a652b SHA256 4794ef677e984bcd564f7c426bdaa6361aa2bfe3cce83bbd1a88647551bca698 DIST cvxopt-1.1.3.tar.gz 2927536 RMD160 cd0fdf51db957b388803b305f43ff323415b2252 SHA1 fe048bd21bb33eb99adb2759eda6f06d7520aa31 SHA256 c9563f04a31516e7b042d9e25344ae24bf6bc3e905c53ed077f9974c0efd9a7a -EBUILD cvxopt-1.1.3.ebuild 988 RMD160 e9df1b914aafaecd26b2adc31a44809d9332a263 SHA1 46e8ee5f96758f617ddb49554a2d571dcd548751 SHA256 e4bf5ddae25eb74d6c52b12d94544ee88af8e69daab3aec59adba25d4dc3d4b6 -MISC ChangeLog 416 RMD160 346711378b73c764ead2af3e1fad3bc34082138f SHA1 ee21b8f97824ece336d3a68e9d9bbe7fee9d00a1 SHA256 ec73bd52a0eebeeacf03e198d80da24245ea08a934e64c837afee98cfa63acd3 -MISC metadata.xml 700 RMD160 0f7133c6997bcc9f6628892cd14df58396b2e964 SHA1 eaff2b19a0158437ebfa252de4b0dddc9cbe38ca SHA256 964ca6fb3e432ca9769b37fd063ce2268749334db92bde64fb4ea373790a6a50 +EBUILD cvxopt-1.1.3.ebuild 1398 RMD160 f1889166a77437d26c23e2c6dd31980d89c8f2f9 SHA1 c2fcfa76df27134976b7d62e9852d66a3f8c2a3b SHA256 9d1ca6849bc2d14fcb5e4502a1c727057eb1472e82daeef4e6cb6c6f3a8d2371 +MISC ChangeLog 854 RMD160 38714bb41cf4e7476c72e811aa07ebdf737bdb94 SHA1 246c56f28f6324fbbdad9b099338253e33e091b3 SHA256 a6ddba47f963efd6e556a59dde9f840bedbd77d97912ec5ee24acc429d7dedd3 +MISC metadata.xml 773 RMD160 0896f77a40bd838a9543fae42d240d7e47fbdaf2 SHA1 5ca51919cac1aabbaafe560fc4689fa83202ae1b SHA256 6e7d1cf0e53dcfb136d3cdc183671ecf3d9fb121eb6e28651e48325dc2b4c40c -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk3H13YACgkQgAnW8HDreRZXegCeNfdmESZDT6m88P/q+v3wN3QJ -nLcAmgJy+l70/ylpiw+4EbSsxAkfRevr -=k38k +iEYEARECAAYFAk4Efy8ACgkQgAnW8HDreRYiXACgjGvWiQFDWTIl6ZvOXHj3yZbt +WD0AoKryiOU0zArNbqsEPjFkYZ6IT7un +=l34+ -----END PGP SIGNATURE----- diff --git a/dev-python/cvxopt/cvxopt-1.1.3.ebuild b/dev-python/cvxopt/cvxopt-1.1.3.ebuild index 93571221b..3539f0777 100644 --- a/dev-python/cvxopt/cvxopt-1.1.3.ebuild +++ b/dev-python/cvxopt/cvxopt-1.1.3.ebuild @@ -3,13 +3,12 @@ # $Header: $ EAPI=3 - PYTHON_DEPEND=2:2.5 SUPPORT_PYTHON_ABIS=1 RESTRICT_PYTHON_ABIS="2.4 3.*" DISTUTILS_USE_SEPARATE_SOURCE_DIRECTORIES=1 -inherit distutils +inherit distutils eutils python DESCRIPTION="A Python Package for Convex Optimization" HOMEPAGE="http://abel.ee.ucla.edu/cvxopt" @@ -22,20 +21,35 @@ SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="fftw glpk gsl" -DEPEND=" - virtual/blas - virtual/cblas +DEPEND="virtual/blas virtual/lapack - + virtual/cblas fftw? ( sci-libs/fftw ) glpk? ( sci-mathematics/glpk ) gsl? ( sci-libs/gsl )" - RDEPEND="${DEPEND}" S=${WORKDIR}/${P}/src src_prepare(){ + epatch "${FILESDIR}/${PN}"-1.1.3-blas.patch + + BLAS=\'$(pkg-config --libs-only-l blas | sed \ + -e 's/^-l//' \ + -e "s/ -l/\',\'/g" \ + -e 's/,.pthread//g' \ + -e "s: ::")\' + LAPACK=\'$(pkg-config --libs-only-l lapack | sed \ + -e 's/^-l//' \ + -e "s/ -l/\',\'/g" \ + -e 's/,.pthread//g' \ + -e "s: ::")\' + + sed -i \ + -e "s:@GENTOO_BLAS:${BLAS}:" \ + -e "s:@GENTOO_LAPACK:${LAPACK}:" \ + setup.py + distutils_src_prepare prepare_builddir() { diff --git a/dev-python/cvxopt/files/cvxopt-1.1.3-blas.patch b/dev-python/cvxopt/files/cvxopt-1.1.3-blas.patch new file mode 100644 index 000000000..12c434990 --- /dev/null +++ b/dev-python/cvxopt/files/cvxopt-1.1.3-blas.patch @@ -0,0 +1,76 @@ +--- setup.py.orig 2011-06-20 15:32:19.584436452 +1200 ++++ setup.py 2011-06-20 15:35:14.962030823 +1200 +@@ -46,14 +48,14 @@ + # optional modules + + if BUILD_GSL: +- gsl = Extension('gsl', libraries = ['m', 'gsl', 'blas'], ++ gsl = Extension('gsl', libraries = ['m', 'gsl', @GENTOO_BLAS], + include_dirs = [ GSL_INC_DIR ], + library_dirs = [ GSL_LIB_DIR ], + sources = ['C/gsl.c'] ) + extmods += [gsl]; + + if BUILD_FFTW: +- fftw = Extension('fftw', libraries = ['fftw3', 'blas'], ++ fftw = Extension('fftw', libraries = ['fftw3', @GENTOO_BLAS], + include_dirs = [ FFTW_INC_DIR ], + library_dirs = [ FFTW_LIB_DIR, ATLAS_LIB_DIR ], + sources = ['C/fftw.c'] ) +@@ -67,7 +69,7 @@ + extmods += [glpk]; + + if BUILD_DSDP: +- dsdp = Extension('dsdp', libraries = ['dsdp', 'blas', 'lapack'], ++ dsdp = Extension('dsdp', libraries = ['dsdp', @GENTOO_LAPACK], + include_dirs = [ DSDP_INC_DIR ], + library_dirs = [ DSDP_LIB_DIR, ATLAS_LIB_DIR ], + sources = ['C/dsdp.c'] ) +@@ -85,17 +87,17 @@ + else: + MACROS = [] + +-base = Extension('base', libraries = ['m','lapack','blas'], ++base = Extension('base', libraries = ['m', @GENTOO_LAPACK], + library_dirs = [ ATLAS_LIB_DIR ], + define_macros = MACROS, + sources = ['C/base.c','C/dense.c','C/sparse.c']) + +-blas = Extension('blas', libraries = ['blas'], ++blas = Extension('blas', libraries = [@GENTOO_BLAS], + library_dirs = [ ATLAS_LIB_DIR ], + define_macros = MACROS, + sources = ['C/blas.c'] ) + +-lapack = Extension('lapack', libraries = ['lapack','blas'], ++lapack = Extension('lapack', libraries = [@GENTOO_LAPACK], + library_dirs = [ ATLAS_LIB_DIR ], + define_macros = MACROS, + sources = ['C/lapack.c'] ) +@@ -106,7 +108,7 @@ + 'C/SuiteSparse/UFconfig' ], + library_dirs = [ ATLAS_LIB_DIR ], + define_macros = MACROS, +- libraries = [ 'blas', 'lapack'], ++ libraries = [@GENTOO_LAPACK], + sources = [ 'C/umfpack.c', + 'C/SuiteSparse/UMFPACK/Source/umfpack_global.c', + 'C/SuiteSparse/UMFPACK/Source/umfpack_tictoc.c' ] + +@@ -118,7 +120,7 @@ + + cholmod = Extension('cholmod', + library_dirs = [ ATLAS_LIB_DIR ], +- libraries = ['lapack', 'blas'], ++ libraries = [@GENTOO_LAPACK], + include_dirs = [ 'C/SuiteSparse/CHOLMOD/Include', + 'C/SuiteSparse/COLAMD', 'C/SuiteSparse/AMD/Include', + 'C/SuiteSparse/UFconfig', 'C/SuiteSparse/COLAMD/Include' ], +@@ -139,7 +141,7 @@ + define_macros = MACROS, + sources = [ 'C/amd.c' ] + glob('C/SuiteSparse/AMD/Source/*.c') ) + +-misc_solvers = Extension('misc_solvers', libraries = ['lapack', 'blas'], ++misc_solvers = Extension('misc_solvers', libraries = [@GENTOO_LAPACK], + library_dirs = [ ATLAS_LIB_DIR ], + define_macros = MACROS, + sources = ['C/misc_solvers.c'] ) diff --git a/dev-python/cvxopt/metadata.xml b/dev-python/cvxopt/metadata.xml index 3bd706c66..9381d9019 100644 --- a/dev-python/cvxopt/metadata.xml +++ b/dev-python/cvxopt/metadata.xml @@ -5,5 +5,8 @@ <longdescription lang="en"> CVXOPT is a free software package for convex optimization based on the Python programming language. It can be used with the interactive Python interpreter, on the command line by executing Python scripts, or integrated in other software via Python extension modules. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python's extensive standard library and on the strengths of Python as a high-level programming language. </longdescription> + <use> + <flag name='glpk'>Use GNU Linear Programming Kit</flag> + </use> </pkgmetadata> diff --git a/dev-python/ffc/Manifest b/dev-python/ffc/Manifest index 85c4d51f2..c37889054 100644 --- a/dev-python/ffc/Manifest +++ b/dev-python/ffc/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST ffc-0.9.4.tar.gz 2655088 RMD160 582aa1522480fe5a446aa582395b03f39704d838 SHA1 7773963845dcb18e94c28ac088da2a366597661d SHA256 e942ce177c442c032e3b51d864bd9d12ba4f85ca160fc029fd2152d65d81cc1a EBUILD ffc-0.9.4.ebuild 499 RMD160 287bb021fbb90e069115ba6b7641f7d7341f5a37 SHA1 bc77175dda0d6479c21846d6deddb3ea3ce86d82 SHA256 7fe2d7174bdc97291184ace2f4695ea4f2229b97a168d0de3ffd80dab3d9d4a5 +MISC ChangeLog 253 RMD160 a0e8fc7083b2f39738bc61b0473533ec8e800c43 SHA1 5a03aa64a018d77afb430d7e2cd2604e1269820a SHA256 b6ec291c1ab1295c42c3055d849cdff11264bd9e612be2e860cd5bf9134f2e37 MISC metadata.xml 554 RMD160 28d22aeea5715a34d255447f8ce0ee0fe8783445 SHA1 55e0f53f9c409347acfb2281f30e92c968439acc SHA256 cda782ed828357bc70586c7ac42c0aa9babf8bd0539b44c56f6a519f30add7ed +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ev8QACgkQgAnW8HDreRbM3wCgn2DpnUTm62r7hZbe62hgCZZN +UCwAn2hEknGX8A3Rl+13kDR3GUrolFty +=bCd0 +-----END PGP SIGNATURE----- diff --git a/dev-python/ffnet/ChangeLog b/dev-python/ffnet/ChangeLog index 8ed1c9d95..e5febd30c 100644 --- a/dev-python/ffnet/ChangeLog +++ b/dev-python/ffnet/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for dev-python/ffnet -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> ffnet-0.6.2.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> ffnet-0.6.2.ebuild: + Added fortran-2.eclass support + 26 Jun 2010; Justin Lecher <jlec@gentoo.org> ffnet-0.6.2.ebuild: Python ABI fixes diff --git a/dev-python/ffnet/Manifest b/dev-python/ffnet/Manifest index 083887523..455ab0c33 100644 --- a/dev-python/ffnet/Manifest +++ b/dev-python/ffnet/Manifest @@ -2,13 +2,13 @@ Hash: SHA1 DIST ffnet-0.6.2.tar.gz 59596 RMD160 756f9287b03d765fa92dfc4a5375876f7fd7de31 SHA1 2858848b5ab04660a824c9e9278fa44fb2c3b75a SHA256 8f75e92b18e8c963876c9112d8ed321b85a5371544aae9facd5c01fffd7cc51a -EBUILD ffnet-0.6.2.ebuild 1117 RMD160 272ce219686811b7d9f681c168f3649bea76d6d0 SHA1 a2f3e3917119583f112c232efd78b38fcbb6e753 SHA256 7a9d94464d1302a94a3d95c85f4fda5bfd4ccf98ea376282be98f09591da08bb -MISC ChangeLog 482 RMD160 2e44463ff08e9190ff2ee7eee5897e27fd5216d3 SHA1 6d3db73fd75cac44879bd37a630969142bcdcbb2 SHA256 ea1253aae02f63328a37b9dd859fce014ad7b893966147bd77ad7b3030cfd857 +EBUILD ffnet-0.6.2.ebuild 993 RMD160 690af17a6253f9a0873081f3f60f43c87e5cbfd7 SHA1 e6b003871a6f159721e7450a47b4b7ab70affee9 SHA256 cb0d7b70f997a9de5c008d6340948bc49cca4e32c0fb875012ecc3e46f027c5b +MISC ChangeLog 688 RMD160 9734fce0092583b6449568132e360a96c6adece1 SHA1 854a9f60079be39a90606d5fbcd8d41850bf70c8 SHA256 ad1837a431d689d548edea0c4f2775a461a4856c2014ae193e3965cedf55dcfa MISC metadata.xml 368 RMD160 147d6b3476a5a4b1fa383def51d0ca28f5c6d596 SHA1 a53c0a8551114670bcabdc8a24630e0bcc7c8984 SHA256 f39f4e999a7bbc60dfce5804cc6913cec1928987a1608baaa2c8b46d913b249d -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkwlt5YACgkQgAnW8HDreRYZogCgv75K2OxCQuRsM9M8RzU/Fc0y -rtgAn1zIr/fxZlPuu4KctI5ujP7ZkyWl -=Q5aC +iEYEARECAAYFAk4C/PgACgkQgAnW8HDreRYj6wCgl+N+SOPI6awZAKXNCOOLcCI0 +utAAoJm+IaULzn24hVZO7v8oD6jd1aPj +=2PSs -----END PGP SIGNATURE----- diff --git a/dev-python/ffnet/ffnet-0.6.2.ebuild b/dev-python/ffnet/ffnet-0.6.2.ebuild index a4c5bd2a5..7795b2109 100644 --- a/dev-python/ffnet/ffnet-0.6.2.ebuild +++ b/dev-python/ffnet/ffnet-0.6.2.ebuild @@ -1,43 +1,41 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=3 PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.*" -inherit distutils flag-o-matic toolchain-funcs +inherit distutils flag-o-matic fortran-2 toolchain-funcs DESCRIPTION="Feed-forward neural network for python" HOMEPAGE="http://ffnet.sourceforge.net/" SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" SLOT="0" -KEYWORDS="~x86 ~amd64" LICENSE="GPL-2" +KEYWORDS="~x86 ~amd64" IUSE="examples graphviz matplotlib" DEPEND=" dev-python/networkx dev-python/numpy sci-libs/scipy + virtual/fortran matplotlib? ( dev-python/matplotlib ) graphviz? ( dev-python/pygraphviz )" RDEPEND="${DEPEND}" -RESTRICT_PYTHON_ABIS="3.*" - pkg_setup() { - [[ -z ${FC} ]] && export FC=$(tc-getFC) - # hack to force F77 to be FC until bug #278772 is fixed - [[ -z ${F77} ]] && export F77=$(tc-getFC) + fortran-2_pkg_setup export FCONFIG="config_fc --noopt --noarch" + append-ldflags -shared + append-fflags -fPIC } src_compile() { - append-ldflags -shared - [[ -n ${FFLAGS} ]] && FFLAGS="${FFLAGS} -fPIC" distutils_src_compile ${FCONFIG} } diff --git a/dev-python/fiat/Manifest b/dev-python/fiat/Manifest index f8dbdedc4..9440268ab 100644 --- a/dev-python/fiat/Manifest +++ b/dev-python/fiat/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST fiat-0.9.2.tar.gz 2770810 RMD160 6d3f8f91484bf736b3d6b7d9b337f227cb8c43d1 SHA1 1da72dd1fce44a02bd6a0768a5770a1dda73333f SHA256 e35f4d13274581847b20e64a2a16c3e83eadee70818b1edccc87d5d463e402be EBUILD fiat-0.9.2.ebuild 530 RMD160 3bb2aa6313ab11476be31bf7a19a20a7d740eccc SHA1 57bf6a509bc6fc84dda9950920d49d46f196fbd5 SHA256 4fa90ac8b20bc25129dfe5fd789dbf8ac5585c19b68c877147b300f5d2a0ddbe +MISC ChangeLog 256 RMD160 b9ea2b39147c6d0eb99d42f5ec20fa40f74f5400 SHA1 62c7e9cf062765e0e7183079bf70c60eb26bd1d4 SHA256 49fb8ff53eba646a47d384a4031ae121bb14803ed5e38ff6ea02c41c2bf3af33 MISC metadata.xml 725 RMD160 72ae2fd86d8932d4318b59299f76e1601a65aa3d SHA1 8ec9f77332d3c4346533b022ab9e5a0569f16ad3 SHA256 8bbf23365efd5f2eb3c7e5ca903d5d015e713dba65f7e99e272a157f232fcdaa +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ev+kACgkQgAnW8HDreRYV5gCgusErlvEnNefX3qLkU0AsP9sl +EwsAn15GZcjXnR+2rIK2t37Ql0HcA25S +=VDJ2 +-----END PGP SIGNATURE----- diff --git a/dev-python/inference/ChangeLog b/dev-python/inference/ChangeLog index a720355da..a1dad065f 100644 --- a/dev-python/inference/ChangeLog +++ b/dev-python/inference/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for dev-python/inference -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> inference-0.4.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> inference-0.4.ebuild: + Added fortran-2.eclass support + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> inference-0.4.ebuild: + Added fortran-2.eclass support + *inference-0.4 (19 Jul 2010) 19 Jul 2010; Sébastien Fabbro <bicatali@gentoo.org> diff --git a/dev-python/inference/Manifest b/dev-python/inference/Manifest index 94c8de41c..603725650 100644 --- a/dev-python/inference/Manifest +++ b/dev-python/inference/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST inference-0.4.tar.gz 132739 RMD160 f92c5fff70b99cb6d5a884ceb27456eaa2af9b81 SHA1 f5aae52f4d6c3510ee6dca4db46559cc03da0ad1 SHA256 78e14c4848bb7ab8bf139957de9c6579c8213bb9d449ec2bf61b168023adcfaf -EBUILD inference-0.4.ebuild 969 RMD160 e2498e1e0517100f382898dabecec37b8618ecfb SHA1 0cb2ccd2f0ab6e2d6cd2cd6e911107b172bd8276 SHA256 0ae582e25c9d1891eb0899ffe1021f88c45877dd46ab76abc5b8c7cf085f8a8e -MISC ChangeLog 264 RMD160 82103ceedfc141de613b347adab511daa0e3a5c2 SHA1 39c50e1d80020892fef86f8a7f3daa72365e1e91 SHA256 a38ab379d459c907bab9165d1552eee01b7eeb82fc7e6aee9eef9977625c8290 +EBUILD inference-0.4.ebuild 920 RMD160 0647c06efc0d0f774d2adcc0937582cd873458d9 SHA1 5a75d18654fc04b604de736be111fb0333edb5cc SHA256 6ad459c5fed4ce882b34904515c91a8000242c10f18729e6a0b74f74e3dcf321 +MISC ChangeLog 577 RMD160 8548ac2fa0add74ed088c98f9d7ccdd3e7ae1de9 SHA1 3c0f0794c7ff0782ec1012fd94ac85b799a17b84 SHA256 697df7333357104d65b5a641d7fccca0e8ed5350ad0a7abcd704d3721bb9f77d MISC metadata.xml 603 RMD160 90e47dd93ea08bc37e091a179d5b390a63568af4 SHA1 20dea5a1f433380a33310aefc0c4bc5b758e4024 SHA256 f1992098c195490aebbcd781742741cc1b44d5075a756ecda9a90f76da82f7ed +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4C/W0ACgkQgAnW8HDreRbdJwCdERtFr8BratDN0OtnpHTWOdPf +lioAoLqaMBdYlYd8NQ44GxnUQfaP4I9/ +=Yc/a +-----END PGP SIGNATURE----- diff --git a/dev-python/inference/inference-0.4.ebuild b/dev-python/inference/inference-0.4.ebuild index c2d30b793..1c4917f2b 100644 --- a/dev-python/inference/inference-0.4.ebuild +++ b/dev-python/inference/inference-0.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -6,34 +6,34 @@ EAPI=3 PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.*" DISTUTILS_SRC_TEST="nosetests" -inherit distutils toolchain-funcs flag-o-matic +inherit distutils flag-o-matic fortran-2 toolchain-funcs DESCRIPTION="Collection of Python modules for statistical inference" HOMEPAGE="http://inference.astro.cornell.edu/" SRC_URI="${HOMEPAGE}/${P}.tar.gz" -IUSE="" SLOT="0" +LICENSE="as-is" KEYWORDS="~amd64 ~x86" -LICENSE="mixed" +IUSE="" -DEPEND="dev-python/scipy" +DEPEND=" + sci-libs/scipy + virtual/fortran" RDEPEND="${DEPEND} dev-python/matplotlib" -RESTRICT_PYTHON_ABIS="3.*" - # buggy tests RESTRICT="test" pkg_setup() { + fortran-2_pkg_setup # The usual numpy.distutils hacks when fortran is used append-ldflags -shared - [[ -z ${FC} ]] && export FC=$(tc-getFC) - [[ -z ${F77} ]] && export F77=$(tc-getFC) - export FFLAGS="${FFLAGS} -fPIC" + append-fflags -fPIC export NUMPY_FCONFIG="config_fc --noopt --noarch" } diff --git a/dev-python/instant/Manifest b/dev-python/instant/Manifest index 33f88b4e1..7a3dee100 100644 --- a/dev-python/instant/Manifest +++ b/dev-python/instant/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST instant-0.9.8.tar.gz 112271 RMD160 e01817f836ff2c4d4eabad3c9286463f82337b79 SHA1 7604620103253e6fd035514c8bb86be7ac277828 SHA256 99286b1147f3eebf0e8a56501cfebbbd335bf0cd98cfba7f60f8d5c17005d896 EBUILD instant-0.9.8.ebuild 447 RMD160 5a9474218e5976d88522d303a927dd195997bc52 SHA1 1692e775e0bcd1eabb693d463ff84191cbd12af3 SHA256 392898f00eb8b9f892d3534b00a4cd9eba60b611e06b77820feec47c632b73b8 +MISC ChangeLog 265 RMD160 dc42bc69598d6a87308860a2a9d38a5e226bcd42 SHA1 c54a195d886576af6e5d0f80bd18eb47dc8a81e9 SHA256 3df1d44bc9f9ffdab4a4aa9a1e9ef526a630e26b705d588f1294fdabbca615d5 MISC metadata.xml 412 RMD160 18f3a82b9e70137231c56529bf1c04cae459551e SHA1 76dfafb931a39988d121f17b389264507e4673fd SHA256 5c71c5edc4a301d061fcdc587769ecb5ef0a23b1402bd72a8e2b9eeefe1b3a01 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ev/cACgkQgAnW8HDreRaxQACeJIv6ryoxPRQg+EaWsMkn3x+I +twwAoLmCq8oybaqYJmyPjRHotJHRo+WL +=Lp4E +-----END PGP SIGNATURE----- diff --git a/dev-python/numpydoc/ChangeLog b/dev-python/numpydoc/ChangeLog index c40c72565..0f35d94db 100644 --- a/dev-python/numpydoc/ChangeLog +++ b/dev-python/numpydoc/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for dev-python/numpydoc -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> numpydoc-0.4.ebuild, + metadata.xml: + 'http://pypi.python.org/packages/source' found in thirdpartymirrors + 03 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> numpydoc-0.4.ebuild: Add ~x86, restrict python-3.*. Thanks to W. Trevor King <wking@drexel.edu> for the report. diff --git a/dev-python/numpydoc/Manifest b/dev-python/numpydoc/Manifest index bb861c10b..0313ca61d 100644 --- a/dev-python/numpydoc/Manifest +++ b/dev-python/numpydoc/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST numpydoc-0.4.tar.gz 28972 RMD160 0eeec5a3570f1d0ea0a2f0090b85e79a96f0cfb9 SHA1 543c78a049a3ee6ab5fe8f85a178c257b20dd0d4 SHA256 20e07c60766a7a044f228de5bdcc0d10b84a9f0b460e0c09422a4f60ef21ff8f -EBUILD numpydoc-0.4.ebuild 752 RMD160 6b846fe8e5308642bc7263ff4dd582b4af5ec9d7 SHA1 6dade749b282a9506a84f3a2cb9e532df5c7a104 SHA256 b0d7e74b835e306ef1a19bec3c893fcfcf6cdf79d0eae684a5841712f1bf7892 -MISC ChangeLog 575 RMD160 64db2e453a4f28ef30d77d0c80c3a8249b62161b SHA1 483922be5c966e39ddae0e7c47e00f2f5b1f10a0 SHA256 5fa0f8da7913c0d24bd62bbb21320514e99c7973eaa4dbf18227ea69b7da5573 -MISC metadata.xml 280 RMD160 441e4b2986b4938c691bafb0d91808a9877c0b21 SHA1 7bc98b170a45c1cb60a544b92bf9c25688c62b19 SHA256 9c43596df399ac2985e164abd28b8993c983d26ba3d1fc0e96f1f2b6f4a99c33 +EBUILD numpydoc-0.4.ebuild 731 RMD160 23c9967ab980922ab128c17be4d8cb01455ea51e SHA1 e9cf7a1482fcad46918be212ac726d001cb985db SHA256 cd34f6b44501743a36b590580d06e14780c1ff35377d5be307929ea141e3ebfc +MISC ChangeLog 730 RMD160 bcff863ba5319a63fb7b650aba0f1b3b50beba8b SHA1 62c770f4be02c5c263d3f1b3ebe84573cfd63fda SHA256 58b26c8e3769b21b365978b3b222001b6af9896d6de1f71bb1f63908e63d5f56 +MISC metadata.xml 283 RMD160 83bacf0f98896f839d05061998440cb6a1ae0d2c SHA1 c176d8d425792226cbe239ee5a05ffba089d8d8f SHA256 e96b84a9959cf90bf941c20ca99da3d62faa683f50fbe2b933c6e99ea9830439 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F7PQACgkQgAnW8HDreRZLSACgiyqpF78QM6EoTUJJV5T9Meej +QYoAoMZps9IUt5ZIihuuHpL+Ma1hgGEy +=8Sz/ +-----END PGP SIGNATURE----- diff --git a/dev-python/numpydoc/metadata.xml b/dev-python/numpydoc/metadata.xml index f1ab7ecf1..8f12a89dd 100644 --- a/dev-python/numpydoc/metadata.xml +++ b/dev-python/numpydoc/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<herd>python</herd> -<longdescription lang="en"> + <herd>sci</herd> + <herd>python</herd> + <longdescription lang="en"> Sphinx extension to support docstrings in Numpy format. </longdescription> </pkgmetadata> diff --git a/dev-python/numpydoc/numpydoc-0.4.ebuild b/dev-python/numpydoc/numpydoc-0.4.ebuild index b8b530296..4e472c9e2 100644 --- a/dev-python/numpydoc/numpydoc-0.4.ebuild +++ b/dev-python/numpydoc/numpydoc-0.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -10,9 +10,10 @@ RESTRICT_PYTHON_ABIS="3.*" inherit distutils DESCRIPTION="Sphinx extension to support docstrings in Numpy format" -HOMEPAGE="http://projects.scipy.org/numpy/browser/trunk/doc/sphinxext - http://pypi.python.org/pypi/numpydoc" -SRC_URI="http://pypi.python.org/packages/source/n/${PN}/${P}.tar.gz" +HOMEPAGE=" + http://projects.scipy.org/numpy/browser/trunk/doc/sphinxext/ + http://pypi.python.org/pypi/numpydoc/" +SRC_URI="mirror://pypi/n/${PN}/${P}.tar.gz" LICENSE="PYTHON BSD" SLOT="0" diff --git a/dev-python/numscons/ChangeLog b/dev-python/numscons/ChangeLog index eb85984a7..e25d3b8b2 100644 --- a/dev-python/numscons/ChangeLog +++ b/dev-python/numscons/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for dev-python/numscons -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> numscons-0.10.1.ebuild, + metadata.xml: + 'http://pypi.python.org/packages/source' found in thirdpartymirrors + 26 Jun 2010; Justin Lecher <jlec@gentoo.org> numscons-0.10.1.ebuild: Python ABI fixes diff --git a/dev-python/numscons/Manifest b/dev-python/numscons/Manifest index 271ad6a94..3cee7b675 100644 --- a/dev-python/numscons/Manifest +++ b/dev-python/numscons/Manifest @@ -1,14 +1,14 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 DIST numscons-0.10.1.tar.bz2 593630 RMD160 fa8d8d1fb01f8ebcced0c4d768d4d4d4ca9717ae SHA1 4c8baf7d714b02f132e242d5ef67a37a39e82b67 SHA256 5fbdb3cfb6ce098d28e6d3af37e424fd5c7e56fe7592265a5096ce20c9cea7da -EBUILD numscons-0.10.1.ebuild 577 RMD160 3ecd91d44cede1304f55cab5d17158776d2f4ce7 SHA1 b805b72ed0d8b102417f7093f8ea56cf6cc693e8 SHA256 e6748ee2654b690c8a4d8a4b0f1875fa10474c896f98e9c65db35485be39a262 -MISC ChangeLog 358 RMD160 815b390f13ed96803dfcc6645481ea6664baa9fd SHA1 f75944da3a90af5ff10c64df06c883c812f8a49a SHA256 2d2d021d1cf5cadd858a091eafb423201585007e06f6fcc02be99734a9526ce6 -MISC metadata.xml 451 RMD160 91291610aa3eb8b5a10046a3545600a0193556cb SHA1 6d8bde1429f1568c2345ccac6b936fcde2fb1f6c SHA256 9d3a2139aa2f0580e7b4a72945a79bae53cf20275f8dda1719a841a826668947 +EBUILD numscons-0.10.1.ebuild 545 RMD160 80a6f8333c21c12bda565b6cdea23e6625195bcd SHA1 528269ac2987df3ac023226735a3b31961bc4f31 SHA256 5ddb13e832063040f28fb6698d4caab52913f5046d76d139325af3c48ace0647 +MISC ChangeLog 516 RMD160 9b2d04007435936f71b82e81ce30ba929bc0f872 SHA1 c7b13261476f1c0b22c93c7d8588a86cfa85e376 SHA256 1b1234e8bf9fdf5961cfd85c4f6155cf53fdc48ce433fb8ca2d0291444fbf657 +MISC metadata.xml 453 RMD160 d8f938d27f45328180b098846c6227ca59d5c1ad SHA1 b8662bb96bb87124292471488d4af8b0fc6abf76 SHA256 ea48eba2cd9ba1b5163c08168605f7acfc9133d723a922f0ddcf1b2e49e15458 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkwlwn4ACgkQgAnW8HDreRZ9fACfTfO1TWJu755IuZpzjgOIDcYb -lz8Anitc3LuaV5FvbpKodFCu0ADxxPEd -=oeJA +iEYEAREIAAYFAk4F7VIACgkQgAnW8HDreRZmOQCfRZ4uDogOinmPeMhwISG6Zzfj +L3kAoIJzMI3Kny5n6/mPHMGW3vlcJwaJ +=asQz -----END PGP SIGNATURE----- diff --git a/dev-python/numscons/metadata.xml b/dev-python/numscons/metadata.xml index 4ee20d43a..34d18a4b3 100644 --- a/dev-python/numscons/metadata.xml +++ b/dev-python/numscons/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>python</herd> -<longdescription lang="en"> + <herd>python</herd> + <longdescription lang="en"> The aim is to provide a library to support most needs for compiled code building in numpy. Concretely, this means more advanced tools ala autoconf, better fortran support, more tools, and support for diff --git a/dev-python/numscons/numscons-0.10.1.ebuild b/dev-python/numscons/numscons-0.10.1.ebuild index 2dd1c1c12..86a7c55ed 100644 --- a/dev-python/numscons/numscons-0.10.1.ebuild +++ b/dev-python/numscons/numscons-0.10.1.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=3 PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" @@ -13,13 +13,13 @@ MP="$(get_version_component_range 1-2)" DESCRIPTION="Support library for building numpy with scons" HOMEPAGE="http://github.com/cournape/numscons/tree/master" -SRC_URI="http://pypi.python.org/packages/source/${PN:0:1}/${PN}/${P}.tar.bz2" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.bz2" IUSE="" SLOT="0" KEYWORDS="~amd64 ~x86" LICENSE="BSD" -DEPEND="dev-util/scons" #yes, it needs scons to work -RDEPEND="dev-util/scons" +DEPEND="dev-util/scons" +RDEPEND="${DEPEND}" diff --git a/dev-python/omniorbpy/ChangeLog b/dev-python/omniorbpy/ChangeLog index f1d4e58ab..945098f50 100644 --- a/dev-python/omniorbpy/ChangeLog +++ b/dev-python/omniorbpy/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/omniorbpy -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> omniorbpy-3.4.ebuild: + Sort inherit and/or USE + 26 Jun 2010; Justin Lecher <jlec@gentoo.org> omniorbpy-3.4.ebuild: Python ABI fixes diff --git a/dev-python/omniorbpy/Manifest b/dev-python/omniorbpy/Manifest index e88b50ded..0f8001a2e 100644 --- a/dev-python/omniorbpy/Manifest +++ b/dev-python/omniorbpy/Manifest @@ -2,13 +2,13 @@ Hash: SHA1 DIST omniORBpy-3.4.tar.gz 721891 RMD160 5b389a31907510800ef0913e2e3855038e6a4cf9 SHA1 e598bd25289d0a2a09da4c7241513202c8b9adb4 SHA256 c786676f5d76082bbe6a4031aed1a08b45345d75c0b5aacc4cdc26b69fb9c782 -EBUILD omniorbpy-3.4.ebuild 2761 RMD160 1eab58c3e0a76d4ddd5940bf911bd1fffcdbb057 SHA1 5bc27e80b8eb35fdfe8ee0eada6451d070bbc7eb SHA256 bbdfb8d67793d468029ce06cd844fec0f43e1b2199365be5f75b04235b5b1b60 -MISC ChangeLog 555 RMD160 a6892f538d24a1d49f91edd4f7b105a671161f3b SHA1 f16cf7b13186bc519258af22e1673aea6a85601a SHA256 cab0702222aed4cebdec2b64c8f89231fb577a7658f30f3b8de0f845042e3e96 +EBUILD omniorbpy-3.4.ebuild 2761 RMD160 927bf01bde7679dc6083e3db07ea928b8733e8ff SHA1 c9750dbc979148b13cb3f40ea184fc99d2b4c108 SHA256 0d64df60f61d7fca265c5a7787ba8ee70da976d03441fd5b764e0274dee0335f +MISC ChangeLog 651 RMD160 179c5750ff7c2f6da64a94cc912e35f795c1609f SHA1 cc2ec30c64c315d945fe127c19455d52a9f863e3 SHA256 719a8e74d219825a3049019d6d7f84479dc260b2fca71981c1bbbd97de036989 MISC metadata.xml 157 RMD160 ed43b99e7bf8bbf62cf4e46152138ab42d3a88c5 SHA1 2182a6de0b10959aad51af2990f1a6c69e34dd97 SHA256 750cb9e46ac2b77e1adf73de43c186a8c2d2234a9c6a89d9358d0969dc5cf8ac -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkwl0M0ACgkQgAnW8HDreRaVBACgrLhleVcJyUsi2Y5PEk6Q3Dyi -9IAAn04SH3Pu28ZaVA/+xwK5dURJ2NdL -=TipB +iEYEARECAAYFAk4Ef1wACgkQgAnW8HDreRaZzQCfRcqIWky8+uxQmxcoSoqjMKQF +bkMAoML/9XsgnRTQeJJasbrMQEI2tSw+ +=sWmm -----END PGP SIGNATURE----- diff --git a/dev-python/omniorbpy/omniorbpy-3.4.ebuild b/dev-python/omniorbpy/omniorbpy-3.4.ebuild index f903ffd5a..d78ffc6bf 100644 --- a/dev-python/omniorbpy/omniorbpy-3.4.ebuild +++ b/dev-python/omniorbpy/omniorbpy-3.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -7,7 +7,7 @@ EAPI="3" PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" -inherit eutils python multilib +inherit eutils multilib python MY_P=${P/omniorb/omniORB} S=${WORKDIR}/${MY_P} diff --git a/dev-python/pymvpa/ChangeLog b/dev-python/pymvpa/ChangeLog new file mode 100644 index 000000000..26f976663 --- /dev/null +++ b/dev-python/pymvpa/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for dev-python/pymvpa +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> pymvpa-0.4.4.ebuild, + metadata.xml: + Dropped keywords because deps are missing + diff --git a/dev-python/pymvpa/Manifest b/dev-python/pymvpa/Manifest index cf6cc99e4..dd6efd24c 100644 --- a/dev-python/pymvpa/Manifest +++ b/dev-python/pymvpa/Manifest @@ -1,12 +1,13 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 -EBUILD pymvpa-0.4.4.ebuild 877 RMD160 65b37f5b8b65a794c5c688bd9e99758750f126dd SHA1 414901debcbc980abd579c5c98bf6239f603db1e SHA256 366e32a76c78f0461ae57fc5ee5fa88c34a64ffc00cedfee0d1aab28ffcb2daa -MISC metadata.xml 670 RMD160 fc2ddb7f9a2c7915959311611ce3cec5a83e1348 SHA1 5b36d5aa5e683147c7994d002787bb1db687072b SHA256 26ebc4000e94e560fd2b48522826b86095c5b2b555cfe314ad1801a1c4289d96 +EBUILD pymvpa-0.4.4.ebuild 891 RMD160 766c4ab2f0e3eb77eab99e840a7f457887f79717 SHA1 04855e4290ef1a73d5bfd0acf6631f2b8c8fc1ca SHA256 dce1147ed0f6fbd370155c8fd5f0d723e6019a1d4f9be3dc217fcb28a69178cd +MISC ChangeLog 247 RMD160 523dae528f91cea2dd61f87c804b4c105f8ca524 SHA1 bc41c207b4af38fc9ac65abefacef27b6e383aff SHA256 39d177de0314e99b2af239df843c26820b62e7842f0a5cc261276eb81ad30aa5 +MISC metadata.xml 673 RMD160 14ecc222d5f5f7cdd602e9f7ce1baa66f336b9b5 SHA1 beb80cd5b15d20c6c24f7c49f409c663a38a2e51 SHA256 89ca1f0539cd89119d1818897091133593e67c67485ed4f8e8fcc445d79e0c97 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk0pyI8ACgkQy0OE/ans1/kiogCeM17RLZVsSCdWNDxEL/eCQrog -ZhwAnR4AClmjgeIK8vA8LThbAuBz/0Pl -=gdW3 +iEYEAREIAAYFAk4F6jkACgkQgAnW8HDreRY7zgCgqBg8QuP5/OjCC+aGGT68VAqC +T0wAoKt0s+anj27SYY6Ju+BouSx9ziMq +=IU5b -----END PGP SIGNATURE----- diff --git a/dev-python/pymvpa/metadata.xml b/dev-python/pymvpa/metadata.xml index 6b37a236c..8473d3d60 100644 --- a/dev-python/pymvpa/metadata.xml +++ b/dev-python/pymvpa/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-mathematics</herd> -<herd>python</herd> -<longdescription lang="en"> + <herd>sci-mathematics</herd> + <herd>python</herd> + <longdescription lang="en"> Python module to ease pattern classification analyses of large datasets. It provides high-level abstraction of typical processing steps (e.g. data preparation, classification, feature selection, diff --git a/dev-python/pymvpa/pymvpa-0.4.4.ebuild b/dev-python/pymvpa/pymvpa-0.4.4.ebuild index 1eb116f07..88a45808b 100644 --- a/dev-python/pymvpa/pymvpa-0.4.4.ebuild +++ b/dev-python/pymvpa/pymvpa-0.4.4.ebuild @@ -1,20 +1,26 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/dev-python/pywavelets/pywavelets-0.2.0.ebuild,v 1.1 2010/04/22 20:14:30 bicatali Exp $ EAPI=2 + +PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.*" + inherit distutils DESCRIPTION="Multivariate pattern analysis with Python" HOMEPAGE="http://www.pymvpa.org/" SRC_URI="" -LICENSE="" + +LICENSE="MIT" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="" IUSE="doc examples minimal test" -DEPEND="dev-lang/swig +DEPEND=" + dev-lang/swig dev-python/lxml dev-python/numpy sys-apps/help2man @@ -33,5 +39,3 @@ RDEPEND="dev-python/numpy sci-libs/libsvm sci-libs/scipy sci-libs/shogun[python] )" - -RESTRICT_PYTHON_ABIS="3.*" diff --git a/dev-python/pythoncgns/ChangeLog b/dev-python/pythoncgns/ChangeLog index 643e48b36..df25ae75c 100644 --- a/dev-python/pythoncgns/ChangeLog +++ b/dev-python/pythoncgns/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/pythoncgns -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> pythoncgns-2009.10.30.ebuild: + 'http://pypi.python.org/packages/source' found in thirdpartymirrors + 26 Jun 2010; Justin Lecher <jlec@gentoo.org> pythoncgns-2009.10.30.ebuild: Python ABI fixes diff --git a/dev-python/pythoncgns/Manifest b/dev-python/pythoncgns/Manifest index 98f8f0ab3..9b7aa7e5c 100644 --- a/dev-python/pythoncgns/Manifest +++ b/dev-python/pythoncgns/Manifest @@ -1,14 +1,14 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 DIST CGNS-2009.10.30.tar.gz 24185 RMD160 aac9c77f620797b5658bde863105d43a8b22e8c3 SHA1 660a0097031474bb939254359b67b44f8bb93805 SHA256 915c57cfbcaceecf8c352de03e96945388c1bd1e10c4b011ea5ac5231814011a -EBUILD pythoncgns-2009.10.30.ebuild 573 RMD160 13696109c9acee62c7f56e2c350696f8ce92cc6b SHA1 9f691ec16e3bda079c1fefc73447e157556ed70b SHA256 9058a47230bc89c3957721140d7c4cc48938b6435d0c532fa36fd906d54841aa -MISC ChangeLog 393 RMD160 bf3f7544e8bce0701d152d16e4c043062834b9e4 SHA1 4a133f47b2dab655a3dd92cfe1aa0eb14d83d560 SHA256 64cf13bffbd79efdcb5c6d991acd13a56b70ea4e0dfe43ed9dad6d03404c9f71 +EBUILD pythoncgns-2009.10.30.ebuild 548 RMD160 96a92f98bced0c842a2c2382e0f9981b0df1ec54 SHA1 4fd6a182a39ed12326e5553cc13bc103958c61c7 SHA256 eebb70ca36f57c224cb15f78969f1a01a57eebf22a144f5e8b8f80042b71d75c +MISC ChangeLog 541 RMD160 715f2d0197f1c82676b8c98317f6b6f22ed789c6 SHA1 f215cd2772ffa2d02a6e27583a6998d6996a12b7 SHA256 693f3e8d6e12fddc301d09f44aaf4f354d848e23970d81081e7a183099cd49ea MISC metadata.xml 157 RMD160 ed43b99e7bf8bbf62cf4e46152138ab42d3a88c5 SHA1 2182a6de0b10959aad51af2990f1a6c69e34dd97 SHA256 750cb9e46ac2b77e1adf73de43c186a8c2d2234a9c6a89d9358d0969dc5cf8ac -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkwl/QcACgkQgAnW8HDreRaMZACfcC+NZIRCV+hhhVqMzoccEpok -enYAnjbnt0KQpW1hM9G8vca4wcjnqasG -=3dDi +iEYEAREIAAYFAk4F7X8ACgkQgAnW8HDreRZOGACfWpn6NP9zc6oO/UclIvkE1HdU +K5gAn3792jcB5EnJcvF437PdfwA09+lD +=a58v -----END PGP SIGNATURE----- diff --git a/dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild b/dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild index 87a505192..adbb3339d 100644 --- a/dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild +++ b/dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild @@ -1,22 +1,21 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 +EAPI=3 PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" +PYTHON_MODNAME="CGNS" inherit distutils -PYTHON_MODNAME="CGNS" - MY_PN="CGNS" MY_P="${MY_PN}-${PV}" DESCRIPTION="Python language bindings for the CGNS library" -HOMEPAGE="http://pypi.python.org/pypi/CGNS" -SRC_URI="http://pypi.python.org/packages/source/C/${MY_PN}/${MY_P}.tar.gz" +HOMEPAGE="http://pypi.python.org/pypi/CGNS/" +SRC_URI="mirror://pypi/C/${MY_PN}/${MY_P}.tar.gz" LICENSE="GPL-3" KEYWORDS="~amd64 ~x86" diff --git a/dev-python/ufl/Manifest b/dev-python/ufl/Manifest index 9f8a21477..2df9ff8c6 100644 --- a/dev-python/ufl/Manifest +++ b/dev-python/ufl/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST ufl-0.5.4.tar.gz 204883 RMD160 7acd9b3883afb3d22a47cf2a4b913c24e9580328 SHA1 7a2f541f9f784014786e7b844aec3c92eb90b00a SHA256 fc032d7a011406764ca3c466d194cfcf7ba165292e1a9da471cde7519ce1a960 EBUILD ufl-0.5.4.ebuild 492 RMD160 87f6bfe90e389f43456c412d383f2c34a4d93200 SHA1 94999fe01e1fd42c9bac68099f107c04b955117a SHA256 c2b5a2ea5a5c96198c5141935853bd9b98a4cb06c22af66037c75bc445fe1493 +MISC ChangeLog 253 RMD160 1d79b4690bc6b2d82de2c37b5cc15f335f6b4547 SHA1 4c4c2c6bbf2c048558c8927c892799378597aec0 SHA256 517250bdaeecf88732d49d835f58ed58a0e9b96e271e65451971ef3611d3148c MISC metadata.xml 504 RMD160 5c7a494cbbeb2be0b58ba7b2b099d59886fc571b SHA1 a415709423532fc7cb8eee3eb5270f03719cd9eb SHA256 82f312f9482ae938ff788d44dd4bff092f31fa4b516f1cfcbb1510cae9859f20 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EwCUACgkQgAnW8HDreRY0wgCgxuKlThruJcGLxxLBvXRtD1Ev +vSMAn3jmf8kygO8LgDFEvNWgTedH2zXS +=4pzz +-----END PGP SIGNATURE----- diff --git a/dev-python/viper/Manifest b/dev-python/viper/Manifest index 136793b4d..a60c88a33 100644 --- a/dev-python/viper/Manifest +++ b/dev-python/viper/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST viper-0.4.6.tar.gz 185997 RMD160 548adcb94db3ab1a1cd12ca1fa6f43c8cb3283b7 SHA1 3618763387c803f4b732eff9f9b1fa3ec54d04e9 SHA256 11a21044f9fcd02e50153e5d9895c41f39ef0dd57b5b074e5fe12923db37cf44 EBUILD viper-0.4.6.ebuild 484 RMD160 27a2fb16e40f472bc509b4f9ce663f3ed20bf820 SHA1 bb26c5dee5f98d616a1f2df24ecb3bdbaf71fd97 SHA256 bfee9fde85465355ace006b547661e4a81fa32cbcc45844a22f5df505ace53d4 +MISC ChangeLog 259 RMD160 cae319e92e233e6868ad7e1f99bbf853f6d35250 SHA1 4e6c71e0ed92db2d6c53d3e9a437a9d1d2f14f85 SHA256 8c249808a83c6917c696ad4bdb05a358b09c41096a787859805e452f73221d84 MISC metadata.xml 345 RMD160 5bc97a9cb5bc6497da0268bccb3ac4eda90dacef SHA1 b6ec4ca8dc5ea51e379591ef478cd1bff3da5582 SHA256 99997559a34647b667fc4457f683615ceb68a03a84aa97879c231b5b8bdb02f3 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EwBEACgkQgAnW8HDreRZAMgCfYl5Ef3eD10VVLduAhD92VqAX +Zk4AnRsK9E1hU83PVfhoWcTpPzsHrEi4 +=kNMh +-----END PGP SIGNATURE----- diff --git a/dev-util/smartgit/ChangeLog b/dev-util/smartgit/ChangeLog index 46567e0c2..9a64eb821 100644 --- a/dev-util/smartgit/ChangeLog +++ b/dev-util/smartgit/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-util/smartgit -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + *smartgit-1.0.2 (10 Jan 2010) 10 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net> diff --git a/dev-util/smartgit/Manifest b/dev-util/smartgit/Manifest index 355a24219..2bcfb3f36 100644 --- a/dev-util/smartgit/Manifest +++ b/dev-util/smartgit/Manifest @@ -3,12 +3,12 @@ Hash: SHA1 DIST smartgit-generic-1_0_2.tar.gz 5641079 RMD160 01eaa9ffeea3c316618f6fe44e76a0e1e1f10a14 SHA1 ab7e822d867b7e28e5092ad56965ab76d1ccef5c SHA256 ec2fad2c9dc798cb29d5070e10bb4e369c6ff2f8a54ef1f181cc9258eaac0d6a EBUILD smartgit-1.0.2.ebuild 1092 RMD160 1b773ef75435bdaf4c7a8d8cdb7d21d55a7568d5 SHA1 24a4150dbef05b6cdb6ff201ac53747134a2e50a SHA256 7bff97c0afbddc844c0ffe6bf1bd98661fabe0c49d1db05fcf2c80468b55ff26 -MISC ChangeLog 1944 RMD160 26b0d84b0e78110d5c0e18f736cf7c1b68ef49f4 SHA1 b8e51b1a05fbaa1cee77a8ef24a60ef4c59f8b5e SHA256 3c4701bcea077f53b661d7d60bb9945ad8d096450798b11699af4a3c304d4470 -MISC metadata.xml 263 RMD160 29af7f646812a941362d89c0ee9566150df25b5b SHA1 8d5988faa6a2e1b34ca739895d1b425ddafcb32e SHA256 1a4b794f9b03c548e77abf998b34c58b16e852d255bf0322f34b48554c003c30 +MISC ChangeLog 2041 RMD160 f383fc1ecfcb674c5c66e7a6133a3edbbbacfa4d SHA1 8cf686bf8d381d2a36909ee0da2067fa8c73658e SHA256 e2c12b110fecdc0a3482314f7a0e3d3f3cd7a3b0517edeccedff4a0fa59c6c95 +MISC metadata.xml 253 RMD160 b3738dd03dc120c9a1a32d708aa149103a0d7b1b SHA1 6300563e9ab32e6b910d2d16fcfd78bcb1ace5b0 SHA256 7063247dbeb973b818df14c75931ab1a18682bc0c480e11703dc6178155691e8 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.11 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEUEARECAAYFAktJnFsACgkQgAnW8HDreRYe0ACgwNbZfxQKvVX/tFGRzcKL1UnP -zDYAmMjOHI4HEtuYbOGTCbralTc8bpk= -=nP4d +iEYEARECAAYFAk4FkXMACgkQgAnW8HDreRYKvQCeLG8m6EKqGyq5nZRx8PhET1zp +0dsAoKuEdLKmSir1Tf5ymx2/QFhnDVs3 +=RpBp -----END PGP SIGNATURE----- diff --git a/dev-util/smartgit/metadata.xml b/dev-util/smartgit/metadata.xml index ede0c5e35..bb9c2dc3f 100644 --- a/dev-util/smartgit/metadata.xml +++ b/dev-util/smartgit/metadata.xml @@ -1,6 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>maintainer-wanted</herd> + <herd>no-herd</herd> <longdescription>SmartSVN is a powerful GUI SVN client written in Java</longdescription> </pkgmetadata> diff --git a/eclass/fortran-2.eclass b/eclass/fortran-2.eclass deleted file mode 100644 index b812f507c..000000000 --- a/eclass/fortran-2.eclass +++ /dev/null @@ -1,172 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -# Author Justin Lecher <jlec@gentoo.org> -# Test functions provided by Sebastien Fabbro and Kacper Kowalik - -# @ECLASS: fortran-2.eclass -# @MAINTAINER: -# jlec@gentoo.org -# sci@gentoo.org -# @BLURB: Packages, which need a fortran compiler should inherit this eclass. -# @DESCRIPTION: -# If you need a fortran compiler, inherit this eclass. This eclass tests for -# working fortran compilers and exports the variables FC and F77. -# Optional, it checks for openmp capability of the -# current fortran compiler through FORTRAN_NEED_OPENMP=1. -# Only phase function exported is pkg_pretend and pkg_setup. -# Need help? Ask the sci team. - -# @ECLASS-VARIABLE: FORTRAN_NEED_OPENMP -# @DESCRIPTION: -# Set FORTRAN_NEED_OPENMP=1 in order to test FC for openmp capabilities -# -# Default is 0 - -# @ECLASS-VARIABLE: FORTRAN_STANDARD -# @DESCRIPTION: -# Set this, if a special dialect needs to be support. Generally not needed. -# -# Valid settings are any combination of -# -# FORTRAN_STANDARD="77 90 95 2003" -# -# Defaults to FORTRAN_STANDARD="77" which is sufficient for most cases. - -inherit toolchain-funcs - -DEPEND="virtual/fortran" -RDEPEND="${DEPEND}" - -# internal function -# -# FUNCTION: _write_testsuite -# DESCRIPTION: writes fortran test code -_write_testsuite() { - local filebase=${T}/test-fortran - - # f77 code - cat <<- EOF > "${filebase}.f" - end - EOF - - # f90/95 code - cat <<- EOF > "${filebase}.f90" - end - EOF - - # f2003 code - cat <<- EOF > "${filebase}.f03" - procedure(), pointer :: p - end - EOF -} - -# internal function -# -# FUNCTION: _compile_test -# DESCRIPTION: -# Takes fortran compiler as first argument and dialect as second. -# Checks whether the passed fortran compiler speaks the fortran dialect -_compile_test() { - local filebase=${T}/test-fortran - local fcomp=${1} - local fdia=${2} - - [[ -z ${fcomp} ]] && die "_compile_test() needs at least one argument" - - [[ -f "${filebase}.f${fdia}" ]] || _write_testsuite - - ${fcomp} "${filebase}.f${fdia}" -o "${filebase}-f${fdia}" >&/dev/null - local ret=$? - - rm -f "${filebase}-f${fdia}" - return ${ret} -} - -# internal function -# -# FUNCTION: _fortran-has-openmp -# DESCRIPTION: -# See if the fortran supports OpenMP. -_fortran-has-openmp() { - local flag - local filebase=${T}/test-fc-openmp - - cat <<- EOF > "${filebase}.f" - call omp_get_num_threads - end - EOF - - for flag in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do - $(tc-getFC "$@") ${flag} "${filebase}.f" -o "${filebase}" >&/dev/null - local ret=$? - (( ${ret} )) || break - done - - rm -f "${filebase}"* - return ${ret} -} - -# internal -# -# FUNCTION: _die_msg -# DESCRIPTION: Detailed description how to handle fortran support -_die_msg() { - echo - eerror "Please install currently selected gcc version with USE=fortran." - eerror "If you intend to use a different compiler then gfortran, please" - eerror "set FC variable accordingly and take care that the neccessary" - eerror "fortran dialects are support." - echo - die "Currently no working fortran compiler is available" -} - -# @FUNCTION: fortran-2_pkg_pretend -# @DESCRIPTION: -# Setup functionallity, checks for a valid fortran compiler and optionally for its openmp support. -fortran-2_pkg_pretend() { - local dialect - - [[ -n ${F77} ]] || F77=$(tc-getFC) - - : ${FORTRAN_STANDARD:=77} - for dialect in ${FORTRAN_STANDARD}; do - case ${dialect} in - 77) _compile_test $(tc-getF77) || _die_msg ;; - 90|95) _compile_test $(tc-getFC) 90 || _die_msg ;; - 2003) _compile_test $(tc-getFC) 03 || _die_msg ;; - 2008) die "Future" ;; - *) die "${dialect} is not a Fortran dialect." ;; - esac - done - - if [[ ${FORTRAN_NEED_OPENMP} == 1 ]]; then - _fortran-has-openmp || \ - die "Please install current gcc with USE=openmp or set the FC variable to a compiler that supports OpenMP" - fi -} - -# @FUNCTION: fortran-2_pkg_setup -# @DESCRIPTION: -# In EAPI < 4 it calls the compiler check. This behavior is deprecated -# and will be removed at 01-Sep-2011. Please migrate to EAPI=4. -# -# Exports the FC and F77 variable according to the compiler checks. -fortran-2_pkg_setup() { - if has ${EAPI:-0} 0 1 2 3; then - ewarn "The support for EAPI=${EAPI} by the fortran-2.eclass" - ewarn "will be end at 01-Sep-2011" - ewarn "Please migrate your package to EAPI=4" - fortran-2_pkg_pretend - fi - [[ -n ${F77} ]] || export F77=$(tc-getFC) - [[ -n ${FC} ]] || export FC=$(tc-getFC) -} - -case "${EAPI:-0}" in - 1|2|3) EXPORT_FUNCTIONS pkg_setup ;; - 4) EXPORT_FUNCTIONS pkg_pretend pkg_setup ;; - *) die "EAPI=${EAPI} is not supported" ;; -esac diff --git a/media-gfx/brlcad/ChangeLog b/media-gfx/brlcad/ChangeLog deleted file mode 100644 index 7acefecd6..000000000 --- a/media-gfx/brlcad/ChangeLog +++ /dev/null @@ -1,89 +0,0 @@ -# ChangeLog for media-gfx/brlcad -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/media-gfx/brlcad/ChangeLog,v 1.2 2011/03/27 19:06:12 dilfridge Exp $ - - 18 Apr 2011; Andreas K. Huettel <dilfridge@gentoo.org> - -brlcad-7.18.4.ebuild, metadata.xml: - Moved to tree, updated metadata - -*brlcad-7.18.2 (27 Mar 2011) - - 15 Apr 2011; Dongxu Li <dongxuli2011@gmail.com> brlcad-7.18.4.ebuild: - Added dev-tcltk/tkpng to RDEPENDS, #363251. Added itk3.4, itcl3.4 to LDPATH - - 12 Apr 2011; Dongxu Li <dongxuli2011@gmail.com> +brlcad-7.18.4.ebuild: - Version bump to 7.18.4 - - 27 Mar 2011; Andreas K. Huettel <dilfridge@gentoo.org> - +brlcad-7.18.2.ebuild: - Version bump - - 27 Mar 2011; Andreas K. Huettel <dilfridge@gentoo.org> - +brlcad-7.16.8.ebuild, +metadata.xml: - Moved from sci-misc to media-gfx - - 18 Jun 2010; Sébastien Fabbro <bicatali@gentoo.org> - -brlcad-7.16.6-r1.ebuild, -files/brlcad-7.16.6-as-needed.patch, - -files/brlcad-7.16.6-stl-headers.patch, brlcad-7.16.8.ebuild: - Now X is forced (does not build without), itcl/itk paths removed from - ebuild. Switched to EAPI3. - -*brlcad-7.16.8 (26 May 2010) - - 26 May 2010; Sébastien Fabbro <bicatali@gentoo.org> - +brlcad-7.16.8.ebuild: - Version bump - - 09 Mar 2010; Sébastien Fabbro <bicatali@gentoo.org> - brlcad-7.16.6-r1.ebuild: - Get the LDPATH right, bug #307867 - -*brlcad-7.16.6-r1 (03 Mar 2010) - - 03 Mar 2010; Sébastien Fabbro <bicatali@gentoo.org> - -brlcad-7.16.6.ebuild, +brlcad-7.16.6-r1.ebuild, metadata.xml: - Added benchmarks which can be run if the tests are enabled. Added a - desktop entry, and itk/itcl library path to the LDPATH environment - - 28 Feb 2010; Sébastien Fabbro <bicatali@gentoo.org> brlcad-7.16.6.ebuild: - Filtered -Werror, still creating problems (bug #307061) - - 26 Feb 2010; Sébastien Fabbro <bicatali@gentoo.org> brlcad-7.16.6.ebuild: - Enabling debug by default, following bug #306841 - -*brlcad-7.16.6 (25 Feb 2010) - - 25 Feb 2010; Sébastien Fabbro <bicatali@gentoo.org> - +brlcad-7.16.6.ebuild, +files/brlcad-7.16.6-as-needed.patch, - +files/brlcad-7.16.6-stl-headers.patch, +metadata.xml: - Version bump and moved to the main tree - - 04 Feb 2010; Sébastien Fabbro <bicatali@gentoo.org> brlcad-7.16.4.ebuild: - Changed man directory to avoid conflicts - -*brlcad-7.16.4 (02 Feb 2010) - - 02 Feb 2010; Sébastien Fabbro <bicatali@gentoo.org> - -brlcad-7.10.4.ebuild, +brlcad-7.16.4.ebuild, - +files/brlcad-7.16.4-as-needed.patch, - -files/brlcad-tcltk-man_install.patch: - Version bump. Rewrote from scratch - - 24 Aug 2008; Tim Cera <timcera@earthlink.net> brlcad-7.10.4.ebuild: - * The BDL (BSD Documentation License) was for content on their wiki. Removed - from software licenses. * Changed the copyright year to 2008. - - 19 Dec 2007; Sébastien Fabbro <bicatali@gentoo.org> - -files/brlcad-7.6.6-gentoo.diff, +files/brlcad-tcltk-man_install.patch, - -files/tcl.m4, -brlcad-7.6.6.ebuild, +brlcad-7.10.4.ebuild: - Version bump - - 26 January 2006; Lucas Chiesa <lucas.chiesa@gmail.com> brlcad-7.6.6.ebuild: - Added brlcad-7.6.6-gentoo.diff which replaces the entire test for - tcl/tk/itcl/iwidgets in configure.ac. It needs some more work. - -*brlcad-7.6.6 (19 January 2006) - - 19 January 2006; Marcus D. Hanwell <cryos@gentoo.org> - +brlcad-7.6.6.ebuild: - Initial import into the science overlay, bug 77197. diff --git a/media-gfx/brlcad/Manifest b/media-gfx/brlcad/Manifest deleted file mode 100644 index d549db31e..000000000 --- a/media-gfx/brlcad/Manifest +++ /dev/null @@ -1,22 +0,0 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA512 - -MISC ChangeLog 3362 RMD160 377e15a8be7cff8aef7f00aeeb415bb7da639b3a SHA1 03bdc48741f0f51f7036d9380d66d7c240c0ba35 SHA256 a20e27a70c94ab94db0c09a068bf3eeacbbdffba981ace961fa3c8a9aec27f57 -MISC metadata.xml 1379 RMD160 7407a87496226206896ad41f07cbf1b4900faf05 SHA1 6fb2b9de93b48435f93a968de325d1b483160a63 SHA256 0374773ad63ea0e195813d44eeca951b9b756a73ad1fe034499532aef7e6078d ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iQIcBAEBCgAGBQJNrMC6AAoJENwGBM22xffefRgP+wTNMfchcBhF8sObJGzZ/Tu1 -Qbp0+whWgsIGu5qEt5SwUonCnYOWTu/72Ipv43UkWoRDNvTpIR4CagZEFON9rBYe -mJ0NTLL3OWDAnSQx5w7mZqSjjqIqgQ1WonKGjrsf+3aRXuXsKyqDokH9ASyC/Nrd -CWbUidn6Ufr0PbuozlDynlZo7rDCOw5W+lEh/VatW6BrNx4AIYIKVaM7f3/tTWws -i4IZbXVLeOXTgyf/LgZFslmHPYxW30VyqlzOHF0w3aOVdXPh5wEkMFnYyUGEtBBT -GJzGbNgNPTVITopw2SrAQPGPDWOGgJHQExQcvbGaol78u1oj8YYlngiMhL7Fo97Z -RfnuRvPqOKcz1LFUhbcSn3910IURhHAbGnzgQYQjbvRb44STFW8iS3DxzWVzZUC0 -LAIgGO7mbW87vDaIhkCjhZOqs7fAli7TM2yPc+xwK62KMx7T6dbT8lko7gcS4Jbv -THX2jp/NiH9AelpGdLhRnC2K5PpKIUj1lrmO6kveDEuQMIaIlXf5dQEUh70/IFqn -kXfCX+KM2ZaaPeWEKjyZzwVvNuF57GGf/DRBt+bB5Heqh4aOnOGnrEwT18hB0L20 -PoPqtVgz5QHci5a+n9C67Yk8dntbtZrtZbhHXAwexCxJKaGqsSh/PF/KhzDEp2rE -gAEYtuIJgpSs7xknBtbn -=CDtq ------END PGP SIGNATURE----- diff --git a/media-gfx/brlcad/metadata.xml b/media-gfx/brlcad/metadata.xml deleted file mode 100644 index cd8783ffa..000000000 --- a/media-gfx/brlcad/metadata.xml +++ /dev/null @@ -1,34 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>dongxuli2011@gmail.com</email> - <description>please assign bugs</description> -</maintainer> -<maintainer> - <email>dilfridge@gentoo.org</email> - <description>proxy-maintainer, please cc on bugs</description> -</maintainer> -<longdescription lang="en"> - BRL-CAD is a Combinatorial/Constructive Solid Geometry (CSG) - solid modeling system that includes an interactive geometry editor, - ray-tracing support for rendering and geometric analysis, - network-distributed framebuffer support, image and signal-processing - tools, and an embedded scripting language. - - The package is a collection of over 400 tools and utilities. Included - is support for various geometric data format conversions, image and - signal processing capabilities, ray-tracing based lighting models, - network distributed ray-tracing, parallel ray-tracing, animation - capabilities, data compression, image handling, and interactive 3-D - geometric editing, and also an implementation of Weiler's n-Manifold - Geometry (NMG) data structures for surface-based solid models and - photon mapping. -</longdescription> -<use> - <flag name="benchmarks"> - Run benchmarks during test phase (need test option enabled) - </flag> -</use> -</pkgmetadata> diff --git a/media-gfx/librecad/ChangeLog b/media-gfx/librecad/ChangeLog index dbaf87f6c..c9a2f7e6c 100644 --- a/media-gfx/librecad/ChangeLog +++ b/media-gfx/librecad/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header$ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> librecad-1.0.0_beta5.ebuild, + librecad-1.0.0_rc1.ebuild, librecad-9999.ebuild: + Sort inherit and/or USE + + 19 Jun 2011; Dongxu Li <dongxuli2011@gmail.com> +librecad-1.0.0_rc1.ebuild: + Version bump to 1.0.0rc1 + 09 Jun 2011; Dongxu Li <dongxuli2011@gmail.com> +librecad-1.0.0_beta5.ebuild: added tagged version 1.0.0beta5 diff --git a/media-gfx/librecad/Manifest b/media-gfx/librecad/Manifest index b28d89239..b288f2289 100644 --- a/media-gfx/librecad/Manifest +++ b/media-gfx/librecad/Manifest @@ -1,4 +1,15 @@ -EBUILD librecad-1.0.0_beta5.ebuild 1026 RMD160 51fcc8a3ea196ebecea814a02cc01eca466e4ed7 SHA1 cb8e1c7f825daacb19fcd40401f4c41690ca4df3 SHA256 dfa8d18c0e22447719eb425a4ae6387c0feb6773f53ad75bbb93813d4caf7f61 -EBUILD librecad-9999.ebuild 996 RMD160 d9ce7fa7f930871a46f7e0f59f6ea0743a6b4261 SHA1 65afe6bae17430931f2c36bd5f2c95eaaf62a2ff SHA256 9042a2a97a40b4ed23c4a9649c263600988a1f660e6a84854f0198ceb2f0de04 -MISC ChangeLog 478 RMD160 0b3a74f5b4bc5cba8bf6d8b5db0a4364c2ca3dbd SHA1 7c25225e00f2195724979643314874245757a6df SHA256 2eec70764f6409ef93c4efb58849f8248773c6fd40bd77313420e0628f02fd8b +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +EBUILD librecad-1.0.0_beta5.ebuild 1026 RMD160 6f3911c70fa4fb9d7c567c59461043703f6361a9 SHA1 ecf63cbc86357ad8d4aab725069c781c0aa4c5a8 SHA256 8bf33da124d924a17e2de727107ecc582efe75c4f09569d32e873effa360f2fa +EBUILD librecad-1.0.0_rc1.ebuild 1022 RMD160 65a83ae087ec90c8737157cc3f94628e18a5f2b1 SHA1 65e9382cf7a3df13685a9c345f96c2f066d13344 SHA256 ebabd9d622e584ac3ce9921469cb233c4d2e222d9ef75db3b5c299f6153701da +EBUILD librecad-9999.ebuild 996 RMD160 0c8e171707187f72a1a224a54649849860a74b06 SHA1 9e51d3ecf5b30329f2b819aef6c9cc98244f80b9 SHA256 dfdd97f8b96ff41a38295544ed7272e6fd93604a8c566ef481391e50f5a47808 +MISC ChangeLog 738 RMD160 8da5b642c518fbe646a1c47aff41d7d9dc463e62 SHA1 588c5f947c13ce5d85745775a97d27cb1a602f4e SHA256 bac2883e23376c1fe285f0bd031be01619000e0d5fccd32b1456727a7371f5c2 MISC metadata.xml 450 RMD160 62a6501cecfe47078279b48be9b1c658d40e59f9 SHA1 c4ea83204f0d636b89b362f43aa2f5f487b9d9c7 SHA256 891d496161866e9f329036a1a953bd667d7be70de7cb1da41eadbb4be21c7df8 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ef3EACgkQgAnW8HDreRb+HgCgoFGcMZjQ5lhkiUrHOwzd1qgr +1EIAn2XOqwdR11leoq6+YmCzzKDweMyC +=21U1 +-----END PGP SIGNATURE----- diff --git a/media-gfx/librecad/librecad-1.0.0_beta5.ebuild b/media-gfx/librecad/librecad-1.0.0_beta5.ebuild index 7e7e71d1d..2830384a5 100644 --- a/media-gfx/librecad/librecad-1.0.0_beta5.ebuild +++ b/media-gfx/librecad/librecad-1.0.0_beta5.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI="3" -inherit qt4-r2 git-2 +inherit git-2 qt4-r2 DESCRIPTION="An generic 2D CAD program" HOMEPAGE="http://www.librecad.org/" diff --git a/media-gfx/librecad/librecad-1.0.0_rc1.ebuild b/media-gfx/librecad/librecad-1.0.0_rc1.ebuild new file mode 100644 index 000000000..19fe1248e --- /dev/null +++ b/media-gfx/librecad/librecad-1.0.0_rc1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="3" +inherit git-2 qt4-r2 + +DESCRIPTION="An generic 2D CAD program" +HOMEPAGE="http://www.librecad.org/" +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc" + +EGIT_REPO_URI="https://github.com/LibreCAD/LibreCAD.git" +EGIT_COMMIT="${PV/_rc/rc}" + +RDEPEND="x11-libs/qt-gui[qt3support]" +DEPEND="${RDEPEND} + x11-libs/qt-assistant:4 + x11-libs/qt-qt3support:4 +" + +src_prepare() +{ +# patch to solve an issue caused by gcc-4.6, by mickele, archlinux + sed -e "s|LiteralMask<Value_t, n>::mask;|LiteralMask<Value_t, static_cast<unsigned int>(n)>::mask;|" \ + -e "s|SimpleSpaceMask<n>::mask;|SimpleSpaceMask<static_cast<unsigned int>(n)>::mask;|" \ + -i fparser/fparser.cc +} + +src_install() +{ + dobin unix/librecad + insinto /usr/share/"${PN}" + doins -r unix/resources/* + if use doc ; then + dohtml -r support/doc/* + fi + doicon res/main/"${PN}".png + make_desktop_entry "${PN}" LibreCAD "${PN}.png" Graphics +} diff --git a/media-gfx/librecad/librecad-9999.ebuild b/media-gfx/librecad/librecad-9999.ebuild index e0c605de1..1d3197adc 100644 --- a/media-gfx/librecad/librecad-9999.ebuild +++ b/media-gfx/librecad/librecad-9999.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI="3" -inherit qt4-r2 git-2 +inherit git-2 qt4-r2 DESCRIPTION="An generic 2D CAD program" HOMEPAGE="http://www.librecad.org/" diff --git a/net-firewall/gcb/ChangeLog b/net-firewall/gcb/ChangeLog index fd9bfd2e6..bed3dabb1 100644 --- a/net-firewall/gcb/ChangeLog +++ b/net-firewall/gcb/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for net-firewall/gcb -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> gcb-1.5.6.ebuild: + Sort inherit and/or USE + *gcb-1.5.6 (23 Oct 2009) 23 Oct 2009; Sébastien Fabbro <bicatali@gentoo.org> +gcb-1.5.6.ebuild, diff --git a/net-firewall/gcb/Manifest b/net-firewall/gcb/Manifest index dd3512a33..198a48086 100644 --- a/net-firewall/gcb/Manifest +++ b/net-firewall/gcb/Manifest @@ -1,5 +1,25 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +- -----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX gcb-1.5.6-shared.patch 4503 RMD160 9c7b263987e2c88d52f8776f87a2f32a6a67f4e0 SHA1 dc84e989ee01b6e98f9b06f7a0f09572d799a02c SHA256 538dcdba63a891137bef77a69c58208cf56e102c2c3e9185f99baf206029acf6 DIST gcb-1.5.6.tar.gz 1326341 RMD160 2cbdd3596ebb521d62e873a55c722c7c14165724 SHA1 229191a7924468ee453956f807b9d2b1ca26df35 SHA256 315ac4f325060d7df7ae03361d959151619cb308841207322cc2bd91193054bb -EBUILD gcb-1.5.6.ebuild 702 RMD160 5a67e5e0a98569d93b4ca3244c40dbf5cf25c5de SHA1 4db56fe352b310a94dd47b80378249d2e6e56a16 SHA256 dde603e802913522936877f247bbe9e1ef941da8e2737d5423afe84c8a6822bf -MISC ChangeLog 302 RMD160 08a5acbcc6c3642c3b5c371ae323d089d152fd88 SHA1 71e9f84f2bf3a1c156d6ec470a37d8489e1f47f4 SHA256 cda30df31ccec034b37143a26c690b18f8b1824ba87774680824e5e8aea1ccc0 -MISC metadata.xml 617 RMD160 38736667fdb338f050bdd626bca46ba439425f82 SHA1 97153fb49e53fbfa1e42dbe1a19066483d48bfc9 SHA256 975d6074d71c61a5c39c46ca6f180102bfbcea670ab86ef6a53bdcd0fd7e1450 +EBUILD gcb-1.5.6.ebuild 633 RMD160 c7571590606fa99303682ea4d51a6f8c4a192ac8 SHA1 3bfcb8b0ce67090bbd946d2ee7c2025aa6a8b597 SHA256 2ff9a5d213144ccc4fb2dc1e270caa2dbdb577057e24984b3183edfebf474d4a +MISC ChangeLog 394 RMD160 67f7590a153d3ce5c3af3cb5fc7bbea811b48817 SHA1 7d3b11a41f3774f0188c7e00cdc2728197dcc771 SHA256 961413bbaddb149723fb51f69c330d3167a1f9d8ea2094eef959953f980bcb2c +MISC metadata.xml 624 RMD160 9e0cbef58198611205cd4e7376dd2d476659522f SHA1 31a8ab7bcd92e11f28d04f57ca69153a9db848c2 SHA256 8de842f610526030ecf12c2b9b8574cd2aa2480d2fe92454c38775310b846d37 +- -----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ewa0ACgkQgAnW8HDreRYiGQCeM1c9FaVswjzbgObfWDchdGUY +dCkAnA7WZNCL7AzLtLXwTykIY20IJQlo +=+2rx +- -----END PGP SIGNATURE----- +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4ExHsACgkQgAnW8HDreRZprACdHid6rRqlDVARgQ3a/M7sqAES +D90AoNFQ60RDGF6hSrx0T8T7czZmAy23 +=54ym +-----END PGP SIGNATURE----- diff --git a/net-firewall/gcb/gcb-1.5.6.ebuild b/net-firewall/gcb/gcb-1.5.6.ebuild index 50d3117d8..2f780fc2d 100644 --- a/net-firewall/gcb/gcb-1.5.6.ebuild +++ b/net-firewall/gcb/gcb-1.5.6.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 +EAPI=4 -inherit eutils autotools +inherit autotools eutils DESCRIPTION="Generic Connection Brokering for communications over firewall/NAT" HOMEPAGE="http://www.cs.wisc.edu/condor/gcb" @@ -15,19 +15,16 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc" -RDEPEND="" -DEPEND="${RDEPEND}" - src_prepare() { epatch "${FILESDIR}"/${P}-shared.patch eautoreconf } src_install() { - emake DESTDIR="${D}" install || die "emake install failed" + emake DESTDIR="${D}" install dodoc AUTHORS ChangeLog NOTICE.txt doc/protocol.txt if use doc; then insinto /usr/share/doc/${PF} - doins doc/*.pdf || die + doins doc/*.pdf fi } diff --git a/net-firewall/gcb/metadata.xml b/net-firewall/gcb/metadata.xml index 0c28ccc79..ad33ad20b 100644 --- a/net-firewall/gcb/metadata.xml +++ b/net-firewall/gcb/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>hp-cluster</herd> -<maintainer> - <email>bicatali@gentoo.org</email> -</maintainer> -<longdescription lang='en'> + <herd>cluster</herd> + <maintainer> + <email>bicatali@gentoo.org</email> + </maintainer> + <longdescription lang="en"> Generic Connection Brokering (GCB) is a firewall/NAT traversal solution that enables communications over firewall/NAT. It consists of daemon processes and a communication library that is supposed to diff --git a/net-ftp/bbftp-server/ChangeLog b/net-ftp/bbftp-server/ChangeLog index 2bef0fdf8..b73e12c55 100644 --- a/net-ftp/bbftp-server/ChangeLog +++ b/net-ftp/bbftp-server/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for net-ftp/bbftp-server -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bbftp-server-3.2.0.ebuild: + Sort inherit and/or USE + 23 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> bbftp-server-3.2.0.ebuild: QA fixes diff --git a/net-ftp/bbftp-server/Manifest b/net-ftp/bbftp-server/Manifest index a0ce6b79e..506a5b6b1 100644 --- a/net-ftp/bbftp-server/Manifest +++ b/net-ftp/bbftp-server/Manifest @@ -4,23 +4,13 @@ Hash: SHA1 AUX 3.2.0-deffixes.patch 2028 RMD160 761794d87412845bb33bd5e595f2350f4aed4385 SHA1 5a0c0d867df6d2ab8778b1a134f8dcb26980a78f SHA256 39cd0800cae958708fa95b94cd30eaffaaeaa5d28c530d5c9c23e35f7d8e03ef AUX bbftpd.init.d 698 RMD160 dc9f9976ff02e2de1e7c37eb0f2ffc21fc4ad65a SHA1 9793f3d17555508b0aa08b2e1e2b986f46b6ca5e SHA256 e7b81c6034f8298ea2fd232338c1f309d3554a76f1dff8d8c1658eefcebe5163 DIST bbftp-server-3.2.0.tar.gz 222600 RMD160 a6c8a79f8bf06dc7674331168a9bf705029edd12 SHA1 dc599051ed69093caaed029e1a0c28614f7f080d SHA256 04fbe472dc4c39f5b3e82520c08a084e8c4fd5301242c6bbb934d6984013b8ff -EBUILD bbftp-server-3.2.0.ebuild 1215 RMD160 c1e253df025d07f2ce7d2b329a7f11f285f58a00 SHA1 41fbd9acc1ba5817257661205352c10b5ddeba5f SHA256 9ea52cfc79d639a2248599e407d68bff0ac51eb0653cf440cfab93c7980e25bc -MISC ChangeLog 499 RMD160 641f3fc8ae7c16a848ad4ae46fb0ed939674e6f8 SHA1 28e55ad2d1eb88033a1eb34a377777c16bbc81ff SHA256 284ed64de2b6ef18f0676ee488707919086c0af67d0202df7e26aed74a31df12 +EBUILD bbftp-server-3.2.0.ebuild 1215 RMD160 cee41bf9efeec5917febc301ccd1df86891f4fad SHA1 ac941a5d23dbf57e6d6f45849331d1c6195a4c8b SHA256 f31e7b1d9945117577a384c6b0452df8dfd75b9d4fc0c4dcecd65abf67e3787f +MISC ChangeLog 600 RMD160 1d4a0971a10887ec18865f2768a22550ab34fffb SHA1 39bc7068fbf8189bdecbf3e72c31b2c4081ed442 SHA256 048779ad4d73cd04408f909fee48624b57a909d9a18c00c9e1068bd4cd3c6f8b MISC metadata.xml 417 RMD160 cee5a58bdcc8778dc746f29717bad69c6d6de8a3 SHA1 d846f619290fff9989b195e6f3a4a6b381b0a7d2 SHA256 7bd69c2ffa53bba43140b5019c71d571bc024d5abb1f9a3e5b638296333324df -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMIltaAAoJENwGBM22xffet3gP/1iVCjCv+f/jo7jWnj1B7OZD -up4Y9v0YbBKm7o3UeEItVes3Vc/b7Jv/C6fGxzFZK684s4gqrLYm/BpiKXuuC7GP -39oMkKPVqSGmXCefEByuPF/DDja1sN3fH1DIjDRghlRaQz8xHKshy2IrMGj4T4vr -btYMTGUn057iGlgCh/w6VAoPiXe7zmzIBPzQdyoTHmr1qs8dwhUts67YTrlmqY89 -UWyUS/7BAMgs47QWf77bb7hmNFfP/IqAFuhGkR6xoFY6XWEVZlCaNjewwawlYdgf -c6SB8/HpfrSx+i7ljmk/swdZM+h6gpmJSA6Lm4CqXuNinZtLDcPeyAdsYRIeqxmF -MP7y/7bwdBX/VCnWzp9jgQVHUhrJJ5p8hqFFdYYdqNayPTA/RnqYCW3eWBDPgol3 -4jkU+ztUYLjjOK3kL4k3q2S1ab+tNvbHETGsvBEy2Mv0BHZ/X9POwdkbsDItE1rq -THSDE2GzrozAvgXHzBGlB6Uu5+qqE3BGzenePItuCZBQyXEur47zXSkgoPaexcSs -PMQ16MstbxBmGWaHd4I2VT0S+5RnBMZzugK0hcf8H4mG2Da1o3kYdvlVaJDelDxF -+QZSUWlgnNa+fnDm2M4vLGpc5JP3KlTqoJV6fu27e2/PjWAdLNRqP2bNXR7jRyTR -PKXKC3Gluzk+NmBTq0ul -=Vn6P +iEYEARECAAYFAk4EgN8ACgkQgAnW8HDreRbt2wCfT/vYe2dn7ALJPDFDQRC+RALY +jxkAnAvuacZXueKW8dXYyWGtgn1iNnER +=U9jk -----END PGP SIGNATURE----- diff --git a/net-ftp/bbftp-server/bbftp-server-3.2.0.ebuild b/net-ftp/bbftp-server/bbftp-server-3.2.0.ebuild index 918134931..7035fa96c 100644 --- a/net-ftp/bbftp-server/bbftp-server-3.2.0.ebuild +++ b/net-ftp/bbftp-server/bbftp-server-3.2.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -13,7 +13,7 @@ S="${WORKDIR}/${P}/bbftpd" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64" -IUSE="ssl pam" +IUSE="pam ssl" DEPEND="ssl? ( dev-libs/openssl )" RDEPEND="${DEPEND}" diff --git a/net-misc/dhcp/ChangeLog b/net-misc/dhcp/ChangeLog new file mode 100644 index 000000000..d743d0076 --- /dev/null +++ b/net-misc/dhcp/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for net-misc/dhcp +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> dhcp-4.2.1_p1-r1.ebuild, + metadata.xml: + RDEPEND is not explicitly assigned -> fixed + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> dhcp-4.2.1_p1-r1.ebuild: + Sort inherit and/or USE + diff --git a/net-misc/dhcp/Manifest b/net-misc/dhcp/Manifest new file mode 100644 index 000000000..84f8e2298 --- /dev/null +++ b/net-misc/dhcp/Manifest @@ -0,0 +1,45 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX dhcp-3.0-fix-perms.patch 485 RMD160 3857270dffed5feee95609aeb37d0c9ef8844945 SHA1 1217265a8a7f1416b781e9f79e8dfb8304268e6c SHA256 a805a60b36e148886887aebb797e80f642386b3e55ef4a0b5132f96a2877e018 +AUX dhcp-3.0-paranoia.patch 5366 RMD160 7c64e3dac5b07ff3859fcaa7a8b0e52a0c50446c SHA1 a30103c138e480766f84644fffb1d0897709c27d SHA256 a8db9eb98397a9c1b3a0de07fc107c39dc4f6a4a331d404fc6fcc4a8dbc7aeae +AUX dhcp-3.0.2-gmake.patch 1872 RMD160 d2d41c0a7e002103d68605d2492bfe716bb2889e SHA1 f60c89233f06ca8554cd5cc9ed0301b597a724f7 SHA256 b2bbfc1d1f5b4d03ff3f53b3974ec32731e5f626de8f8d127328591e4c721215 +AUX dhcp-3.0.3-dhclient-dbus.patch 2774 RMD160 250582d89894a58a297786c4a6884b54219c4b6f SHA1 74760ca00712ff529e6b97457408515098563f88 SHA256 d70292c5b61648ba5970ab436429ced33e807bd6f68ba06dcd2b9d4073b02ea4 +AUX dhcp-3.0.3-dhclient-hostname.patch 523 RMD160 38c20bcc417822ae858626eb5d0eaf7e669c1ca0 SHA1 5d2c3a1da74a1d151c9fbf08e01e4545e989078c SHA256 57c09edd2bf48cd65745e3b14499f7f3c26d529f60fd2ab122887ae968e26bbd +AUX dhcp-3.0.3-dhclient-metric.patch 7270 RMD160 04187868f66e03a62dafd31b4cdcdd2029283ce5 SHA1 1d726d1526ae97adbdf1b259bb55e05145060375 SHA256 7e5ace014ed55d7d4e90a6cdac7dec4842ea9d178bb19bf6cdccf295eba9da7d +AUX dhcp-3.0.3-dhclient-mtu.patch 6413 RMD160 2517c7fe58d7dca95bdbdc80e96b6260cc205e56 SHA1 da342800bafee86726570aa0a5e4e3c8bd5f1371 SHA256 0a4bff3c4c44252125f66a3a4423f677465592b84a8f7f500bad9ba4e3b5cb06 +AUX dhcp-3.0.3-dhclient-no-down.patch 2332 RMD160 26d0c88534b71070e81c86c12b76a2b4ec7c9c2c SHA1 b2a00d46754414e937dc6c3d63a28b63b3b57ac9 SHA256 a5a67de79f6435d9bc4eeea416aff7a904ab567e5e8d75ecf34495bc9f2c5a44 +AUX dhcp-3.0.3-dhclient-ntp.patch 5862 RMD160 73d001b7b2df36cf84aba9db76a1753c8d423a7d SHA1 cc3db6430f07f956c2ad25ed00e47d468eef2600 SHA256 80ab30eee75fb03c099416c25f031d03744011a582e8940c73077d5ee587c1ee +AUX dhcp-3.0.3-libdst.patch 322 RMD160 5216c754a912cfcfc65683afcf44dbe1a7871212 SHA1 804bab67ae06269336c51183d5ff1e8ba45c20b5 SHA256 68e9a081739736980c0ad834dfa6197f940982f53d4d16054715c0346b5b9eca +AUX dhcp-3.0.3-no_isc_blurb.patch 3002 RMD160 d70f89e1763bfeb23ce8f09399426983df01f7c8 SHA1 99a9fe69988226d29ccc6c2dc745ffab9b66817c SHA256 09c451cd9667fc8effcecd640f4cbe8629d41f6abacf9d1f2f923aab1f6e0bbb +AUX dhcp-3.0.4-dhclient-stdin-conf.patch 2176 RMD160 fae08899f6b57da3ec7ab0068e288bbdf2fbf2ae SHA1 c10c35dcf4a94f45f4bc98147a70e9dcf3f01dd5 SHA256 80141fe71e52774f1c7b1a02f2cbd49bc646f19753ceefc1c3605104df0cae5f +AUX dhcp-3.0.5-bpf-nofallback.patch 1473 RMD160 1a5ece77cb481416935b0d2eea53e85dc4c4ee93 SHA1 d4cad638075a98606e07c633551c8a1d2f78f2e7 SHA256 b215c5ff4a282b475f28168250c05bbbc85e7c37e7af92616571d499b8c14da6 +AUX dhcp-3.1.0a1-dhclient-resolvconf.patch 10316 RMD160 183bedd1660bf5a5f9dc7d002199e76aec12341c SHA1 1e0332ea31cfdbe92f3053405587f08117de8f8b SHA256 112b2ed44aab92592eb3810c61ada7f30d9d01fe43b647667326972a37b412a1 +AUX dhcp-3.1.2_p1-CVE-2009-1892.patch 427 RMD160 fe7daa6834faa0f6078ef125525f6a2db0c05f37 SHA1 eb6dcedecef536f743e97e7d0b5eea0a08f5e55a SHA256 55bb136138b76d6fa9c9165b348fb2c6975b935b3bba72ea551fc8bcae4fcc9b +AUX dhcp-3.1.3-dhclient-no-down.patch 2762 RMD160 bea58f58f745cbcee5d2d43f0dbabe54a1eaaafa SHA1 6ceb33afe42734b21b5ea91076b06c4fb4e9b81f SHA256 94c9dbe45063c6c600976ffab4c1fc9ac6f52f4e8077b5074f5142816ea626c4 +AUX dhcp-4.0-dhclient-ntp.patch 7966 RMD160 d6dd1c3363f06712a82231eae1eb559f5a45bbb5 SHA1 3c1b373c6649c1ccb44f205fbee116c134514f4e SHA256 e93bda7f2baae9163f96ab0408bfbe885caa96a8698f9e566b8a9dc04de9359b +AUX dhcp-4.0.1-dhclient-stdin-conf.patch 2965 RMD160 2c3dd3994f0a7f15f3fe51972dd04a2e6055613a SHA1 f4a9d51126ea489f75fcf29053ab432b68e5055d SHA256 0b25bc74ae258656dd1f0e6f4ffd6b4ef8b4ad56956624c0b6070941a180e57c +AUX dhcp-4.2.0-errwarn-message.patch 1508 RMD160 604c680c22b620ae11e4c1ab83902a0c3dacaa62 SHA1 8d645f2510dac8c68d6114cb3f3c0077d832f8c0 SHA256 e2baa7b6097a6ca20b66afcd7b0e399840a8b0f251b3750a49a03f0d5b714231 +AUX dhcp-4.2.0-improved-xid.patch 5135 RMD160 396725be4f0e179730652c516e3b926021370b72 SHA1 bad02db8b7d5eb316aee08c25b1bf231d919e26c SHA256 2b770ba1ec8108c6e6c6c89cab066307f3653d859f1563286ac8846f9d8efdff +AUX dhcp-4.2.0-lpf-ib.patch 17023 RMD160 5ce926287739144a9ca3130e5b75fa91340d205c SHA1 ac73c6cfbd914f07b612a7874eb123526d1114b1 SHA256 39b6835dadd156f4070ef4c4b43a4fdcaf4f61c1d763a37211ad493ce9933bdc +AUX dhcp-4.2.0-options.patch 14611 RMD160 456569e5228779869a5e823cb4b5eaa1de9d836c SHA1 376fbe71cb39481cefbe209a74ecc984434f690e SHA256 8555cc3ada3894de53c93127bfe15a8a161515137d8f0a9cc6844acca7637e2e +AUX dhcp-4.2.0-xen-checksum.patch 8710 RMD160 1f16ae824b60c56c05063ad29196ca570b1eafca SHA1 6a6509a031bfb39cda38205c99609ac4c4b8924a SHA256 d6dfbea187e943c09b350d156c570be6f3cbb648ac96ba838ad707280a63b3e9 +AUX dhcp-4.2.1-dhclient-resolvconf.patch 13742 RMD160 e226e793ab4d1302dbaf288c3077f3f6c8758b97 SHA1 d4ea97c3383c7f7769ab36c8d36674a3297dc1f9 SHA256 ddc284623b421098702d3e0cc1849b37c015e78dc510aa7efdd2e5fc9b6a849c +AUX dhcp-4.2.1-nogateway.patch 1648 RMD160 820956e072e4a84ffabdee6714377ae23827b7bf SHA1 5c6c8118ee6b4b8524451827756aab052766ca09 SHA256 694caca5fbcf900cef2223307a43fb21a66fd672728cebfd873313730029acc4 +AUX dhcpd.conf 1092 RMD160 936bb112c7cdf8e669b695599252d1f6626be2f3 SHA1 cbabbcea73a0cbc9692462683b983c96d6f18b0c SHA256 b86d27e0560689057b01a352474582fceb3a398eaf3b17f901378ec56284c4d5 +AUX dhcpd.init2 2421 RMD160 baa01ae97b227edba7653cd51735613be2dac652 SHA1 f2068ceb2d79d7992f46b31e6a6e3277a0167dce SHA256 fef93e5a7264780044a977ade27e9cc70de824063791bcd07d3db81c11c16df5 +AUX dhcpd.init3 2525 RMD160 d56c77e6f2e3981c78c3fefad04347615e9d9d60 SHA1 c04f470d0cc3b262cf87cc766ceee5a35aec8b43 SHA256 69f5e6bee391a9a03554bead07c9dd5775e1fbb2a0ae515b7930cec328a8959c +AUX dhcrelay.conf 421 RMD160 456edbc9bcc8d3a44db5bb6dbf0c3003c3e7419c SHA1 78ecdb000382893fb49d0052ced063955b0ad9cf SHA256 409b895ed489e75c1a08f72961b45d641b93fd9357f528abc78b1fd036b7f730 +AUX dhcrelay.init 736 RMD160 04566b87bd6dbb8bb754b26409ca30b878ef3ca3 SHA1 72742b308314b2e1476b27e94212fbf4d179adc4 SHA256 cfdaff3a723be3935d06c14e171d4008f2ad3329bd05ac2e49c19bc0e14bc59c +AUX dhcrelay.init2 712 RMD160 2baeaf7c0fb8a5796792b5721f32104907243798 SHA1 ced20da5625b6517fa6044ce179e1c5d9a17297e SHA256 6cca726147474c600662b0c2e49eb5aa148a7a9af1358dbc56f16b1d08255ae3 +DIST dhcp-4.2.1-P1.tar.gz 8797289 RMD160 e3607828ea12eb718c0877430f9607d336d78c36 SHA1 7767019313b4128357054a1eb053c66799831dd6 SHA256 6cd5e06512c53ad43d71400f39071ce0bd07f074e416c727d5bc7e5949ec55ec +EBUILD dhcp-4.2.1_p1-r1.ebuild 6878 RMD160 c6b512021e9aaefc753437a99e410f6b32b7762b SHA1 bb749bc393eebf05ed2ec16e9b22401ea65b597f SHA256 7c93402e1a501f5ed2e53cf4d410a350ca6bee6c5499a80a4126522f18a560df +MISC ChangeLog 348 RMD160 140574ebdec8c3293b81b76444f11f942e22bc65 SHA1 44c98802fab59d59eba55e44f4655e389ee85eee SHA256 962de6f2bba37062163d90bb1d0089ce617c9ee34781575d6487da91db95f53b +MISC metadata.xml 554 RMD160 8dd1a37b5afc3652e3071f11ad13949b216a26f9 SHA1 7b971bf09188a332c9026c358193840d8a54bb49 SHA256 64f78ebffdcfdd9d8e39eb8fee99ed1799569561bc90383ded51ebdc8f9033b5 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F5VUACgkQgAnW8HDreRYltwCfdUBWXcVYo5gh3uU6MiAbiFnM +ZUMAoJfETVuvUJhGYUU+CSS12LZ1DvAd +=aEtu +-----END PGP SIGNATURE----- diff --git a/net-misc/dhcp/dhcp-4.2.1_p1-r1.ebuild b/net-misc/dhcp/dhcp-4.2.1_p1-r1.ebuild new file mode 100644 index 000000000..c7966f92b --- /dev/null +++ b/net-misc/dhcp/dhcp-4.2.1_p1-r1.ebuild @@ -0,0 +1,231 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/net-misc/dhcp/dhcp-4.2.1_p1.ebuild,v 1.2 2011/04/15 21:40:50 ulm Exp $ + +EAPI="2" + +inherit eutils + +MY_PV="${PV//_alpha/a}" +MY_PV="${MY_PV//_beta/b}" +MY_PV="${MY_PV//_rc/rc}" +MY_PV="${MY_PV//_p/-P}" +MY_P="${PN}-${MY_PV}" +DESCRIPTION="ISC Dynamic Host Configuration Protocol (DHCP) client/server" +HOMEPAGE="http://www.isc.org/products/DHCP" +SRC_URI="ftp://ftp.isc.org/isc/dhcp/${MY_P}.tar.gz" + +LICENSE="as-is BSD" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~sparc-fbsd ~x86 ~x86-fbsd" +IUSE="+client infiniband ipv6 kernel_linux ldap selinux +server ssl vim-syntax" + +DEPEND="selinux? ( sec-policy/selinux-dhcp ) + kernel_linux? ( sys-apps/net-tools ) + vim-syntax? ( app-vim/dhcpd-syntax ) + ldap? ( + net-nds/openldap + ssl? ( dev-libs/openssl ) + )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + # Gentoo patches - these will probably never be accepted upstream + # Fix some permission issues + epatch "${FILESDIR}"/${PN}-3.0-fix-perms.patch + # Enable dhclient to equery NTP servers + epatch "${FILESDIR}"/${PN}-4.0-dhclient-ntp.patch + # resolvconf support in dhclient-script + epatch "${FILESDIR}"/${PN}-4.2.1-dhclient-resolvconf.patch + # Stop downing the interface on Linux as that breaks link daemons + # such as wpa_supplicant and netplug + epatch "${FILESDIR}"/${PN}-3.0.3-dhclient-no-down.patch + epatch "${FILESDIR}"/${PN}-4.2.0-errwarn-message.patch + # Enable dhclient to get extra configuration from stdin + epatch "${FILESDIR}"/${PN}-4.0.1-dhclient-stdin-conf.patch + epatch "${FILESDIR}"/${PN}-4.2.1-nogateway.patch #265531 + + # NetworkManager support patches + # If they fail to apply to future versions they will be dropped + # Add dbus support to dhclient + epatch "${FILESDIR}"/${PN}-3.0.3-dhclient-dbus.patch + + # Infiniband stuff + if use infiniband; then + epatch "${FILESDIR}/${PN}-4.2.0-improved-xid.patch" + epatch "${FILESDIR}/${PN}-lpf-ib.patch" + epatch "${FILESDIR}/${PN}-options.patch" + epatch "${FILESDIR}/${PN}-xen-checksum.patch" + fi + + # Brand the version with Gentoo + sed -i \ + -e "/VERSION=/s:'$: Gentoo-${PR}':" \ + configure || die + + # Change the hook script locations of the scripts + sed -i \ + -e 's,/etc/dhclient-exit-hooks,/etc/dhcp/dhclient-exit-hooks,g' \ + -e 's,/etc/dhclient-enter-hooks,/etc/dhcp/dhclient-enter-hooks,g' \ + client/scripts/* || die + + # No need for the linux script to force bash, #158540. + sed -i -e 's,#!/bin/bash,#!/bin/sh,' client/scripts/linux || die + + # Quiet the freebsd logger a little + sed -i -e '/LOGGER=/ s/-s -p user.notice //g' client/scripts/freebsd || die + + # Remove these options from the sample config + sed -i \ + -e "/\(script\|host-name\|domain-name\) / d" \ + client/dhclient.conf || die + + if use client && ! use server ; then + sed -i -r \ + -e '/^SUBDIRS/s:\<(dhcpctl|relay|server)\>::g' \ + Makefile.in || die + elif ! use client && use server ; then + sed -i -r \ + -e '/^SUBDIRS/s:\<client\>::' \ + Makefile.in || die + fi + + # Only install different man pages if we don't have en + if [[ " ${LINGUAS} " != *" en "* ]]; then + # Install Japanese man pages + if [[ " ${LINGUAS} " == *" ja "* && -d doc/ja_JP.eucJP ]]; then + einfo "Installing Japanese documention" + cp doc/ja_JP.eucJP/dhclient* client + cp doc/ja_JP.eucJP/dhcp* common + fi + fi + # Now remove the non-english docs so there are no errors later + rm -rf doc/ja_JP.eucJP +} + +src_configure() { + econf \ + --enable-paranoia \ + --sysconfdir=/etc/dhcp \ + --with-cli-pid-file=/var/run/dhcp/dhclient.pid \ + --with-cli-lease-file=/var/lib/dhcp/dhclient.leases \ + --with-cli6-pid-file=/var/run/dhcp/dhclient6.pid \ + --with-cli6-lease-file=/var/lib/dhcp/dhclient6.leases \ + --with-srv-pid-file=/var/run/dhcp/dhcpd.pid \ + --with-srv-lease-file=/var/lib/dhcp/dhcpd.leases \ + --with-srv6-pid-file=/var/run/dhcp/dhcpd6.pid \ + --with-srv6-lease-file=/var/lib/dhcp/dhcpd6.leases \ + --with-relay-pid-file=/var/run/dhcp/dhcrelay.pid \ + $(use_enable ipv6 dhcpv6) \ + $(use_with ldap) \ + $(use ldap && use_with ssl ldapcrypto || echo --without-ldapcrypto) +} + +src_install() { + emake install DESTDIR="${D}" || die + + dodoc README RELNOTES doc/{api+protocol,IANA-arp-parameters} + dohtml doc/References.html + + if [[ -e client/dhclient ]] ; then + # move the client to / + dodir /sbin + mv "${D}"/usr/sbin/dhclient "${D}"/sbin/ || die + + exeinto /sbin + if use kernel_linux ; then + newexe "${S}"/client/scripts/linux dhclient-script || die + else + newexe "${S}"/client/scripts/freebsd dhclient-script || die + fi + + insinto /etc/dhcp + doins client/dhclient.conf || die + + keepdir /var/lib/dhclient + fi + + if [[ -e server/dhcpd ]] ; then + if use ldap ; then + insinto /etc/openldap/schema + doins contrib/ldap/dhcp.* || die + dosbin contrib/ldap/dhcpd-conf-to-ldap || die + fi + + newinitd "${FILESDIR}"/dhcpd.init3 dhcpd + newinitd "${FILESDIR}"/dhcrelay.init2 dhcrelay + newconfd "${FILESDIR}"/dhcpd.conf dhcpd + newconfd "${FILESDIR}"/dhcrelay.conf dhcrelay + + insinto /etc/dhcp + doins server/dhcpd.conf || die + + keepdir /var/{lib,run}/dhcp + fi +} + +pkg_preinst() { + enewgroup dhcp + enewuser dhcp -1 -1 /var/lib/dhcp dhcp + + # Keep the user files over the sample ones + local f + for f in dhclient dhcpd ; do + f="/etc/dhcp/${f}.conf" + if [ -e "${ROOT}"${f} ] ; then + cp -p "${ROOT}"${f} "${D}"${f} + fi + done +} + +pkg_postinst() { + chown -R dhcp:dhcp "${ROOT}"/var/{lib,run}/dhcp + + if [[ -e "${ROOT}"/etc/init.d/dhcp ]] ; then + ewarn + ewarn "WARNING: The dhcp init script has been renamed to dhcpd" + ewarn "/etc/init.d/dhcp and /etc/conf.d/dhcp need to be removed and" + ewarn "and dhcp should be removed from the default runlevel" + ewarn + fi + + einfo "You can edit /etc/conf.d/dhcpd to customize dhcp settings." + einfo + einfo "If you would like to run dhcpd in a chroot, simply configure the" + einfo "DHCPD_CHROOT directory in /etc/conf.d/dhcpd and then run:" + einfo " emerge --config =${PF}" +} + +pkg_config() { + local CHROOT="$( + sed -n -e 's/^[[:blank:]]\?DHCPD_CHROOT="*\([^#"]\+\)"*/\1/p' \ + "${ROOT}"/etc/conf.d/dhcpd + )" + + if [[ -z ${CHROOT} ]]; then + eerror "CHROOT not defined in /etc/conf.d/dhcpd" + return 1 + fi + + CHROOT="${ROOT}/${CHROOT}" + + if [[ -d ${CHROOT} ]] ; then + ewarn "${CHROOT} already exists - aborting" + return 0 + fi + + ebegin "Setting up the chroot directory" + mkdir -m 0755 -p "${CHROOT}/"{dev,etc,var/lib,var/run/dhcp} + cp /etc/{localtime,resolv.conf} "${CHROOT}"/etc + cp -R /etc/dhcp "${CHROOT}"/etc + cp -R /var/lib/dhcp "${CHROOT}"/var/lib + ln -s ../../var/lib/dhcp "${CHROOT}"/etc/dhcp/lib + chown -R dhcp:dhcp "${CHROOT}"/var/{lib,run}/dhcp + eend 0 + + local logger="$(best_version virtual/logger)" + einfo "To enable logging from the dhcpd server, configure your" + einfo "logger (${logger}) to listen on ${CHROOT}/dev/log" +} diff --git a/net-misc/dhcp/files/dhcp-3.0-fix-perms.patch b/net-misc/dhcp/files/dhcp-3.0-fix-perms.patch new file mode 100644 index 000000000..13debb20e --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0-fix-perms.patch @@ -0,0 +1,15 @@ +--- server/dhcpd.c 2003-11-05 14:08:09.000000000 -0800 ++++ server/dhcpd.c 2003-11-05 14:15:32.000000000 -0800 +@@ -602,6 +602,12 @@ + if (lftest) + exit (0); + ++#if defined (PARANOIA) ++ /* Set proper permissions... */ ++ if (lchown (path_dhcpd_db, set_uid, set_gid)) ++ log_fatal ("lchown(%s, %d, %d): %m", path_dhcpd_db, (int) set_uid, (int) set_gid); ++#endif /* PARANOIA */ ++ + /* Discover all the network interfaces and initialize them. */ + discover_interfaces (DISCOVER_SERVER); + diff --git a/net-misc/dhcp/files/dhcp-3.0-paranoia.patch b/net-misc/dhcp/files/dhcp-3.0-paranoia.patch new file mode 100644 index 000000000..886f5cb5f --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0-paranoia.patch @@ -0,0 +1,207 @@ + +paranoia (non-root/chroot) patch for ISC dhcp 3.0 +file to patch: dhcp-3.0/server/dhcpd.c + +update from paranoia patch for ISC dhcp 2.0 + +Adds 3 options: + + -user <user> + -group <group> + -chroot <chroot_dir> + +Notes: + -DPARANOIA must be passed as an argument to the --copts option + of configure. Otherwise, the paranoia code will not be compiled + in. Example: ./configure --copts -DPARANOIA + + The chroot() call has been delayed in order to allow /dev/log to + be reopened after the configuration file has been read. This is + beneficial for systems on which /dev/log is a unix domain socket. + The main side effect is that dhcpd.conf should be placed in /etc, + instead of <chroot_dir>/etc. + + If dhcpd is to be run on a sysV-style architecture (or, more + generally, if /dev/log is a character device), one may opt to + create the <chroot_dir>/dev/log character device and add + -DEARLY_CHROOT to the --copts option of configure (in addition to + -DPARANOIA). This will perform the chroot() call at the earliest + convenience (before reading the configuration file). + + If the -user option is used, the lease and pid file directories + should be writable to the server process after it drops + privileges. + + +ari edelkind (12/10/2001) +last modified 12/10/2001 + + +--- dhcp-3.0/server/dhcpd.c Thu Jun 21 22:12:58 2001 ++++ dhcp-3.0+paranoia/server/dhcpd.c Wed Oct 17 08:23:00 2001 +@@ -56,6 +56,16 @@ + #include "version.h" + #include <omapip/omapip_p.h> + ++#if defined (PARANOIA) ++# include <sys/types.h> ++# include <unistd.h> ++# include <pwd.h> ++/* get around the ISC declaration of group */ ++# define group real_group ++# include <grp.h> ++# undef group ++#endif /* PARANOIA */ ++ + static void usage PROTO ((void)); + + TIME cur_time; +@@ -204,6 +214,22 @@ + omapi_object_dereference (&listener, MDL); + } + ++#if defined (PARANOIA) ++/* to be used in one of two possible scenarios */ ++static void setup_chroot (char *chroot_dir) { ++ if (geteuid()) ++ log_fatal ("you must be root to use chroot"); ++ ++ if (chroot(chroot_dir)) { ++ log_fatal ("chroot(\"%s\"): %m", chroot_dir); ++ } ++ if (chdir ("/")) { ++ /* probably permission denied */ ++ log_fatal ("chdir(\"/\"): %m"); ++ } ++} ++#endif /* PARANOIA */ ++ + int main (argc, argv, envp) + int argc; + char **argv, **envp; +@@ -236,6 +262,14 @@ + char *traceinfile = (char *)0; + char *traceoutfile = (char *)0; + #endif ++#if defined (PARANOIA) ++ char *set_user = 0; ++ char *set_group = 0; ++ char *set_chroot = 0; ++ ++ uid_t set_uid = 0; ++ gid_t set_gid = 0; ++#endif /* PARANOIA */ + + /* Make sure we have stdin, stdout and stderr. */ + status = open ("/dev/null", O_RDWR); +@@ -298,6 +332,20 @@ + if (++i == argc) + usage (); + server = argv [i]; ++#if defined (PARANOIA) ++ } else if (!strcmp (argv [i], "-user")) { ++ if (++i == argc) ++ usage (); ++ set_user = argv [i]; ++ } else if (!strcmp (argv [i], "-group")) { ++ if (++i == argc) ++ usage (); ++ set_group = argv [i]; ++ } else if (!strcmp (argv [i], "-chroot")) { ++ if (++i == argc) ++ usage (); ++ set_chroot = argv [i]; ++#endif /* PARANOIA */ + } else if (!strcmp (argv [i], "-cf")) { + if (++i == argc) + usage (); +@@ -397,6 +445,44 @@ + trace_seed_stop, MDL); + #endif + ++#if defined (PARANOIA) ++ /* get user and group info if those options were given */ ++ if (set_user) { ++ struct passwd *tmp_pwd; ++ ++ if (geteuid()) ++ log_fatal ("you must be root to set user"); ++ ++ if (!(tmp_pwd = getpwnam(set_user))) ++ log_fatal ("no such user: %s", set_user); ++ ++ set_uid = tmp_pwd->pw_uid; ++ ++ /* use the user's group as the default gid */ ++ if (!set_group) ++ set_gid = tmp_pwd->pw_gid; ++ } ++ ++ if (set_group) { ++/* get around the ISC declaration of group */ ++#define group real_group ++ struct group *tmp_grp; ++ ++ if (geteuid()) ++ log_fatal ("you must be root to set group"); ++ ++ if (!(tmp_grp = getgrnam(set_group))) ++ log_fatal ("no such group: %s", set_group); ++ ++ set_gid = tmp_grp->gr_gid; ++#undef group ++ } ++ ++# if defined (EARLY_CHROOT) ++ if (set_chroot) setup_chroot (set_chroot); ++# endif /* EARLY_CHROOT */ ++#endif /* PARANOIA */ ++ + /* Default to the DHCP/BOOTP port. */ + if (!local_port) + { +@@ -500,6 +586,10 @@ + + postconf_initialization (quiet); + ++#if defined (PARANOIA) && !defined (EARLY_CHROOT) ++ if (set_chroot) setup_chroot (set_chroot); ++#endif /* PARANOIA && !EARLY_CHROOT */ ++ + /* test option should cause an early exit */ + if (cftest && !lftest) + exit(0); +@@ -543,6 +633,22 @@ + exit (0); + } + ++#if defined (PARANOIA) ++ /* change uid to the specified one */ ++ ++ if (set_gid) { ++ if (setgroups (0, (void *)0)) ++ log_fatal ("setgroups: %m"); ++ if (setgid (set_gid)) ++ log_fatal ("setgid(%d): %m", (int) set_gid); ++ } ++ ++ if (set_uid) { ++ if (setuid (set_uid)) ++ log_fatal ("setuid(%d): %m", (int) set_uid); ++ } ++#endif /* PARANOIA */ ++ + /* Read previous pid file. */ + if ((i = open (path_dhcpd_pid, O_RDONLY)) >= 0) { + status = read (i, pbuf, (sizeof pbuf) - 1); +@@ -888,6 +994,10 @@ + + log_fatal ("Usage: dhcpd [-p <UDP port #>] [-d] [-f]%s%s%s%s", + "\n [-cf config-file] [-lf lease-file]", ++#if defined (PARANOIA) ++ /* meld into the following string */ ++ "\n [-user user] [-group group] [-chroot dir]" ++#endif /* PARANOIA */ + #if defined (TRACING) + "\n [-tf trace-output-file]", + "\n [-play trace-input-file]", diff --git a/net-misc/dhcp/files/dhcp-3.0.2-gmake.patch b/net-misc/dhcp/files/dhcp-3.0.2-gmake.patch new file mode 100644 index 000000000..4ab99a2b7 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0.2-gmake.patch @@ -0,0 +1,66 @@ +Index: dhcp-3.0.2/Makefile +=================================================================== +--- dhcp-3.0.2.orig/Makefile ++++ dhcp-3.0.2/Makefile +@@ -33,7 +33,7 @@ all: + if [ ! -d work.$$sysname ]; then \ + echo No build directory for $$sysname - please run ./configure.; \ + else \ +- (cd work.$$sysname; make all); \ ++ (cd work.$$sysname; $(MAKE) all); \ + fi + + install: +@@ -41,7 +41,7 @@ install: + if [ ! -d work.$$sysname ]; then \ + echo No build directory for $$sysname - please run ./configure.; \ + else \ +- (cd work.$$sysname; make install); \ ++ (cd work.$$sysname; $(MAKE) install); \ + fi + + depend: +@@ -49,7 +49,7 @@ depend: + if [ ! -d work.$$sysname ]; then \ + echo No build directory for $$sysname - please run ./configure.; \ + else \ +- (cd work.$$sysname; make depend); \ ++ (cd work.$$sysname; $(MAKE) depend); \ + fi + + clean: +@@ -57,7 +57,7 @@ clean: + if [ ! -d work.$$sysname ]; then \ + echo No build directory for $$sysname - please run ./configure.; \ + else \ +- (cd work.$$sysname; make clean); \ ++ (cd work.$$sysname; $(MAKE) clean); \ + fi + + realclean: +@@ -65,7 +65,7 @@ realclean: + if [ ! -d work.$$sysname ]; then \ + echo No build directory for $$sysname - please run ./configure.; \ + else \ +- (cd work.$$sysname; make realclean); \ ++ (cd work.$$sysname; $(MAKE) realclean); \ + fi + + distclean: +@@ -73,7 +73,7 @@ distclean: + if [ ! -d work.$$sysname ]; then \ + echo No build directory for $$sysname - please run ./configure.; \ + else \ +- (cd work.$$sysname; make distclean); \ ++ (cd work.$$sysname; $(MAKE) distclean); \ + fi + + links: +@@ -81,6 +81,6 @@ links: + if [ ! -d work.$$sysname ]; then \ + echo No build directory for $$sysname - please run ./configure.; \ + else \ +- (cd work.$$sysname; make links); \ ++ (cd work.$$sysname; $(MAKE) links); \ + fi + diff --git a/net-misc/dhcp/files/dhcp-3.0.3-dhclient-dbus.patch b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-dbus.patch new file mode 100644 index 000000000..579d72f48 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-dbus.patch @@ -0,0 +1,84 @@ +--- client/scripts/bsdos ++++ client/scripts/bsdos +@@ -47,6 +47,11 @@ + . /etc/dhcp/dhclient-exit-hooks + fi + # probably should do something with exit status of the local script ++ if [ x$dhc_dbus != x -a $exit_status -eq 0 ]; then ++ dbus-send --system --dest=com.redhat.dhcp \ ++ --type=method_call /com/redhat/dhcp/$interface com.redhat.dhcp.set \ ++ 'string:'"`env | grep -Ev '^(PATH|SHLVL|_|PWD|dhc_dbus)\='`" ++ fi + exit $exit_status + } + +--- client/scripts/freebsd ++++ client/scripts/freebsd +@@ -57,6 +57,11 @@ + . /etc/dhcp/dhclient-exit-hooks + fi + # probably should do something with exit status of the local script ++ if [ x$dhc_dbus != x -a $exit_status -eq 0 ]; then ++ dbus-send --system --dest=com.redhat.dhcp \ ++ --type=method_call /com/redhat/dhcp/$interface com.redhat.dhcp.set \ ++ 'string:'"`env | grep -Ev '^(PATH|SHLVL|_|PWD|dhc_dbus)\='`" ++ fi + exit $exit_status + } + +--- client/scripts/linux ++++ client/scripts/linux +@@ -69,6 +69,11 @@ + . /etc/dhcp/dhclient-exit-hooks + fi + # probably should do something with exit status of the local script ++ if [ x$dhc_dbus != x -a $exit_status -eq 0 ]; then ++ dbus-send --system --dest=com.redhat.dhcp \ ++ --type=method_call /com/redhat/dhcp/$interface com.redhat.dhcp.set \ ++ 'string:'"`env | grep -Ev '^(PATH|SHLVL|_|PWD|dhc_dbus)\='`" ++ fi + exit $exit_status + } + +--- client/scripts/netbsd ++++ client/scripts/netbsd +@@ -47,6 +47,11 @@ + . /etc/dhcp/dhclient-exit-hooks + fi + # probably should do something with exit status of the local script ++ if [ x$dhc_dbus != x -a $exit_status -eq 0 ]; then ++ dbus-send --system --dest=com.redhat.dhcp \ ++ --type=method_call /com/redhat/dhcp/$interface com.redhat.dhcp.set \ ++ 'string:'"`env | grep -Ev '^(PATH|SHLVL|_|PWD|dhc_dbus)\='`" ++ fi + exit $exit_status + } + +--- client/scripts/openbsd ++++ client/scripts/openbsd +@@ -47,6 +47,11 @@ + . /etc/dhcp/dhclient-exit-hooks + fi + # probably should do something with exit status of the local script ++ if [ x$dhc_dbus != x -a $exit_status -eq 0 ]; then ++ dbus-send --system --dest=com.redhat.dhcp \ ++ --type=method_call /com/redhat/dhcp/$interface com.redhat.dhcp.set \ ++ 'string:'"`env | grep -Ev '^(PATH|SHLVL|_|PWD|dhc_dbus)\='`" ++ fi + exit $exit_status + } + +--- client/scripts/solaris ++++ client/scripts/solaris +@@ -47,6 +47,11 @@ + . /etc/dhcp/dhclient-exit-hooks + fi + # probably should do something with exit status of the local script ++ if [ x$dhc_dbus != x -a $exit_status -eq 0 ]; then ++ dbus-send --system --dest=com.redhat.dhcp \ ++ --type=method_call /com/redhat/dhcp/$interface com.redhat.dhcp.set \ ++ 'string:'"`env | grep -Ev '^(PATH|SHLVL|_|PWD|dhc_dbus)\='`" ++ fi + exit $exit_status + } + diff --git a/net-misc/dhcp/files/dhcp-3.0.3-dhclient-hostname.patch b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-hostname.patch new file mode 100644 index 000000000..9a6e7b969 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-hostname.patch @@ -0,0 +1,16 @@ +--- client/scripts/linux ++++ client/scripts/linux +@@ -138,10 +138,12 @@ + [ x$reason = xREBIND ] || [ x$reason = xREBOOT ]; then + current_hostname=`hostname` + if [ x$current_hostname = x ] || \ ++ [ x$current_hostname = "x(none)" ] || \ ++ [ x$current_hostname = xlocalhost ] || \ + [ x$current_hostname = x$old_host_name ]; then + if [ x$current_hostname = x ] || \ + [ x$new_host_name != x$old_host_name ]; then +- hostname $new_host_name ++ hostname "$new_host_name" + fi + fi + diff --git a/net-misc/dhcp/files/dhcp-3.0.3-dhclient-metric.patch b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-metric.patch new file mode 100644 index 000000000..040ef779d --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-metric.patch @@ -0,0 +1,200 @@ +--- client/scripts/bsdos ++++ client/scripts/bsdos +@@ -84,6 +84,9 @@ + if [ x$new_interface_mtu != x ]; then + mtu_arg="mtu $new_interface_mtu" + fi ++if [ x$IF_METRIC != x ]; then ++ metric_arg="metric $IF_METRIC" ++fi + + if [ x$reason = xMEDIUM ]; then + eval "ifconfig $interface $medium" +@@ -141,7 +144,7 @@ + if [ x$old_ip_address = x ] || [ x$old_ip_address != x$new_ip_address ] || \ + [ x$reason = xBOUND ] || [ x$reason = xREBOOT ]; then + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $mtu_arg $medium" ++ $new_broadcast_arg $mtu_arg $metric_arg $medium" + route add $new_ip_address 127.1 >/dev/null 2>&1 + for router in $new_routers; do + route add default $router >/dev/null 2>&1 +@@ -198,7 +201,7 @@ + route delete $alias_ip_address 127.0.0.1 > /dev/null 2>&1 + fi + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $mtu_arg $medium" ++ $new_broadcast_arg $mtu_arg $metric_arg $medium" + sleep 1 + if [ "$new_routers" != "" ]; then + set $new_routers +--- client/scripts/freebsd ++++ client/scripts/freebsd +@@ -94,6 +94,9 @@ + if [ x$new_interface_mtu != x ]; then + mtu_arg="mtu $new_interface_mtu" + fi ++if [ x$IF_METRIC != x ]; then ++ metric_arg="metric $IF_METRIC" ++fi + + if [ x$reason = xMEDIUM ]; then + eval "ifconfig $interface $medium" +@@ -151,7 +154,7 @@ + if [ x$old_ip_address = x ] || [ x$old_ip_address != x$new_ip_address ] || \ + [ x$reason = xBOUND ] || [ x$reason = xREBOOT ]; then + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $mtu_arg $medium" ++ $new_broadcast_arg $mtu_arg $metric_arg $medium" + $LOGGER "New IP Address ($interface): $new_ip_address" + $LOGGER "New Subnet Mask ($interface): $new_subnet_mask" + $LOGGER "New Broadcast Address ($interface): $new_broadcast_address" +@@ -215,7 +218,7 @@ + route delete $alias_ip_address 127.0.0.1 > /dev/null 2>&1 + fi + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $mtu_arg $medium" ++ $new_broadcast_arg $mtu_arg $metric_arg $medium" + $LOGGER "New IP Address ($interface): $new_ip_address" + $LOGGER "New Subnet Mask ($interface): $new_subnet_mask" + $LOGGER "New Broadcast Address ($interface): $new_broadcast_address" +--- client/scripts/linux ++++ client/scripts/linux +@@ -83,11 +83,6 @@ + fi + fi + +-release=`uname -r` +-release=`expr $release : '\(.*\)\..*'` +-relminor=`echo $release |sed -e 's/[0-9]*\.\([0-9][0-9]*\)\(\..*\)*$/\1/'` +-relmajor=`echo $release |sed -e 's/\([0-9][0-9]*\)\..*$/\1/'` +- + if [ x$new_broadcast_address != x ]; then + new_broadcast_arg="broadcast $new_broadcast_address" + fi +@@ -106,6 +101,9 @@ + if [ x$new_interface_mtu != x ]; then + mtu_arg="mtu $new_interface_mtu" + fi ++if [ x$IF_METRIC != x ]; then ++ metric_arg="metric $IF_METRIC" ++fi + + if [ x$reason = xMEDIUM ]; then + # Linux doesn't do mediums (ok, ok, media). +@@ -117,15 +115,7 @@ + # Bring down alias interface. Its routes will disappear too. + ifconfig $interface:0- inet 0 + fi +- if [ $relmajor -lt 2 ] || ( [ $relmajor -eq 2 ] && [ $relminor -eq 0 ] ) +- then +- ifconfig $interface inet 0.0.0.0 netmask 0.0.0.0 \ +- broadcast 255.255.255.255 up +- # Add route to make broadcast work. Do not omit netmask. +- route add default dev $interface netmask 0.0.0.0 +- else +- ifconfig $interface 0 up +- fi ++ ifconfig $interface 0 up + + # We need to give the kernel some time to get the interface up. + sleep 1 +@@ -164,12 +154,14 @@ + ifconfig $interface inet $new_ip_address $new_subnet_arg \ + $new_broadcast_arg $mtu_arg + # Add a network route to the computed network address. +- if [ $relmajor -lt 2 ] || \ +- ( [ $relmajor -eq 2 ] && [ $relminor -eq 0 ] ); then +- route add -net $new_network_number $new_subnet_arg dev $interface ++ if [ x$IF_METRIC != x ] && [ x$IF_METRIC != x0 ]; then ++ route del -net $new_network_number $new_subnet_arg \ ++ dev $interface ++ route add -net $new_network_number $new_subnet_arg $metric_arg \ ++ dev $interface + fi + for router in $new_routers; do +- route add default gw $router ++ route add default gw $router $metric_arg dev $interface + done + fi + if [ x$new_ip_address != x$alias_ip_address ] && [ x$alias_ip_address != x ]; +@@ -213,12 +205,15 @@ + ifconfig $interface:0 inet $alias_ip_address $alias_subnet_arg + route add -host $alias_ip_address dev $interface:0 + fi +- if [ $relmajor -lt 2 ] || \ +- ( [ $relmajor -eq 2 ] && [ $relminor -eq 0 ] ); then +- route add -net $new_network_number ++ # Add a network route to the computed network address. ++ if [ x$IF_METRIC != x ] && [ x$IF_METRIC != x0 ]; then ++ route del -net $new_network_number $new_subnet_arg \ ++ dev $interface ++ route add -net $new_network_number $new_subnet_arg $metric_arg \ ++ dev $interface + fi + for router in $new_routers; do +- route add default gw $router ++ route add default gw $router $metric_arg dev $interface + done + make_resolv_conf + exit_with_hooks 0 +--- client/scripts/netbsd ++++ client/scripts/netbsd +@@ -84,6 +84,9 @@ + if [ x$new_interface_mtu != x ]; then + mtu_arg="mtu $new_interface_mtu" + fi ++if [ x$IF_METRIC != x ]; then ++ metric_arg="metric $IF_METRIC" ++fi + + if [ x$reason = xMEDIUM ]; then + eval "ifconfig $interface $medium" +@@ -141,7 +144,7 @@ + if [ x$old_ip_address = x ] || [ x$old_ip_address != x$new_ip_address ] || \ + [ x$reason = xBOUND ] || [ x$reason = xREBOOT ]; then + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $mtu_arg $medium" ++ $new_broadcast_arg $mtu_arg $metric_arg $medium" + route add $new_ip_address 127.1 >/dev/null 2>&1 + for router in $new_routers; do + route add default $router >/dev/null 2>&1 +@@ -198,7 +201,7 @@ + route delete $alias_ip_address 127.0.0.1 > /dev/null 2>&1 + fi + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $mtu_arg $medium" ++ $new_broadcast_arg $mtu_arg $metric_arg $medium" + sleep 1 + if [ "$new_routers" != "" ]; then + set $new_routers +--- client/scripts/solaris ++++ client/scripts/solaris +@@ -79,6 +79,9 @@ + if [ x$new_interface_mtu != x ]; then + mtu_arg="mtu $new_interface_mtu" + fi ++if [ x$IF_METRIC != x ]; then ++ metric_arg="metric $IF_METRIC" ++fi + + ifconfig=/sbin/ifconfig + +@@ -141,7 +144,7 @@ + if [ x$old_ip_address = x ] || [ x$old_ip_address != x$new_ip_address ] || \ + [ x$reason = xBOUND ] || [ x$reason = xREBOOT ]; then + eval "$ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $mtu_arg $medium" ++ $new_broadcast_arg $mtu_arg $metric_arg $medium" + route add $new_ip_address 127.1 1 >/dev/null 2>&1 + for router in $new_routers; do + route add default $router 1 >/dev/null 2>&1 +@@ -182,7 +185,7 @@ + route delete $alias_ip_address 127.0.0.1 > /dev/null 2>&1 + fi + eval "$ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $mtu_arg $medium" ++ $new_broadcast_arg $mtu_arg $metric_arg $medium" + sleep 1 + set $new_routers + if ping -s -n -I 1 $1 64 1; then diff --git a/net-misc/dhcp/files/dhcp-3.0.3-dhclient-mtu.patch b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-mtu.patch new file mode 100644 index 000000000..5ef4442d8 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-mtu.patch @@ -0,0 +1,180 @@ +--- client/scripts/bsdos ++++ client/scripts/bsdos +@@ -81,6 +81,9 @@ + if [ x$alias_subnet_mask != x ]; then + alias_subnet_arg="netmask $alias_subnet_mask" + fi ++if [ x$new_interface_mtu != x ]; then ++ mtu_arg="mtu $new_interface_mtu" ++fi + + if [ x$reason = xMEDIUM ]; then + eval "ifconfig $interface $medium" +@@ -138,7 +141,7 @@ + if [ x$old_ip_address = x ] || [ x$old_ip_address != x$new_ip_address ] || \ + [ x$reason = xBOUND ] || [ x$reason = xREBOOT ]; then + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $medium" ++ $new_broadcast_arg $mtu_arg $medium" + route add $new_ip_address 127.1 >/dev/null 2>&1 + for router in $new_routers; do + route add default $router >/dev/null 2>&1 +@@ -195,7 +198,7 @@ + route delete $alias_ip_address 127.0.0.1 > /dev/null 2>&1 + fi + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $medium" ++ $new_broadcast_arg $mtu_arg $medium" + sleep 1 + if [ "$new_routers" != "" ]; then + set $new_routers +--- client/scripts/freebsd ++++ client/scripts/freebsd +@@ -91,6 +91,9 @@ + if [ x$alias_subnet_mask != x ]; then + alias_subnet_arg="netmask $alias_subnet_mask" + fi ++if [ x$new_interface_mtu != x ]; then ++ mtu_arg="mtu $new_interface_mtu" ++fi + + if [ x$reason = xMEDIUM ]; then + eval "ifconfig $interface $medium" +@@ -148,7 +151,7 @@ + if [ x$old_ip_address = x ] || [ x$old_ip_address != x$new_ip_address ] || \ + [ x$reason = xBOUND ] || [ x$reason = xREBOOT ]; then + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $medium" ++ $new_broadcast_arg $mtu_arg $medium" + $LOGGER "New IP Address ($interface): $new_ip_address" + $LOGGER "New Subnet Mask ($interface): $new_subnet_mask" + $LOGGER "New Broadcast Address ($interface): $new_broadcast_address" +@@ -212,7 +215,7 @@ + route delete $alias_ip_address 127.0.0.1 > /dev/null 2>&1 + fi + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $medium" ++ $new_broadcast_arg $mtu_arg $medium" + $LOGGER "New IP Address ($interface): $new_ip_address" + $LOGGER "New Subnet Mask ($interface): $new_subnet_mask" + $LOGGER "New Broadcast Address ($interface): $new_broadcast_address" +--- client/scripts/linux ++++ client/scripts/linux +@@ -103,6 +103,9 @@ + if [ x$alias_subnet_mask != x ]; then + alias_subnet_arg="netmask $alias_subnet_mask" + fi ++if [ x$new_interface_mtu != x ]; then ++ mtu_arg="mtu $new_interface_mtu" ++fi + + if [ x$reason = xMEDIUM ]; then + # Linux doesn't do mediums (ok, ok, media). +@@ -159,7 +162,7 @@ + [ x$reason = xBOUND ] || [ x$reason = xREBOOT ]; then + + ifconfig $interface inet $new_ip_address $new_subnet_arg \ +- $new_broadcast_arg ++ $new_broadcast_arg $mtu_arg + # Add a network route to the computed network address. + if [ $relmajor -lt 2 ] || \ + ( [ $relmajor -eq 2 ] && [ $relminor -eq 0 ] ); then +@@ -201,7 +204,7 @@ + ifconfig $interface:0- inet 0 + fi + ifconfig $interface inet $new_ip_address $new_subnet_arg \ +- $new_broadcast_arg ++ $new_broadcast_arg $mtu_arg + set $new_routers + ############## what is -w in ping? + if ping -q -c 1 $1; then +--- client/scripts/netbsd ++++ client/scripts/netbsd +@@ -81,6 +81,9 @@ + if [ x$alias_subnet_mask != x ]; then + alias_subnet_arg="netmask $alias_subnet_mask" + fi ++if [ x$new_interface_mtu != x ]; then ++ mtu_arg="mtu $new_interface_mtu" ++fi + + if [ x$reason = xMEDIUM ]; then + eval "ifconfig $interface $medium" +@@ -138,7 +141,7 @@ + if [ x$old_ip_address = x ] || [ x$old_ip_address != x$new_ip_address ] || \ + [ x$reason = xBOUND ] || [ x$reason = xREBOOT ]; then + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $medium" ++ $new_broadcast_arg $mtu_arg $medium" + route add $new_ip_address 127.1 >/dev/null 2>&1 + for router in $new_routers; do + route add default $router >/dev/null 2>&1 +@@ -195,7 +198,7 @@ + route delete $alias_ip_address 127.0.0.1 > /dev/null 2>&1 + fi + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $medium" ++ $new_broadcast_arg $mtu_arg $medium" + sleep 1 + if [ "$new_routers" != "" ]; then + set $new_routers +--- client/scripts/openbsd ++++ client/scripts/openbsd +@@ -81,6 +81,9 @@ + if [ x$alias_subnet_mask != x ]; then + alias_subnet_arg="netmask $alias_subnet_mask" + fi ++if [ x$new_interface_mtu != x ]; then ++ mtu_arg="mtu $new_interface_mtu" ++fi + + if [ x$reason = xMEDIUM ]; then + eval "ifconfig $interface $medium" +@@ -138,7 +141,7 @@ + if [ x$old_ip_address = x ] || [ x$old_ip_address != x$new_ip_address ] || \ + [ x$reason = xBOUND ] || [ x$reason = xREBOOT ]; then + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $medium" ++ $new_broadcast_arg $mtu_arg $medium" + route add $new_ip_address 127.1 >/dev/null 2>&1 + for router in $new_routers; do + route add default $router >/dev/null 2>&1 +@@ -195,7 +198,7 @@ + route delete $alias_ip_address 127.0.0.1 > /dev/null 2>&1 + fi + eval "ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $medium" ++ $new_broadcast_arg $mtu_arg $medium" + sleep 1 + if [ "$new_routers" != "" ]; then + set $new_routers +--- client/scripts/solaris ++++ client/scripts/solaris +@@ -76,6 +76,9 @@ + if [ x$alias_subnet_mask != x ]; then + alias_subnet_arg="netmask $alias_subnet_mask" + fi ++if [ x$new_interface_mtu != x ]; then ++ mtu_arg="mtu $new_interface_mtu" ++fi + + ifconfig=/sbin/ifconfig + +@@ -138,7 +141,7 @@ + if [ x$old_ip_address = x ] || [ x$old_ip_address != x$new_ip_address ] || \ + [ x$reason = xBOUND ] || [ x$reason = xREBOOT ]; then + eval "$ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $medium" ++ $new_broadcast_arg $mtu_arg $medium" + route add $new_ip_address 127.1 1 >/dev/null 2>&1 + for router in $new_routers; do + route add default $router 1 >/dev/null 2>&1 +@@ -179,7 +182,7 @@ + route delete $alias_ip_address 127.0.0.1 > /dev/null 2>&1 + fi + eval "$ifconfig $interface inet $new_ip_address $new_netmask_arg \ +- $new_broadcast_arg $medium" ++ $new_broadcast_arg $mtu_arg $medium" + sleep 1 + set $new_routers + if ping -s -n -I 1 $1 64 1; then diff --git a/net-misc/dhcp/files/dhcp-3.0.3-dhclient-no-down.patch b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-no-down.patch new file mode 100644 index 000000000..518efec11 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-no-down.patch @@ -0,0 +1,70 @@ +--- client/scripts/linux ++++ client/scripts/linux +@@ -118,9 +118,9 @@ + if [ x$reason = xPREINIT ]; then + if [ x$alias_ip_address != x ]; then + # Bring down alias interface. Its routes will disappear too. +- ifconfig $interface:0- inet 0 ++ ifconfig $interface:0- inet 0.0.0.0 + fi +- ifconfig $interface 0 up ++ ifconfig $interface 0.0.0.0 up + + # We need to give the kernel some time to get the interface up. + sleep 1 +@@ -145,12 +145,12 @@ + if [ x$old_ip_address != x ] && [ x$alias_ip_address != x ] && \ + [ x$alias_ip_address != x$old_ip_address ]; then + # Possible new alias. Remove old alias. +- ifconfig $interface:0- inet 0 ++ ifconfig $interface:0- inet 0.0.0.0 + fi + if [ x$old_ip_address != x ] && [ x$old_ip_address != x$new_ip_address ]; then + # IP address changed. Bringing down the interface will delete all routes, + # and clear the ARP cache. +- ifconfig $interface inet 0 down ++ ifconfig $interface inet 0.0.0.0 + + fi + if [ x$old_ip_address = x ] || [ x$old_ip_address != x$new_ip_address ] || \ +@@ -171,7 +171,7 @@ + fi + if [ x$new_ip_address != x$alias_ip_address ] && [ x$alias_ip_address != x ]; + then +- ifconfig $interface:0- inet 0 ++ ifconfig $interface:0- inet 0.0.0.0 + ifconfig $interface:0 inet $alias_ip_address $alias_subnet_arg + route add -host $alias_ip_address $interface:0 + fi +@@ -183,11 +183,11 @@ + || [ x$reason = xSTOP ]; then + if [ x$alias_ip_address != x ]; then + # Turn off alias interface. +- ifconfig $interface:0- inet 0 ++ ifconfig $interface:0- inet 0.0.0.0 + fi + if [ x$old_ip_address != x ]; then + # Shut down interface, which will delete routes and clear arp cache. +- ifconfig $interface inet 0 down ++ ifconfig $interface inet 0.0.0.0 + fi + if [ x$alias_ip_address != x ]; then + ifconfig $interface:0 inet $alias_ip_address $alias_subnet_arg +@@ -198,7 +198,7 @@ + + if [ x$reason = xTIMEOUT ]; then + if [ x$alias_ip_address != x ]; then +- ifconfig $interface:0- inet 0 ++ ifconfig $interface:0- inet 0.0.0.0 + fi + ifconfig $interface inet $new_ip_address $new_subnet_arg \ + $new_broadcast_arg $mtu_arg +@@ -223,7 +223,7 @@ + make_resolv_conf + exit_with_hooks 0 + fi +- ifconfig $interface inet 0 down ++ ifconfig $interface inet 0.0.0.0 + exit_with_hooks 1 + fi + diff --git a/net-misc/dhcp/files/dhcp-3.0.3-dhclient-ntp.patch b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-ntp.patch new file mode 100644 index 000000000..d84e6f613 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0.3-dhclient-ntp.patch @@ -0,0 +1,186 @@ +--- client/clparse.c ++++ client/clparse.c +@@ -51,6 +51,7 @@ + DHO_DOMAIN_NAME, + DHO_DOMAIN_NAME_SERVERS, + DHO_HOST_NAME, ++ DHO_NTP_SERVERS, + 0 + }; + +--- client/scripts/bsdos ++++ client/scripts/bsdos +@@ -7,6 +7,26 @@ + echo nameserver $nameserver >>/etc/resolv.conf + done + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf ++} ++ ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ x$new_ntp_servers != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi + } + + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. +--- client/scripts/freebsd ++++ client/scripts/freebsd +@@ -32,8 +32,28 @@ + done + fi + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf + } + ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ "x$new_ntp_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi ++} ++ + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. + exit_with_hooks() { + exit_status=$1 +--- client/scripts/linux ++++ client/scripts/linux +@@ -30,6 +30,26 @@ + echo nameserver $nameserver >>/etc/resolv.conf + done + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf ++} ++ ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ "x$new_ntp_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi + } + + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. +--- client/scripts/netbsd ++++ client/scripts/netbsd +@@ -7,6 +7,26 @@ + echo nameserver $nameserver >>/etc/resolv.conf + done + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf ++} ++ ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ "x$new_ntp_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi + } + + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. +--- client/scripts/openbsd ++++ client/scripts/openbsd +@@ -7,6 +7,26 @@ + echo nameserver $nameserver >>/etc/resolv.conf + done + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf ++} ++ ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ "x$new_ntp_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi + } + + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. +--- client/scripts/solaris ++++ client/scripts/solaris +@@ -7,6 +7,26 @@ + echo nameserver $nameserver >>/etc/resolv.conf + done + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf ++} ++ ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ "x$new_ntp_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi + } + + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. diff --git a/net-misc/dhcp/files/dhcp-3.0.3-libdst.patch b/net-misc/dhcp/files/dhcp-3.0.3-libdst.patch new file mode 100644 index 000000000..8e93ac95b --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0.3-libdst.patch @@ -0,0 +1,14 @@ +--- dst/Makefile.dist.old 2004-12-24 13:31:22.986061032 +0000 ++++ dst/Makefile.dist 2004-12-24 13:47:19.036913364 +0000 +@@ -31,6 +31,10 @@ + all: libdst.a + + install: ++ mkdir -p $(DESTDIR)$(LIBDIR) ++ $(INSTALL) libdst.a $(DESTDIR)$(LIBDIR) ++ $(CHMOD) 644 $(DESTDIR)$(LIBDIR)/libdst.a ++ + + libdst.a: $(OBJ) + rm -f dst.a + diff --git a/net-misc/dhcp/files/dhcp-3.0.3-no_isc_blurb.patch b/net-misc/dhcp/files/dhcp-3.0.3-no_isc_blurb.patch new file mode 100644 index 000000000..38f7713f5 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0.3-no_isc_blurb.patch @@ -0,0 +1,105 @@ +Patch nobbled from RedHat, and adapted to work with dhclient and dhrelay +by Roy Marples <uberlord@gentoo.org> + +--- dhcp-3.0.3/omapip/errwarn.c.no_isc_blurb 2004-09-30 16:38:32.000000000 -0400 ++++ dhcp-3.0.3/omapip/errwarn.c 2005-04-18 13:45:49.037158000 -0400 +@@ -45,6 +45,8 @@ + int log_perror = 1; + #endif + int log_priority; ++int log_isc_blurb=1; ++ + void (*log_cleanup) (void); + + #define CVT_BUF_MAX 1023 +@@ -76,7 +78,9 @@ + write (STDERR_FILENO, "\n", 1); + } + +-#if !defined (NOMINUM) ++#if !defined(NOMINUM) ++ if ( log_isc_blurb ) ++ { + log_error ("%s", ""); + log_error ("If you did not get this software from ftp.isc.org, please"); + log_error ("get the latest from ftp.isc.org and install that before"); +@@ -94,7 +98,12 @@ + log_error ("the README file."); + log_error ("%s", ""); + log_error ("exiting."); ++ }else ++ { ++ log_error ("exiting."); ++ } + #endif ++ + if (log_cleanup) + (*log_cleanup) (); + exit (1); +--- dhcp-3.0.3/client/dhclient.c.no_isc_blurb 2005-04-18 13:21:08.509169000 -0400 ++++ dhcp-3.0.3/client/dhclient.c 2005-04-18 13:49:27.574402000 -0400 +@@ -34,7 +34,7 @@ + static char ocopyright[] = + "$Id: dhcp-3.0.3-no_isc_blurb.patch,v 1.1 2005/12/09 14:13:30 uberlord Exp $ Copyright (c) 2004 Internet Systems Consortium. All rights reserved.\n"; + #endif /* not lint */ +- ++ + #include "dhcpd.h" + #include "version.h" + +@@ -81,6 +81,8 @@ + + void do_release(struct client_state *); + ++extern int log_isc_blurb; ++ + int main (argc, argv, envp) + int argc; + char **argv, **envp; +@@ -176,6 +178,7 @@ + } else if (!strcmp (argv [i], "-q")) { + quiet = 1; + quiet_interface_discovery = 1; ++ log_isc_blurb = 0; + } else if (!strcmp (argv [i], "-s")) { + if (++i == argc) + usage (); +--- dhcp-3.0.3/server/dhcpd.c.no_isc_blurb 2005-12-08 10:01:40.000000000 +0000 ++++ dhcp-3.0.3/server/dhcpd.c 2005-12-08 10:05:55.000000000 +0000 +@@ -62,6 +62,9 @@ + struct iaddr server_identifier; + int server_identifier_matched; + ++ ++extern int log_isc_blurb; ++ + #if defined (NSUPDATE) + + /* This stuff is always executed to figure the default values for certain +@@ -368,6 +371,7 @@ + } else if (!strcmp (argv [i], "-q")) { + quiet = 1; + quiet_interface_discovery = 1; ++ log_isc_blurb = 0; + } else if (!strcmp (argv [i], "--version")) { + log_info ("isc-dhcpd-%s", DHCP_VERSION); + exit (0); +--- dhcp-3.0.3/relay/dhcrelay.c.no_isc_blurb 2005-12-08 10:21:00.000000000 +0000 ++++ dhcp-3.0.3/relay/dhcrelay.c 2005-12-08 10:21:50.000000000 +0000 +@@ -102,6 +102,8 @@ + static char message [] = "Internet Systems Consortium DHCP Relay Agent"; + static char url [] = "For info, please visit http://www.isc.org/sw/dhcp/"; + ++extern int log_isc_blurb; ++ + int main (argc, argv, envp) + int argc; + char **argv, **envp; +@@ -170,6 +172,7 @@ + } else if (!strcmp (argv [i], "-q")) { + quiet = 1; + quiet_interface_discovery = 1; ++ log_isc_blurb = 0; + } else if (!strcmp (argv [i], "-a")) { + add_agent_options = 1; + } else if (!strcmp (argv [i], "-c")) { diff --git a/net-misc/dhcp/files/dhcp-3.0.4-dhclient-stdin-conf.patch b/net-misc/dhcp/files/dhcp-3.0.4-dhclient-stdin-conf.patch new file mode 100644 index 000000000..3fedc7c0e --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0.4-dhclient-stdin-conf.patch @@ -0,0 +1,83 @@ +--- common/conflex.c.orig 2006-02-21 16:21:45.000000000 +0000 ++++ common/conflex.c 2006-02-21 16:23:06.000000000 +0000 +@@ -90,7 +90,7 @@ + struct parse **cfile; + { + /* "Memory" config files have no file. */ +- if ((*cfile)->file != -1) ++ if ((*cfile)->file != -1 && (*cfile)->file != fileno(stdin)) + close((*cfile)->file); + + if ((*cfile)->bufsiz) +--- client/clparse.c.orig 2006-02-22 09:37:12.000000000 +0000 ++++ client/clparse.c 2006-02-22 09:38:26.000000000 +0000 +@@ -97,6 +97,11 @@ + status = read_client_conf_file (path_dhclient_conf, + (struct interface_info *)0, + &top_level_config); ++ ++ /* Read any extra configuration from stdin */ ++ read_client_conf_stdin ((struct interface_info *)0, ++ &top_level_config); ++ + if (status != ISC_R_SUCCESS) { + ; + #ifdef LATER +@@ -148,20 +153,17 @@ + return status; + } + +-int read_client_conf_file (const char *name, struct interface_info *ip, +- struct client_config *client) ++int read_client_conf_actual (int file, const char *name, ++ struct interface_info *ip, ++ struct client_config *client) + { +- int file; + struct parse *cfile; + const char *val; + int token; + isc_result_t status; + +- if ((file = open (name, O_RDONLY)) < 0) +- return uerr2isc (errno); +- + cfile = (struct parse *)0; +- new_parse (&cfile, file, (char *)0, 0, path_dhclient_conf, 0); ++ new_parse (&cfile, file, (char *)0, 0, name , 0); + + do { + token = peek_token (&val, (unsigned *)0, cfile); +@@ -177,6 +179,32 @@ + return status; + } + ++int read_client_conf_file (const char *name, struct interface_info *ip, ++ struct client_config *client) ++{ ++ int file; ++ isc_result_t status; ++ ++ if ((file = open (name, O_RDONLY)) < 0) ++ return uerr2isc (errno); ++ ++ status = read_client_conf_actual(file, name, ip, client); ++ ++ return status; ++} ++ ++ ++int read_client_conf_stdin (struct interface_info *ip, ++ struct client_config *client) ++{ ++ int file = fileno(stdin); ++ isc_result_t status; ++ ++ if (isatty(file)) return ISC_R_NOTFOUND; ++ status = read_client_conf_actual(file, "stdin", ip, client); ++ ++ return status; ++} + + /* lease-file :== client-lease-statements END_OF_FILE + client-lease-statements :== <nil> diff --git a/net-misc/dhcp/files/dhcp-3.0.5-bpf-nofallback.patch b/net-misc/dhcp/files/dhcp-3.0.5-bpf-nofallback.patch new file mode 100644 index 000000000..2fae6f220 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.0.5-bpf-nofallback.patch @@ -0,0 +1,44 @@ +diff -ur common.orig/bpf.c common/bpf.c +--- common.orig/bpf.c 2006-09-20 12:52:47 +0100 ++++ common/bpf.c 2006-09-20 12:53:22 +0100 +@@ -354,10 +354,6 @@ + int result; + int fudge; + +- if (!strcmp (interface -> name, "fallback")) +- return send_fallback (interface, packet, raw, +- len, from, to, hto); +- + /* Assemble the headers... */ + assemble_hw_header (interface, (unsigned char *)hw, &hbufp, hto); + assemble_udp_ip_header (interface, +@@ -531,17 +527,5 @@ + + void maybe_setup_fallback () + { +- isc_result_t status; +- struct interface_info *fbi = (struct interface_info *)0; +- if (setup_fallback (&fbi, MDL)) { +- if_register_fallback (fbi); +- status = omapi_register_io_object ((omapi_object_t *)fbi, +- if_readsocket, 0, +- fallback_discard, 0, 0); +- if (status != ISC_R_SUCCESS) +- log_fatal ("Can't register I/O handle for %s: %s", +- fbi -> name, isc_result_totext (status)); +- interface_dereference (&fbi, MDL); +- } + } + #endif +diff -ur includes.orig/osdep.h includes/osdep.h +--- includes.orig/osdep.h 2006-09-20 12:54:52 +0100 ++++ includes/osdep.h 2006-09-20 12:56:40 +0100 +@@ -190,7 +190,7 @@ + Currently, all low-level packet interfaces use BSD sockets as a + fallback. */ + +-#if defined (USE_BPF_SEND) || defined (USE_NIT_SEND) || \ ++#if defined (USE_NIT_SEND) || \ + defined (USE_DLPI_SEND) || defined (USE_UPF_SEND) || \ + defined (USE_LPF_SEND) || \ + (defined (USE_SOCKET_SEND) && defined (HAVE_SO_BINDTODEVICE)) diff --git a/net-misc/dhcp/files/dhcp-3.1.0a1-dhclient-resolvconf.patch b/net-misc/dhcp/files/dhcp-3.1.0a1-dhclient-resolvconf.patch new file mode 100644 index 000000000..5c420ae6e --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.1.0a1-dhclient-resolvconf.patch @@ -0,0 +1,254 @@ +diff -ur client.orig/scripts/bsdos client/scripts/bsdos +--- client.orig/scripts/bsdos 2006-09-07 18:53:10.476329752 +0100 ++++ client/scripts/bsdos 2006-09-07 19:19:53.000000000 +0100 +@@ -1,21 +1,22 @@ + #!/bin/sh + + make_resolv_conf() { +- if [ x"$new_domain_name_servers" != x ]; then +- cat /dev/null > /etc/resolv.conf.dhclient +- if [ "x$new_domain_search" != x ]; then +- echo search $new_domain_search >> /etc/resolv.conf.dhclient +- elif [ "x$new_domain_name" != x ]; then +- # Note that the DHCP 'Domain Name Option' is really just a domain +- # name, and that this practice of using the domain name option as +- # a search path is both nonstandard and deprecated. +- echo search $new_domain_name >> /etc/resolv.conf.dhclient ++ if [ x$PEER_DNS = x ] || [ x$PEER_DNS = xyes ]; then ++ if [ "x$new_domain_name" != x ] || [ "x$new_domain_name_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ if [ "x$new_domain_name" != x ]; then ++ conf="${conf}search $new_domain_name\n" ++ fi ++ for nameserver in $new_domain_name_servers; do ++ conf="${conf}nameserver $nameserver\n" ++ done ++ if [ -x /sbin/resolvconf ]; then ++ printf "$conf" | resolvconf -a "$interface" ++ else ++ printf "$conf" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf ++ fi + fi +- for nameserver in $new_domain_name_servers; do +- echo nameserver $nameserver >> /etc/resolv.conf.dhclient +- done +- +- mv /etc/resolv.conf.dhclient /etc/resolv.conf + fi + # If we're making confs, may as well make an ntp.conf too + make_ntp_conf +diff -ur client.orig/scripts/freebsd client/scripts/freebsd +--- client.orig/scripts/freebsd 2006-09-07 18:53:10.476329752 +0100 ++++ client/scripts/freebsd 2006-09-07 19:19:32.000000000 +0100 +@@ -11,38 +11,20 @@ + fi + + make_resolv_conf() { +- if [ x"$new_domain_name_servers" != x ]; then +- ( cat /dev/null > /etc/resolv.conf.dhclient ) +- exit_status=$? +- if [ $exit_status -ne 0 ]; then +- $LOGGER "Unable to create /etc/resolv.conf.dhclient: Error $exit_status" +- else +- if [ "x$new_domain_search" != x ]; then +- ( echo search $new_domain_search >> /etc/resolv.conf.dhclient ) +- exit_status=$? +- elif [ "x$new_domain_name" != x ]; then +- # Note that the DHCP 'Domain Name Option' is really just a domain +- # name, and that this practice of using the domain name option as +- # a search path is both nonstandard and deprecated. +- ( echo search $new_domain_name >> /etc/resolv.conf.dhclient ) +- exit_status=$? ++ if [ x$PEER_DNS = x ] || [ x$PEER_DNS = xyes ]; then ++ if [ "x$new_domain_name" != x ] || [ "x$new_domain_name_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ if [ "x$new_domain_name" != x ]; then ++ conf="${conf}search $new_domain_name\n" + fi + for nameserver in $new_domain_name_servers; do +- if [ $exit_status -ne 0 ]; then +- break +- fi +- ( echo nameserver $nameserver >>/etc/resolv.conf.dhclient ) +- exit_status=$? ++ conf="${conf}nameserver $nameserver\n" + done +- +- # If there were no errors, attempt to mv the new file into place. +- if [ $exit_status -eq 0 ]; then +- ( mv /etc/resolv.conf.dhclient /etc/resolv.conf ) +- exit_status = $? +- fi +- +- if [ $exit_status -ne 0 ]; then +- $LOGGER "Error while writing new /etc/resolv.conf." ++ if [ -x /sbin/resolvconf ]; then ++ printf "$conf" | resolvconf -a "$interface" ++ else ++ printf "$conf" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf + fi + fi + fi +diff -ur client.orig/scripts/linux client/scripts/linux +--- client.orig/scripts/linux 2006-09-07 18:53:10.476329752 +0100 ++++ client/scripts/linux 2006-09-07 19:18:57.000000000 +0100 +@@ -23,22 +23,22 @@ + # of the $1 in its args. + + make_resolv_conf() { +- if [ x"$new_domain_name_servers" != x ]; then +- cat /dev/null > /etc/resolv.conf.dhclient +- chmod 644 /etc/resolv.conf.dhclient +- if [ x"$new_domain_search" != x ]; then +- echo search $new_domain_search >> /etc/resolv.conf.dhclient +- elif [ x"$new_domain_name" != x ]; then +- # Note that the DHCP 'Domain Name Option' is really just a domain +- # name, and that this practice of using the domain name option as +- # a search path is both nonstandard and deprecated. +- echo search $new_domain_name >> /etc/resolv.conf.dhclient ++ if [ x$PEER_DNS = x ] || [ x$PEER_DNS = xyes ]; then ++ if [ "x$new_domain_name" != x ] || [ "x$new_domain_name_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ if [ "x$new_domain_name" != x ]; then ++ conf="${conf}search $new_domain_name\n" ++ fi ++ for nameserver in $new_domain_name_servers; do ++ conf="${conf}nameserver $nameserver\n" ++ done ++ if [ -x /sbin/resolvconf ]; then ++ printf "$conf" | resolvconf -a "$interface" ++ else ++ printf "$conf" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf ++ fi + fi +- for nameserver in $new_domain_name_servers; do +- echo nameserver $nameserver >>/etc/resolv.conf.dhclient +- done +- +- mv /etc/resolv.conf.dhclient /etc/resolv.conf + fi + # If we're making confs, may as well make an ntp.conf too + make_ntp_conf +diff -ur client.orig/scripts/netbsd client/scripts/netbsd +--- client.orig/scripts/netbsd 2006-09-07 18:53:10.476329752 +0100 ++++ client/scripts/netbsd 2006-09-07 19:20:10.000000000 +0100 +@@ -1,21 +1,22 @@ + #!/bin/sh + + make_resolv_conf() { +- if [ "x$new_domain_name" != x ] && [ x"$new_domain_name_servers" != x ]; then +- cat /dev/null > /etc/resolv.conf.dhclient +- if [ "x$new_domain_search != x ]; then +- echo search $new_domain_search >> /etc/resolv.conf.dhclient +- elif [ "x$new_domain_name != x ]; then +- # Note that the DHCP 'Domain Name Option' is really just a domain +- # name, and that this practice of using the domain name option as +- # a search path is both nonstandard and deprecated. +- echo search $new_domain_name >> /etc/resolv.conf.dhclient ++ if [ x$PEER_DNS = x ] || [ x$PEER_DNS = xyes ]; then ++ if [ "x$new_domain_name" != x ] || [ "x$new_domain_name_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ if [ "x$new_domain_name" != x ]; then ++ conf="${conf}search $new_domain_name\n" ++ fi ++ for nameserver in $new_domain_name_servers; do ++ conf="${conf}nameserver $nameserver\n" ++ done ++ if [ -x /sbin/resolvconf ]; then ++ printf "$conf" | resolvconf -a "$interface" ++ else ++ printf "$conf" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf ++ fi + fi +- for nameserver in $new_domain_name_servers; do +- echo nameserver $nameserver >>/etc/resolv.conf.dhclient +- done +- +- mv /etc/resolv.conf.dhclient /etc/resolv.conf + fi + # If we're making confs, may as well make an ntp.conf too + make_ntp_conf +diff -ur client.orig/scripts/openbsd client/scripts/openbsd +--- client.orig/scripts/openbsd 2006-09-07 18:53:10.476329752 +0100 ++++ client/scripts/openbsd 2006-09-07 19:20:38.000000000 +0100 +@@ -1,21 +1,22 @@ + #!/bin/sh + + make_resolv_conf() { +- if x"$new_domain_name_servers" != x ]; then +- cat /dev/null > /etc/resolv.conf.dhclient +- if [ x"$new_domain_search" != x ]; then +- echo search $new_domain_search >> /etc/resolv.conf.dhclient +- elif [ x"$new_domain_name" != x ]; then +- # Note that the DHCP 'Domain Name Option' is really just a domain +- # name, and that this practice of using the domain name option as +- # a search path is both nonstandard and deprecated. +- echo search $new_domain_name >> /etc/resolv.conf.dhclient ++ if [ x$PEER_DNS = x ] || [ x$PEER_DNS = xyes ]; then ++ if [ "x$new_domain_name" != x ] || [ "x$new_domain_name_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ if [ "x$new_domain_name" != x ]; then ++ conf="${conf}search $new_domain_name\n" ++ fi ++ for nameserver in $new_domain_name_servers; do ++ conf="${conf}nameserver $nameserver\n" ++ done ++ if [ -x /sbin/resolvconf ]; then ++ printf "$conf" | resolvconf -a "$interface" ++ else ++ printf "$conf" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf ++ fi + fi +- for nameserver in $new_domain_name_servers; do +- echo nameserver $nameserver >>/etc/resolv.conf.dhclient +- done +- +- mv /etc/ersolv.conf.dhclient /etc/resolv.conf + fi + # If we're making confs, may as well make an ntp.conf too + make_ntp_conf +diff -ur client.orig/scripts/solaris client/scripts/solaris +--- client.orig/scripts/solaris 2006-09-07 18:53:10.476329752 +0100 ++++ client/scripts/solaris 2006-09-07 19:21:12.000000000 +0100 +@@ -1,21 +1,22 @@ + #!/bin/sh + + make_resolv_conf() { +- if [ x"$new_domain_name_servers" != x ]; then +- cat /dev/null > /etc/resolv.conf.dhclient +- if [ x"$new_domain_search" != x ]; then +- echo search $new_domain_search >> /etc/resolv.conf.dhclient +- elif [ x"$new_domain_name" != x ]; then +- # Note that the DHCP 'Domain Name Option' is really just a domain +- # name, and that this practice of using the domain name option as +- # a search path is both nonstandard and deprecated. +- echo search $new_domain_name >> /etc/resolv.conf.dhclient ++ if [ x$PEER_DNS = x ] || [ x$PEER_DNS = xyes ]; then ++ if [ "x$new_domain_name" != x ] || [ "x$new_domain_name_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ if [ "x$new_domain_name" != x ]; then ++ conf="${conf}search $new_domain_name\n" ++ fi ++ for nameserver in $new_domain_name_servers; do ++ conf="${conf}nameserver $nameserver\n" ++ done ++ if [ -x /sbin/resolvconf ]; then ++ printf "$conf" | resolvconf -a "$interface" ++ else ++ printf "$conf" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf ++ fi + fi +- for nameserver in $new_domain_name_servers; do +- echo nameserver $nameserver >>/etc/resolv.conf.dhclient +- done +- +- mv /etc/resolv.conf.dhclient /etc/resolv.conf + fi + # If we're making confs, may as well make an ntp.conf too + make_ntp_conf diff --git a/net-misc/dhcp/files/dhcp-3.1.2_p1-CVE-2009-1892.patch b/net-misc/dhcp/files/dhcp-3.1.2_p1-CVE-2009-1892.patch new file mode 100644 index 000000000..ae1b92af8 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.1.2_p1-CVE-2009-1892.patch @@ -0,0 +1,12 @@ +diff -uNr dhcp-3.1.2.ORIG/server/dhcp.c dhcp-3.1.2/server/dhcp.c +--- dhcp-3.1.2.ORIG/server/dhcp.c 2009-07-13 14:26:15.000000000 +0100 ++++ dhcp-3.1.2/server/dhcp.c 2009-07-13 14:26:33.000000000 +0100 +@@ -1747,6 +1747,8 @@ + host_reference (&host, h, MDL); + } + if (!host) { ++ if (hp) ++ host_dereference (&hp, MDL); + find_hosts_by_haddr (&hp, + packet -> raw -> htype, + packet -> raw -> chaddr, diff --git a/net-misc/dhcp/files/dhcp-3.1.3-dhclient-no-down.patch b/net-misc/dhcp/files/dhcp-3.1.3-dhclient-no-down.patch new file mode 100644 index 000000000..89935df82 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-3.1.3-dhclient-no-down.patch @@ -0,0 +1,77 @@ +diff -Nuar --exclude '*.orig' dhcp-3.1.3.orig//client/scripts/linux dhcp-3.1.3//client/scripts/linux +--- dhcp-3.1.3.orig//client/scripts/linux 2010-10-15 04:59:15.890664245 +0000 ++++ dhcp-3.1.3//client/scripts/linux 2010-10-15 05:04:57.940396350 +0000 +@@ -118,7 +118,7 @@ + if [ x$reason = xPREINIT ]; then + if [ x$alias_ip_address != x ]; then + # Bring down alias interface. Its routes will disappear too. +- ifconfig $interface:0- inet 0 ++ ifconfig $interface:0- inet 0.0.0.0 + fi + if [ $relmajor -lt 2 ] || ( [ $relmajor -eq 2 ] && [ $relminor -eq 0 ] ) + then +@@ -127,7 +127,7 @@ + # Add route to make broadcast work. Do not omit netmask. + route add default dev $interface netmask 0.0.0.0 + else +- ifconfig $interface 0 up ++ ifconfig $interface 0.0.0.0 up + fi + + # We need to give the kernel some time to get the interface up. +@@ -155,12 +155,12 @@ + if [ x$old_ip_address != x ] && [ x$alias_ip_address != x ] && \ + [ x$alias_ip_address != x$old_ip_address ]; then + # Possible new alias. Remove old alias. +- ifconfig $interface:0- inet 0 ++ ifconfig $interface:0- inet 0.0.0.0 + fi + if [ x$old_ip_address != x ] && [ x$old_ip_address != x$new_ip_address ]; then + # IP address changed. Bringing down the interface will delete all routes, + # and clear the ARP cache. +- ifconfig $interface inet 0 down ++ ifconfig $interface inet 0.0.0.0 + + fi + if [ x$old_ip_address = x ] || [ x$old_ip_address != x$new_ip_address ] || \ +@@ -179,7 +179,7 @@ + fi + if [ x$new_ip_address != x$alias_ip_address ] && [ x$alias_ip_address != x ]; + then +- ifconfig $interface:0- inet 0 ++ ifconfig $interface:0- inet 0.0.0.0 + ifconfig $interface:0 inet $alias_ip_address $alias_subnet_arg + route add -host $alias_ip_address $interface:0 + fi +@@ -191,11 +191,11 @@ + || [ x$reason = xSTOP ]; then + if [ x$alias_ip_address != x ]; then + # Turn off alias interface. +- ifconfig $interface:0- inet 0 ++ ifconfig $interface:0- inet 0.0.0.0 + fi + if [ x$old_ip_address != x ]; then + # Shut down interface, which will delete routes and clear arp cache. +- ifconfig $interface inet 0 down ++ ifconfig $interface inet 0.0.0.0 + fi + if [ x$alias_ip_address != x ]; then + ifconfig $interface:0 inet $alias_ip_address $alias_subnet_arg +@@ -206,7 +206,7 @@ + + if [ x$reason = xTIMEOUT ]; then + if [ x$alias_ip_address != x ]; then +- ifconfig $interface:0- inet 0 ++ ifconfig $interface:0- inet 0.0.0.0 + fi + ifconfig $interface inet $new_ip_address $new_subnet_arg \ + $new_broadcast_arg $mtu_arg +@@ -227,7 +227,7 @@ + make_resolv_conf + exit_with_hooks 0 + fi +- ifconfig $interface inet 0 down ++ ifconfig $interface inet 0.0.0.0 + exit_with_hooks 1 + fi + diff --git a/net-misc/dhcp/files/dhcp-4.0-dhclient-ntp.patch b/net-misc/dhcp/files/dhcp-4.0-dhclient-ntp.patch new file mode 100644 index 000000000..d3f29714b --- /dev/null +++ b/net-misc/dhcp/files/dhcp-4.0-dhclient-ntp.patch @@ -0,0 +1,216 @@ +diff -uNr dhcp-4.0.0.ORIG/client/clparse.c dhcp-4.0.0/client/clparse.c +--- dhcp-4.0.0.ORIG/client/clparse.c 2008-09-01 11:38:51.000000000 +0100 ++++ dhcp-4.0.0/client/clparse.c 2008-09-01 11:48:17.000000000 +0100 +@@ -37,7 +37,7 @@ + + struct client_config top_level_config; + +-#define NUM_DEFAULT_REQUESTED_OPTS 9 ++#define NUM_DEFAULT_REQUESTED_OPTS 10 + struct option *default_requested_options[NUM_DEFAULT_REQUESTED_OPTS + 1]; + + static void parse_client_default_duid(struct parse *cfile); +@@ -98,15 +98,20 @@ + dhcp_universe.code_hash, &code, 0, MDL); + + /* 8 */ +- code = D6O_NAME_SERVERS; ++ code = DHO_NTP_SERVERS; + option_code_hash_lookup(&default_requested_options[7], +- dhcpv6_universe.code_hash, &code, 0, MDL); ++ dhcp_universe.code_hash, &code, 0, MDL); + + /* 9 */ +- code = D6O_DOMAIN_SEARCH; ++ code = D6O_NAME_SERVERS; + option_code_hash_lookup(&default_requested_options[8], + dhcpv6_universe.code_hash, &code, 0, MDL); + ++ /* 10 */ ++ code = D6O_DOMAIN_SEARCH; ++ option_code_hash_lookup(&default_requested_options[9], ++ dhcpv6_universe.code_hash, &code, 0, MDL); ++ + for (code = 0 ; code < NUM_DEFAULT_REQUESTED_OPTS ; code++) { + if (default_requested_options[code] == NULL) + log_fatal("Unable to find option definition for " +diff -uNr dhcp-4.0.0.ORIG/client/scripts/bsdos dhcp-4.0.0/client/scripts/bsdos +--- dhcp-4.0.0.ORIG/client/scripts/bsdos 2008-09-01 11:38:51.000000000 +0100 ++++ dhcp-4.0.0/client/scripts/bsdos 2008-09-01 11:39:30.000000000 +0100 +@@ -29,6 +29,26 @@ + + mv /etc/resolv.conf.dhclient6 /etc/resolv.conf + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf ++} ++ ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ x$new_ntp_servers != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi + } + + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. +diff -uNr dhcp-4.0.0.ORIG/client/scripts/freebsd dhcp-4.0.0/client/scripts/freebsd +--- dhcp-4.0.0.ORIG/client/scripts/freebsd 2008-09-01 11:38:51.000000000 +0100 ++++ dhcp-4.0.0/client/scripts/freebsd 2008-09-01 11:39:30.000000000 +0100 +@@ -73,6 +73,26 @@ + fi + fi + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf ++} ++ ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ "x$new_ntp_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi + } + + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. +diff -uNr dhcp-4.0.0.ORIG/client/scripts/linux dhcp-4.0.0/client/scripts/linux +--- dhcp-4.0.0.ORIG/client/scripts/linux 2008-09-01 11:38:51.000000000 +0100 ++++ dhcp-4.0.0/client/scripts/linux 2008-09-01 11:39:30.000000000 +0100 +@@ -55,6 +55,26 @@ + + mv /etc/resolv.conf.dhclient6 /etc/resolv.conf + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf ++} ++ ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ "x$new_ntp_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi + } + + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. +diff -uNr dhcp-4.0.0.ORIG/client/scripts/netbsd dhcp-4.0.0/client/scripts/netbsd +--- dhcp-4.0.0.ORIG/client/scripts/netbsd 2008-09-01 11:38:51.000000000 +0100 ++++ dhcp-4.0.0/client/scripts/netbsd 2008-09-01 11:39:30.000000000 +0100 +@@ -29,6 +29,26 @@ + + mv /etc/resolv.conf.dhclient6 /etc/resolv.conf + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf ++} ++ ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ "x$new_ntp_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi + } + + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. +diff -uNr dhcp-4.0.0.ORIG/client/scripts/openbsd dhcp-4.0.0/client/scripts/openbsd +--- dhcp-4.0.0.ORIG/client/scripts/openbsd 2008-09-01 11:38:51.000000000 +0100 ++++ dhcp-4.0.0/client/scripts/openbsd 2008-09-01 11:39:30.000000000 +0100 +@@ -29,6 +29,26 @@ + + mv /etc/resolv.conf.dhclient6 /etc/resolv.conf + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf ++} ++ ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ "x$new_ntp_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi + } + + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. +diff -uNr dhcp-4.0.0.ORIG/client/scripts/solaris dhcp-4.0.0/client/scripts/solaris +--- dhcp-4.0.0.ORIG/client/scripts/solaris 2008-09-01 11:38:51.000000000 +0100 ++++ dhcp-4.0.0/client/scripts/solaris 2008-09-01 11:39:30.000000000 +0100 +@@ -17,6 +17,26 @@ + + mv /etc/resolv.conf.dhclient /etc/resolv.conf + fi ++ # If we're making confs, may as well make an ntp.conf too ++ make_ntp_conf ++} ++ ++make_ntp_conf() { ++ if [ x$PEER_NTP = x ] || [ x$PEER_NTP = xyes ]; then ++ if [ "x$new_ntp_servers" != x ]; then ++ conf="# Generated by dhclient for interface $interface\n" ++ conf="${conf}restrict default noquery notrust nomodify\n" ++ conf="${conf}restrict 127.0.0.1\n" ++ for ntpserver in $new_ntp_servers; do ++ conf="${conf}restrict $ntpserver nomodify notrap noquery\n" ++ conf="${conf}server $ntpserver\n" ++ done ++ conf="${conf}driftfile /var/lib/ntp/ntp.drift\n" ++ conf="${conf}logfile /var/log/ntp.log\n" ++ printf "${conf}" > /etc/ntp.conf ++ chmod 644 /etc/ntp.conf ++ fi ++ fi + } + + # Must be used on exit. Invokes the local dhcp client exit hooks, if any. diff --git a/net-misc/dhcp/files/dhcp-4.0.1-dhclient-stdin-conf.patch b/net-misc/dhcp/files/dhcp-4.0.1-dhclient-stdin-conf.patch new file mode 100644 index 000000000..ddbe4a39d --- /dev/null +++ b/net-misc/dhcp/files/dhcp-4.0.1-dhclient-stdin-conf.patch @@ -0,0 +1,114 @@ +diff -uNr dhcp-4.0.1.ORIG/client/clparse.c dhcp-4.0.1/client/clparse.c +--- dhcp-4.0.1.ORIG/client/clparse.c 2009-03-30 13:54:47.000000000 +0100 ++++ dhcp-4.0.1/client/clparse.c 2009-03-30 13:58:02.000000000 +0100 +@@ -174,6 +174,10 @@ + #endif + } + ++ /* Read any extra configuration from stdin */ ++ read_client_conf_stdin ((struct interface_info *)0, ++ &top_level_config); ++ + /* Set up state and config structures for clients that don't + have per-interface configuration statements. */ + config = (struct client_config *)0; +@@ -203,23 +207,13 @@ + return status; + } + +-int read_client_conf_file (const char *name, struct interface_info *ip, ++int read_client_conf_actual (struct parse *cfile, struct interface_info *ip, + struct client_config *client) + { +- int file; +- struct parse *cfile; + const char *val; + int token; + isc_result_t status; + +- if ((file = open (name, O_RDONLY)) < 0) +- return uerr2isc (errno); +- +- cfile = NULL; +- status = new_parse(&cfile, file, NULL, 0, path_dhclient_conf, 0); +- if (status != ISC_R_SUCCESS || cfile == NULL) +- return status; +- + do { + token = peek_token (&val, (unsigned *)0, cfile); + if (token == END_OF_FILE) +@@ -230,10 +224,74 @@ + status = (cfile -> warnings_occurred + ? ISC_R_BADPARSE + : ISC_R_SUCCESS); ++ return status; ++} ++ ++int read_client_conf_file (const char *name, struct interface_info *ip, ++ struct client_config *client) ++{ ++ int file; ++ struct parse *cfile; ++ isc_result_t status; ++ ++ if ((file = open (name, O_RDONLY)) < 0) ++ return uerr2isc (errno); ++ ++ cfile = (struct parse *)0; ++ new_parse (&cfile, file, (char *)0, 0, path_dhclient_conf, 0); ++ status = read_client_conf_actual(cfile, ip, client); + end_parse (&cfile); + return status; + } + ++int read_client_conf_stdin (struct interface_info *ip, ++ struct client_config *client) ++{ ++ int file; ++ char *buffer = NULL, *p; ++ unsigned buflen, len = 0; ++ struct parse *cfile; ++ size_t bytes; ++ isc_result_t status; ++ ++ file = fileno(stdin); ++ if (isatty (file)) ++ return ISC_R_NOTFOUND; ++ if (fcntl (file, F_SETFL, O_NONBLOCK) < 0) ++ log_fatal ("could not set stdin to non blocking!"); ++ ++ buflen = BUFSIZ; ++ buffer = malloc (BUFSIZ + 1); ++ p = buffer; ++ do { ++ bytes = read (file, p, BUFSIZ); ++ if (bytes == 0) ++ break; ++ if (bytes == -1) ++ log_fatal ("failed to read stdin!"); ++ if (bytes >= BUFSIZ) { ++ buflen += BUFSIZ; ++ len += BUFSIZ; ++ buffer = realloc (buffer, buflen + 1); ++ if (!buffer) ++ log_fatal ("not enough buffer to read stdin!"); ++ p = buffer + len; ++ } else { ++ len += bytes; ++ break; ++ } ++ } while(1); ++ buffer[len] = '\0'; ++ ++ cfile = (struct parse *)0; ++ status = new_parse (&cfile, -1, buffer, len, "stdin", 0); ++ if (status == ISC_R_SUCCESS) { ++ status = read_client_conf_actual (cfile, ip, client); ++ end_parse (&cfile); ++ } ++ free(buffer); ++ return status; ++} + + /* lease-file :== client-lease-statements END_OF_FILE + client-lease-statements :== <nil> diff --git a/net-misc/dhcp/files/dhcp-4.2.0-errwarn-message.patch b/net-misc/dhcp/files/dhcp-4.2.0-errwarn-message.patch new file mode 100644 index 000000000..f882a1345 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-4.2.0-errwarn-message.patch @@ -0,0 +1,31 @@ +ripped from Fedora & tweaked + +--- dhcp-4.2.0/omapip/errwarn.c ++++ dhcp-4.2.0/omapip/errwarn.c +@@ -76,20 +76,13 @@ + + #if !defined (NOMINUM) + log_error ("%s", ""); +- log_error ("If you did not get this software from ftp.isc.org, please"); +- log_error ("get the latest from ftp.isc.org and install that before"); +- log_error ("requesting help."); ++ log_error ("This version of ISC DHCP is based on the release available"); ++ log_error ("on ftp.isc.org. Features have been added and other changes"); ++ log_error ("have been made to the base software release in order to make"); ++ log_error ("it work better with this distribution."); + log_error ("%s", ""); +- log_error ("If you did get this software from ftp.isc.org and have not"); +- log_error ("yet read the README, please read it before requesting help."); +- log_error ("If you intend to request help from the dhcp-server@isc.org"); +- log_error ("mailing list, please read the section on the README about"); +- log_error ("submitting bug reports and requests for help."); +- log_error ("%s", ""); +- log_error ("Please do not under any circumstances send requests for"); +- log_error ("help directly to the authors of this software - please"); +- log_error ("send them to the appropriate mailing list as described in"); +- log_error ("the README file."); ++ log_error ("Please report for this software via the Gentoo Bugzilla site:"); ++ log_error (" http://bugs.gentoo.org/"); + log_error ("%s", ""); + log_error ("exiting."); + #endif diff --git a/net-misc/dhcp/files/dhcp-4.2.0-improved-xid.patch b/net-misc/dhcp/files/dhcp-4.2.0-improved-xid.patch new file mode 100644 index 000000000..567601f06 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-4.2.0-improved-xid.patch @@ -0,0 +1,138 @@ +diff -up dhcp-4.2.0/client/dhclient.c.xid dhcp-4.2.0/client/dhclient.c
+--- dhcp-4.2.0/client/dhclient.c.xid 2010-09-23 06:21:03.000000000 -0400
++++ dhcp-4.2.0/client/dhclient.c 2010-09-23 09:14:09.000000000 -0400
+@@ -805,6 +805,26 @@ main(int argc, char **argv) {
+ }
+ }
+
++ /* We create a backup seed before rediscovering interfaces in order to
++ have a seed built using all of the available interfaces
++ It's interesting if required interfaces doesn't let us defined
++ a really unique seed due to a lack of valid HW addr later
++ (this is the case with DHCP over IB)
++ We only use the last device as using a sum could broke the
++ uniqueness of the seed among multiple nodes
++ */
++ unsigned backup_seed = 0;
++ for (ip = interfaces; ip; ip = ip -> next) {
++ int junk;
++ if ( ip -> hw_address.hlen <= sizeof seed )
++ continue;
++ memcpy (&junk,
++ &ip -> hw_address.hbuf [ip -> hw_address.hlen -
++ sizeof seed], sizeof seed);
++ backup_seed = junk;
++ }
++
++
+ /* At this point, all the interfaces that the script thinks
+ are relevant should be running, so now we once again call
+ discover_interfaces(), and this time ask it to actually set
+@@ -819,14 +839,36 @@ main(int argc, char **argv) {
+ Not much entropy, but we're booting, so we're not likely to
+ find anything better. */
+ seed = 0;
++ int seed_flag = 0;
+ for (ip = interfaces; ip; ip = ip->next) {
+ int junk;
++ if ( ip -> hw_address.hlen <= sizeof seed )
++ continue;
+ memcpy(&junk,
+ &ip->hw_address.hbuf[ip->hw_address.hlen -
+ sizeof seed], sizeof seed);
+ seed += junk;
++ seed_flag = 1;
+ }
+- srandom(seed + cur_time);
++ if ( seed_flag == 0 ) {
++ if ( backup_seed != 0 ) {
++ seed = backup_seed;
++ log_info ("xid: rand init seed (0x%x) built using all"
++ " available interfaces",seed);
++ }
++ else {
++ seed = cur_time^((unsigned) gethostid()) ;
++ log_info ("xid: warning: no netdev with useable HWADDR found"
++ " for seed's uniqueness enforcement");
++ log_info ("xid: rand init seed (0x%x) built using gethostid",
++ seed);
++ }
++ /* we only use seed and no current time as a broadcast reply */
++ /* will certainly be used by the hwaddrless interface */
++ srandom(seed);
++ }
++ else
++ srandom(seed + cur_time);
+
+ /* Setup specific Infiniband options */
+ for (ip = interfaces; ip; ip = ip->next) {
+@@ -1310,7 +1352,7 @@ void dhcpack (packet)
+ return;
+ }
+
+- log_info ("DHCPACK from %s", piaddr (packet -> client_addr));
++ log_info ("DHCPACK from %s (xid=0x%x)", piaddr (packet -> client_addr), client -> xid);
+
+ lease = packet_to_lease (packet, client);
+ if (!lease) {
+@@ -2010,7 +2052,7 @@ void dhcpnak (packet)
+ return;
+ }
+
+- log_info ("DHCPNAK from %s", piaddr (packet -> client_addr));
++ log_info ("DHCPNAK from %s (xid=0x%x)", piaddr (packet -> client_addr), client -> xid);
+
+ if (!client -> active) {
+ #if defined (DEBUG)
+@@ -2136,10 +2178,10 @@ void send_discover (cpp)
+ client -> packet.secs = htons (65535);
+ client -> secs = client -> packet.secs;
+
+- log_info ("DHCPDISCOVER on %s to %s port %d interval %ld",
++ log_info ("DHCPDISCOVER on %s to %s port %d interval %ld (xid=0x%x)",
+ client -> name ? client -> name : client -> interface -> name,
+ inet_ntoa (sockaddr_broadcast.sin_addr),
+- ntohs (sockaddr_broadcast.sin_port), (long)(client -> interval));
++ ntohs (sockaddr_broadcast.sin_port), (long)(client -> interval), client -> xid);
+
+ /* Send out a packet. */
+ result = send_packet (client -> interface, (struct packet *)0,
+@@ -2394,10 +2436,10 @@ void send_request (cpp)
+ client -> packet.secs = htons (65535);
+ }
+
+- log_info ("DHCPREQUEST on %s to %s port %d",
++ log_info ("DHCPREQUEST on %s to %s port %d (xid=0x%x)",
+ client -> name ? client -> name : client -> interface -> name,
+ inet_ntoa (destination.sin_addr),
+- ntohs (destination.sin_port));
++ ntohs (destination.sin_port), client -> xid);
+
+ if (destination.sin_addr.s_addr != INADDR_BROADCAST &&
+ fallback_interface)
+@@ -2427,10 +2469,10 @@ void send_decline (cpp)
+
+ int result;
+
+- log_info ("DHCPDECLINE on %s to %s port %d",
++ log_info ("DHCPDECLINE on %s to %s port %d (xid=0x%x)",
+ client -> name ? client -> name : client -> interface -> name,
+ inet_ntoa (sockaddr_broadcast.sin_addr),
+- ntohs (sockaddr_broadcast.sin_port));
++ ntohs (sockaddr_broadcast.sin_port), client -> xid);
+
+ /* Send out a packet. */
+ result = send_packet (client -> interface, (struct packet *)0,
+@@ -2470,10 +2512,10 @@ void send_release (cpp)
+ return;
+ }
+
+- log_info ("DHCPRELEASE on %s to %s port %d",
++ log_info ("DHCPRELEASE on %s to %s port %d (xid=0x%x)",
+ client -> name ? client -> name : client -> interface -> name,
+ inet_ntoa (destination.sin_addr),
+- ntohs (destination.sin_port));
++ ntohs (destination.sin_port), client -> xid);
+
+ if (fallback_interface)
+ result = send_packet (fallback_interface,
diff --git a/net-misc/dhcp/files/dhcp-4.2.0-lpf-ib.patch b/net-misc/dhcp/files/dhcp-4.2.0-lpf-ib.patch new file mode 100644 index 000000000..52a7aa8a2 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-4.2.0-lpf-ib.patch @@ -0,0 +1,538 @@ +diff -up dhcp-4.2.0/common/lpf.c.ib dhcp-4.2.0/common/lpf.c
+--- dhcp-4.2.0/common/lpf.c.ib 2010-09-23 05:24:09.000000000 -0400
++++ dhcp-4.2.0/common/lpf.c 2010-09-23 06:21:03.000000000 -0400
+@@ -42,6 +42,7 @@
+ #include "includes/netinet/udp.h"
+ #include "includes/netinet/if_ether.h"
+ #include <net/if.h>
++#include <ifaddrs.h>
+
+ #ifndef PACKET_AUXDATA
+ #define PACKET_AUXDATA 8
+@@ -59,6 +60,15 @@ struct tpacket_auxdata
+ /* Reinitializes the specified interface after an address change. This
+ is not required for packet-filter APIs. */
+
++/* Default broadcast address for IPoIB */
++static unsigned char default_ib_bcast_addr[20] = {
++ 0x00, 0xff, 0xff, 0xff,
++ 0xff, 0x12, 0x40, 0x1b,
++ 0x00, 0x00, 0x00, 0x00,
++ 0x00, 0x00, 0x00, 0x00,
++ 0xff, 0xff, 0xff, 0xff
++};
++
+ #ifdef USE_LPF_SEND
+ void if_reinitialize_send (info)
+ struct interface_info *info;
+@@ -86,10 +96,21 @@ int if_register_lpf (info)
+ struct sockaddr common;
+ } sa;
+ struct ifreq ifr;
++ int type;
++ int protocol;
+
+ /* Make an LPF socket. */
+- if ((sock = socket(PF_PACKET, SOCK_RAW,
+- htons((short)ETH_P_ALL))) < 0) {
++ get_hw_addr(info);
++
++ if (info->hw_address.hbuf[0] == HTYPE_INFINIBAND) {
++ type = SOCK_DGRAM;
++ protocol = ETHERTYPE_IP;
++ } else {
++ type = SOCK_RAW;
++ protocol = ETH_P_ALL;
++ }
++
++ if ((sock = socket(PF_PACKET, type, htons((short)protocol))) < 0) {
+ if (errno == ENOPROTOOPT || errno == EPROTONOSUPPORT ||
+ errno == ESOCKTNOSUPPORT || errno == EPFNOSUPPORT ||
+ errno == EAFNOSUPPORT || errno == EINVAL) {
+@@ -111,6 +132,7 @@ int if_register_lpf (info)
+ /* Bind to the interface name */
+ memset (&sa, 0, sizeof sa);
+ sa.ll.sll_family = AF_PACKET;
++ sa.ll.sll_protocol = htons(protocol);
+ sa.ll.sll_ifindex = ifr.ifr_ifindex;
+ if (bind (sock, &sa.common, sizeof sa)) {
+ if (errno == ENOPROTOOPT || errno == EPROTONOSUPPORT ||
+@@ -126,8 +148,6 @@ int if_register_lpf (info)
+ log_fatal ("Bind socket to interface: %m");
+ }
+
+- get_hw_addr(info->name, &info->hw_address);
+-
+ return sock;
+ }
+ #endif /* USE_LPF_SEND || USE_LPF_RECEIVE */
+@@ -182,6 +202,8 @@ void if_deregister_send (info)
+ in bpf includes... */
+ extern struct sock_filter dhcp_bpf_filter [];
+ extern int dhcp_bpf_filter_len;
++extern struct sock_filter dhcp_ib_bpf_filter [];
++extern int dhcp_ib_bpf_filter_len;
+
+ #if defined (HAVE_TR_SUPPORT)
+ extern struct sock_filter dhcp_bpf_tr_filter [];
+@@ -199,11 +221,13 @@ void if_register_receive (info)
+ /* Open a LPF device and hang it on this interface... */
+ info -> rfdesc = if_register_lpf (info);
+
+- val = 1;
+- if (setsockopt (info -> rfdesc, SOL_PACKET, PACKET_AUXDATA, &val,
+- sizeof val) < 0) {
+- if (errno != ENOPROTOOPT)
+- log_fatal ("Failed to set auxiliary packet data: %m");
++ if (info->hw_address.hbuf[0] != HTYPE_INFINIBAND) {
++ val = 1;
++ if (setsockopt (info -> rfdesc, SOL_PACKET, PACKET_AUXDATA,
++ &val, sizeof val) < 0) {
++ if (errno != ENOPROTOOPT)
++ log_fatal ("Failed to set auxiliary packet data: %m");
++ }
+ }
+
+ #if defined (HAVE_TR_SUPPORT)
+@@ -249,15 +273,28 @@ static void lpf_gen_filter_setup (info)
+
+ memset(&p, 0, sizeof(p));
+
+- /* Set up the bpf filter program structure. This is defined in
+- bpf.c */
+- p.len = dhcp_bpf_filter_len;
+- p.filter = dhcp_bpf_filter;
+-
+- /* Patch the server port into the LPF program...
+- XXX changes to filter program may require changes
+- to the insn number(s) used below! XXX */
+- dhcp_bpf_filter [8].k = ntohs ((short)local_port);
++ if (info->hw_address.hbuf[0] == HTYPE_INFINIBAND) {
++ /* Set up the bpf filter program structure. */
++ p.len = dhcp_ib_bpf_filter_len;
++ p.filter = dhcp_ib_bpf_filter;
++
++ /* Patch the server port into the LPF program...
++ XXX
++ changes to filter program may require changes
++ to the insn number(s) used below!
++ XXX */
++ dhcp_ib_bpf_filter[6].k = ntohs ((short)local_port);
++ } else {
++ /* Set up the bpf filter program structure.
++ This is defined in bpf.c */
++ p.len = dhcp_bpf_filter_len;
++ p.filter = dhcp_bpf_filter;
++
++ /* Patch the server port into the LPF program...
++ XXX changes to filter program may require changes
++ to the insn number(s) used below! XXX */
++ dhcp_bpf_filter [8].k = ntohs ((short)local_port);
++ }
+
+ if (setsockopt (info -> rfdesc, SOL_SOCKET, SO_ATTACH_FILTER, &p,
+ sizeof p) < 0) {
+@@ -314,6 +351,54 @@ static void lpf_tr_filter_setup (info)
+ #endif /* USE_LPF_RECEIVE */
+
+ #ifdef USE_LPF_SEND
++ssize_t send_packet_ib(interface, packet, raw, len, from, to, hto)
++ struct interface_info *interface;
++ struct packet *packet;
++ struct dhcp_packet *raw;
++ size_t len;
++ struct in_addr from;
++ struct sockaddr_in *to;
++ struct hardware *hto;
++{
++ unsigned ibufp = 0;
++ double ih [1536 / sizeof (double)];
++ unsigned char *buf = (unsigned char *)ih;
++ ssize_t result;
++
++ union sockunion {
++ struct sockaddr sa;
++ struct sockaddr_ll sll;
++ struct sockaddr_storage ss;
++ } su;
++
++ assemble_udp_ip_header (interface, buf, &ibufp, from.s_addr,
++ to->sin_addr.s_addr, to->sin_port,
++ (unsigned char *)raw, len);
++ memcpy (buf + ibufp, raw, len);
++
++ memset(&su, 0, sizeof(su));
++ su.sll.sll_family = AF_PACKET;
++ su.sll.sll_protocol = htons(ETHERTYPE_IP);
++
++ if (!(su.sll.sll_ifindex = if_nametoindex(interface->name))) {
++ errno = ENOENT;
++ log_error ("send_packet_ib: %m - failed to get if index");
++ return -1;
++ }
++
++ su.sll.sll_hatype = htons(HTYPE_INFINIBAND);
++ su.sll.sll_halen = sizeof(interface->bcast_addr);
++ memcpy(&su.sll.sll_addr, interface->bcast_addr, 20);
++
++ result = sendto(interface->wfdesc, buf, ibufp + len, 0,
++ &su.sa, sizeof(su));
++
++ if (result < 0)
++ log_error ("send_packet_ib: %m");
++
++ return result;
++}
++
+ ssize_t send_packet (interface, packet, raw, len, from, to, hto)
+ struct interface_info *interface;
+ struct packet *packet;
+@@ -334,6 +419,11 @@ ssize_t send_packet (interface, packet,
+ return send_fallback (interface, packet, raw,
+ len, from, to, hto);
+
++ if (interface->hw_address.hbuf[0] == HTYPE_INFINIBAND) {
++ return send_packet_ib(interface, packet, raw, len, from,
++ to, hto);
++ }
++
+ if (hto == NULL && interface->anycast_mac_addr.hlen)
+ hto = &interface->anycast_mac_addr;
+
+@@ -355,6 +445,42 @@ ssize_t send_packet (interface, packet,
+ #endif /* USE_LPF_SEND */
+
+ #ifdef USE_LPF_RECEIVE
++ssize_t receive_packet_ib (interface, buf, len, from, hfrom)
++ struct interface_info *interface;
++ unsigned char *buf;
++ size_t len;
++ struct sockaddr_in *from;
++ struct hardware *hfrom;
++{
++ int length = 0;
++ int offset = 0;
++ unsigned char ibuf [1536];
++ unsigned bufix = 0;
++ unsigned paylen;
++
++ length = read(interface->rfdesc, ibuf, sizeof(ibuf));
++
++ if (length <= 0)
++ return length;
++
++ offset = decode_udp_ip_header(interface, ibuf, bufix, from,
++ (unsigned)length, &paylen, 0);
++
++ if (offset < 0)
++ return 0;
++
++ bufix += offset;
++ length -= offset;
++
++ if (length < paylen)
++ log_fatal("Internal inconsistency at %s:%d.", MDL);
++
++ /* Copy out the data in the packet... */
++ memcpy(buf, &ibuf[bufix], paylen);
++
++ return (ssize_t)paylen;
++}
++
+ ssize_t receive_packet (interface, buf, len, from, hfrom)
+ struct interface_info *interface;
+ unsigned char *buf;
+@@ -381,6 +507,10 @@ ssize_t receive_packet (interface, buf,
+ };
+ struct cmsghdr *cmsg;
+
++ if (interface->hw_address.hbuf[0] == HTYPE_INFINIBAND) {
++ return receive_packet_ib(interface, buf, len, from, hfrom);
++ }
++
+ length = recvmsg (interface -> rfdesc, &msg, 0);
+ if (length <= 0)
+ return length;
+@@ -461,33 +591,41 @@ void maybe_setup_fallback ()
+ }
+
+ void
+-get_hw_addr(const char *name, struct hardware *hw) {
+- int sock;
+- struct ifreq tmp;
+- struct sockaddr *sa;
++get_hw_addr(struct interface_info *info)
++{
++ struct hardware *hw = &info->hw_address;
++ char *name = info->name;
++ struct ifaddrs *ifaddrs;
++ struct ifaddrs *ifa;
++ struct sockaddr_ll *sll = NULL;
+
+- if (strlen(name) >= sizeof(tmp.ifr_name)) {
+- log_fatal("Device name too long: \"%s\"", name);
+- }
++ if (getifaddrs(&ifaddrs) == -1)
++ log_fatal("Failed to get interfaces");
++
++ for (ifa = ifaddrs; ifa != NULL; ifa = ifa->ifa_next) {
++
++ if (ifa->ifa_addr->sa_family != AF_PACKET)
++ continue;
+
+- sock = socket(AF_INET, SOCK_DGRAM, 0);
+- if (sock < 0) {
+- log_fatal("Can't create socket for \"%s\": %m", name);
++ if (ifa->ifa_flags & IFF_LOOPBACK)
++ continue;
++
++ if (strcmp(ifa->ifa_name, name) == 0) {
++ sll = (struct sockaddr_ll *)(void *)ifa->ifa_addr;
++ break;
++ }
+ }
+
+- memset(&tmp, 0, sizeof(tmp));
+- strcpy(tmp.ifr_name, name);
+- if (ioctl(sock, SIOCGIFHWADDR, &tmp) < 0) {
+- log_fatal("Error getting hardware address for \"%s\": %m",
+- name);
++ if (sll == NULL) {
++ freeifaddrs(ifaddrs);
++ log_fatal("Failed to get HW address for %s\n", name);
+ }
+
+- sa = &tmp.ifr_hwaddr;
+- switch (sa->sa_family) {
++ switch (sll->sll_hatype) {
+ case ARPHRD_ETHER:
+ hw->hlen = 7;
+ hw->hbuf[0] = HTYPE_ETHER;
+- memcpy(&hw->hbuf[1], sa->sa_data, 6);
++ memcpy(&hw->hbuf[1], sll->sll_addr, 6);
+ break;
+ case ARPHRD_IEEE802:
+ #ifdef ARPHRD_IEEE802_TR
+@@ -495,18 +633,36 @@ get_hw_addr(const char *name, struct har
+ #endif /* ARPHRD_IEEE802_TR */
+ hw->hlen = 7;
+ hw->hbuf[0] = HTYPE_IEEE802;
+- memcpy(&hw->hbuf[1], sa->sa_data, 6);
++ memcpy(&hw->hbuf[1], sll->sll_addr, 6);
+ break;
+ case ARPHRD_FDDI:
+ hw->hlen = 17;
+ hw->hbuf[0] = HTYPE_FDDI;
+- memcpy(&hw->hbuf[1], sa->sa_data, 16);
++ memcpy(&hw->hbuf[1], sll->sll_addr, 16);
++ break;
++ case ARPHRD_INFINIBAND:
++ /* For Infiniband, save the broadcast address and store
++ * the port GUID into the hardware address.
++ */
++ if (ifa->ifa_flags & IFF_BROADCAST) {
++ struct sockaddr_ll *bll;
++
++ bll = (struct sockaddr_ll *)ifa->ifa_broadaddr;
++ memcpy(&info->bcast_addr, bll->sll_addr, 20);
++ } else {
++ memcpy(&info->bcast_addr, default_ib_bcast_addr,
++ 20);
++ }
++
++ hw->hlen = 1;
++ hw->hbuf[0] = HTYPE_INFINIBAND;
+ break;
+ default:
++ freeifaddrs(ifaddrs);
+ log_fatal("Unsupported device type %ld for \"%s\"",
+- (long int)sa->sa_family, name);
++ (long int)sll->sll_family, name);
+ }
+
+- close(sock);
++ freeifaddrs(ifaddrs);
+ }
+ #endif
+diff -up dhcp-4.2.0/includes/dhcp.h.ib dhcp-4.2.0/includes/dhcp.h
+--- dhcp-4.2.0/includes/dhcp.h.ib 2009-11-19 20:49:01.000000000 -0500
++++ dhcp-4.2.0/includes/dhcp.h 2010-09-23 06:21:03.000000000 -0400
+@@ -79,6 +79,7 @@ struct dhcp_packet {
+ #define HTYPE_ETHER 1 /* Ethernet 10Mbps */
+ #define HTYPE_IEEE802 6 /* IEEE 802.2 Token Ring... */
+ #define HTYPE_FDDI 8 /* FDDI... */
++#define HTYPE_INFINIBAND 32 /* Infiniband IPoIB */
+
+ /* Magic cookie validating dhcp options field (and bootp vendor
+ extensions field). */
+diff -up dhcp-4.2.0/client/dhclient.c.ib dhcp-4.2.0/client/dhclient.c
+--- dhcp-4.2.0/client/dhclient.c.ib 2010-09-23 06:11:14.000000000 -0400
++++ dhcp-4.2.0/client/dhclient.c 2010-09-23 06:21:03.000000000 -0400
+@@ -98,6 +98,29 @@ static void usage(void);
+
+ static isc_result_t write_duid(struct data_string *duid);
+
++static void setup_ib_interface(struct interface_info *ip)
++{
++ struct group *g;
++
++ /* Set the broadcast flag */
++ ip->client->config->bootp_broadcast_always = 1;
++
++ /*
++ * Find out if a dhcp-client-identifier option was specified either
++ * in the config file or on the command line
++ */
++ for (g = ip->client->config->on_transmission; g != NULL; g = g->next) {
++ if ((g->statements != NULL) &&
++ (strcmp(g->statements->data.option->option->name,
++ "dhcp-client-identifier") == 0)) {
++ return;
++ }
++ }
++
++ /* No client ID specified */
++ log_fatal("dhcp-client-identifier must be specified for InfiniBand");
++}
++
+ int
+ main(int argc, char **argv) {
+ int fd;
+@@ -805,6 +828,14 @@ main(int argc, char **argv) {
+ }
+ srandom(seed + cur_time);
+
++ /* Setup specific Infiniband options */
++ for (ip = interfaces; ip; ip = ip->next) {
++ if (ip->client &&
++ (ip->hw_address.hbuf[0] == HTYPE_INFINIBAND)) {
++ setup_ib_interface(ip);
++ }
++ }
++
+ /* Start a configuration state machine for each interface. */
+ #ifdef DHCPv6
+ if (local_family == AF_INET6) {
+diff -up dhcp-4.2.0/common/bpf.c.ib dhcp-4.2.0/common/bpf.c
+--- dhcp-4.2.0/common/bpf.c.ib 2010-09-23 05:24:01.000000000 -0400
++++ dhcp-4.2.0/common/bpf.c 2010-09-23 06:37:48.000000000 -0400
+@@ -116,7 +116,7 @@ int if_register_bpf (info)
+ log_fatal ("Can't attach interface %s to bpf device %s: %m",
+ info -> name, filename);
+
+- get_hw_addr(info->name, &info->hw_address);
++ get_hw_addr(info);
+
+ return sock;
+ }
+@@ -198,11 +198,44 @@ struct bpf_insn dhcp_bpf_filter [] = {
+ BPF_STMT(BPF_RET+BPF_K, 0),
+ };
+
++/* Packet filter program for DHCP over Infiniband.
++ *
++ * XXX
++ * Changes to the filter program may require changes to the constant offsets
++ * used in lpf_gen_filter_setup to patch the port in the BPF program!
++ * XXX
++ */
++struct bpf_insn dhcp_ib_bpf_filter [] = {
++ /* Packet filter for Infiniband */
++ /* Make sure it's a UDP packet... */
++ BPF_STMT(BPF_LD + BPF_B + BPF_ABS, 9),
++ BPF_JUMP(BPF_JMP + BPF_JEQ + BPF_K, IPPROTO_UDP, 0, 6),
++
++ /* Make sure this isn't a fragment... */
++ BPF_STMT(BPF_LD + BPF_H + BPF_ABS, 6),
++ BPF_JUMP(BPF_JMP + BPF_JSET + BPF_K, 0x1fff, 4, 0),
++
++ /* Get the IP header length... */
++ BPF_STMT(BPF_LDX + BPF_B + BPF_MSH, 0),
++
++ /* Make sure it's to the right port... */
++ BPF_STMT(BPF_LD + BPF_H + BPF_IND, 2),
++ BPF_JUMP(BPF_JMP + BPF_JEQ + BPF_K, 67, 0, 1),
++
++ /* If we passed all the tests, ask for the whole packet. */
++ BPF_STMT(BPF_RET + BPF_K, (u_int)-1),
++
++ /* Otherwise, drop it. */
++ BPF_STMT(BPF_RET + BPF_K, 0),
++};
++
+ #if defined (DEC_FDDI)
+ struct bpf_insn *bpf_fddi_filter;
+ #endif
+
+ int dhcp_bpf_filter_len = sizeof dhcp_bpf_filter / sizeof (struct bpf_insn);
++int dhcp_ib_bpf_filter_len = sizeof dhcp_ib_bpf_filter / sizeof (struct bpf_insn);
++
+ #if defined (HAVE_TR_SUPPORT)
+ struct bpf_insn dhcp_bpf_tr_filter [] = {
+ /* accept all token ring packets due to variable length header */
+@@ -552,7 +585,9 @@ void maybe_setup_fallback ()
+ }
+
+ void
+-get_hw_addr(const char *name, struct hardware *hw) {
++get_hw_addr(struct interface_info *info) {
++ struct hardware *hw = &info->hw_address;
++ char *name = info->name;
+ struct ifaddrs *ifa;
+ struct ifaddrs *p;
+ struct sockaddr_dl *sa;
+diff -up dhcp-4.2.0/common/socket.c.ib dhcp-4.2.0/common/socket.c
+--- dhcp-4.2.0/common/socket.c.ib 2009-11-19 20:49:01.000000000 -0500
++++ dhcp-4.2.0/common/socket.c 2010-09-23 06:21:03.000000000 -0400
+@@ -283,7 +283,7 @@ if_register_socket(struct interface_info
+
+ /* If this is a normal IPv4 address, get the hardware address. */
+ if ((local_family == AF_INET) && (strcmp(info->name, "fallback") != 0))
+- get_hw_addr(info->name, &info->hw_address);
++ get_hw_addr(info);
+
+ return sock;
+ }
+@@ -429,7 +429,7 @@ if_register6(struct interface_info *info
+ if (req_multi)
+ if_register_multicast(info);
+
+- get_hw_addr(info->name, &info->hw_address);
++ get_hw_addr(info);
+
+ if (!quiet_interface_discovery) {
+ if (info->shared_network != NULL) {
+diff -up dhcp-4.2.0/includes/dhcpd.h.ib dhcp-4.2.0/includes/dhcpd.h
+--- dhcp-4.2.0/includes/dhcpd.h.ib 2010-09-23 06:07:17.000000000 -0400
++++ dhcp-4.2.0/includes/dhcpd.h 2010-09-23 06:21:03.000000000 -0400
+@@ -1214,6 +1214,7 @@ struct interface_info {
+ struct shared_network *shared_network;
+ /* Networks connected to this interface. */
+ struct hardware hw_address; /* Its physical address. */
++ u_int8_t bcast_addr[20]; /* Infiniband broadcast address */
+ struct in_addr *addresses; /* Addresses associated with this
+ * interface.
+ */
+@@ -2324,7 +2325,7 @@ void print_dns_status (int, struct dhcp_
+ #endif
+ const char *print_time(TIME);
+
+-void get_hw_addr(const char *name, struct hardware *hw);
++void get_hw_addr(struct interface_info *info);
+
+ /* socket.c */
+ #if defined (USE_SOCKET_SEND) || defined (USE_SOCKET_RECEIVE) \
+diff -up dhcp-4.2.0/common/dlpi.c.ib dhcp-4.2.0/common/dlpi.c
+--- dhcp-4.2.0/common/dlpi.c.ib 2010-09-23 05:24:05.000000000 -0400
++++ dhcp-4.2.0/common/dlpi.c 2010-09-23 06:39:26.000000000 -0400
+@@ -1342,7 +1342,9 @@ void maybe_setup_fallback ()
+ #endif /* USE_DLPI_SEND */
+
+ void
+-get_hw_addr(const char *name, struct hardware *hw) {
++get_hw_addr(struct interface_info *info) {
++ struct hardware *hw = &info->hw_address;
++ char *name = info->name;
+ int sock, unit;
+ long buf[DLPI_MAXDLBUF];
+ union DL_primitives *dlp;
diff --git a/net-misc/dhcp/files/dhcp-4.2.0-options.patch b/net-misc/dhcp/files/dhcp-4.2.0-options.patch new file mode 100644 index 000000000..6c2062afa --- /dev/null +++ b/net-misc/dhcp/files/dhcp-4.2.0-options.patch @@ -0,0 +1,401 @@ +diff -up dhcp-4.2.0/client/clparse.c.options dhcp-4.2.0/client/clparse.c
+--- dhcp-4.2.0/client/clparse.c.options 2009-11-19 20:48:58.000000000 -0500
++++ dhcp-4.2.0/client/clparse.c 2010-09-23 06:07:17.000000000 -0400
+@@ -136,6 +136,7 @@ isc_result_t read_client_conf ()
+ /* Requested lease time, used by DHCPv6 (DHCPv4 uses the option cache)
+ */
+ top_level_config.requested_lease = 7200;
++ top_level_config.bootp_broadcast_always = 0;
+
+ group_allocate (&top_level_config.on_receipt, MDL);
+ if (!top_level_config.on_receipt)
+@@ -303,7 +304,8 @@ void read_client_leases ()
+ interface-declaration |
+ LEASE client-lease-statement |
+ ALIAS client-lease-statement |
+- KEY key-definition */
++ KEY key-definition |
++ BOOTP_BROADCAST_ALWAYS */
+
+ void parse_client_statement (cfile, ip, config)
+ struct parse *cfile;
+@@ -717,6 +719,12 @@ void parse_client_statement (cfile, ip,
+ parse_reject_statement (cfile, config);
+ return;
+
++ case BOOTP_BROADCAST_ALWAYS:
++ token = next_token(&val, (unsigned*)0, cfile);
++ config -> bootp_broadcast_always = 1;
++ parse_semi (cfile);
++ return;
++
+ default:
+ lose = 0;
+ stmt = (struct executable_statement *)0;
+diff -up dhcp-4.2.0/client/dhclient.c.options dhcp-4.2.0/client/dhclient.c
+--- dhcp-4.2.0/client/dhclient.c.options 2010-02-17 15:33:55.000000000 -0500
++++ dhcp-4.2.0/client/dhclient.c 2010-09-23 06:11:14.000000000 -0400
+@@ -39,6 +39,12 @@
+ #include <limits.h>
+ #include <dns/result.h>
+
++/*
++ * Defined in stdio.h when _GNU_SOURCE is set, but we don't want to define
++ * that when building ISC code.
++ */
++extern int asprintf(char **strp, const char *fmt, ...);
++
+ TIME default_lease_time = 43200; /* 12 hours... */
+ TIME max_lease_time = 86400; /* 24 hours... */
+
+@@ -82,6 +88,9 @@ int wanted_ia_na = -1; /* the absolute
+ int wanted_ia_ta = 0;
+ int wanted_ia_pd = 0;
+ char *mockup_relay = NULL;
++int bootp_broadcast_always = 0;
++
++extern u_int32_t default_requested_options[];
+
+ void run_stateless(int exit_mode);
+
+@@ -112,6 +121,15 @@ main(int argc, char **argv) {
+ int local_family_set = 0;
+ #endif /* DHCPv6 */
+ char *s;
++ char *dhcp_client_identifier_arg = NULL;
++ char *dhcp_host_name_arg = NULL;
++ char *dhcp_fqdn_arg = NULL;
++ char *dhcp_vendor_class_identifier_arg = NULL;
++ char *dhclient_request_options = NULL;
++
++ int timeout_arg = 0;
++ char *arg_conf = NULL;
++ int arg_conf_len = 0;
+
+ /* Initialize client globals. */
+ memset(&default_duid, 0, sizeof(default_duid));
+@@ -297,6 +315,88 @@ main(int argc, char **argv) {
+ } else if (!strcmp(argv[i], "--version")) {
+ log_info("isc-dhclient-%s", PACKAGE_VERSION);
+ exit(0);
++ } else if (!strcmp(argv[i], "-I")) {
++ if ((++i == argc) || (argv[i] == NULL) || (*(argv[i])=='\0')) {
++ usage();
++ exit(1);
++ }
++
++ if (strlen(argv[i]) >= DHCP_MAX_OPTION_LEN) {
++ log_error("-I option dhcp-client-identifier string \"%s\" is too long - maximum length is: %d", argv[i], DHCP_MAX_OPTION_LEN-1);
++ exit(1);
++ }
++
++ dhcp_client_identifier_arg = argv[i];
++ } else if (!strcmp(argv[i], "-B")) {
++ bootp_broadcast_always = 1;
++ } else if (!strcmp(argv[i], "-H")) {
++ if ((++i == argc) || (argv[i] == NULL) || (*(argv[i])=='\0')) {
++ usage();
++ exit(1);
++ }
++
++ if (strlen(argv[i]) >= DHCP_MAX_OPTION_LEN) {
++ log_error("-H option host-name string \"%s\" is too long - maximum length is: %d", argv[i], DHCP_MAX_OPTION_LEN-1);
++ exit(1);
++ }
++
++ if (dhcp_host_name_arg != NULL) {
++ log_error("The -H <host-name> and -F <fqdn> arguments are mutually exclusive");
++ exit(1);
++ }
++
++ dhcp_host_name_arg = argv[i];
++ } else if (!strcmp(argv[i], "-F")) {
++ if ((++i == argc) || (argv[i] == NULL) || (*(argv[i])=='\0')) {
++ usage();
++ exit(1);
++ }
++
++ if (strlen(argv[i]) >= DHCP_MAX_OPTION_LEN) {
++ log_error("-F option fqdn.fqdn string \"%s\" is too long - maximum length is: %d", argv[i], DHCP_MAX_OPTION_LEN-1);
++ exit(1);
++ }
++
++ if (dhcp_fqdn_arg != NULL) {
++ log_error("Only one -F <fqdn> argument can be specified");
++ exit(1);
++ }
++
++ if (dhcp_host_name_arg != NULL) {
++ log_error("The -F <fqdn> and -H <host-name> arguments are mutually exclusive");
++ exit(1);
++ }
++
++ dhcp_fqdn_arg = argv[i];
++ } else if (!strcmp(argv[i], "-timeout")) {
++ if ((++i == argc) || (argv[i] == NULL) || (*(argv[i])=='\0')) {
++ usage();
++ exit(1);
++ }
++
++ if ((timeout_arg = atoi(argv[i])) <= 0) {
++ log_error("-T timeout option must be > 0 - bad value: %s",argv[i]);
++ exit(1);
++ }
++ } else if (!strcmp(argv[i], "-V")) {
++ if ((++i == argc) || (argv[i] == NULL) || (*(argv[i])=='\0')) {
++ usage();
++ exit(1);
++ }
++
++ if (strlen(argv[i]) >= DHCP_MAX_OPTION_LEN) {
++ log_error("-V option vendor-class-identifier string \"%s\" is too long - maximum length is: %d", argv[i], DHCP_MAX_OPTION_LEN-1);
++ exit(1);
++ }
++
++ dhcp_vendor_class_identifier_arg = argv[i];
++ } else if (!strcmp(argv[i], "-R")) {
++ if ((++i == argc) || (argv[i] == NULL) || (*(argv[i])=='\0')) {
++ usage();
++ exit(1);
++ }
++
++ dhclient_request_options = argv[i];
+ } else if (argv[i][0] == '-') {
+ usage();
+ } else if (interfaces_requested < 0) {
+@@ -466,6 +566,166 @@ main(int argc, char **argv) {
+ /* Parse the dhclient.conf file. */
+ read_client_conf();
+
++ /* Parse any extra command line configuration arguments: */
++ if ((dhcp_client_identifier_arg != NULL) && (*dhcp_client_identifier_arg != '\0')) {
++ arg_conf_len = asprintf(&arg_conf, "send dhcp-client-identifier \"%s\";", dhcp_client_identifier_arg);
++
++ if ((arg_conf == 0) || (arg_conf_len <= 0))
++ log_fatal("Unable to send -I option dhcp-client-identifier");
++ }
++
++ if ((dhcp_host_name_arg != NULL) && (*dhcp_host_name_arg != '\0')) {
++ if (arg_conf == 0) {
++ arg_conf_len = asprintf(&arg_conf, "send host-name \"%s\";", dhcp_host_name_arg);
++
++ if ((arg_conf == 0) || (arg_conf_len <= 0))
++ log_fatal("Unable to send -H option host-name");
++ } else {
++ char *last_arg_conf = arg_conf;
++ arg_conf = NULL;
++ arg_conf_len = asprintf(&arg_conf, "%s\nsend host-name \"%s\";", last_arg_conf, dhcp_host_name_arg);
++
++ if ((arg_conf == 0) || (arg_conf_len <= 0))
++ log_fatal("Unable to send -H option host-name");
++
++ free(last_arg_conf);
++ }
++ }
++
++ if ((dhcp_fqdn_arg != NULL) && (*dhcp_fqdn_arg != '\0')) {
++ if (arg_conf == 0) {
++ arg_conf_len = asprintf(&arg_conf, "send fqdn.fqdn \"%s\";", dhcp_fqdn_arg);
++
++ if ((arg_conf == 0) || (arg_conf_len <= 0))
++ log_fatal("Unable to send -F option fqdn.fqdn");
++ } else {
++ char *last_arg_conf = arg_conf;
++ arg_conf = NULL;
++ arg_conf_len = asprintf(&arg_conf, "%s\nsend fqdn.fqdn \"%s\";", last_arg_conf, dhcp_fqdn_arg);
++
++ if ((arg_conf == 0) || (arg_conf_len <= 0))
++ log_fatal("Unable to send -F option fqdn.fqdn");
++
++ free(last_arg_conf);
++ }
++ }
++
++ if (timeout_arg) {
++ if (arg_conf == 0) {
++ arg_conf_len = asprintf(&arg_conf, "timeout %d;", timeout_arg);
++
++ if ((arg_conf == 0) || (arg_conf_len <= 0))
++ log_fatal("Unable to process -timeout timeout argument");
++ } else {
++ char *last_arg_conf = arg_conf;
++ arg_conf = NULL;
++ arg_conf_len = asprintf(&arg_conf, "%s\ntimeout %d;", last_arg_conf, timeout_arg);
++
++ if ((arg_conf == 0) || (arg_conf_len == 0))
++ log_fatal("Unable to process -timeout timeout argument");
++
++ free(last_arg_conf);
++ }
++ }
++
++ if ((dhcp_vendor_class_identifier_arg != NULL) && (*dhcp_vendor_class_identifier_arg != '\0')) {
++ if (arg_conf == 0) {
++ arg_conf_len = asprintf(&arg_conf, "send vendor-class-identifier \"%s\";", dhcp_vendor_class_identifier_arg);
++
++ if ((arg_conf == 0) || (arg_conf_len <= 0))
++ log_fatal("Unable to send -V option vendor-class-identifier");
++ } else {
++ char *last_arg_conf = arg_conf;
++ arg_conf = NULL;
++ arg_conf_len = asprintf(&arg_conf, "%s\nsend vendor-class-identifier \"%s\";", last_arg_conf, dhcp_vendor_class_identifier_arg);
++
++ if ((arg_conf == 0) || (arg_conf_len <= 0))
++ log_fatal("Unable to send -V option vendor-class-identifier");
++
++ free(last_arg_conf);
++ }
++ }
++
++ if (dhclient_request_options != NULL) {
++ if (arg_conf == 0) {
++ arg_conf_len = asprintf(&arg_conf, "request %s;", dhclient_request_options);
++
++ if ((arg_conf == 0) || (arg_conf_len <= 0))
++ log_fatal("Unable to parse -R <request options list> argument");
++ } else {
++ char *last_arg_conf = arg_conf;
++ arg_conf = NULL;
++ arg_conf_len = asprintf(&arg_conf, "%s\nrequest %s;", last_arg_conf, dhclient_request_options);
++
++ if ((arg_conf == 0) || (arg_conf_len <= 0))
++ log_fatal("Unable to parse -R <request options list> argument");
++
++ free(last_arg_conf);
++ }
++ }
++
++ if (arg_conf) {
++ if (arg_conf_len == 0)
++ if ((arg_conf_len = strlen(arg_conf)) == 0)
++ /* huh ? cannot happen ! */
++ log_fatal("Unable to process -I/-H/-F/-timeout/-V/-R configuration arguments");
++
++ /* parse the extra dhclient.conf configuration arguments
++ * into top level config: */
++ struct parse *cfile = (struct parse *)0;
++ const char *val = NULL;
++ int token;
++
++ status = new_parse(&cfile, -1, arg_conf, arg_conf_len, "extra dhclient -I/-H/-F/-timeout/-V/-R configuration arguments", 0);
++
++ if ((status != ISC_R_SUCCESS) || (cfile -> warnings_occurred))
++ log_fatal("Cannot parse -I/-H/-F/-timeout/-V/-R configuration arguments !");
++ /* more detailed parse failures will be logged */
++
++ do {
++ token = peek_token(&val, (unsigned *)0, cfile);
++ if (token == END_OF_FILE)
++ break;
++
++ parse_client_statement(cfile, (struct interface_info *)0, &top_level_config);
++ } while (1);
++
++ if (cfile -> warnings_occurred)
++ log_fatal("Cannot parse -I/-H/-F/-timeout/-V/-R configuration arguments !");
++ end_parse(&cfile);
++
++ if (timeout_arg) {
++ /* we just set the toplevel timeout, but per-client
++ * timeouts may still be at defaults. Also, it makes no
++ * sense having the reboot_timeout or backoff_cutoff
++ * greater than the timeout:
++ */
++ if ((top_level_config.backoff_cutoff == 15) && (top_level_config.backoff_cutoff > (timeout_arg / 2)))
++ top_level_config.backoff_cutoff = (((unsigned long)(timeout_arg / 2)) == 0) ? timeout_arg : (unsigned long)(timeout_arg / 2);
++
++ for (ip=interfaces; ip; ip = ip->next) {
++ if (ip->client->config->timeout == 60)
++ ip->client->config->timeout = timeout_arg;
++
++ if ((ip->client->config->reboot_timeout == 10) && (ip->client->config->reboot_timeout > ip->client->config->timeout))
++ ip->client->config->reboot_timeout = ip->client->config->timeout;
++ if ((ip->client->config->backoff_cutoff == 15) && (ip->client->config->backoff_cutoff > top_level_config.backoff_cutoff))
++ ip->client->config->backoff_cutoff = top_level_config.backoff_cutoff;
++ }
++ }
++
++ if ((dhclient_request_options != 0) && (top_level_config.requested_options != (void *) default_requested_options)) {
++ for (ip=interfaces; ip; ip = ip->next) {
++ if (ip->client->config->requested_options == (void *) default_requested_options)
++ ip->client->config->requested_options = top_level_config.requested_options;
++ }
++ }
++
++ free(arg_conf);
++ arg_conf = NULL;
++ arg_conf_len = 0;
++ }
++
+ /* Parse the lease database. */
+ read_client_leases();
+
+@@ -2337,7 +2597,8 @@ void make_discover (client, lease)
+ client -> packet.xid = random ();
+ client -> packet.secs = 0; /* filled in by send_discover. */
+
+- if (can_receive_unicast_unconfigured (client -> interface))
++ if ((!(bootp_broadcast_always || client->config->bootp_broadcast_always))
++ && can_receive_unicast_unconfigured(client->interface))
+ client -> packet.flags = 0;
+ else
+ client -> packet.flags = htons (BOOTP_BROADCAST);
+@@ -2421,7 +2682,9 @@ void make_request (client, lease)
+ } else {
+ memset (&client -> packet.ciaddr, 0,
+ sizeof client -> packet.ciaddr);
+- if (can_receive_unicast_unconfigured (client -> interface))
++ if ((!(bootp_broadcast_always ||
++ client ->config->bootp_broadcast_always)) &&
++ can_receive_unicast_unconfigured (client -> interface))
+ client -> packet.flags = 0;
+ else
+ client -> packet.flags = htons (BOOTP_BROADCAST);
+@@ -2483,7 +2746,8 @@ void make_decline (client, lease)
+ client -> packet.hops = 0;
+ client -> packet.xid = client -> xid;
+ client -> packet.secs = 0; /* Filled in by send_request. */
+- if (can_receive_unicast_unconfigured (client -> interface))
++ if ((!(bootp_broadcast_always || client->config-> bootp_broadcast_always))
++ && can_receive_unicast_unconfigured (client->interface))
+ client -> packet.flags = 0;
+ else
+ client -> packet.flags = htons (BOOTP_BROADCAST);
+diff -up dhcp-4.2.0/common/conflex.c.options dhcp-4.2.0/common/conflex.c
+--- dhcp-4.2.0/common/conflex.c.options 2010-03-24 17:49:47.000000000 -0400
++++ dhcp-4.2.0/common/conflex.c 2010-09-23 06:07:17.000000000 -0400
+@@ -803,6 +803,8 @@ intern(char *atom, enum dhcp_token dfv)
+ return BALANCE;
+ if (!strcasecmp (atom + 1, "ound"))
+ return BOUND;
++ if (!strcasecmp (atom + 1, "ootp-broadcast-always"))
++ return BOOTP_BROADCAST_ALWAYS;
+ break;
+ case 'c':
+ if (!strcasecmp(atom + 1, "ase"))
+diff -up dhcp-4.2.0/includes/dhcpd.h.options dhcp-4.2.0/includes/dhcpd.h
+--- dhcp-4.2.0/includes/dhcpd.h.options 2010-09-23 05:24:32.000000000 -0400
++++ dhcp-4.2.0/includes/dhcpd.h 2010-09-23 06:07:17.000000000 -0400
+@@ -1119,6 +1119,9 @@ struct client_config {
+ int do_forward_update; /* If nonzero, and if we have the
+ information we need, update the
+ A record for the address we get. */
++
++ int bootp_broadcast_always; /* If nonzero, always set the BOOTP_BROADCAST
++ flag in requests */
+ };
+
+ /* Per-interface state used in the dhcp client... */
+diff -up dhcp-4.2.0/includes/dhctoken.h.options dhcp-4.2.0/includes/dhctoken.h
+--- dhcp-4.2.0/includes/dhctoken.h.options 2010-02-17 15:33:55.000000000 -0500
++++ dhcp-4.2.0/includes/dhctoken.h 2010-09-23 06:08:18.000000000 -0400
+@@ -357,7 +357,8 @@ enum dhcp_token {
+ CONFLICT_DONE = 660,
+ AUTO_PARTNER_DOWN = 661,
+ GETHOSTNAME = 662,
+- REWIND = 663
++ REWIND = 663,
++ BOOTP_BROADCAST_ALWAYS = 664
+ };
+
+ #define is_identifier(x) ((x) >= FIRST_TOKEN && \
diff --git a/net-misc/dhcp/files/dhcp-4.2.0-xen-checksum.patch b/net-misc/dhcp/files/dhcp-4.2.0-xen-checksum.patch new file mode 100644 index 000000000..fe33bdf50 --- /dev/null +++ b/net-misc/dhcp/files/dhcp-4.2.0-xen-checksum.patch @@ -0,0 +1,245 @@ +diff -up dhcp-4.2.0/common/bpf.c.xen dhcp-4.2.0/common/bpf.c
+--- dhcp-4.2.0/common/bpf.c.xen 2009-11-19 20:48:59.000000000 -0500
++++ dhcp-4.2.0/common/bpf.c 2010-09-23 05:24:01.000000000 -0400
+@@ -485,7 +485,7 @@ ssize_t receive_packet (interface, buf,
+ offset = decode_udp_ip_header (interface,
+ interface -> rbuf,
+ interface -> rbuf_offset,
+- from, hdr.bh_caplen, &paylen);
++ from, hdr.bh_caplen, &paylen, 0);
+
+ /* If the IP or UDP checksum was bad, skip the packet... */
+ if (offset < 0) {
+diff -up dhcp-4.2.0/common/dlpi.c.xen dhcp-4.2.0/common/dlpi.c
+--- dhcp-4.2.0/common/dlpi.c.xen 2009-11-19 20:49:00.000000000 -0500
++++ dhcp-4.2.0/common/dlpi.c 2010-09-23 05:24:05.000000000 -0400
+@@ -694,7 +694,7 @@ ssize_t receive_packet (interface, buf,
+ length -= offset;
+ #endif
+ offset = decode_udp_ip_header (interface, dbuf, bufix,
+- from, length, &paylen);
++ from, length, &paylen, 0);
+
+ /*
+ * If the IP or UDP checksum was bad, skip the packet...
+diff -up dhcp-4.2.0/common/lpf.c.xen dhcp-4.2.0/common/lpf.c
+--- dhcp-4.2.0/common/lpf.c.xen 2009-07-23 14:52:19.000000000 -0400
++++ dhcp-4.2.0/common/lpf.c 2010-09-23 05:24:09.000000000 -0400
+@@ -29,18 +29,33 @@
+ #include "dhcpd.h"
+ #if defined (USE_LPF_SEND) || defined (USE_LPF_RECEIVE)
+ #include <sys/ioctl.h>
++#include <sys/socket.h>
+ #include <sys/uio.h>
+ #include <errno.h>
+
+ #include <asm/types.h>
+ #include <linux/filter.h>
+ #include <linux/if_ether.h>
++#include <linux/if_packet.h>
+ #include <netinet/in_systm.h>
+ #include "includes/netinet/ip.h"
+ #include "includes/netinet/udp.h"
+ #include "includes/netinet/if_ether.h"
+ #include <net/if.h>
+
++#ifndef PACKET_AUXDATA
++#define PACKET_AUXDATA 8
++
++struct tpacket_auxdata
++{
++ __u32 tp_status;
++ __u32 tp_len;
++ __u32 tp_snaplen;
++ __u16 tp_mac;
++ __u16 tp_net;
++};
++#endif
++
+ /* Reinitializes the specified interface after an address change. This
+ is not required for packet-filter APIs. */
+
+@@ -66,10 +81,14 @@ int if_register_lpf (info)
+ struct interface_info *info;
+ {
+ int sock;
+- struct sockaddr sa;
++ union {
++ struct sockaddr_ll ll;
++ struct sockaddr common;
++ } sa;
++ struct ifreq ifr;
+
+ /* Make an LPF socket. */
+- if ((sock = socket(PF_PACKET, SOCK_PACKET,
++ if ((sock = socket(PF_PACKET, SOCK_RAW,
+ htons((short)ETH_P_ALL))) < 0) {
+ if (errno == ENOPROTOOPT || errno == EPROTONOSUPPORT ||
+ errno == ESOCKTNOSUPPORT || errno == EPFNOSUPPORT ||
+@@ -84,11 +103,16 @@ int if_register_lpf (info)
+ log_fatal ("Open a socket for LPF: %m");
+ }
+
++ memset (&ifr, 0, sizeof ifr);
++ strncpy (ifr.ifr_name, (const char *)info -> ifp, sizeof ifr.ifr_name);
++ if (ioctl (sock, SIOCGIFINDEX, &ifr))
++ log_fatal ("Failed to get interface index: %m");
++
+ /* Bind to the interface name */
+ memset (&sa, 0, sizeof sa);
+- sa.sa_family = AF_PACKET;
+- strncpy (sa.sa_data, (const char *)info -> ifp, sizeof sa.sa_data);
+- if (bind (sock, &sa, sizeof sa)) {
++ sa.ll.sll_family = AF_PACKET;
++ sa.ll.sll_ifindex = ifr.ifr_ifindex;
++ if (bind (sock, &sa.common, sizeof sa)) {
+ if (errno == ENOPROTOOPT || errno == EPROTONOSUPPORT ||
+ errno == ESOCKTNOSUPPORT || errno == EPFNOSUPPORT ||
+ errno == EAFNOSUPPORT || errno == EINVAL) {
+@@ -170,9 +194,18 @@ static void lpf_gen_filter_setup (struct
+ void if_register_receive (info)
+ struct interface_info *info;
+ {
++ int val;
++
+ /* Open a LPF device and hang it on this interface... */
+ info -> rfdesc = if_register_lpf (info);
+
++ val = 1;
++ if (setsockopt (info -> rfdesc, SOL_PACKET, PACKET_AUXDATA, &val,
++ sizeof val) < 0) {
++ if (errno != ENOPROTOOPT)
++ log_fatal ("Failed to set auxiliary packet data: %m");
++ }
++
+ #if defined (HAVE_TR_SUPPORT)
+ if (info -> hw_address.hbuf [0] == HTYPE_IEEE802)
+ lpf_tr_filter_setup (info);
+@@ -294,7 +327,6 @@ ssize_t send_packet (interface, packet,
+ double hh [16];
+ double ih [1536 / sizeof (double)];
+ unsigned char *buf = (unsigned char *)ih;
+- struct sockaddr sa;
+ int result;
+ int fudge;
+
+@@ -315,15 +347,7 @@ ssize_t send_packet (interface, packet,
+ (unsigned char *)raw, len);
+ memcpy (buf + ibufp, raw, len);
+
+- /* For some reason, SOCK_PACKET sockets can't be connected,
+- so we have to do a sentdo every time. */
+- memset (&sa, 0, sizeof sa);
+- sa.sa_family = AF_PACKET;
+- strncpy (sa.sa_data,
+- (const char *)interface -> ifp, sizeof sa.sa_data);
+-
+- result = sendto (interface -> wfdesc,
+- buf + fudge, ibufp + len - fudge, 0, &sa, sizeof sa);
++ result = write (interface -> wfdesc, buf + fudge, ibufp + len - fudge);
+ if (result < 0)
+ log_error ("send_packet: %m");
+ return result;
+@@ -340,14 +364,35 @@ ssize_t receive_packet (interface, buf,
+ {
+ int length = 0;
+ int offset = 0;
++ int nocsum = 0;
+ unsigned char ibuf [1536];
+ unsigned bufix = 0;
+ unsigned paylen;
++ unsigned char cmsgbuf[CMSG_LEN(sizeof(struct tpacket_auxdata))];
++ struct iovec iov = {
++ .iov_base = ibuf,
++ .iov_len = sizeof ibuf,
++ };
++ struct msghdr msg = {
++ .msg_iov = &iov,
++ .msg_iovlen = 1,
++ .msg_control = cmsgbuf,
++ .msg_controllen = sizeof(cmsgbuf),
++ };
++ struct cmsghdr *cmsg;
+
+- length = read (interface -> rfdesc, ibuf, sizeof ibuf);
++ length = recvmsg (interface -> rfdesc, &msg, 0);
+ if (length <= 0)
+ return length;
+
++ for (cmsg = CMSG_FIRSTHDR(&msg); cmsg; cmsg = CMSG_NXTHDR(&msg, cmsg)) {
++ if (cmsg->cmsg_level == SOL_PACKET &&
++ cmsg->cmsg_type == PACKET_AUXDATA) {
++ struct tpacket_auxdata *aux = (void *)CMSG_DATA(cmsg);
++ nocsum = aux->tp_status & TP_STATUS_CSUMNOTREADY;
++ }
++ }
++
+ bufix = 0;
+ /* Decode the physical header... */
+ offset = decode_hw_header (interface, ibuf, bufix, hfrom);
+@@ -364,7 +409,7 @@ ssize_t receive_packet (interface, buf,
+
+ /* Decode the IP and UDP headers... */
+ offset = decode_udp_ip_header (interface, ibuf, bufix, from,
+- (unsigned)length, &paylen);
++ (unsigned)length, &paylen, nocsum);
+
+ /* If the IP or UDP checksum was bad, skip the packet... */
+ if (offset < 0)
+diff -up dhcp-4.2.0/common/nit.c.xen dhcp-4.2.0/common/nit.c
+--- dhcp-4.2.0/common/nit.c.xen 2009-11-19 20:49:01.000000000 -0500
++++ dhcp-4.2.0/common/nit.c 2010-09-23 05:24:18.000000000 -0400
+@@ -369,7 +369,7 @@ ssize_t receive_packet (interface, buf,
+
+ /* Decode the IP and UDP headers... */
+ offset = decode_udp_ip_header (interface, ibuf, bufix,
+- from, length, &paylen);
++ from, length, &paylen, 0);
+
+ /* If the IP or UDP checksum was bad, skip the packet... */
+ if (offset < 0)
+diff -up dhcp-4.2.0/common/packet.c.xen dhcp-4.2.0/common/packet.c
+--- dhcp-4.2.0/common/packet.c.xen 2009-07-23 14:52:20.000000000 -0400
++++ dhcp-4.2.0/common/packet.c 2010-09-23 05:24:21.000000000 -0400
+@@ -211,7 +211,7 @@ ssize_t
+ decode_udp_ip_header(struct interface_info *interface,
+ unsigned char *buf, unsigned bufix,
+ struct sockaddr_in *from, unsigned buflen,
+- unsigned *rbuflen)
++ unsigned *rbuflen, int nocsum)
+ {
+ unsigned char *data;
+ struct ip ip;
+@@ -322,7 +322,7 @@ decode_udp_ip_header(struct interface_in
+ 8, IPPROTO_UDP + ulen))));
+
+ udp_packets_seen++;
+- if (usum && usum != sum) {
++ if (!nocsum && usum && usum != sum) {
+ udp_packets_bad_checksum++;
+ if (udp_packets_seen > 4 &&
+ (udp_packets_seen / udp_packets_bad_checksum) < 2) {
+diff -up dhcp-4.2.0/common/upf.c.xen dhcp-4.2.0/common/upf.c
+--- dhcp-4.2.0/common/upf.c.xen 2009-11-19 20:49:01.000000000 -0500
++++ dhcp-4.2.0/common/upf.c 2010-09-23 05:24:25.000000000 -0400
+@@ -320,7 +320,7 @@ ssize_t receive_packet (interface, buf,
+
+ /* Decode the IP and UDP headers... */
+ offset = decode_udp_ip_header (interface, ibuf, bufix,
+- from, length, &paylen);
++ from, length, &paylen, 0);
+
+ /* If the IP or UDP checksum was bad, skip the packet... */
+ if (offset < 0)
+diff -up dhcp-4.2.0/includes/dhcpd.h.xen dhcp-4.2.0/includes/dhcpd.h
+--- dhcp-4.2.0/includes/dhcpd.h.xen 2010-06-01 13:29:59.000000000 -0400
++++ dhcp-4.2.0/includes/dhcpd.h 2010-09-23 05:24:32.000000000 -0400
+@@ -2769,7 +2769,7 @@ ssize_t decode_hw_header PROTO ((struct
+ unsigned, struct hardware *));
+ ssize_t decode_udp_ip_header PROTO ((struct interface_info *, unsigned char *,
+ unsigned, struct sockaddr_in *,
+- unsigned, unsigned *));
++ unsigned, unsigned *, int));
+
+ /* ethernet.c */
+ void assemble_ethernet_header PROTO ((struct interface_info *, unsigned char *,
diff --git a/net-misc/dhcp/files/dhcp-4.2.1-dhclient-resolvconf.patch b/net-misc/dhcp/files/dhcp-4.2.1-dhclient-resolvconf.patch new file mode 100644 index 000000000..6d8caecdf --- /dev/null +++ b/net-misc/dhcp/files/dhcp-4.2.1-dhclient-resolvconf.patch @@ -0,0 +1,384 @@ +--- a/client/scripts/bsdos ++++ b/client/scripts/bsdos +@@ -1,34 +1,41 @@ + #!/bin/sh + + make_resolv_conf() { ++ if [ x"$PEER_DNS" != x ] && [ x$"PEER_DNS" != xyes ]; then ++ return 0 ++ fi ++ local conf= + if [ x"$new_domain_name_servers" != x ]; then +- cat /dev/null > /etc/resolv.conf.dhclient + if [ "x$new_domain_search" != x ]; then +- echo search $new_domain_search >> /etc/resolv.conf.dhclient ++ conf="${conf}search ${new_domain_search}\n" + elif [ "x$new_domain_name" != x ]; then + # Note that the DHCP 'Domain Name Option' is really just a domain + # name, and that this practice of using the domain name option as + # a search path is both nonstandard and deprecated. +- echo search $new_domain_name >> /etc/resolv.conf.dhclient ++ conf="${conf}search ${new_domain_name}\n" + fi + for nameserver in $new_domain_name_servers; do +- echo nameserver $nameserver >> /etc/resolv.conf.dhclient ++ conf="${conf}nameserver ${nameserver}\n" + done +- +- mv /etc/resolv.conf.dhclient /etc/resolv.conf + elif [ "x${new_dhcp6_name_servers}" != x ] ; then +- cat /dev/null > /etc/resolv.conf.dhclient6 +- chmod 644 /etc/resolv.conf.dhclient6 +- + if [ "x${new_dhcp6_domain_search}" != x ] ; then +- echo search ${new_dhcp6_domain_search} >> /etc/resolv.conf.dhclient6 ++ conf="${conf}search ${new_dhcp6_domain_search}\n" + fi + for nameserver in ${new_dhcp6_name_servers} ; do +- echo nameserver ${nameserver} >> /etc/resolv.conf.dhclient6 ++ conf="${conf}nameserver ${nameserver}\n" + done ++ fi + +- mv /etc/resolv.conf.dhclient6 /etc/resolv.conf ++ if [ x"$conf" != x ]; then ++ conf="# Generated by dhclient or interface $interface\n${conf}" ++ if type resolvconf >/dev/null 2>&1; then ++ printf "${conf}" | resolvconf -a $interface ++ else ++ printf "${conf}" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf ++ fi + fi ++ + # If we're making confs, may as well make an ntp.conf too + make_ntp_conf + } +--- a/client/scripts/freebsd ++++ b/client/scripts/freebsd +@@ -11,68 +11,41 @@ + fi + + make_resolv_conf() { ++ if [ x"$PEER_DNS" != x ] && [ x$"PEER_DNS" != xyes ]; then ++ return 0 ++ fi ++ local conf= + if [ x"$new_domain_name_servers" != x ]; then +- ( cat /dev/null > /etc/resolv.conf.dhclient ) +- exit_status=$? +- if [ $exit_status -ne 0 ]; then +- $LOGGER "Unable to create /etc/resolv.conf.dhclient: Error $exit_status" +- else +- if [ "x$new_domain_search" != x ]; then +- ( echo search $new_domain_search >> /etc/resolv.conf.dhclient ) +- exit_status=$? +- elif [ "x$new_domain_name" != x ]; then +- # Note that the DHCP 'Domain Name Option' is really just a domain +- # name, and that this practice of using the domain name option as +- # a search path is both nonstandard and deprecated. +- ( echo search $new_domain_name >> /etc/resolv.conf.dhclient ) +- exit_status=$? +- fi +- for nameserver in $new_domain_name_servers; do +- if [ $exit_status -ne 0 ]; then +- break +- fi +- ( echo nameserver $nameserver >>/etc/resolv.conf.dhclient ) +- exit_status=$? +- done +- +- # If there were no errors, attempt to mv the new file into place. +- if [ $exit_status -eq 0 ]; then +- ( mv /etc/resolv.conf.dhclient /etc/resolv.conf ) +- exit_status=$? +- fi +- +- if [ $exit_status -ne 0 ]; then +- $LOGGER "Error while writing new /etc/resolv.conf." +- fi ++ if [ "x$new_domain_search" != x ]; then ++ conf="${conf}search ${new_domain_search}\n" ++ elif [ "x$new_domain_name" != x ]; then ++ # Note that the DHCP 'Domain Name Option' is really just a domain ++ # name, and that this practice of using the domain name option as ++ # a search path is both nonstandard and deprecated. ++ conf="${conf}search ${new_domain_name}\n" + fi ++ for nameserver in $new_domain_name_servers; do ++ conf="${conf}nameserver ${nameserver}\n" ++ done + elif [ "x${new_dhcp6_name_servers}" != x ] ; then +- ( cat /dev/null > /etc/resolv.conf.dhclient6 ) +- exit_status=$? +- if [ $exit_status -ne 0 ] ; then +- $LOGGER "Unable to create /etc/resolv.conf.dhclient6: Error $exit_status" +- else +- if [ "x${new_dhcp6_domain_search}" != x ] ; then +- ( echo search ${new_dhcp6_domain_search} >> /etc/resolv.conf.dhclient6 ) +- exit_status=$? +- fi +- for nameserver in ${new_dhcp6_name_servers} ; do +- if [ $exit_status -ne 0 ] ; then +- break +- fi +- ( echo nameserver ${nameserver} >> /etc/resolv.conf.dhclient6 ) +- exit_status=$? +- done +- +- if [ $exit_status -eq 0 ] ; then +- ( mv /etc/resolv.conf.dhclient6 /etc/resolv.conf ) +- exit_status=$? +- fi ++ if [ "x${new_dhcp6_domain_search}" != x ] ; then ++ conf="${conf}search ${new_dhcp6_domain_search}\n" ++ fi ++ for nameserver in ${new_dhcp6_name_servers} ; do ++ conf="${conf}nameserver ${nameserver}\n" ++ done ++ fi + +- if [ $exit_status -ne 0 ] ; then +- $LOGGER "Error while writing new /etc/resolv.conf." +- fi ++ if [ x"$conf" != x ]; then ++ conf="# Generated by dhclient or interface $interface\n${conf}" ++ if type resolvconf >/dev/null 2>&1; then ++ printf "${conf}" | resolvconf -a $interface ++ else ++ printf "${conf}" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf + fi + fi ++ + # If we're making confs, may as well make an ntp.conf too + make_ntp_conf + } +--- a/client/scripts/linux ++++ b/client/scripts/linux +@@ -26,35 +26,41 @@ + ip=/sbin/ip + + make_resolv_conf() { ++ if [ x"$PEER_DNS" != x ] && [ x$"PEER_DNS" != xyes ]; then ++ return 0 ++ fi ++ local conf= + if [ x"$new_domain_name_servers" != x ]; then +- cat /dev/null > /etc/resolv.conf.dhclient +- chmod 644 /etc/resolv.conf.dhclient +- if [ x"$new_domain_search" != x ]; then +- echo search $new_domain_search >> /etc/resolv.conf.dhclient +- elif [ x"$new_domain_name" != x ]; then ++ if [ "x$new_domain_search" != x ]; then ++ conf="${conf}search ${new_domain_search}\n" ++ elif [ "x$new_domain_name" != x ]; then + # Note that the DHCP 'Domain Name Option' is really just a domain + # name, and that this practice of using the domain name option as + # a search path is both nonstandard and deprecated. +- echo search $new_domain_name >> /etc/resolv.conf.dhclient ++ conf="${conf}search ${new_domain_name}\n" + fi + for nameserver in $new_domain_name_servers; do +- echo nameserver $nameserver >>/etc/resolv.conf.dhclient ++ conf="${conf}nameserver ${nameserver}\n" + done +- +- mv /etc/resolv.conf.dhclient /etc/resolv.conf + elif [ "x${new_dhcp6_name_servers}" != x ] ; then +- cat /dev/null > /etc/resolv.conf.dhclient6 +- chmod 644 /etc/resolv.conf.dhclient6 +- + if [ "x${new_dhcp6_domain_search}" != x ] ; then +- echo search ${new_dhcp6_domain_search} >> /etc/resolv.conf.dhclient6 ++ conf="${conf}search ${new_dhcp6_domain_search}\n" + fi + for nameserver in ${new_dhcp6_name_servers} ; do +- echo nameserver ${nameserver} >> /etc/resolv.conf.dhclient6 ++ conf="${conf}nameserver ${nameserver}\n" + done ++ fi + +- mv /etc/resolv.conf.dhclient6 /etc/resolv.conf ++ if [ x"$conf" != x ]; then ++ conf="# Generated by dhclient or interface $interface\n${conf}" ++ if type resolvconf >/dev/null 2>&1; then ++ printf "${conf}" | resolvconf -a $interface ++ else ++ printf "${conf}" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf ++ fi + fi ++ + # If we're making confs, may as well make an ntp.conf too + make_ntp_conf + } +--- a/client/scripts/netbsd ++++ b/client/scripts/netbsd +@@ -1,34 +1,41 @@ + #!/bin/sh + + make_resolv_conf() { +- if [ "x$new_domain_name" != x ] && [ x"$new_domain_name_servers" != x ]; then +- cat /dev/null > /etc/resolv.conf.dhclient +- if [ "x$new_domain_search" != x ]; then +- echo search $new_domain_search >> /etc/resolv.conf.dhclient +- elif [ "x$new_domain_name" != x ]; then ++ if [ x"$PEER_DNS" != x ] && [ x$"PEER_DNS" != xyes ]; then ++ return 0 ++ fi ++ local conf= ++ if [ x"$new_domain_name_servers" != x ]; then ++ if [ "x$new_domain_search" != x ]; then ++ conf="${conf}search ${new_domain_search}\n" ++ elif [ "x$new_domain_name" != x ]; then + # Note that the DHCP 'Domain Name Option' is really just a domain + # name, and that this practice of using the domain name option as + # a search path is both nonstandard and deprecated. +- echo search $new_domain_name >> /etc/resolv.conf.dhclient ++ conf="${conf}search ${new_domain_name}\n" + fi + for nameserver in $new_domain_name_servers; do +- echo nameserver $nameserver >>/etc/resolv.conf.dhclient ++ conf="${conf}nameserver ${nameserver}\n" + done +- +- mv /etc/resolv.conf.dhclient /etc/resolv.conf + elif [ "x${new_dhcp6_name_servers}" != x ] ; then +- cat /dev/null > /etc/resolv.conf.dhclient6 +- chmod 644 /etc/resolv.conf.dhclient6 +- + if [ "x${new_dhcp6_domain_search}" != x ] ; then +- echo search ${new_dhcp6_domain_search} >> /etc/resolv.conf.dhclient6 ++ conf="${conf}search ${new_dhcp6_domain_search}\n" + fi + for nameserver in ${new_dhcp6_name_servers} ; do +- echo nameserver ${nameserver} >> /etc/resolv.conf.dhclient6 ++ conf="${conf}nameserver ${nameserver}\n" + done ++ fi + +- mv /etc/resolv.conf.dhclient6 /etc/resolv.conf ++ if [ x"$conf" != x ]; then ++ conf="# Generated by dhclient or interface $interface\n${conf}" ++ if type resolvconf >/dev/null 2>&1; then ++ printf "${conf}" | resolvconf -a $interface ++ else ++ printf "${conf}" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf ++ fi + fi ++ + # If we're making confs, may as well make an ntp.conf too + make_ntp_conf + } +--- a/client/scripts/openbsd ++++ b/client/scripts/openbsd +@@ -1,34 +1,41 @@ + #!/bin/sh + + make_resolv_conf() { +- if x"$new_domain_name_servers" != x ]; then +- cat /dev/null > /etc/resolv.conf.dhclient +- if [ x"$new_domain_search" != x ]; then +- echo search $new_domain_search >> /etc/resolv.conf.dhclient +- elif [ x"$new_domain_name" != x ]; then ++ if [ x"$PEER_DNS" != x ] && [ x$"PEER_DNS" != xyes ]; then ++ return 0 ++ fi ++ local conf= ++ if [ x"$new_domain_name_servers" != x ]; then ++ if [ "x$new_domain_search" != x ]; then ++ conf="${conf}search ${new_domain_search}\n" ++ elif [ "x$new_domain_name" != x ]; then + # Note that the DHCP 'Domain Name Option' is really just a domain + # name, and that this practice of using the domain name option as + # a search path is both nonstandard and deprecated. +- echo search $new_domain_name >> /etc/resolv.conf.dhclient ++ conf="${conf}search ${new_domain_name}\n" + fi + for nameserver in $new_domain_name_servers; do +- echo nameserver $nameserver >>/etc/resolv.conf.dhclient ++ conf="${conf}nameserver ${nameserver}\n" + done +- +- mv /etc/ersolv.conf.dhclient /etc/resolv.conf + elif [ "x${new_dhcp6_name_servers}" != x ] ; then +- cat /dev/null > /etc/resolv.conf.dhclient6 +- chmod 644 /etc/resolv.conf.dhclient6 +- + if [ "x${new_dhcp6_domain_search}" != x ] ; then +- echo search ${new_dhcp6_domain_search} >> /etc/resolv.conf.dhclient6 ++ conf="${conf}search ${new_dhcp6_domain_search}\n" + fi + for nameserver in ${new_dhcp6_name_servers} ; do +- echo nameserver ${nameserver} >> /etc/resolv.conf.dhclient6 ++ conf="${conf}nameserver ${nameserver}\n" + done ++ fi + +- mv /etc/resolv.conf.dhclient6 /etc/resolv.conf ++ if [ x"$conf" != x ]; then ++ conf="# Generated by dhclient or interface $interface\n${conf}" ++ if type resolvconf >/dev/null 2>&1; then ++ printf "${conf}" | resolvconf -a $interface ++ else ++ printf "${conf}" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf ++ fi + fi ++ + # If we're making confs, may as well make an ntp.conf too + make_ntp_conf + } +--- a/client/scripts/solaris ++++ b/client/scripts/solaris +@@ -1,22 +1,41 @@ + #!/bin/sh + + make_resolv_conf() { ++ if [ x"$PEER_DNS" != x ] && [ x$"PEER_DNS" != xyes ]; then ++ return 0 ++ fi ++ local conf= + if [ x"$new_domain_name_servers" != x ]; then +- cat /dev/null > /etc/resolv.conf.dhclient +- if [ x"$new_domain_search" != x ]; then +- echo search $new_domain_search >> /etc/resolv.conf.dhclient +- elif [ x"$new_domain_name" != x ]; then ++ if [ "x$new_domain_search" != x ]; then ++ conf="${conf}search ${new_domain_search}\n" ++ elif [ "x$new_domain_name" != x ]; then + # Note that the DHCP 'Domain Name Option' is really just a domain + # name, and that this practice of using the domain name option as + # a search path is both nonstandard and deprecated. +- echo search $new_domain_name >> /etc/resolv.conf.dhclient ++ conf="${conf}search ${new_domain_name}\n" + fi + for nameserver in $new_domain_name_servers; do +- echo nameserver $nameserver >>/etc/resolv.conf.dhclient ++ conf="${conf}nameserver ${nameserver}\n" ++ done ++ elif [ "x${new_dhcp6_name_servers}" != x ] ; then ++ if [ "x${new_dhcp6_domain_search}" != x ] ; then ++ conf="${conf}search ${new_dhcp6_domain_search}\n" ++ fi ++ for nameserver in ${new_dhcp6_name_servers} ; do ++ conf="${conf}nameserver ${nameserver}\n" + done ++ fi + +- mv /etc/resolv.conf.dhclient /etc/resolv.conf ++ if [ x"$conf" != x ]; then ++ conf="# Generated by dhclient or interface $interface\n${conf}" ++ if type resolvconf >/dev/null 2>&1; then ++ printf "${conf}" | resolvconf -a $interface ++ else ++ printf "${conf}" > /etc/resolv.conf ++ chmod 644 /etc/resolv.conf ++ fi + fi ++ + # If we're making confs, may as well make an ntp.conf too + make_ntp_conf + } diff --git a/net-misc/dhcp/files/dhcp-4.2.1-nogateway.patch b/net-misc/dhcp/files/dhcp-4.2.1-nogateway.patch new file mode 100644 index 000000000..11aaacefd --- /dev/null +++ b/net-misc/dhcp/files/dhcp-4.2.1-nogateway.patch @@ -0,0 +1,46 @@ +http://bugs.gentoo.org/265531 + +--- dhcp-4.2.1/client/scripts/linux ++++ dhcp-4.2.1/client/scripts/linux +@@ -193,12 +193,14 @@ + ifconfig $interface inet $new_ip_address $new_subnet_arg \ + $new_broadcast_arg $mtu_arg + # Add a network route to the computed network address. +- for router in $new_routers; do +- if [ "x$new_subnet_mask" = "x255.255.255.255" ] ; then +- route add -host $router dev $interface +- fi +- route add default gw $router $metric_arg dev $interface +- done ++ if [ x$PEER_ROUTERS = x ] || [ x$PEER_ROUTERS = xyes ]; then ++ for router in $new_routers; do ++ if [ "x$new_subnet_mask" = "x255.255.255.255" ] ; then ++ route add -host $router dev $interface ++ fi ++ route add default gw $router $metric_arg dev $interface ++ done ++ fi + fi + if [ x$new_ip_address != x$alias_ip_address ] && [ x$alias_ip_address != x ]; + then +@@ -244,12 +246,14 @@ + ifconfig $interface:0 inet $alias_ip_address $alias_subnet_arg + route add -host $alias_ip_address dev $interface:0 + fi +- for router in $new_routers; do +- if [ "x$new_subnet_mask" = "x255.255.255.255" ] ; then +- route add -host $router dev $interface +- fi +- route add default gw $router $metric_arg dev $interface +- done ++ if [ x$PEER_ROUTERS = x ] || [ x$PEER_ROUTERS = xyes ]; then ++ for router in $new_routers; do ++ if [ "x$new_subnet_mask" = "x255.255.255.255" ] ; then ++ route add -host $router dev $interface ++ fi ++ route add default gw $router $metric_arg dev $interface ++ done ++ fi + make_resolv_conf + exit_with_hooks 0 + fi diff --git a/net-misc/dhcp/files/dhcpd.conf b/net-misc/dhcp/files/dhcpd.conf new file mode 100644 index 000000000..1672633c8 --- /dev/null +++ b/net-misc/dhcp/files/dhcpd.conf @@ -0,0 +1,29 @@ +# /etc/conf.d/dhcpd: config file for /etc/init.d/dhcpd + +# If you require more than one instance of dhcpd you can create symbolic +# links to dhcpd service like so +# cd /etc/init.d +# ln -s dhcpd dhcpd.foo +# cd ../conf.d +# cp dhcpd dhcpd.foo +# Now you can edit dhcpd.foo and specify a different configuration file. +# You'll also need to specify a pidfile in that dhcpd.conf file. +# See the pid-file-name option in the dhcpd.conf man page for details. + +# If you wish to run dhcpd in a chroot, uncomment the following line +# DHCPD_CHROOT="/chroot/dhcp" + +# Then run emerge dhcp --config +# All file paths below are relative to the chroot. +# You can specify a different chroot directory but MAKE SURE it's empty. + +# Specify a configuration file - the default is /etc/dhcp/dhcpd.conf +# DHCPD_CONF="/etc/dhcp/dhcpd.conf" + +# Configure which interface or interfaces to for dhcpd to listen on. +# List all interfaces space separated. If this is not specified then +# we listen on all interfaces. +# DHCPD_IFACE="" + +# Insert any other dhcpd options - see the man page for a full list. +# DHCPD_OPTS="" diff --git a/net-misc/dhcp/files/dhcpd.init2 b/net-misc/dhcp/files/dhcpd.init2 new file mode 100644 index 000000000..82cb26e77 --- /dev/null +++ b/net-misc/dhcp/files/dhcpd.init2 @@ -0,0 +1,94 @@ +#!/sbin/runscript +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/net-misc/dhcp/files/dhcpd.init2,v 1.1 2009/07/09 14:45:22 chainsaw Exp $ + +opts="configtest" + +DHCPD_CONF=${DHCPD_CONF:-/etc/dhcp/dhcpd.conf} + +depend() { + need net + use logger dns +} + +get_var() { + sed -n 's/^[[:blank:]]\?'"$1"' "*\([^#";]\+\).*/\1/p' \ + "${DHCPD_CHROOT}/${DHCPD_CONF}" +} + +checkconfig() { + /usr/sbin/dhcpd -cf ${DHCPD_CHROOT}/${DHCPD_CONF} -t 1>/dev/null 2>&1 + ret=$? + if [ $ret -ne 0 ]; then + eerror "${SVCNAME} has detected a syntax error in your configuration files:" + /usr/sbin/dhcpd -cf ${DHCPD_CHROOT}/${DHCPD_CONF} -t + fi + + return $ret +} + +configtest() { + ebegin "Checking ${SVCNAME} configuration" + checkconfig + eend $? +} + +start() { + # Work out our cffile if it's on our DHCPD_OPTS + case " ${DHCPD_OPTS} " in + *" -cf "*) + DHCPD_CONF=" ${DHCPD_OPTS} " + DHCPD_CONF="${DHCPD_CONF##* -cf }" + DHCPD_CONF="${DHCPD_CONF%% *}" + ;; + *) DHCPD_OPTS="${DHCPD_OPTS} -cf ${DHCPD_CONF}" + ;; + esac + + if [ ! -f "${DHCPD_CHROOT}/${DHCPD_CONF}" ] ; then + eerror "${DHCPD_CHROOT}/${DHCPD_CONF} does not exist" + return 1 + fi + + checkconfig || return 1 + + local leasefile="$(get_var lease-file-name)" + leasefile="${DHCPD_CHROOT}/${leasefile:-/var/lib/dhcp/dhcpd.leases}" + if [ ! -f "${leasefile}" ] ; then + ebegin "Creating ${leasefile}" + touch "${leasefile}" + chown dhcp:dhcp "${leasefile}" + eend $? || return 1 + fi + + # Setup LD_PRELOAD so name resolution works in our chroot. + if [ -n "${DHCPD_CHROOT}" ] ; then + LD_PRELOAD="${LD_PRELOAD} /usr/lib/libresolv.so" + export LD_PRELOAD="${LD_PRELOAD} /usr/lib/libnss_dns.so" + fi + + local pidfile="$(get_var pid-file-name)" + pidfile="${pidfile:-/var/run/dhcp/dhcpd.pid}" + + ebegin "Starting ${DHCPD_CHROOT:+chrooted }${SVCNAME}" + start-stop-daemon --start --exec /usr/sbin/dhcpd \ + --pidfile "${DHCPD_CHROOT}/${pidfile}" \ + -- ${DHCPD_OPTS} -q -pf "${pidfile}" \ + -user dhcp -group dhcp \ + ${DHCPD_CHROOT:+-chroot} ${DHCPD_CHROOT} ${DHCPD_IFACE} + eend $? \ + && save_options chroot "${DHCPD_CHROOT}" \ + && save_options pidfile "${pidfile}" +} + +stop() { + local chroot="$(get_options chroot)" + + checkconfig || return 1 + + ebegin "Stopping ${chroot:+chrooted }${SVCNAME}" + start-stop-daemon --stop --exec /usr/sbin/dhcpd \ + --pidfile "${chroot}/$(get_options pidfile)" + eend $? +} diff --git a/net-misc/dhcp/files/dhcpd.init3 b/net-misc/dhcp/files/dhcpd.init3 new file mode 100755 index 000000000..3b0053142 --- /dev/null +++ b/net-misc/dhcp/files/dhcpd.init3 @@ -0,0 +1,94 @@ +#!/sbin/runscript +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/net-misc/dhcp/files/dhcpd.init3,v 1.1 2011/03/05 23:59:20 vapier Exp $ + +opts="configtest" + +DHCPD_CONF=${DHCPD_CONF:-/etc/dhcp/${SVCNAME}.conf} + +depend() { + need net + use logger dns +} + +get_var() { + sed -n 's/^[[:blank:]]\?'"$1"' "*\([^#";]\+\).*/\1/p' \ + "${DHCPD_CHROOT}/${DHCPD_CONF}" +} + +checkconfig() { + dhcpd ${DHCPD_OPTS} ${DHCPD_CHROOT:+-chroot} ${DHCPD_CHROOT} -t 1>/dev/null 2>&1 + local ret=$? + if [ $ret -ne 0 ] ; then + eerror "${SVCNAME} has detected a syntax error in your configuration files:" + dhcpd ${DHCPD_OPTS} ${DHCPD_CHROOT:+-chroot} ${DHCPD_CHROOT} -t + fi + + return $ret +} + +configtest() { + ebegin "Checking ${SVCNAME} configuration" + checkconfig + eend $? +} + +start() { + # Work out our cffile if it's in our DHCPD_OPTS + case " ${DHCPD_OPTS} " in + *" -cf "*) + DHCPD_CONF=" ${DHCPD_OPTS} " + DHCPD_CONF="${DHCPD_CONF##* -cf }" + DHCPD_CONF="${DHCPD_CONF%% *}" + ;; + *) DHCPD_OPTS="${DHCPD_OPTS} -cf ${DHCPD_CONF}" + ;; + esac + + if [ ! -f "${DHCPD_CHROOT}/${DHCPD_CONF}" ] ; then + eerror "${DHCPD_CHROOT}/${DHCPD_CONF} does not exist" + return 1 + fi + + checkconfig || return 1 + + checkpath -d -o dhcp:dhcp /var/run/dhcp /var/lib/dhcp + + local leasefile="$(get_var lease-file-name)" + leasefile="${leasefile:-/var/lib/dhcp/${SVCNAME}.leases}" + if [ ! -f "${DHCPD_CHROOT}${leasefile}" ] ; then + ebegin "Creating ${leasefile}" + touch "${DHCPD_CHROOT}${leasefile}" + chown dhcp:dhcp "${DHCPD_CHROOT}${leasefile}" + eend $? || return 1 + fi + + # Setup LD_PRELOAD so name resolution works in our chroot. + if [ -n "${DHCPD_CHROOT}" ] ; then + LD_PRELOAD="${LD_PRELOAD} /usr/lib/libresolv.so" + export LD_PRELOAD="${LD_PRELOAD} /usr/lib/libnss_dns.so" + fi + + local pidfile="$(get_var pid-file-name)" + pidfile="${pidfile:-/var/run/dhcp/${SVCNAME}.pid}" + + ebegin "Starting ${DHCPD_CHROOT:+chrooted }${SVCNAME}" + start-stop-daemon --start --exec /usr/sbin/dhcpd \ + --pidfile "${DHCPD_CHROOT}/${pidfile}" \ + -- ${DHCPD_OPTS} -q -pf "${pidfile}" -lf "${leasefile}" \ + -user dhcp -group dhcp \ + ${DHCPD_CHROOT:+-chroot} ${DHCPD_CHROOT} ${DHCPD_IFACE} + eend $? \ + && save_options chroot "${DHCPD_CHROOT}" \ + && save_options pidfile "${pidfile}" +} + +stop() { + local chroot="$(get_options chroot)" + + ebegin "Stopping ${chroot:+chrooted }${SVCNAME}" + start-stop-daemon --stop --exec /usr/sbin/dhcpd \ + --pidfile "${chroot}/$(get_options pidfile)" + eend $? +} diff --git a/net-misc/dhcp/files/dhcrelay.conf b/net-misc/dhcp/files/dhcrelay.conf new file mode 100644 index 000000000..1102d3a41 --- /dev/null +++ b/net-misc/dhcp/files/dhcrelay.conf @@ -0,0 +1,13 @@ +# /etc/conf.d/dhcrelay: config file for /etc/init.d/dhcrelay + +# Configure which interface or interfaces to for dhcrelay to listen on +# and send to. +# List all interfaces space separated. If this is not specified then +# we use all interfaces. +#IFACE="" + +# Insert any other options needed. See dhcrelay(8) for details. +#DHCRELAY_OPTS="" + +# Space separated list of IPs to forward BOOTP/DHCP packets to. +DHCRELAY_SERVERS="" diff --git a/net-misc/dhcp/files/dhcrelay.init b/net-misc/dhcp/files/dhcrelay.init new file mode 100644 index 000000000..2f92956be --- /dev/null +++ b/net-misc/dhcp/files/dhcrelay.init @@ -0,0 +1,32 @@ +#!/sbin/runscript +# Copyright 1999-2004 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/net-misc/dhcp/files/dhcrelay.init,v 1.2 2007/03/22 15:36:59 uberlord Exp $ + +depend() { + need net + use logger +} + +start() { + if [ -z "${DHCRELAY_SERVERS}" ]; then + eerror "No DHCRELAY_SERVERS specified in /etc/conf.d/dhcrelay" + return 1 + fi + + local IFACES= i= + for i in ${IFACE} ; do + IFACES="${IFACES} -i ${i}" + done + + ebegin "Starting dhcrelay" + start-stop-daemon --start --exec /usr/sbin/dhcrelay \ + -- -q ${IFACES} ${DHCRELAY_OPTS} ${DHCRELAY_SERVERS} + eend $? +} + +stop() { + ebegin "Stopping dhcrelay" + start-stop-daemon --stop --pidfile /var/run/dhcrelay.pid + eend $? +} diff --git a/net-misc/dhcp/files/dhcrelay.init2 b/net-misc/dhcp/files/dhcrelay.init2 new file mode 100755 index 000000000..4f09249a6 --- /dev/null +++ b/net-misc/dhcp/files/dhcrelay.init2 @@ -0,0 +1,29 @@ +#!/sbin/runscript +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/net-misc/dhcp/files/dhcrelay.init2,v 1.2 2011/03/08 20:13:26 vapier Exp $ + +depend() { + need net + use logger +} + +start() { + if [ -z "${DHCRELAY_SERVERS}" ]; then + eerror "No DHCRELAY_SERVERS specified in /etc/conf.d/dhcrelay" + return 1 + fi + + checkpath -d /var/run/dhcp + + ebegin "Starting dhcrelay" + start-stop-daemon --start --exec /usr/sbin/dhcrelay \ + -- -q $(printf -- '-i %s ' ${IFACE}) ${DHCRELAY_OPTS} ${DHCRELAY_SERVERS} + eend $? +} + +stop() { + ebegin "Stopping dhcrelay" + start-stop-daemon --stop --pidfile /var/run/dhcp/dhcrelay.pid + eend $? +} diff --git a/net-misc/dhcp/metadata.xml b/net-misc/dhcp/metadata.xml new file mode 100644 index 000000000..de6dcfd48 --- /dev/null +++ b/net-misc/dhcp/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>base-system</herd> + <longdescription lang="en">The ISC DHCP client/server package.</longdescription> + <longdescription lang="ja">ISC DHCP クライアント/サーバ・パッケージです。</longdescription> + <use> + <flag name="client">Install the dhclient program</flag> + <flag name="server">Install the dhcpd and dhcrelay programs</flag> + <flag name="infiniband">Enable ipoib support</flag> + </use> +</pkgmetadata> diff --git a/perl-core/encoding-warnings/ChangeLog b/perl-core/encoding-warnings/ChangeLog index 0e46fef6b..cce70e111 100644 --- a/perl-core/encoding-warnings/ChangeLog +++ b/perl-core/encoding-warnings/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for perl-core/encoding-warnings -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> encoding-warnings-0.11.ebuild: + RDEPEND is not explicitly assigned -> fixed + *encoding-warnings-0.11 (22 Jun 2010) 22 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> diff --git a/perl-core/encoding-warnings/Manifest b/perl-core/encoding-warnings/Manifest index bb2a3c43d..989f211c2 100644 --- a/perl-core/encoding-warnings/Manifest +++ b/perl-core/encoding-warnings/Manifest @@ -1,14 +1,14 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA512 +Hash: SHA256 DIST encoding-warnings-0.11.tar.gz 16110 RMD160 ba26a43222f7988d2ba5025d9ecdbb1112e9ca84 SHA1 c03e57cb0be7ed0186c80c663076e86a6933dbcb SHA256 67faf727b59ab1132d2b147bc1f927dc752897ce1f57b303efc46c3a969bf25e -EBUILD encoding-warnings-0.11.ebuild 461 RMD160 2f0b4e68563245bdd128beb2326cacb8ffc0ccdb SHA1 bfb3ca0b502f428e33a90ed02a9d1fdcc7944e69 SHA256 33fb7c8fa8e41443774b82abc7ff759d6588806939d0e9fe78d5fceaa126e238 -MISC ChangeLog 297 RMD160 62fd6f46460f1cf3d9fa9c36ab74a5cc16eaa38a SHA1 ae76b7ff43e8c37dc70d55703c264acab7e5fdef SHA256 5bb69e39f8503fed87dad38212ceb2db4702e7c429033ea84303b956c506a861 +EBUILD encoding-warnings-0.11.ebuild 481 RMD160 fa57947e876ba7c52f68c9263fa7ab770d098859 SHA1 6b47d0c4408ecc249cc33c4a23f6d91e33f135fb SHA256 6976f916546f9f5929f8792dabc0e35831b37d62762b7302471e93f6e72c1e69 +MISC ChangeLog 422 RMD160 c1ce3303b972135850f89a53ab050a614ffcf6ae SHA1 f40b12da52e74ef420b2f0c18026b02b05c8e6e6 SHA256 f270473fc535ffc7d394128027c545f9e41e47e4d24aa9ec5289a06f56ca7f0d MISC metadata.xml 225 RMD160 aa7d7690bc9d41aa160500739ec29a5aecb24958 SHA1 a7fa143a3c80636c1f82827063de2327d4380d57 SHA256 3b760abcba804d12e90e8101abef730ff1be333e8c01f273f7a05e68f5f1df88 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEAREKAAYFAkwg6HEACgkQL+gLs3iH94c9KQCfUuXHvLzT39sN4lMX4v78ptTt -2doAn2bY/ekwAHnLb4KOEa7toxOFlJ8N -=MUT8 +iEYEAREIAAYFAk4F5fQACgkQgAnW8HDreRZlOgCguElHEwgvhk+FmlvnPX35W7/I +pfEAn0+jwHr8r0qLKA1D2Wkx6aOp/quM +=DWPt -----END PGP SIGNATURE----- diff --git a/perl-core/encoding-warnings/encoding-warnings-0.11.ebuild b/perl-core/encoding-warnings/encoding-warnings-0.11.ebuild index 1a37e29f8..b4d3f0c1b 100644 --- a/perl-core/encoding-warnings/encoding-warnings-0.11.ebuild +++ b/perl-core/encoding-warnings/encoding-warnings-0.11.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -15,3 +15,4 @@ KEYWORDS="~amd64 ~x86" IUSE="" DEPEND="dev-lang/perl" +RDEPEND="${DEPEND}" diff --git a/profiles/package.mask b/profiles/package.mask index a83b0833f..3e279a9be 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,11 +30,15 @@ #--- END OF EXAMPLES --- -# Sebastien Fabbro (07 Jan 2011) -# svn trunk development of root ->=sci-physics/root-9999 +# Justin Lecher <jlec@gentoo.org> (24 Jun 2011) +# fftw dep is masked +sci-libs/pfft -# Justin Lecher <jlec> (04 Jan 2011) +# Justin Lecher <jlec@gentoo.org> (24 Jun 2011) +# paraview dep is masked +sci-visualization/vtkPOFFReader + +# Justin Lecher <jlec@gentoo.org> (04 Jan 2011) # Masked for several QA reasons: # portage screams during processing this ebuild # Author uses @gentoo.org address, although not a dev @@ -48,76 +52,57 @@ # #348029 sci-biology/tablet-bin -# Sebastien Fabbro (29 Sep 2010) -# alpha software ->=sci-libs/fftw-3.3_alpha1 - -# Justin Lecher (jlec) (1 Aug 09) -# jlec@gentoo.org +# Christoph Junghans <ottxor@gentoo.org> (20 Apr 2011) # mask live ebuild -=sci-chemistry/burrow-owl-9999_pre15 +=sci-physics/espresso-9999 -# Christoph Junghans (ottxor) (23 Jan 11) -# ottxor@gentoo.org +# Christoph Junghans <ottxor@gentoo.org> (23 Jan 2011) # mask live ebuild =sys-cluster/nullmpi-9999 -# Christoph Junghans (ottxor) (20 Apr 11) -# ottxor@gentoo.org -# mask live ebuild -=sci-physics/espresso-9999 +# Francois Bissey (kiwifb) (29 Oct 2010) +# f.r.bissey@massey.ac.nz +# mask paraview-3.8.* as there are no stable versions in the tree +# Avoid accidental upgrade +>=sci-visualization/paraview-3.8.0 -# Christoph Junghans (ottxor) (03 Oct 10) -# ottxor@gentoo.org +# Christoph Junghans <ottxor@gentoo.org> (03 Oct 2010) # masked for testing =sci-libs/openmm-2.0 -# Christoph Junghans (ottxor) (31 Jul 10) -# ottxor@gentoo.org +# Sebastien Fabbro (29 Sep 2010) +# alpha software +>=sci-libs/fftw-3.3_alpha1 + +# Christoph Junghans <ottxor@gentoo.org> (31 Jul 2010) # mask live ebuilds =sci-chemistry/gromacs-4.0.9999 =sci-chemistry/gromacs-4.5.9999 =sci-chemistry/gromacs-9999 =app-doc/gromacs-manual-9999 -# Christoph Junghans (ottxor) (23 Jan 10) -# ottxor@gentoo.org +# Christoph Junghans <ottxor@gentoo.org> (23 Jan 2010) # mask live ebuilds =sci-libs/votca-tools-9999 =sci-chemistry/votca-csg-9999 =app-doc/votca-csg-manual-9999 -# Justin Lecher (jlec) (08 Jun 09) -# jlec@gentoo.org -# mask live ebuilds -=sci-chemistry/pymol-apbs-plugin-9999 -=sci-chemistry/coot-9999 -=sci-chemistry/pymol-9999 - -# Christoph Junghans (ottxor) (02 Nov 09) -# ottxor@gentoo.org +# Christoph Junghans <ottxor@gentoo.org> (02 Nov 2009) # live cvs ebuild, deps changing constantly # report to bug #232363 =sci-visualization/gnuplot-4.4.9999 =sci-visualization/gnuplot-4.5.9999 -# Justin Lecher (jlec) (11 May 09) -# jlec@gentoo.org -# work in progress -=sci-chemistry/almost-1.0.3-r1 - -# Francois Bissey (kiwifb) (29 Oct 2010) -# f.r.bissey@massey.ac.nz -# mask paraview-3.8.* as there are no stable versions in the tree -# Avoid accidental upgrade ->=sci-visualization/paraview-3.8.0 +# Justin Lecher <jlec@gentoo.org> (1 Aug 2009) +# mask live ebuild +=sci-chemistry/burrow-owl-9999_pre15 -# Andreas K. Huettel (dilfridge) (23 Jun 2010) -# mask dev-lang/aldor for removal in 30d since there is no source available anymore -# (was a svn checkout, but the server is dead) -=dev-lang/aldor-1.1.0 +# Justin Lecher <jlec@gentoo.org> (08 Jun 2009) +# mask live ebuilds +=sci-chemistry/pymol-apbs-plugin-9999 +=sci-chemistry/coot-9999 +=sci-chemistry/pymol-9999 -# Andreas K. Huettel (dilfridge) (27 Jun 2010) -# mask for removal in 30d since there is no source anymore -# (fetch restricted, and the ftp server does not respond; no hint of program at HOMEPAGE) -sci-biology/newbler +# Justin Lecher <jlec@gentoo.org> (11 May 2009) +# work in progress +=sci-chemistry/almost-1.0.3-r1 diff --git a/sci-astronomy/casacore/ChangeLog b/sci-astronomy/casacore/ChangeLog new file mode 100644 index 000000000..b66cfa96f --- /dev/null +++ b/sci-astronomy/casacore/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-astronomy/casacore +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> casacore-1.2.20110516.ebuild: + Sort inherit and/or USE + diff --git a/sci-astronomy/casacore/Manifest b/sci-astronomy/casacore/Manifest index 6e081f258..cfca214ff 100644 --- a/sci-astronomy/casacore/Manifest +++ b/sci-astronomy/casacore/Manifest @@ -1,6 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX 1.2.20110516-headers.patch 936 RMD160 0775642a72727df99130b41c484d69f034410992 SHA1 7ede5cb0f92cc5cf6ed9ce1d1beda191ad7d5c4e SHA256 34769b047fabff24e6da4069d040c6f5f44e393170831925c14d5391394d9444 AUX 1.2.20110516-implicits.patch 6423 RMD160 01569cd7ec3b5f4cb6498722945fb1a9eccf87a2 SHA1 512e292f7a9ea90ec87950a9a5c70e94cf91a020 SHA256 7f537b6a7404d185580b3ad12676f87a718f9e92ffab24229888959f323879f4 AUX 1.2.20110516-libdir.patch 8284 RMD160 dcecff84020fff3f7fb91386a3c338b5fda26c44 SHA1 1fdc9e7f8087918d6511d1ccdf717c1e078f1be7 SHA256 112112db01eca5657a08a492b923f96c183d6e77aa9d6ca1d2402fd7aedb72a2 DIST casacore-1.2.20110516.tar.bz2 4649168 RMD160 3d0f7df94b88b93a3cd36b5f76e01538f37b0877 SHA1 57e9b1b19a61c846d7ceeeeb575ff92998b011fc SHA256 d47a113038bf26a4431bbbeb4821b0e245a452fc1d63ffe4d9df2af0d3155ca7 -EBUILD casacore-1.2.20110516.ebuild 1099 RMD160 76ece8f9079b711e047819a6c89f9a8f3216dd12 SHA1 1f8b3e97e52db514f1724ce69a563e28b8622bca SHA256 686eb5146c308be21d3bb886565ed227bd2334545e3e85ef9e42848407a419f7 +EBUILD casacore-1.2.20110516.ebuild 1099 RMD160 16c1a52947aef05bb0b9e659b1186de0b4853bdc SHA1 d13dee016b957873fc9697890714f326a6890895 SHA256 304fd4e2bf4bd89aaa822a4fc416a5decc62dbe90620560b23aaccf17d3865dc +MISC ChangeLog 227 RMD160 0d357dccfeb0a6901a4ccc9c76b4c2504a6f9778 SHA1 7d6e4e2958d8c32529cf17799d0e3969f2af9de0 SHA256 bc19d04dfc4d26a88d22b044b6ef22dffa673a176740292d834020bbf7af336e MISC metadata.xml 391 RMD160 2b9d91edfd432ddf16694c417d25e89eaa13da42 SHA1 c6300dc3bf52bdd055804ad2f2c2480cc2304dcb SHA256 58c9dd33f794ccc2a1243b05da6f787660e1d844ba29c62f264b780793ab01b8 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EgYUACgkQgAnW8HDreRZWgQCdH+9ScWjLhwnS2K4iuHeSZQ94 +zVYAn2Saqxtf69UPwG1llHMrkeg2ND2t +=b+gh +-----END PGP SIGNATURE----- diff --git a/sci-astronomy/casacore/casacore-1.2.20110516.ebuild b/sci-astronomy/casacore/casacore-1.2.20110516.ebuild index deec38284..c535e9523 100644 --- a/sci-astronomy/casacore/casacore-1.2.20110516.ebuild +++ b/sci-astronomy/casacore/casacore-1.2.20110516.ebuild @@ -4,7 +4,7 @@ EAPI=4 -inherit eutils cmake-utils +inherit cmake-utils eutils DESCRIPTION="Core libraries for the Common Astronomy Software Applications" HOMEPAGE="http://code.google.com/p/casacore/" diff --git a/sci-astronomy/eye/ChangeLog b/sci-astronomy/eye/ChangeLog index e91d1227f..205be6502 100644 --- a/sci-astronomy/eye/ChangeLog +++ b/sci-astronomy/eye/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-astronomy/eye -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> eye-1.4.1.ebuild: + Sort inherit and/or USE + *eye-1.4.1 (18 Nov 2010) 18 Nov 2010; Sébastien Fabbro <bicatali@gentoo.org> +eye-1.4.1.ebuild, diff --git a/sci-astronomy/eye/Manifest b/sci-astronomy/eye/Manifest index 135e266ff..7f6594d04 100644 --- a/sci-astronomy/eye/Manifest +++ b/sci-astronomy/eye/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX eye-1.4.1-configure.patch 1521 RMD160 4e21ded936e19e7745a815b02d5121a5de7e791d SHA1 b0a81827e9f052ccf91ac93571ef2ce2872a93c8 SHA256 426d54714b01cf7616e31401e6f36f93642a28e50f13bbb30718d5d949ae4e0b DIST eye-1.4.1.tar.gz 744173 RMD160 886d85638f099276d393dd14c841efb41c06d50a SHA1 73815581cb93c6c579f4a8c8de88f274890439e9 SHA256 f3b480be936ea8143d9f469d2901b227092ec8e7692fd2578b8ecdbcd8875824 -EBUILD eye-1.4.1.ebuild 808 RMD160 1039d52c0e522cf478a30a0d538f203eef832207 SHA1 529358d63d93e12ab19819c8f62282bb5cdc0387 SHA256 91cd62943c309ca1144b9e16059664587cca96fed5f4c8b3dd494d990c84a369 -MISC ChangeLog 287 RMD160 4b3e10bc31fa606eb2cb115a22855778e3106666 SHA1 57c0fb40b5d38466cb59009fe3fd1e017b2c9dde SHA256 9fd0826f218d876a694714f944f61006f2105f23825ea13f82fb6cae779c3b03 +EBUILD eye-1.4.1.ebuild 808 RMD160 e82521ff4555390253da4101a4f6611d6b58ce87 SHA1 e6847c2dd4f0b9d3f30413413036d7dbe1114bb5 SHA256 077abf77b9498f9523663c2a88ea87b5ff54fb4f3dd9bb451a18ac1e368d0623 +MISC ChangeLog 379 RMD160 1f5edf69d0645a9e4e313386c8700cedd8b6ed36 SHA1 05d2519b348918e5adb5b303fe1d7ce227c6f57c SHA256 85420060f74136642827d24c07b6ee0c30203bd1000a3feb3004229f2e9ef8ad MISC metadata.xml 655 RMD160 fcec85388054934d37c4188bd508c00e00c281d2 SHA1 e51a4415f87217fbd8ade88e15fa2c10f1de83a2 SHA256 a4dca7403f21df6c4862cfd17549594c627b82633cb5cea7e808834f6c08959e +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EglcACgkQgAnW8HDreRZx1QCgjHsaSmcpZQMsysuvjSEXlF/a +nycAoJyW/sXiWmudK29m4fBrTVeWTBtg +=Ry2X +-----END PGP SIGNATURE----- diff --git a/sci-astronomy/eye/eye-1.4.1.ebuild b/sci-astronomy/eye/eye-1.4.1.ebuild index e389ca03b..5cb826551 100644 --- a/sci-astronomy/eye/eye-1.4.1.ebuild +++ b/sci-astronomy/eye/eye-1.4.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=3 -inherit eutils autotools +inherit autotools eutils DESCRIPTION="Enhance astronomical object extraction with neural network filters" HOMEPAGE="http://www.astromatic.net/software/eye" diff --git a/sci-astronomy/missfits/ChangeLog b/sci-astronomy/missfits/ChangeLog index be0a06fb0..8a7e0eb1c 100644 --- a/sci-astronomy/missfits/ChangeLog +++ b/sci-astronomy/missfits/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-astronomy/missfits -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> missfits-2.4.0.ebuild, + metadata.xml: + Cleaned ebuild, unused local USE-description: 'plplot' + *missfits-2.4.0 (18 Nov 2010) 18 Nov 2010; Sébastien Fabbro <bicatali@gentoo.org> +missfits-2.4.0.ebuild, diff --git a/sci-astronomy/missfits/Manifest b/sci-astronomy/missfits/Manifest index 64c28807b..57320f9f5 100644 --- a/sci-astronomy/missfits/Manifest +++ b/sci-astronomy/missfits/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + AUX missfits-2.4.0-configure.patch 3223 RMD160 7a3da312bf067a655202624cc1e156666b25dfd5 SHA1 a2652ebb1ad4e799308fbebadd47a70765a55d94 SHA256 57d8c51435573043c35b532e779f8f67eee54d8f17e63cb9fd3b892d7153fa35 DIST missfits-2.4.0.tar.gz 381606 RMD160 0cc4e7aa2d27607c5137e424581dc173ab692bcb SHA1 f2ff6fa889bcab66fffa3210a7d179b5f1d0b641 SHA256 40cd9de9d539ac95d34c108afa0ade4b26475adf4772a95ee42b0f9ab6edaf21 -EBUILD missfits-2.4.0.ebuild 851 RMD160 c59aee8c7d741cf37df62935259427301d8a7be1 SHA1 4acd3cb235fa73ec2d8974e40f4863dffefa16d7 SHA256 ae82c035800bc8f06e916dd5346787e73f7375f54f5466afd504d7a7bd8935f1 -MISC ChangeLog 307 RMD160 5bb0694d4a94cc0bcebc26913cc7e162bc3d735f SHA1 dbce0224932ff301488e7320010f80b7cf30420e SHA256 9ad3b334e8e711d90f1e8b5b8eca95a1591da4538cbe71d7fad66e01729dbc12 -MISC metadata.xml 665 RMD160 24b25af62924fef76691b176c6a39a4c6e728f02 SHA1 0d3c8fc603cb07359d885486273e0dc077c0d02a SHA256 5b9a3023094ce5da8f5787ab3aac15f728d466b0ac29c23ae22fab5f187a49bf +EBUILD missfits-2.4.0.ebuild 686 RMD160 479a50099efd2546a939186d2516b4baabf0afaf SHA1 71eb8d465aef1a4c279a4bf9f14a3a4cfb9d8126 SHA256 30f8d0024e63818852e0ae100d23909f341b5a90da23a36872cfd0e256646ac6 +MISC ChangeLog 451 RMD160 2a3817063c4b042617072685618ffb3c832c40d9 SHA1 ba5d8d96687be98cdb33419daa9988d45b8e069a SHA256 eda78d1d6a24df563ec11f957886d878976bed13a0f301c38500663949ff31cb +MISC metadata.xml 543 RMD160 0ba62e9208ce536ee9a2c08ed24b0ba0b8f02083 SHA1 65a101f1e363e77f9555655bc66458c514d193f3 SHA256 fcfb63c372b73a4553c56f39d6940a0cf8d8d8d15e5beef95ffcb5acab405d17 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F7tQACgkQgAnW8HDreRZYtwCfczBxyOBZSaFSdizjB6Adaf30 +7zYAoIlovwtLBhTIDcftTq9+FPiuh4b/ +=bzQS +-----END PGP SIGNATURE----- diff --git a/sci-astronomy/missfits/metadata.xml b/sci-astronomy/missfits/metadata.xml index 9abf5c25b..e8c098543 100644 --- a/sci-astronomy/missfits/metadata.xml +++ b/sci-astronomy/missfits/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> MissFITS is a program that performs basic maintenance and packaging tasks on FITS files using an optimised FITS library. MissFITS can: * add/edit/remove FITS header keywords @@ -10,7 +10,4 @@ * unpile/pile FITS data-cubes * create/check/update FITS checksums, using R. Seaman’s protocol. </longdescription> -<use> - <flag name="plplot">Build with <pkg>sci-libs/plplot</pkg> to allow diagnostic plots during processing</flag> -</use> </pkgmetadata> diff --git a/sci-astronomy/missfits/missfits-2.4.0.ebuild b/sci-astronomy/missfits/missfits-2.4.0.ebuild index d710b9f85..cf97ed926 100644 --- a/sci-astronomy/missfits/missfits-2.4.0.ebuild +++ b/sci-astronomy/missfits/missfits-2.4.0.ebuild @@ -1,12 +1,13 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-astronomy/scamp/scamp-1.7.0.ebuild,v 1.1 2010/05/03 21:44:04 bicatali Exp $ -EAPI=3 -inherit eutils autotools +EAPI=4 + +inherit autotools eutils DESCRIPTION="Performs basic maintenance and packaging tasks on FITS files" -HOMEPAGE="http://www.astromatic.net/software/missfits" +HOMEPAGE="http://www.astromatic.net/software/missfits/" SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz" LICENSE="GPL-3" @@ -14,19 +15,15 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc" -RDEPEND="" -DEPEND="${RDEPEND}" - src_prepare() { epatch "${FILESDIR}"/${P}-configure.patch eautoreconf } src_install () { - emake DESTDIR="${D}" install || die "emake install failed" - dodoc AUTHORS ChangeLog HISTORY README THANKS BUGS + default if use doc; then insinto /usr/share/doc/${PF} - doins doc/*.pdf || die "pdf doc install failed" + doins doc/*.pdf fi } diff --git a/sci-astronomy/psfex/Manifest b/sci-astronomy/psfex/Manifest index a89bca695..e38a380d7 100644 --- a/sci-astronomy/psfex/Manifest +++ b/sci-astronomy/psfex/Manifest @@ -2,12 +2,12 @@ Hash: SHA1 DIST psfex-3.9.1.tar.gz 2364495 RMD160 54c1a32c7f9305a91b973a974c4ae527a4dc3143 SHA1 af164b4e3d1bf61cdd738e8c52730f8564460ae0 SHA256 1758a1a40166ef59475d8fab6abda33ca0ed0a837531ff7ad577d8bce4e511f7 -EBUILD psfex-3.9.1.ebuild 1183 RMD160 8d6a5d0516905461ad7396048041a8b77b80ba72 SHA1 5efaa2f2a3e61efd61fea3cdd63ff09b58b76974 SHA256 db8a963587ebcedbc59342e771b1083a1c449dcf4b7bdab856a39800ba66416e +EBUILD psfex-3.9.1.ebuild 1183 RMD160 26f4f8c2c4e6e6bee033972d051f5ca949a58877 SHA1 88f82e87f8258be728318d1930dfcf93cec51022 SHA256 afe364cee799aabbe1a474fbd62f88db3288f7078292be05965f437e81083d55 MISC metadata.xml 608 RMD160 16d7fe8c80598c89ae9a28647326731fa17579b5 SHA1 aa50c8cf441f11b93cf3cb133113d819cb55178b SHA256 11164a313edba70d4453e479bc6ee510c190f60dfe8ddaf6e1df74cde674d07b -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkzkbYoACgkQ1ycZbhPLE2A7MACcDGkfh4bbgwggd+IENWm4izNH -rsMAnRXGJG+TOyOuFMkgQ0Ny1FlxIDAL -=wt/K +iEYEARECAAYFAk4EhyIACgkQgAnW8HDreRbrjACfStyPlJje9jUp1Iii4zNJzaVe +EAwAn0mOjSRI8gK34Pgnt2HxijHc5BIB +=zk3W -----END PGP SIGNATURE----- diff --git a/sci-astronomy/psfex/psfex-3.9.1.ebuild b/sci-astronomy/psfex/psfex-3.9.1.ebuild index 9d95745bc..3530ea969 100644 --- a/sci-astronomy/psfex/psfex-3.9.1.ebuild +++ b/sci-astronomy/psfex/psfex-3.9.1.ebuild @@ -12,7 +12,7 @@ SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="doc threads plplot" +IUSE="doc plplot threads" RDEPEND="virtual/cblas sci-libs/lapack-atlas diff --git a/sci-astronomy/skymaker/Manifest b/sci-astronomy/skymaker/Manifest index 828a78e4a..5e57a4766 100644 --- a/sci-astronomy/skymaker/Manifest +++ b/sci-astronomy/skymaker/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX skymaker-configure.patch 1152 RMD160 ac9808398cf1e2e0dcb17ca7a0e0e54814e1803c SHA1 1ddbe2391e66a48c5220a00a3500cb5a6cbfe356 SHA256 a27412b932426c28b61e98eb6eb9be8c83c8ad56c020b3892ecf4e6ae2235374 DIST skymaker-3.3.3.tar.gz 415740 RMD160 8f9809a1fcf6659a6d76b6d8f6cc1a9154306262 SHA1 781e4e1955a04bfadb74904243ddfd8f507839d5 SHA256 75ddcfcc577591b3ad430171fa867cc7a573bb93f541fd82ef6ebe873c1816f4 -EBUILD skymaker-3.3.3.ebuild 698 RMD160 d7c98c777616a773ca64baa85c3d753a37d92c52 SHA1 3cbf5ce62625e29d6eeda11ee6797c3a4cd7b024 SHA256 949a15f774162c4d47fc515c2d8a3e0b6f02fb04ee29ff6df602943e31860de3 +EBUILD skymaker-3.3.3.ebuild 698 RMD160 5086f36d06bdd0bcf82f1066233c1d6c2bfb324a SHA1 a78b52ddf0b7294864d08794b466815cc08605e3 SHA256 5c6ff7aae00edf2b7a61027a1cc258e30fe972cb5c457b9d2905e7d28f2e38f7 MISC ChangeLog 504 RMD160 3278dbafae2c1350b3ee2132d40feb2884ad24d9 SHA1 9ad54a932a7d3dd7a237e095fa69e29eca1f81f2 SHA256 954c491b6107fe2867ecdb7a6ff89d89c45dd16220b88a31d76c8ba496f8b1fc MISC metadata.xml 522 RMD160 82a2f56adf45447226214d63b733d5ee59a7a28f SHA1 f3fd9b95737eec4ac3bb5d7103b6237b21089d20 SHA256 d86351847a40cd61b3b7da6a9794b11a34de5192952dcb849d91cbc442b05646 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EhycACgkQgAnW8HDreRYIKwCg0aUQ4uxJxWREhEsQkfzXoXWp +7XUAn2DgdbrunHDwK76kE9aJme7it8Jj +=k3Vm +-----END PGP SIGNATURE----- diff --git a/sci-astronomy/skymaker/skymaker-3.3.3.ebuild b/sci-astronomy/skymaker/skymaker-3.3.3.ebuild index 07fc85770..99dd48b0d 100644 --- a/sci-astronomy/skymaker/skymaker-3.3.3.ebuild +++ b/sci-astronomy/skymaker/skymaker-3.3.3.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI=2 -inherit eutils autotools +inherit autotools eutils DESCRIPTION="Program that simulates astronomical images" HOMEPAGE="http://www.astromatic.net/software/skymaker" diff --git a/sci-astronomy/stuff/Manifest b/sci-astronomy/stuff/Manifest index 2dfa594fd..a38923192 100644 --- a/sci-astronomy/stuff/Manifest +++ b/sci-astronomy/stuff/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX stuff-configure.patch 1734 RMD160 cd80f40b8bf4757a7f30219a68393bc014dad63d SHA1 ba572bd637a09246ca2fcdb0f576ec183ce798b0 SHA256 7cdcd8b57aae0d2b80534794d3f9d34a72fde74e20cd6220f70e7d286fce11a9 DIST stuff-1.19.tar.gz 4017086 RMD160 c8ac8d3bbe7cd4a7e48b81b98de60b6c777e6e74 SHA1 acf5b26e5cc10eac757b55b8cca59d5ca3d3ab94 SHA256 592e6bfff704d1391b150a0820b52258ef69a99b698ac07eb0a8f04daf5b0210 -EBUILD stuff-1.19.ebuild 690 RMD160 7efea25ad8594cc817f98d78cb1aad60222118fe SHA1 3522b40dfe6a16c70fb6199e47bcbd6530cffb33 SHA256 cc7da95766f458816f763308e9ae697c101a810652d25d030c6f62394b636d92 +EBUILD stuff-1.19.ebuild 690 RMD160 d131ccfb5b7ad8fe0a8f272ed3d8b2323f7190d7 SHA1 1321ff319e1d02027374dbaaf4404da7584b56d5 SHA256 a6a667a18447e04baeace961941cc8c7d114f0f39535b516b45211c9ce8060c0 MISC ChangeLog 393 RMD160 1b8d57da8f964e6b587cb88039da9a7d096f7517 SHA1 b1224d92a265403f6473771b8887d9bc9b094a4c SHA256 49ac0889dbb5ce913e6f1068db7d490f3590071faec88b8ecc3b34c6e916a2f5 MISC metadata.xml 397 RMD160 1b501841d3d65e5f322607b8f336e077ded9cb7e SHA1 5c5037a6ce527cf3c559426e9355fa804ad6e2db SHA256 69add15cada8ac23ffc005025d85d26e369d568ee8d3b88755d0a99571d6bd3f +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EhywACgkQgAnW8HDreRayhgCfUDhqlPx5iUku6SQJpMNK8yZ/ +JX8AnApgK1ToA9ofIO/qUVr5FufOwh7w +=2Vnj +-----END PGP SIGNATURE----- diff --git a/sci-astronomy/stuff/stuff-1.19.ebuild b/sci-astronomy/stuff/stuff-1.19.ebuild index 9231d7b27..39abdb39e 100644 --- a/sci-astronomy/stuff/stuff-1.19.ebuild +++ b/sci-astronomy/stuff/stuff-1.19.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI=2 -inherit eutils autotools +inherit autotools eutils DESCRIPTION="Tool for automatic generation of astronomical catalogs" HOMEPAGE="http://astromatic.iap.fr/software/stuff/" diff --git a/sci-astronomy/weightwatcher/ChangeLog b/sci-astronomy/weightwatcher/ChangeLog index c2f6ee227..b886eb169 100644 --- a/sci-astronomy/weightwatcher/ChangeLog +++ b/sci-astronomy/weightwatcher/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-astronomy/weightwatcher -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> weightwatcher-1.8.10.ebuild, + metadata.xml: + Cleaned ebuild, no eauto* function called + 18 Nov 2010; Sébastien Fabbro <bicatali@gentoo.org> ChangeLog: Initial import diff --git a/sci-astronomy/weightwatcher/Manifest b/sci-astronomy/weightwatcher/Manifest index dc26d6c97..9826603bc 100644 --- a/sci-astronomy/weightwatcher/Manifest +++ b/sci-astronomy/weightwatcher/Manifest @@ -1,13 +1,14 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 DIST weightwatcher-1.8.10.tar.gz 403372 RMD160 530b81d4b40354f85eb21bcd62b473457033ce4d SHA1 00c824fdc068299db04e48263558e1da223baeff SHA256 7f8a09deb586bb118c79d7ebcb8c6958d9ea49862f7d5a2dfdf229c550e8f740 -EBUILD weightwatcher-1.8.10.ebuild 692 RMD160 811a7bbe0512a2d86a5f3d16448250a0ab2c8bda SHA1 42140a2587530c735d5383b47ffe5bda9ab1de02 SHA256 4c13bdf29fecb952cc815fda3965f75ddd51a28999c4f7b05dabf22e674a363d -MISC metadata.xml 479 RMD160 2abe17c2742f23806adee6a24fcee03e357ddf3c SHA1 804697574ded40d4b802df5aa31aaec9cbc22b30 SHA256 8e8e110f13856ad59bea1abc02de7f0fe172e7951c147fb7f780036f3a65de52 +EBUILD weightwatcher-1.8.10.ebuild 517 RMD160 cc2f96177bbb6af7bb746c85669e2616d50f1e70 SHA1 4bafd53f0944f6045c70370fd72f8a2619e275e9 SHA256 9a19a994c35259bfc6743fe13995b380c5c8368d670f3ab5b99d9ae07ffb2b1f +MISC ChangeLog 349 RMD160 1f074aee3274c53f77def751a5ef77754e44e58e SHA1 0051d0f751f75ce7e167e6c80a65aa3af9f0dd4d SHA256 4959c4d7230fb771495634b9c1416a5085750f08831fde056761f29725e3e341 +MISC metadata.xml 481 RMD160 3335871d604c67ce9b43c7d863f951b9e1735eb4 SHA1 31775493c9b40dfce2fb7aa638b6d325bf9911ce SHA256 af2d3375fefbb033ababcc44c8a2f9cd3765b3ec0d786bdb6d37d7dd356a141f -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkzkbVwACgkQ1ycZbhPLE2DZQACdEbXHKnrW/sS4WjVUCATXIsZ/ -GQoAoJNwPc9xAew9DlmagSNIXWWxgF45 -=Q4TL +iEYEAREIAAYFAk4F7xoACgkQgAnW8HDreRaeOACfZ5L1wH10RAKUbSrEzywHmv7i +iJIAoLdCz8gJ36paAzfxnrmJAWzYyvqA +=KJ7w -----END PGP SIGNATURE----- diff --git a/sci-astronomy/weightwatcher/metadata.xml b/sci-astronomy/weightwatcher/metadata.xml index 098d83643..278512904 100644 --- a/sci-astronomy/weightwatcher/metadata.xml +++ b/sci-astronomy/weightwatcher/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> WeightWatcher is a program that combines weight-maps, flag-maps and polygon data in order to produce control maps which can directly be used in astronomical image-processing packages like Drizzle, diff --git a/sci-astronomy/weightwatcher/weightwatcher-1.8.10.ebuild b/sci-astronomy/weightwatcher/weightwatcher-1.8.10.ebuild index a2c96fba4..c4a277050 100644 --- a/sci-astronomy/weightwatcher/weightwatcher-1.8.10.ebuild +++ b/sci-astronomy/weightwatcher/weightwatcher-1.8.10.ebuild @@ -1,12 +1,13 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 -inherit eutils autotools +EAPI=4 + +inherit eutils DESCRIPTION="Combine weight maps and polygon for astronomical images weighting" -HOMEPAGE="http://www.astromatic.net/software/weightwatcher" +HOMEPAGE="http://www.astromatic.net/software/weightwatcher/" SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz" LICENSE="GPL-3" @@ -14,14 +15,10 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc threads" -RDEPEND="" -DEPEND="${RDEPEND}" - src_install () { - emake DESTDIR="${D}" install || die "emake install failed" - dodoc AUTHORS ChangeLog HISTORY README THANKS BUGS + default if use doc; then insinto /usr/share/doc/${PF} - doins doc/*.pdf || die "pdf doc install failed" + doins doc/*.pdf fi } diff --git a/sci-biology/OBO-Edit/ChangeLog b/sci-biology/OBO-Edit/ChangeLog new file mode 100644 index 000000000..e1de6ad37 --- /dev/null +++ b/sci-biology/OBO-Edit/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/OBO-Edit +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> OBO-Edit-2.1_beta8.ebuild: + Cleaned ebuild + diff --git a/sci-biology/OBO-Edit/Manifest b/sci-biology/OBO-Edit/Manifest index b12079377..7d3684c16 100644 --- a/sci-biology/OBO-Edit/Manifest +++ b/sci-biology/OBO-Edit/Manifest @@ -1,4 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + AUX response.varfile 161 RMD160 3fbf3bb5a79dafecefdd64314f4fcfbb05ecc8d0 SHA1 46c6214c7072221455e74a9aa502c85b8edca0be SHA256 4a5793bb5bf94fcb10732cf9f821eacfa41b8a36d1a5fc4bae76408f19d85c02 DIST oboedit_2_1_8_linux_install4j.rpm 51962024 RMD160 b1ce3c7704c2fbe5185e36c6ad6c63f7fcf065fb SHA1 6a8a1605b9d6f16b6dc34469442a520029135eaa SHA256 e29edfe6531be9f64235e2891426b3ecf9f5a12f0f0f09a0b461f440dbcacfdd -EBUILD OBO-Edit-2.1_beta8.ebuild 1202 RMD160 e344bfb70b7291a04f3a21e41d9a8cdbeb75af36 SHA1 7f3df8619ec1ca9d9fc0912e175a159d86ddd6da SHA256 41fcb00811757696c332c9d4d1941ea186d7265ab7d2bfe05c923e9486125b51 +EBUILD OBO-Edit-2.1_beta8.ebuild 1011 RMD160 9214f2ed58107aceb10259e9960380a2e42a508d SHA1 52ccbf82bb26a9764c73f43edd5749297c43bd0f SHA256 efbeebf397b2176e07fc80aaf020cd9d9e4d2b4523315a820939761d3902a8c7 +MISC ChangeLog 213 RMD160 b8548e6d5f3b28a81e670bea1bad94cf72b68541 SHA1 aed23b323ab6ec8f1ba26a4e0583e139d9b4c50e SHA256 60ac52b6c2696252417f779b77704412a18162fa69c7923c53722072ac6deb90 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F9AUACgkQgAnW8HDreRaa7QCghXG6JSHPKGLWYGFRHT83RWD3 +oscAoJucwotuTlZpVfq0ImuGVTIQcThj +=RaKC +-----END PGP SIGNATURE----- diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1_beta8.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.1_beta8.ebuild index debd89f27..8842bcdb3 100644 --- a/sci-biology/OBO-Edit/OBO-Edit-2.1_beta8.ebuild +++ b/sci-biology/OBO-Edit/OBO-Edit-2.1_beta8.ebuild @@ -2,7 +2,9 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 + +inherit rpm DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format" HOMEPAGE="http://www.oboedit.org/" @@ -15,19 +17,16 @@ KEYWORDS="~amd64 ~x86" IUSE="" DEPEND="app-arch/rpm2targz" -RDEPEND="${DEPEND} - virtual/jre" +RDEPEND="virtual/jre" -src_unpack() { - cd "${WORKDIR}" - rpm2targz "${DISTDIR}/oboedit_2_1_8_linux_install4j.rpm" || die - tar -xzf "${WORKDIR}/oboedit_2_1_8_linux_install4j.tar.gz" || die -} +S="${WORKDIR}"/opt src_install(){ # sh "${DISTDIR}"/oboedit_2_1_8_unix_install4j.sh -q -overwrite --var-file="${FILESDIR}"/response.varfile --destination="${D}"/opt/OBO-Edit2 - mkdir -p "${D}"/opt/ || die - cp -rp opt/OBO-Edit2 "${D}"/opt/ || die - find "${D}"/opt -name firstrun | xargs rm -f # drop a world writable file - find "${D}"/opt -name .svn | xargs rm -rf + find . -name firstrun -delete + find . -name .svn -exec rm -rf '{}' \; + + insinto /opt/ + doins -r OBO-Edit2 + chmod 755 "${ED}"/opt/OBO-Edit2/* } diff --git a/sci-biology/ONTO-PERL/ChangeLog b/sci-biology/ONTO-PERL/ChangeLog new file mode 100644 index 000000000..847ef31f3 --- /dev/null +++ b/sci-biology/ONTO-PERL/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/ONTO-PERL +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> ONTO-PERL-1.31.ebuild: + Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors + diff --git a/sci-biology/ONTO-PERL/Manifest b/sci-biology/ONTO-PERL/Manifest index cea366935..66f2b8d5b 100644 --- a/sci-biology/ONTO-PERL/Manifest +++ b/sci-biology/ONTO-PERL/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST ONTO-PERL-1.31.tar.gz 721117 RMD160 0253abe13b159578955aff5cd0b294ddc3c8c9ed SHA1 93147c710ab0c3e5d227c91ff22dea1de6d2c6fa SHA256 89a85cbe2f7ced1a394d863d9b6fbc54fae2cc8a3c2531fcaaebaf50489866b8 -EBUILD ONTO-PERL-1.31.ebuild 656 RMD160 e29e0b2bb9382c7cac680448c0e7a62850a2437f SHA1 f04ae934a75027f6f1f3f028994aab634bc0dc86 SHA256 3ab67cb3df24b53241929631c974c1b97455ad5977e4bc3ea587a2fa58bef316 +EBUILD ONTO-PERL-1.31.ebuild 549 RMD160 369b3febfed860468843bbf9ae3819c44929faf9 SHA1 84ef7853cae41bea9cc8c3ddf10eedd1429a5cf3 SHA256 cafd5f1e96a254aa4c8107214afe3795e6a6ced10a9dc6203b96e551f179dec3 +MISC ChangeLog 268 RMD160 7ee93ecde2424e9e58e287496593e5335ff877b0 SHA1 a5a25c4ccfee8d1f2c05c68ee0e869069bb31dff SHA256 2b597424fede3c8c80631c215da408b7050da0454e739b837d2a8563ddb6459e MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F8lEACgkQgAnW8HDreRboOACgxyF0eel2GS+hFJWZFkewTKAJ +l7EAoL/6f7pEw0MjEOHc4KkxAuGV160N +=3aoL +-----END PGP SIGNATURE----- diff --git a/sci-biology/ONTO-PERL/ONTO-PERL-1.31.ebuild b/sci-biology/ONTO-PERL/ONTO-PERL-1.31.ebuild index efb4f7a46..473a145f9 100644 --- a/sci-biology/ONTO-PERL/ONTO-PERL-1.31.ebuild +++ b/sci-biology/ONTO-PERL/ONTO-PERL-1.31.ebuild @@ -1,18 +1,19 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/dev-perl/Geo-IP/Geo-IP-1.38.ebuild,v 1.1 2009/05/19 12:22:20 tove Exp $ +# $Header: $ EAPI=2 MODULE_AUTHOR=EASR -inherit perl-module multilib + +inherit multilib perl-module DESCRIPTION="Manipulates OBO- and OWL-formatted ontologies (like the Gene Ontology)" +SRC_URI="mirror://cpan/authors/id/E/EA/EASR/ONTO-PERL/ONTO-PERL-1.31.tar.gz" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -SRC_URI="http://search.cpan.org/CPAN/authors/id/E/EA/EASR/ONTO-PERL/ONTO-PERL-1.31.tar.gz" DEPEND="" RDEPEND="${DEPEND} diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest index 0f80e3de9..b9e41a1a5 100644 --- a/sci-biology/amos/Manifest +++ b/sci-biology/amos/Manifest @@ -1,4 +1,13 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX amos.m4.patch 1597 RMD160 f59e198aa725132f9e63d95a7efb05281d83a26f SHA1 5f4dfd9ffc40b2d06a3e8b4996aed2cbbe1297e7 SHA256 c5015f3548b2465fe235a8f2906fc0da2ecc96e50ebe2d7818aa2e17202aa01d EBUILD amos-9999.ebuild 1443 RMD160 020608c038facb917a9b52fe33cf5a70964fcffb SHA1 092e11d2844a4ea917d91c8edfd3d0682408ad34 SHA256 8e6ed1e4926c6e13531dc719d751028d5499e093b58a38ba8fb542d0db00da61 -MISC ChangeLog 213 RMD160 de502e7771dc17bd94b9bcd73b8288ebeff8892c SHA1 c0ea21e961752ecc7d8ed29334a31beb631ffc00 SHA256 423e7fb2941c5d867e363f2c6cbd26ed39b5efee85724fd76ac3d3c1803bd2d5 -MISC metadata.xml 549 RMD160 aaaa14a78b782644b19b4319869cfe78d2db5836 SHA1 f587b263a39731a1af3c80854aa5959f8edb7db6 SHA256 175313bbe3f6d424690f879605a71e0e2661d84b4c4cdd884d4a5cb05c04c7b9 +MISC metadata.xml 557 RMD160 3c1fa25a5d69a810652841110b688036a6971a64 SHA1 004c2081cbbcc715c82273022e7f4afce45c6da6 SHA256 fd4ffdf2f6037866d7ff2acf02e8d0c6bc9950888c1276c3de09958d4b141509 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EwEoACgkQgAnW8HDreRZnVACdEvKREzWpDhIjVPoRWZUAm18J +ZwkAn0MRMmjUrZeECCipLdsKQmR7bYci +=hr7y +-----END PGP SIGNATURE----- diff --git a/sci-biology/apollo/Manifest b/sci-biology/apollo/Manifest index 056646de8..5f874bbc5 100644 --- a/sci-biology/apollo/Manifest +++ b/sci-biology/apollo/Manifest @@ -1,2 +1,12 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + EBUILD apollo-9999.ebuild 1048 RMD160 21152d198e3c6a17442d1cde53f4bdf81d6089a1 SHA1 637631379bc584f26caba8fd4f4faea0597ba13e SHA256 6c8177a03caa6e4166d055da0fcb9b88feb2edaf00e3d38f996f73f644c6dc47 -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ev5QACgkQgAnW8HDreRYwLgCeKqTedlqvgkrkXwKNBfFfYN9o +o40AoJ8xTGL9Ko6q8XwA0X222+RUCPr3 +=ALTA +-----END PGP SIGNATURE----- diff --git a/sci-biology/argo-bin/ChangeLog b/sci-biology/argo-bin/ChangeLog new file mode 100644 index 000000000..7f9152a7a --- /dev/null +++ b/sci-biology/argo-bin/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/argo-bin +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> argo-bin-1.0.31.ebuild: + Cleaned ebuild + diff --git a/sci-biology/argo-bin/Manifest b/sci-biology/argo-bin/Manifest index ddf9aded8..12adf4d3e 100644 --- a/sci-biology/argo-bin/Manifest +++ b/sci-biology/argo-bin/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST argo.jar 26624770 RMD160 d789a09818e3d6d3cb87b11411c49959a050fa79 SHA1 305a668897ebd8f9c9c12484b3518a591121e51d SHA256 33ece2dba7ee5cc36f5aab99b3e7df2d641b261d86aacac00745e9d4a2e914cf -EBUILD argo-bin-1.0.31.ebuild 826 RMD160 43c29f959b336d944cd7864e5483f43fcd42a2dc SHA1 0b6778565dcc6d1f0a87340eefa2c9c5c5480586 SHA256 a4c2363eab488198df4762ecfc9f5a4549a0d58da895ddce6cbb4aaa0d7b6188 -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +EBUILD argo-bin-1.0.31.ebuild 750 RMD160 48f92a7e0bc78e52758d23e03187a3c064b66ce4 SHA1 f0dd3eea6eeebd45c2e07f894d5d6f4ec031af61 SHA256 5a2c0b5e82bdac568e5d671730595a8969bdd7e33d051e3f2133379805302b90 +MISC ChangeLog 210 RMD160 c00a3a468c7cad5ff65f84c0d9f3357bc9fa25a9 SHA1 b98c0ed89efdef2754c6d89da9ae28b5bb93b544 SHA256 8789c4325700c8afd94e30292e96c792d1282177baa879b3ce548f08db288726 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F75cACgkQgAnW8HDreRbZLgCeLx70kw5eOyWwmJv7iQTwcWxo +9DEAn0X1CgF0j1rrThydYJYRVfUwSX9+ +=ErKe +-----END PGP SIGNATURE----- diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild index ee72f80a9..7ed58fad2 100644 --- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild +++ b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild @@ -1,14 +1,12 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v 1.2 2010/10/10 21:20:04 ulm Exp $ -EAPI=3 +EAPI=4 -inherit toolchain-funcs java-utils-2 +inherit java-utils-2 toolchain-funcs -DESCRIPTION="The Argo Genome Browser is a production tool for - visualizing and manually annotating whole genomes - stored in .gff3 files" +DESCRIPTION="Visualization and manually annotating whole genomes" HOMEPAGE="http://www.broadinstitute.org/annotation/argo/" SRC_URI="http://www.broadinstitute.org/annotation/argo/argo.jar" #SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz" @@ -26,4 +24,3 @@ src_install() { java-pkg_newjar "${DISTDIR}"/argo.jar argo.jar java-pkg_dolauncher } - diff --git a/sci-biology/argo/Manifest b/sci-biology/argo/Manifest index a23395d9c..62322c09d 100644 --- a/sci-biology/argo/Manifest +++ b/sci-biology/argo/Manifest @@ -1,3 +1,13 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST workspace-2008-03-11.tgz 109194467 RMD160 873b9c3facfe872108a4c8849a774d5c8c74893f SHA1 382642ae8d7498bb8c21764fa625aa47b4107cfb SHA256 0ee6acb0ebdc17cfbedfedb8559ba950ddd4c5c4ef5f7875fa93f3fad885b99e -EBUILD argo-1.0.24.ebuild 935 RMD160 54eb968965979b8b37e236f94faa554ebb7d21df SHA1 65eda8fec914b3a43184e039c52a91d6381d8005 SHA256 f06f6d3ca2e10a5eee2e4f233bedfcacaaa918b4294d945a861399ffd95e40c3 -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +EBUILD argo-1.0.24.ebuild 879 RMD160 7288ffba9db9f8380326957a0b2e780434b190fb SHA1 d662bcdf91e2a10bf6a49ae643d3d7552748f3ae SHA256 558fcb91ff7a7188d49a86343ae7c58ce5053995c0cdfd9e17fe7e7b8308e026 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ei+4ACgkQgAnW8HDreRav7wCdFTNQA2y8/m1P5MN+B1mIVE+l +5ucAnRUBfKPrUIvcaEfPasGiSs4CVkcM +=wbss +-----END PGP SIGNATURE----- diff --git a/sci-biology/argo/argo-1.0.24.ebuild b/sci-biology/argo/argo-1.0.24.ebuild index 30fba8746..055979850 100644 --- a/sci-biology/argo/argo-1.0.24.ebuild +++ b/sci-biology/argo/argo-1.0.24.ebuild @@ -4,11 +4,9 @@ EAPI=3 -inherit toolchain-funcs java-utils-2 java-pkg-2 java-ant-2 +inherit java-pkg-2 java-ant-2 java-utils-2 toolchain-funcs -DESCRIPTION="The Argo Genome Browser is a production tool for - visualizing and manually annotating whole genomes - stored in .gff3 files" +DESCRIPTION="Production tool for visualizing and manually annotating whole genomes" HOMEPAGE="http://www.broadinstitute.org/annotation/argo/" SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz" @@ -18,8 +16,9 @@ KEYWORDS="~amd64 ~x86" IUSE="" RDEPEND=">=virtual/jre-1.5" -DEPEND=">=virtual/jdk-1.5 - dev-java/ant-core" +DEPEND=" + >=virtual/jdk-1.5 + dev-java/ant-core" S="${WORKDIR}"/workspace-2008-03-11 diff --git a/sci-biology/autoeditor/ChangeLog b/sci-biology/autoeditor/ChangeLog new file mode 100644 index 000000000..a95258201 --- /dev/null +++ b/sci-biology/autoeditor/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/autoeditor +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> autoeditor-1.20.ebuild: + Shorten Summary + diff --git a/sci-biology/autoeditor/Manifest b/sci-biology/autoeditor/Manifest index c6f9f202c..641dc429b 100644 --- a/sci-biology/autoeditor/Manifest +++ b/sci-biology/autoeditor/Manifest @@ -1,6 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX Makefile.patch 3051 RMD160 bca80507a7d1b401a96b654e7049a54c8f68bd05 SHA1 453ce786ab004f25eb19842d8558ad450bb34560 SHA256 534d67e7effdb072d6a2c7469e67b50ff82da5c5c9bf16de57d30609b024055d AUX sample_expected.out 1118 RMD160 38f3a997add481e6ac8b2f981e32aab6113302ce SHA1 5c1afa013888ccdeb4325935a4bc362dfdebe2e1 SHA256 bb51ba6b15a9916c65b0209742ff3dc3a8832c1355f65cbf35738ce88047ce9b DIST autoEditor-1.20-sample.tar.gz 71953287 RMD160 bfb859a3badec0db85ee31086d2574cd43ebe3a3 SHA1 a36668f1d041552229684c20d9789e7b6301d57e SHA256 f25beb3668ab2b3f2018e5e3b9615995ba5a16b5ce002ff50806287f28f5ef25 DIST autoEditor-1.20.tar.gz 2438903 RMD160 598ac977eb424959fc052b4c857ef4487b7e13f9 SHA1 985b5e880148a904b157295053945f9530718d30 SHA256 c0c399eda52a10deb0e0362b4caf909014768a4d08e90c900392cdf712cefd66 -EBUILD autoeditor-1.20.ebuild 1304 RMD160 1090965e8b9dcfdbf5ed192976dd2ddde4164cdb SHA1 17c7245826480ec3e3ea93b1f373a1077dbdec70 SHA256 a3f44b7e1eb317350ec8e676068601d164e50f997ff0d9919282d4d68abb5711 -MISC metadata.xml 1152 RMD160 0c202dd48bd4242879dccee9f566e9003857db84 SHA1 bf658a22a72370f46e76da50b1960f5fbb189aae SHA256 a6323415c0ec7864b776e4454845e6e659f23e978669c86aa4188ac0bbad24b8 +EBUILD autoeditor-1.20.ebuild 1134 RMD160 9a60610118475e6bdcfc54676887e1a809fa526f SHA1 297b5566c27274765b52345a6c943d62d750d00f SHA256 8e62b735c19f1ea2a5a1a9fc729fb55f68706f9d6ddf68c6e51eaad02a686345 +MISC ChangeLog 213 RMD160 dad86b527258c7be58b278fd8afcb94f83c4f9a1 SHA1 e37a2303e9c3d7f86446da6094bcb684ff1989bf SHA256 e3e26aff923684c1790497a3cb2c2b04a094d0dba50a2944de58008857873971 +MISC metadata.xml 1160 RMD160 1006598866055875c6ad7f39e0634def718002db SHA1 2b13d7786cc0dac0434b14bace3467126904ddc2 SHA256 fb86e548211f36d0f56372b98bd47ff6228e9e81862714937afb1292e9004079 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EwNcACgkQgAnW8HDreRb6RACgkYKEo++8/u1PQglFS2rPcO1y +Va4An3GZWl1Zj/OwpNTKqys8QJwLFVpn +=4wrn +-----END PGP SIGNATURE----- diff --git a/sci-biology/autoeditor/autoeditor-1.20.ebuild b/sci-biology/autoeditor/autoeditor-1.20.ebuild index bbe990805..f39f43dd5 100644 --- a/sci-biology/autoeditor/autoeditor-1.20.ebuild +++ b/sci-biology/autoeditor/autoeditor-1.20.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -6,20 +6,21 @@ EAPI=3 inherit eutils -DESCRIPTION="AutoEditor is a program that can automatically correct discrepancies in a -multiple alignment by reanalyzing the chromatograms of the discrepant bases." +DESCRIPTION="Automatic correct of discrepancies in multiple sequence alignments" HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AutoEditor" -SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20.tar.gz - test? ( ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20-sample.tar.gz )" +SRC_URI=" + ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20.tar.gz + test? ( ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20-sample.tar.gz )" LICENSE="Artistic" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND=">=sci-libs/io_lib-1.8.11 - sys-libs/zlib - sci-biology/tigr-foundation-libs" +DEPEND=" + >=sci-libs/io_lib-1.8.11 + sci-biology/tigr-foundation-libs + sys-libs/zlib" RDEPEND="${DEPEND}" S="${WORKDIR}"/autoEditor-1.20 @@ -29,14 +30,6 @@ src_prepare(){ rm -rf TigrFoundation-2.0 || die "Failed to drop TigrFoundation-2.0/" } -src_compile(){ - emake || die -} - -src_install(){ - emake install DESTDIR="${D}" || die -} - # TODO: # * QA Notice: Package has poor programming practices which may compile # * fine but exhibit random runtime failures. diff --git a/sci-biology/bamtools/ChangeLog b/sci-biology/bamtools/ChangeLog new file mode 100644 index 000000000..111c436cf --- /dev/null +++ b/sci-biology/bamtools/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/bamtools +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bamtools-9999.ebuild: + Moved from 'git' to 'git-2' + diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest index 2d1817498..0fc975819 100644 --- a/sci-biology/bamtools/Manifest +++ b/sci-biology/bamtools/Manifest @@ -1,4 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST bamtools-20101215.tar.gz 142100 RMD160 615f64659faaf21d0d83a11e9d0748b5220888be SHA1 1c5d44928434e9e99187035630724205d10bc337 SHA256 3b90c8317207398d94bb7b7cf6470ee8ae8f3b306332c498d1696c80659dce07 EBUILD bamtools-20101215.ebuild 758 RMD160 d0dd72604cfde877a8ce64261a964c2a145a4b15 SHA1 7c0d41b89cf09f0c0a81f7d9ed7a5a3d44ea3837 SHA256 740ee79b8830e455363c5aafb47fe44675000ab119b915107de48f95b4345415 -EBUILD bamtools-9999.ebuild 885 RMD160 ecfefc0a74541f88fa2a331ad6799be05bef80ea SHA1 c1f10f3348ee88c90e278dd6b33c6bebd910303a SHA256 3424284b41b44b8087629335fcb894d89b6d58493410270a65f5f1b6251c7543 -MISC metadata.xml 547 RMD160 1b58f37f70cc5873715f4b77795428f1f393b7ee SHA1 a1900126a5dee33d7c9ed138923ea2f0db28fa9d SHA256 4573902d3d9a0bc60d9e253439e87462cba88e1cf6dd2ac7e1be35242f38b4d8 +EBUILD bamtools-9999.ebuild 887 RMD160 edac08fd4f626ddcd46e70e7e3a33629975526e6 SHA1 2b451d5e08c68ede6b0cea58e32c295e9449ddb1 SHA256 d9c89d10dbe417fc40c60d97ca12059ee562c9a9e0da1c2f453c61478a129d97 +MISC ChangeLog 221 RMD160 68ce47391131977af697c1358c535193098e7f8a SHA1 9f93a33b9fd78f6b33225cdc7bf523f602e9cc45 SHA256 965f3bb7dc9bba900ee96e9a82fc344d9b58743d39f27a9a1ccaf69fe9ec31ad +MISC metadata.xml 555 RMD160 4562689d2995eb95550c28a48c7d9516b81bb572 SHA1 02ce41839a3b77ac7122a736b2dc71acc9408dc6 SHA256 8a592c3fc8ff1340d59d088fb6b1e5e3184433d6a1546985e09fa14b79869b09 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4ExvcACgkQgAnW8HDreRb9AgCghOuvXFxkcw3fHAPV4PTuTwD/ +UoAAoIlUD9lYLJRJ1QYyHKYPPEGo4bQT +=3c+9 +-----END PGP SIGNATURE----- diff --git a/sci-biology/bamtools/bamtools-9999.ebuild b/sci-biology/bamtools/bamtools-9999.ebuild index 6448e0a00..e23dc3974 100644 --- a/sci-biology/bamtools/bamtools-9999.ebuild +++ b/sci-biology/bamtools/bamtools-9999.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=3 -inherit cmake-utils git +inherit cmake-utils git-2 DESCRIPTION="BamTools provides a fast, flexible C++ API for reading and writing BAM files." HOMEPAGE="http://sourceforge.net/projects/bamtools" diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog new file mode 100644 index 000000000..3fd80712f --- /dev/null +++ b/sci-biology/bedtools/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/bedtools +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bedtools-2.10.1.ebuild: + SOme ebuild cleaning + diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index 7f721ba90..e3af7c57a 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST BEDTools.v2.10.1.tar.gz 904396 RMD160 db6b9f103bff28a04479d243b05de7c8cb38c208 SHA1 67ece0f2747b6886de8ab9642365fa071d0fe32c SHA256 b128ee474827aad2a3bd8808aeaeca484120fc202ac5f1f7b805c21d0be76458 -EBUILD bedtools-2.10.1.ebuild 656 RMD160 618b0fa2740c6da5a3ace6300ce93d5199fe8edc SHA1 61f2299b782ab680895de9f3698142afe038f29f SHA256 b78bf69a0aa265139238ce3689cfdded2b3fd6c35007cbca1201e453c781a07b -MISC metadata.xml 365 RMD160 97d6bbddf5c26e472d3c6c19ec50c2db87d88dda SHA1 8e10d068960e7e258db3e33397f679dc56bf0545 SHA256 0209b66105b6f3fd1059f6c16366807c71d96fe6021b80cd115adc745192981b +EBUILD bedtools-2.10.1.ebuild 485 RMD160 039c6cbbceb4154a022fe95635bb00fac8e443fc SHA1 bacae16709812d7687b14a9f07fe6a4f680f38fa SHA256 efb1a05b1f80ac6a04747572380b6fe53827423cfa7c0a4e63f0f1228d4238ad +MISC ChangeLog 216 RMD160 6779ba4504285979c47f966da1e0141322da629f SHA1 4fc8043870c49461873e220c9768396ea90376a3 SHA256 ebf9a0ba64734c49cad21cadb00c7c5633fc9680211dbf60975b5eb06a3a4907 +MISC metadata.xml 373 RMD160 492d63a640c8667cd2c3e48f9f79916348eaa425 SHA1 57afd5cc95b7a6fd4ed4ecdc8a2dd40f3036d6ba SHA256 9cd28401c75e322432ebbf23f9e9ba4c32154e951171de78c83668a33147e042 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ex3AACgkQgAnW8HDreRbomwCgwPWuLzeea794YNTaqD2BSnlJ +lf0AoJ++a1yEa9u42KNdO7XvDohVFNbo +=sZl+ +-----END PGP SIGNATURE----- diff --git a/sci-biology/bedtools/bedtools-2.10.1.ebuild b/sci-biology/bedtools/bedtools-2.10.1.ebuild index f03a4f761..541b05647 100644 --- a/sci-biology/bedtools/bedtools-2.10.1.ebuild +++ b/sci-biology/bedtools/bedtools-2.10.1.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 -DESCRIPTION="BEDTools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats" +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats" HOMEPAGE="http://code.google.com/p/bedtools/" SRC_URI="http://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz" @@ -13,16 +13,8 @@ SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - -src_compile(){ - cd BEDTools-Version-2.10.1 || die - emake all || die -} +S="${WORKDIR}"BEDTools-Version-${PV} src_install(){ - cd BEDTools-Version-2.10.1 || die - mv bin/overlap bin/bt_ovelap # prevent file collision with sci-biology/wgs-assembler - dobin bin/* + newbin bin/overlap bt_ovelap } diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest index c832cecf0..82c2f4fcc 100644 --- a/sci-biology/caftools/Manifest +++ b/sci-biology/caftools/Manifest @@ -1,7 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX Makefile.in-2.0.2.patch 1619 RMD160 a36fc2e878424df24e4a2501769b5959d2997362 SHA1 255d22883c245bbbcb29cf1afaeafc08d067bd8f SHA256 4d24755beabe400afcfcdb987bbe85d117a2098ce6f05879cc813166448569c2 AUX Makefile.in.patch 1633 RMD160 2942a5da7112bfb9f9c6bbd40d26b85d6688265b SHA1 b96e4ebd6b3805c04f7690b240729ca5228dfd3e SHA256 c8bb87d532e664683b41ae0f46a08f9232e1724a574f8a03e658130b0e13d223 DIST caftools-2.0.2.tar.gz 2645554 RMD160 66ebb894e8899e10349742de1bae67a565a35a9c SHA1 071a170d265ddef46ae2f5effa478421e9cce6ff SHA256 7be5eafbd6817a7869f73c7540b5fdfe184b0be28624cc6ca9a01c52a140d4a2 DIST caftools-2.0.tar.gz 2644892 RMD160 29f389d0861f8c60efa137a53816abed5286214a SHA1 9ed7ed3d8be2bcde86aab8a79d4a61408cdc49f2 SHA256 b41f323ceb3fd260d6c2ecff1f285548f40301065cea54687eb96717534eaad9 EBUILD caftools-2.0.2.ebuild 1581 RMD160 bacc32349fcdcb76f6569db199385bd9fb51d6f5 SHA1 c5b411c13045623376779d615e310c4e375c0937 SHA256 3df664db4d5435f9b396fab721ec74cce26d997ced582028dbc662aac8d09b37 EBUILD caftools-2.0.ebuild 1068 RMD160 bdc6a4b5b423bfca1cf310f37db1f36ed5da9660 SHA1 0fde3ae97fda1cf06e2035e45f9cacefffa54c21 SHA256 613629e32ff2b43ca4f6ddc9428212542f1deccf69b868882a94ed20246d9e53 -MISC metadata.xml 531 RMD160 4e24b3b35b7b5399437676b65deb40c1533d7e15 SHA1 c0ac47f9d1d505bc7dddf2dbb5a2ef5e4905643d SHA256 8da1039b073c1c438b5a93089e469c9e35b7dc1297d6ac181e7d81809dee6049 +MISC metadata.xml 539 RMD160 811d93c4d63a12d2534865e7f848b41974c82a43 SHA1 5ddac4a5841b1c2e487f847d37e1a5e2dafa1c8f SHA256 84f5eb9ec596906c56f2e74dd64eba9d46895a45d1178e0b8c3bf7ff19bd8c36 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ex5oACgkQgAnW8HDreRbRtgCfaasNnmY98tewV7p1jbGiD0F4 +zXsAoMEJI0ipeTsvrhxZ6PDwE/jEfrLr +=v2js +-----END PGP SIGNATURE----- diff --git a/sci-biology/cap3-bin/Manifest b/sci-biology/cap3-bin/Manifest index e93a18b35..3148a591a 100644 --- a/sci-biology/cap3-bin/Manifest +++ b/sci-biology/cap3-bin/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST cap3.linux.i686_xeon64.tar 430080 RMD160 f5a5e6643747b35de14fa2dab3f5b0d6756abc8c SHA1 b1e06785286f3509a8d08cd2e3400e2abb9e7888 SHA256 fd7112a89dd349e0d11820d4bfab34c3556eb570828f71a8db18b68bd6aa1c2c DIST cap3.linux.tar 409600 RMD160 a3e4fc661ac349791b2c9f1d5982d6b34f502122 SHA1 0de4f5de7fd3a4f6bae9d402f5bcd4937fe15ea2 SHA256 49916f0ac2dc7b6f28fd88e79f98eb097e059839bd9311593ef3fc6f77bc4648 -EBUILD cap3-bin-20071221.ebuild 1463 RMD160 cc06270e4c2e9fc0204296d552eb6f749a92c386 SHA1 ea015dee363244e53a16b771a161476e42ea0397 SHA256 b7adefe5ea1f7e31a9d3f7f420c3aa1bd7e3539bfabb2de884d562b3433c32a0 -MISC metadata.xml 391 RMD160 1af9555e8977c2e8b9bb8ba330498a8e5d050907 SHA1 0068e6453a108df09f7adb2875f61fec6c73140b SHA256 019499f4ccf9bcdf115a3ffff6af37bdf9a14ae2613d087f73149dfdc6eebdda +EBUILD cap3-bin-20071221.ebuild 1479 RMD160 2c2726cbb00ad6596b4c2b44824e342256bf5ecf SHA1 a1f5a59778f37c78b4c2819f89edff08c727fa1f SHA256 1268644cbc1d0ee100906fecb4debbc11b239c6c5ba40503e12f35f1ab938fef +MISC metadata.xml 399 RMD160 b4d8b61da12d50650bc9a7240664b2ccb11b4c3b SHA1 33c15e90cea2a4d530c4a4bc998bbad10f850edf SHA256 169911bbc957ca5de82f7f818e746c917a9698ade71b03d99e60a5912620c226 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ey3IACgkQgAnW8HDreRZdKQCfcQFotsJkMbnzcnXjXdgeVlXy +XTUAoMigo6CG32wshx1VhQ/SgvaRIsr1 +=unOA +-----END PGP SIGNATURE----- diff --git a/sci-biology/cap3-bin/cap3-bin-20071221.ebuild b/sci-biology/cap3-bin/cap3-bin-20071221.ebuild index fadedf7a9..cc6f5e30e 100644 --- a/sci-biology/cap3-bin/cap3-bin-20071221.ebuild +++ b/sci-biology/cap3-bin/cap3-bin-20071221.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 DESCRIPTION="CAP3 is for small-scale assembly of EST sequences with or without quality value" HOMEPAGE="http://seq.cs.iastate.edu" @@ -18,25 +18,27 @@ HOMEPAGE="http://seq.cs.iastate.edu" # http://seq.cs.iastate.edu/pub/CAP3/cap3.linux.itanium.tar # http://seq.cs.iastate.edu/pub/CAP3/cap3.linux.powerpc32.tar # http://seq.cs.iastate.edu/pub/CAP3/cap3.linux.powerpc64.tar -SRC_URI="x86? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.tar ) - amd64? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.i686_xeon64.tar )" +SRC_URI=" + x86? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.tar ) + amd64? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.i686_xeon64.tar )" LICENSE="Artistic" SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" +S="${WORKDIR}/CAP3" src_install() { - cd "${WORKDIR}/CAP3" || die - dobin cap3 formcon || die - dodoc README || die - newdoc doc cap3.txt || die + exeinto /opt/${PN} + doexe cap3 formcon + dosym ../${PN}/cap3 /opt/bin/cap3 + dosym ../${PN}/formcon /opt/bin/formcon + dodoc README + newdoc doc cap3.txt # other examples # http://seq.cs.iastate.edu/pub/CAP3/data.tar - dodir /usr/share/cap3/examples || die - insinto /usr/share/cap3 || die - doins -r example || die + dodir /usr/share/cap3/examples + insinto /usr/share/cap3 + doins -r example } diff --git a/sci-biology/clover/Manifest b/sci-biology/clover/Manifest index 74679997b..d19acf301 100644 --- a/sci-biology/clover/Manifest +++ b/sci-biology/clover/Manifest @@ -1,45 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 -- -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - DIST clover-2010-02-19.tar.gz 15641 RMD160 aeeefc128976ce299e5ad65129cc0891104f0348 SHA1 ad30ac6440c6abfe53876ccc94149eec34e16b2f SHA256 f6de99b9ce5676af8b4179e12c4701f81f0b17ac5dadacfe7affa38ad2a585f5 DIST jaspar2005core 14913 RMD160 6fe43472cc1a2e0389ad9290801db56488773d3e SHA1 be8cdff62cf35f430c0c17f53564529b08000c9c SHA256 498a560c67411789106b50ccdfd9bc41f571d77c2fe9bfba7e95128c0a122fe4 -EBUILD clover-2010.02.19.ebuild 1068 RMD160 ee85f019c8e3914d41e7a902f1afd1b250c22b7f SHA1 056c74812ac0ee941c6975c706ad3e94c177a8ad SHA256 d13347e138e155e7d12588dfd15457510d2d8caecdf5f7bb26c82408572467f1 +EBUILD clover-2010.02.19.ebuild 1068 RMD160 33df8e6f80650fc17ce9d0fbda7d9ec318dfef7c SHA1 9763b5036cfc7feeeee887148cf962bf0404017c SHA256 514616a014b196e736d8f4b2f0f5b6df78ed4ab51498e92e05fa7d578f8420ce MISC ChangeLog 670 RMD160 76fec21f730ded591f166b128cee5ad87730e387 SHA1 45db195b3b23a9f0da9dc81a33a8f23303770faa SHA256 446dad253d4a186f03678f0aef1d9b6f0c683bb7390814c1c7b27ed7c829a2f4 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -- -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) - -iQIcBAEBAgAGBQJMcsvnAAoJENwGBM22xffeL5sP/jDmo45oY5thDk+pt3owS+GP -jX5BnheYpo1yRarTGbkYHflROiV5tuXMv/lKj6WFft/OlVIZfVyx0lpcie+OAppQ -b3c3MOUOWRTQz4MYBZ/HbagJ3ArVWHfw3BArSI24lcsGfeMTxQt0E2TyCNNOnmO3 -HAR+KxaKKjdz3lKWPg1fVqbDYt+T6fhWtG8BcTONAzB72y78qYG7twKiO52AcWSp -sEGyK7RlPqduJmeX2yyzJQcQRnI1kq7/FjVuzcw470BXQe4S1MGlPvKim8QLyoti -1jh2Vt9hiSb4NLmothqEFs4dUwXOrclPzia1DfNJynCBFrhj3h/Qk4f+rIHLtp3I -IhiRLHEawZzJNdeUfMwDCY6IuwWi7H9gLpVeJSiYIN47baCuUVjQDZ0NTa0/wuHU -9IGyjn2XZGGzs9r/dJu3MVN8FJz/V+lmXKJQ/QPVJIjLosFM7yJBaeaPHKrAFlnV -u6rRkDzIgyoqLxdSUdMHxIDSgKoI5NvnA02dnCK/I2ANM/18ku1UoyKK1N8LJcTD -n8bAU4rWCt7+w+D1ltHeDvOa8eALT1aGGbqzJeAgtOZxp3USWwWj0wDG4vPb/SeO -VTaNV1OprAZ8eC3uV806RaXRXHAqvBkcyBJdle38RQOuBw4bJ3PkXQv3JON/WcSI -rZgPMzMkbwCkKnq9Ppro -=7fhm -- -----END PGP SIGNATURE----- +MISC metadata.xml 225 RMD160 281076a863af4791e194c7c0b39ccd572e95d0f2 SHA1 62bd67899a22705ac2475b479d5b31a331cb26bf SHA256 fd7f5bfdfd9dce3dd874edd9ff9fd12dcd83aba1c73b0c62399e8aba52e435fc -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMcswRAAoJENwGBM22xffei/0P/14eh/3mDWL54PJMGPc38Wnv -nl7rJDdeZJf2LdjhgRGS7a1VoP34Jmg+TFwA1LHNhqEcuxQV7z4oQGi/HLHYI5i9 -64r1+agm+RIk9+VhGgf/r22y5v6ZwqzBN+SxC29mHvSJuwbjw+jHvJdqzhKSDkvd -caiFdE1oYwhGQ1qXiBrElTZkfprpaNwjwYRSOkyefj5P+FV7PFK3tzVsTq7m79Ab -pNHyIc9zTYI2YhyQ9v3jFJhGJsDb9JqoEwqYHLtPda+b7/ekpv4frLBgNSajKJeu -lHR6eVS4tA0WcCVnUHjCPAOJisCtOLQcao1c5ViftpvfofNs+BHtvmlBm7moPCvv -sAB8JVbzBIZ4rcFwy/7mjYe7MZ1MsmiLZR2D3X71K0LmRp5UgjjaJjczTUQ0Fqtg -9WbJOiDR7IPfxjhmfAZK4aeSnXD+rVjZ+MPOGRUuD2zplj9NuQK3PTgndCdI1Yo8 -jGSTkRNa5Civ4c2FEQW4UlCrKB+u35+ocyZsPniFkdP0hlN66eHfsOxIE562qaFU -GkSvN4HWiW5yS4fdEcGh8EM/ojUnRQN/2T9flkA+JHdhAy/+6+ilVv10pVlJ0Ala -af+rxjDbkPaeo+8kBYQvhSChVv84gQOBj72KSziBTmSgDWYXs4BFXPj3Pmx7Bwcr -+MSjiUj5Bhc185SjfZOA -=T+d9 +iEYEARECAAYFAk4Eh/gACgkQgAnW8HDreRY8tACgzJ1dGICxmztGGCVYJ05z+hba +QMEAoKTiqkCsI+B26uZICnG+Z4Vy9jla +=PGkq -----END PGP SIGNATURE----- diff --git a/sci-biology/clover/clover-2010.02.19.ebuild b/sci-biology/clover/clover-2010.02.19.ebuild index f14b70a16..239cc30e4 100644 --- a/sci-biology/clover/clover-2010.02.19.ebuild +++ b/sci-biology/clover/clover-2010.02.19.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit versionator toolchain-funcs +inherit toolchain-funcs versionator MY_PV=$(replace_all_version_separators '-') diff --git a/sci-biology/clover/metadata.xml b/sci-biology/clover/metadata.xml index 7e3286984..9e64bf890 100644 --- a/sci-biology/clover/metadata.xml +++ b/sci-biology/clover/metadata.xml @@ -1,5 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>maintainer-wanted</herd> +<herd>sci</herd> +<maintainer><email>maintainer-wanted@gentoo.org</email></maintainer> </pkgmetadata> diff --git a/sci-biology/codonw/Manifest b/sci-biology/codonw/Manifest index eb2e90af1..5802e4d51 100644 --- a/sci-biology/codonw/Manifest +++ b/sci-biology/codonw/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST CodonWSourceCode_1_4_4.tar.gz 161908 RMD160 9e01d48525e5308e8719f89276a12a3909d64a09 SHA1 a440d1ebdca328ed1f5efa7342267b7a2e764b3b SHA256 951e2a686f7849e0fa225b83b09842d4cf822ecafd67bff0438fc815512183b8 -EBUILD codonw-1.4.4-r1.ebuild 928 RMD160 06354dac3504df4e4feccf6cf6261a0c1c8a6dfa SHA1 acd84fdeef62f055a8cdf6a033edfe7f883d8f10 SHA256 c99157862f6ee0a30e0c62888ac9d9d5977eee9e12cdd4fd650801eac9824e38 +EBUILD codonw-1.4.4-r1.ebuild 928 RMD160 c8c1a14377188542889d6ede54538223ee865223 SHA1 d98279ddd25dba4cb8c1c7d55ef492e0c5bf7270 SHA256 382bd0ffef52b148657497df54f58be47081dc2165478dc9180711a14e39f295 MISC ChangeLog 435 RMD160 be5677fe4fe3cce0464834389b5c02e1dfb06ff5 SHA1 6318f550aa8e0f901ac5f3b57a52e2f404aeba0b SHA256 9d4201e4ff6acccc66c516e3a970b415a4820f167010fa8fd3dc11c5217847ce MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Eh/0ACgkQgAnW8HDreRb2gwCdEWq45ZAa7F0/PYnbNYE0DWSQ +t18AoLHX5NDr2XRfGcckk5HnSCY1JMPu +=+KUN +-----END PGP SIGNATURE----- diff --git a/sci-biology/codonw/codonw-1.4.4-r1.ebuild b/sci-biology/codonw/codonw-1.4.4-r1.ebuild index 3563ddfab..05ed6ea14 100644 --- a/sci-biology/codonw/codonw-1.4.4-r1.ebuild +++ b/sci-biology/codonw/codonw-1.4.4-r1.ebuild @@ -4,7 +4,7 @@ EAPI=2 -inherit versionator toolchain-funcs +inherit toolchain-funcs versionator MY_PV=$(replace_all_version_separators '_') diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest index 73cf624e3..73899c6a7 100644 --- a/sci-biology/consed/Manifest +++ b/sci-biology/consed/Manifest @@ -1,6 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX nLine.h.patch 237 RMD160 2fa26b40e186f5a5a840a244386484be17350edc SHA1 a842928142ca4228c8a94b1f7daca37ed77cc301 SHA256 376f61dbbd142b6927c2f0b1984d03499ad1e7ffc70b646bad46c5fe006e0350 AUX nextPhredPipeline.cpp.patch 439 RMD160 747bc2e640d04525e9e085e4aa33bc45ad1c3eb5 SHA1 5d658507a91af26fe4477608aeaf6db87bd6bc27 SHA256 3ac55169665cc74507ea5f405a67d43a37a3d2733d74b877f732674c4e2e8e82 DIST consed-20-linux.tar.gz 31407408 RMD160 8ab84f5216bb433884c75806738a6f7f20dea915 SHA1 9ccf1a2db890e30f042188d20e52098e1e37987a SHA256 ebde602163743d018ac8bf49f04ff0afbd0cccb3b7ef065a154943a68e95ad27 DIST consed-20-sources.tar.gz 7418118 RMD160 2dafda72027ecefd20333bddcec0b3e24d102412 SHA1 a222ef3a34c4940eabc8e0250ae88a86c5ee27b5 SHA256 8d12191e08d9dfc73c3284a057b7fd80d1aefe4a60d11a0de1db6ba9ce9ba4b7 -EBUILD consed-20-r1.ebuild 2495 RMD160 2a1832e72bbea1b782cbcea2cc98053dc3fbcbc6 SHA1 81dd87503c95c853464f6ce4100e8f8d3f499136 SHA256 7a84e27608e40ff07e49c488ab7d9754d30ff376541617ca5a529010708e9ad1 +EBUILD consed-20-r1.ebuild 2495 RMD160 41aca137feda9859a997dc2c8adc04790231bd76 SHA1 37228fa4128d4f091384d821f63001df368c275e SHA256 f7831b85683c057afbd48d7830147aca7c2f6d8e03485477948e3b323a9686ec MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EiAIACgkQgAnW8HDreRYZQgCcDET079yuAcbfOjok/M99Uvzw +Sk0AnRGjhAhntG3bxr5+HuCAWTJZ8h44 +=X0Ic +-----END PGP SIGNATURE----- diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild index 5c65e660b..0ddce15bc 100644 --- a/sci-biology/consed/consed-20-r1.ebuild +++ b/sci-biology/consed/consed-20-r1.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit toolchain-funcs eutils +inherit eutils toolchain-funcs DESCRIPTION="A genome sequence finishing program" HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" diff --git a/sci-biology/dawg/ChangeLog b/sci-biology/dawg/ChangeLog index ff3e5fed1..ad8b3b952 100644 --- a/sci-biology/dawg/ChangeLog +++ b/sci-biology/dawg/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/dawg -# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + 24 Jun 2008; weaver <weaver@gentoo.org> +files/dawg-1.1.1-gcc43.patch, +dawg-1.1.1.ebuild: New package diff --git a/sci-biology/dawg/Manifest b/sci-biology/dawg/Manifest index bac910e38..7c2b7c109 100644 --- a/sci-biology/dawg/Manifest +++ b/sci-biology/dawg/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX dawg-1.1.1-gcc43.patch 251 RMD160 432f37ab9d976958161cc05c8176aefca2d34047 SHA1 aa560bc5086e8ef17437d23d091be46044080f63 SHA256 85ac21adb231fa971d11597dc9e5f3725a7900889841e6665119ac1bf807722d DIST dawg-1.1.1-release.tar.gz 213877 RMD160 d2be74cf13c5aecb30cc08f4404d954f6f4272c8 SHA1 fe2942ab9d73d22fd02a8dd06bd8874b7470d487 SHA256 dd621d7913fc1511b52ed2bdc5856e1e591464ddf8ee5c2e7eaa45ac81705286 EBUILD dawg-1.1.1.ebuild 607 RMD160 7832fc450b66ec3763bca33070ef6f6573f813c5 SHA1 c2b987a3e3c2a001eedf4fe01a265aaacc30a087 SHA256 33421468781252e7fff1a238b0ca30c7e2be9c433985e70986e82c5597866333 -MISC ChangeLog 227 RMD160 56af05e22cc08ee72a7bd7e75ab928b3c9e07e6a SHA1 83e5a13bbdd76547150cf934ae0ef2a043d18767 SHA256 3ae2b976f9eca9d456a198f01294bb489a03096c49021212216798be97b5cfd9 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 +MISC ChangeLog 324 RMD160 fa6ced37eca55f0a9b6a3009df761e83e59938e0 SHA1 d4f71cc8ba5e0f9944d181fc3d94e73f49e17f77 SHA256 7632e828e8ff7464d35516a70ee32cdb99e6f2d8956c88dfdb1565ce37b09ff6 +MISC metadata.xml 158 RMD160 9b441c987a00c5a66c06850c0d587a2abd70893c SHA1 7a8997eb2fc55fda167d3e95cdffb43c8f817fdf SHA256 dae7918daac89b300804812d32584889aa1c4e8b9edeced06006900494457a6d +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4FkaIACgkQgAnW8HDreRacngCcCzOtR+z/0GLQ5EFv4EnHQT2r +gbIAoKQnApG+KCVRKqKuAig2S0IuvX3o +=fw2v +-----END PGP SIGNATURE----- diff --git a/sci-biology/dawg/metadata.xml b/sci-biology/dawg/metadata.xml index 7e3286984..897aa2e6b 100644 --- a/sci-biology/dawg/metadata.xml +++ b/sci-biology/dawg/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>maintainer-wanted</herd> + <herd>sci</herd> </pkgmetadata> diff --git a/sci-biology/embassy-cbstools/ChangeLog b/sci-biology/embassy-cbstools/ChangeLog index f4ed9e2c6..5588b77aa 100644 --- a/sci-biology/embassy-cbstools/ChangeLog +++ b/sci-biology/embassy-cbstools/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/ChangeLog,v 1.5 2010/01/15 22:44:35 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-cbstools-1.0.0-r2.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 19 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-cbstools-1.0.0-r2.ebuild, files/embassy-cbstools-1.0.0-r2.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest index 4bd6e4a83..095dd6797 100644 --- a/sci-biology/embassy-cbstools/Manifest +++ b/sci-biology/embassy-cbstools/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-cbstools-1.0.0-r2.patch 9656 RMD160 152ea616559e1d8377267ae6e5d8035e525e6e19 SHA1 8974cde7df8b76c99551760a93bd007211993986 SHA256 79a0b8fb574fe2d55bbcd8fca7ef2822c3c7e1e573565996c3656645f3b41845 DIST embassy-cbstools-1.0.0.tar.gz 389856 RMD160 019d278d482c621c1cecf75dac99493168a5de65 SHA1 c16abdf8c3d5b8a4e31fdcd20a556f35bdd671c6 SHA256 fd1c6a5f588d548791c98d2c31841705ac6971163a7f95345542932960080b5e -EBUILD embassy-cbstools-1.0.0-r2.ebuild 383 RMD160 dd1457128ca42fb18d433650407f1debe4db1c48 SHA1 2a17d9167f913f6c53c8e5516a7ecba656ff749d SHA256 ed41ac5a77816c74b339ce80d3cea9a8edea0489a81aadc95925f5c3d188ff36 -MISC ChangeLog 1522 RMD160 9f1b5c8d47838c8764bf60677f0ce1e790192307 SHA1 bece2c6805129a8d404aad819da50c0749bf8fec SHA256 18976a4da34e830371ca4740038094e538e6b6401f5042c6c195ee9df871bb2f +EBUILD embassy-cbstools-1.0.0-r2.ebuild 378 RMD160 279ff65e206230320b07b33d1cefe89341f2c152 SHA1 1dcee934c0e4b6009f0fba68622f7d3221808298 SHA256 a210592d8effa9a3c87000434bb7c083a2a697d5439b169bc9141464510504b5 +MISC ChangeLog 1675 RMD160 27a45eefb1bf4e2be1de18428b6dceb184ee5c01 SHA1 d214a352d09171307ca3dffdcf1f0e229e7daff2 SHA256 7d7467dc1a93ef7f0093ab1c988b47f7ddc720c344776783fe7b3dc9a463ecc0 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2EopUACgkQgAnW8HDreRYUtwCdFuOfcGcCw2mPkyk8q6w+PwiV -en8An2GIRROpmUwVBJKfBU7WYMPAKHo8 -=K1MY +iEYEAREIAAYFAk4GAa4ACgkQgAnW8HDreRaMxwCeLAXLPbDyAloWfdMalhLVUIaa +Lv0AoIyXED7qXOduh+ylvlzKOZNzty+m +=gIH2 -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r2.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r2.ebuild index 4642b30c7..78c619eab 100644 --- a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r2.ebuild +++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r2.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="applications from the CBS group" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-domainatrix/ChangeLog b/sci-biology/embassy-domainatrix/ChangeLog index 819cf4f6b..9377854f3 100644 --- a/sci-biology/embassy-domainatrix/ChangeLog +++ b/sci-biology/embassy-domainatrix/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.29 2010/01/01 21:48:13 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-domainatrix-0.1.0-r5.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 19 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-domainatrix-0.1.0-r5.ebuild, files/embassy-domainatrix-0.1.0-r5.patch: diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest index c29621bf6..a93e8fe43 100644 --- a/sci-biology/embassy-domainatrix/Manifest +++ b/sci-biology/embassy-domainatrix/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-domainatrix-0.1.0-r5.patch 9588 RMD160 51633db082a16f45274fb96371e6a384ce3a2fcf SHA1 afc886fc9f34cb71a66f2f09f3dd5b3ed3a448dc SHA256 818d81968350bae8d0492e4103ef7d4f41dd651321735c5d5dc04f4b35bfb8c4 DIST embassy-domainatrix-0.1.0.tar.gz 426218 RMD160 da6136665c4e951a6ca93362692fc299be2c05d2 SHA1 b7c9d14203fb1e9fff2fb7608c8edf87a346c133 SHA256 f6afe128cfb42dac7e734e979910d3bc7dd879ad1a677012f12f33572bd70989 -EBUILD embassy-domainatrix-0.1.0-r5.ebuild 383 RMD160 bc0f0c1b39241e06bd6a95d2859b0d2d4845bba3 SHA1 cbb23311c6b95338a5f9729e1ce4491406d19c62 SHA256 0ea008c9157a53bd78955754df81048975f887d1b06fac2b3e8c651046c68d06 -MISC ChangeLog 5357 RMD160 bc43bd64d16b91290adefb005d01ede07fd679fa SHA1 8ff260f7a1c872f443de4c2891d178875883a08a SHA256 6c12cccf3481e054a7aa36b84c96286c13ad236ba560481a3bf3a032eafaf691 +EBUILD embassy-domainatrix-0.1.0-r5.ebuild 378 RMD160 d8868e7626926173256b56b2fb638d454866b3e8 SHA1 b0a505534e84fd6c80b5b421987b577d71b7fbff SHA256 d01a3257f3af0d6b4fb47585634e3a188d7b7fe19f43c240e9c04f2c122a9895 +MISC ChangeLog 5513 RMD160 31a6d5ce03f35c9710701a5db981355b2c14e69f SHA1 2af219fff22fa4a1dd718adc4da9dd99335ce936 SHA256 af41911a9f76481c9b90f39bc24f3d4ca81a8893dde7093268a83944aacc66ed MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2EpJYACgkQgAnW8HDreRapUwCdHO/9eJaP+C+s1nkSG/k/Izsb -MS8AoIOouBCvYaN7202LceJGUXF2QP+P -=6j4K +iEYEAREIAAYFAk4GAcUACgkQgAnW8HDreRYImACgwoi57Dmd7C/3RU95IhaMwIYe +eAMAn00tr+YqkE7Ra8IluzEMxzuxo/6W +=15FX -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r5.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r5.ebuild index 9ba3995ed..8892a8061 100644 --- a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r5.ebuild +++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r5.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Protein domain analysis add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-domalign/ChangeLog b/sci-biology/embassy-domalign/ChangeLog index 5d5d4cdba..171f1a209 100644 --- a/sci-biology/embassy-domalign/ChangeLog +++ b/sci-biology/embassy-domalign/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.20 2010/01/01 21:51:36 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-domalign-0.1.0-r5.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 19 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-domalign-0.1.0-r5.ebuild, files/embassy-domalign-0.1.0-r5.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest index a4bbcaedf..10e364c4b 100644 --- a/sci-biology/embassy-domalign/Manifest +++ b/sci-biology/embassy-domalign/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-domalign-0.1.0-r5.patch 9586 RMD160 60830ec72285bdafd6e36a3667bf9c8f38aa4796 SHA1 89516869d482d4a3540bcca8fda28da063478b0a SHA256 551e01c1c91596e9f8454e6a53015edca265d0d22eec3ec6e675c6e49eeb2b87 DIST embassy-domalign-0.1.0.tar.gz 441025 RMD160 ba356997be2baa4c526740f52f65d4bc016461ca SHA1 5260a40297f43633e68e1577325275b0a196c60a SHA256 345db267970cb9a8c9c41f53a5063185d36d13bf61dcc8941569d9bb2d18c567 -EBUILD embassy-domalign-0.1.0-r5.ebuild 378 RMD160 d295d835790077174b267bcd375ea18558704e94 SHA1 624c3144ed9ac1020e2ddd793431a26a9d707d7f SHA256 9d53dc57f4025cd13a56ad835bd48efaa5f36af6392454b83723ecd8ff05b684 -MISC ChangeLog 3495 RMD160 69c9e2bf25d7510826059ea6eb02e411259940ec SHA1 d8c9eff4cf959d5e15806ae97bffb5d83dee4868 SHA256 1451fbc4949551cbaae77e1170b64ac12ad34227c94a4a777b794b056c60d72a +EBUILD embassy-domalign-0.1.0-r5.ebuild 373 RMD160 5c7e9a075f2b32e7c7ccdec112354742dcfa7a4b SHA1 43eafab9510280266add0d43cced378049c697dc SHA256 e44e64c7c79ba070270d9237a7a2d39d854e2d248c4fd7ab5486bbd319523518 +MISC ChangeLog 3648 RMD160 0aff0ada60e9ed7285f83ab5707f417bb890abef SHA1 13492eae0cbac60e10675c866fe0acc663a0e76c SHA256 3e704961800746684e8c2407b04a7155ad79523850ff0030ea86e47cb4d94b6e MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2Ep5gACgkQgAnW8HDreRY9/wCgyI/ZyvRYyUmTG/brxelHWhRM -FwUAoJE4IT9Yxj8XTgKYZ5RhIekpoRPT -=3Dze +iEYEAREIAAYFAk4GAdgACgkQgAnW8HDreRafSwCfSiAnnJawmlZ2G25XOHQzl0ZF +ThAAnjsXPG3PeC6qzPWdorU18vwM2IkC +=UGgf -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r5.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r5.ebuild index b1d116394..4751d1fd8 100644 --- a/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r5.ebuild +++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r5.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Protein domain alignment add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-domsearch/ChangeLog b/sci-biology/embassy-domsearch/ChangeLog index 5a4cb2995..e206e653e 100644 --- a/sci-biology/embassy-domsearch/ChangeLog +++ b/sci-biology/embassy-domsearch/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/ChangeLog,v 1.19 2010/01/01 21:53:24 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-domsearch-0.1.0-r5.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 19 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-domsearch-0.1.0-r5.ebuild, files/embassy-domsearch-0.1.0-r5.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest index 149bc5139..2fa7e0c50 100644 --- a/sci-biology/embassy-domsearch/Manifest +++ b/sci-biology/embassy-domsearch/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-domsearch-0.1.0-r5.patch 9557 RMD160 b4af6f43b44fd408e867034309c21a1fd847b3f4 SHA1 e4a20f94557dcda2ef3533e60c7c4b7b2e1c97df SHA256 4c69c017bc435c3aaedee62238d643d93c749344f1a0c6d3776ff890cb3c0afe DIST embassy-domsearch-0.1.0.tar.gz 452787 RMD160 3a3b58bd700e1b4cb4ddf78ca944f9fff12262df SHA1 2f85959b2fe7314372d23b5f993af2a174a85997 SHA256 8f64eae467246389306196847f3428e848628a0b6e051d54bcf4659595f4aa75 -EBUILD embassy-domsearch-0.1.0-r5.ebuild 377 RMD160 28a9f1b73e72d6c6a9e92586bb070af2b04c5e10 SHA1 b090777e23aa2121dc339581fa6cd6ac7f2c1433 SHA256 d4c09ce57950316c31825f4bdb0a4d27192bbe74cd11ab2e14f3e57019a7c60d -MISC ChangeLog 3432 RMD160 a279f1c1029b4993c8834d34930576c61848a3a2 SHA1 a4aba7565e390d5508c94b30c9360522fcbc7cc7 SHA256 943be6cb1a1dd33a7b16ccf736e4013c73299c04530dc2287235f980d8517ff0 +EBUILD embassy-domsearch-0.1.0-r5.ebuild 372 RMD160 32b82d2df1c34e131172251b985b6dd455d51951 SHA1 1e1ec3fa74cf64b65ad0e29fbe0ba9690c4e7f56 SHA256 0cb78f65aa00dd4a6160647b4c662e83b2fa8c5916b1ddd99f2b6b492fbcfcc1 +MISC ChangeLog 3586 RMD160 c19f6c3613d5b6b62538370346f4fadb48ae9b19 SHA1 27e8ba66d9601062b45ee52412332546c2ebe9ad SHA256 55035e184a7bacaf580222538854d055e58b3885664b56e876c926573197ad32 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2FBfgACgkQgAnW8HDreRYKMwCfcj7s7+X9tk/vW9BydpnDyM27 -Hb8AnRLbC9ouyjwoTMeaOeN5ru6BJfLk -=Tx4K +iEYEAREIAAYFAk4GAh0ACgkQgAnW8HDreRb/1ACfUmPO6RawkId8RnI8aKqeGmr9 +huwAn2pionTN7GsFtH7XUJGUm388DkMq +=z4Ki -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r5.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r5.ebuild index 3deb535d7..56e828ce5 100644 --- a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r5.ebuild +++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r5.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Protein domain search add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-emnu/ChangeLog b/sci-biology/embassy-emnu/ChangeLog index 6334ae1bc..94f00fd9f 100644 --- a/sci-biology/embassy-emnu/ChangeLog +++ b/sci-biology/embassy-emnu/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.29 2010/01/01 21:55:20 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-emnu-1.05-r7.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-emnu-1.05-r7.ebuild, files/embassy-emnu-1.05-r7.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest index 176a2067b..5a09c1d7b 100644 --- a/sci-biology/embassy-emnu/Manifest +++ b/sci-biology/embassy-emnu/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-emnu-1.05-r7.patch 10038 RMD160 4cbbe9c049346f8dddcbb0e2663a5a6bcec7eb85 SHA1 9c5970fac281da1bcd301f69bb1eda3f0e558b46 SHA256 ee578534c253c43078a03b7018b686157e9ad695dae654549a66348a46a12db7 DIST embassy-emnu-1.05.tar.gz 373798 RMD160 9844ed22591a7ee857920f2fd4eee5626de39ba6 SHA1 8c8781cf48a8d95aacc452d1edf5e77144a34987 SHA256 70568ed4f68c174706f17df27cfb3db05c9e0e0d3cf42029ea4fe96328588ca6 -EBUILD embassy-emnu-1.05-r7.ebuild 469 RMD160 311fc0e38196ab39662202405df455ec5b35849a SHA1 72866f2913cbbe147748902ca4dff070ecba83fc SHA256 69e268026d4b3efc10ccd6e5dac655338227e22f214cd85a92b3733a3130ff73 -MISC ChangeLog 4756 RMD160 f0db438642e887a45f7299c2f54efc7aaf13ba16 SHA1 b01fe739268f8f0882459afec6c6d54e3ef49803 SHA256 b409401952b3b7c483e7ed704c4bb13e639e7b869f2da6967df5bb8b7b81a574 +EBUILD embassy-emnu-1.05-r7.ebuild 464 RMD160 840d4d0699b90c315537e9262d1e8eb1739fe11a SHA1 aac132dd4babd270bd625931053259bdd70011cb SHA256 7bb1e373c7705f203e014dfd046081a94cd411e1da9b6c75eb0ab9f80c24caf1 +MISC ChangeLog 4902 RMD160 42e8d7ff1bee5eb0b5d22a1dacf08f4477cc350f SHA1 0bcdb16f557a205d33cfe64507a97ba630641cce SHA256 5272ed4038aa5d624fe95ebb88a702c96b15ec842c6cadb509070497df81de5f MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F4lQACgkQgAnW8HDreRa/MgCgi09tcMG3fsvH50XVyDAoMGRb -p2wAoLOl5ylsIuxOCUTIkdeCMGeCnRBk -=G5AP +iEYEAREIAAYFAk4GAj4ACgkQgAnW8HDreRZBbACguK+C+YhKqKyR5oGGy73cXRIf +xhgAoJAaFZvCpigtqzCjpEbd/yuVHbU6 +=R9Ct -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05-r7.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05-r7.ebuild index 0bf55dc39..f4538cdf2 100644 --- a/sci-biology/embassy-emnu/embassy-emnu-1.05-r7.ebuild +++ b/sci-biology/embassy-emnu/embassy-emnu-1.05-r7.ebuild @@ -9,7 +9,7 @@ EBO_EXTRA_ECONF="$(use_with ncurses curses)" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" IUSE+=" ncurses" RDEPEND+=" ncurses? ( sys-libs/ncurses )" diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog index 0e7dd091e..5629297ac 100644 --- a/sci-biology/embassy-esim4/ChangeLog +++ b/sci-biology/embassy-esim4/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.28 2010/01/01 21:58:14 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-esim4-1.0.0-r7.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-esim4-1.0.0-r7.ebuild, files/embassy-esim4-1.0.0-r7.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest index 7632db279..65a511896 100644 --- a/sci-biology/embassy-esim4/Manifest +++ b/sci-biology/embassy-esim4/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-esim4-1.0.0-r7.patch 9399 RMD160 34b108e0ad6ee283ff8c5752fce3225ffbf16091 SHA1 d104d8d4c84ab4ac80e28df25ce8310c1ee04d33 SHA256 42277736c23d9bb66ef7033447b5509f8313293727661acc17cd53f4fef38ece DIST embassy-esim4-1.0.0.tar.gz 415096 RMD160 9043eaaed74aab481b1a2e690a06932211421003 SHA1 76a2ea556a23241d94e17fdfdcc05bfa17dd8bfb SHA256 7abd69516d6e12ae58f568662db3bfa19bb3a15c03413db61ecda3f013b144f5 -EBUILD embassy-esim4-1.0.0-r7.ebuild 373 RMD160 a4b8e7a9425af8f41894f024b581529a9e65d76c SHA1 7844efd50e9002306cd98e8c0040f89a349aef3e SHA256 967f831aeac261c52c9bb7e217b32e64423180b419d115e04bd743da4f57dfd3 -MISC ChangeLog 4746 RMD160 a81634edd5ce8167ff9dd4748157359cf36ba7f6 SHA1 00a37eae5e7289b15a55629d70442c549bcc94d6 SHA256 cbc4902a8864403323771479866ceb373d61edf8d2f112a1139dae37a5e57c20 +EBUILD embassy-esim4-1.0.0-r7.ebuild 368 RMD160 69787846d2661b4267346554a6d65335f32245c8 SHA1 2140b8b390d30e8b08803e876b5f623a89a3d308 SHA256 4ca9027576eeb78a49cc6ce8c35ca5f8ba5caaf925bd82f6cdf39ee13568363e +MISC ChangeLog 4894 RMD160 6fc8d939262883ed53ee63f506afffa89eaa0773 SHA1 ea898c2ee001a0ce17b43645916839ea4aa0a241 SHA256 89674c146a18b749f9a0dd0ea7b6d665c89daf03cada834e981e9629b096cb30 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F43oACgkQgAnW8HDreRYTyQCghtcrpiPBAeGNUfKJwSvSfxV9 -GAEAoIMuWbUohsePxwyN2TsxrAVpNkLJ -=INXE +iEYEAREIAAYFAk4GAlMACgkQgAnW8HDreRY9pgCfQOorfDkF+7V+EqLAcTcJ2/9v +WAIAn2blUNlwv3Zioel2YOMVxpi6ZV9q +=w9ca -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild index 3662f65d5..eba377747 100644 --- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-hmmer/ChangeLog b/sci-biology/embassy-hmmer/ChangeLog index 3979e4956..a24cbb09f 100644 --- a/sci-biology/embassy-hmmer/ChangeLog +++ b/sci-biology/embassy-hmmer/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.30 2010/01/01 22:00:05 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-hmmer-2.3.2-r4.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-hmmer-2.3.2-r4.ebuild, files/embassy-hmmer-2.3.2-r4.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest index 2527c1aa5..0382f8de2 100644 --- a/sci-biology/embassy-hmmer/Manifest +++ b/sci-biology/embassy-hmmer/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-hmmer-2.3.2-r4.patch 9564 RMD160 01329277e61caee71a6ee2a2cce0645c87e62883 SHA1 da160acedea05872176894c3a95388cbaa66582c SHA256 373996ef3b99630663b0e414386f540548ac643be980fc724d87c0efdd7529d6 DIST embassy-hmmer-2.3.2.tar.gz 569581 RMD160 1c2fdbe0b2aa4e5d3de45d9177c9ae9833acc352 SHA1 0ec9d34dc2a137b5c1b21102bebbd5c28354ad37 SHA256 d4c5ec18f9bdd049be7de138d4c560b4bcb39d9a239f791c6713c0857ea29c89 -EBUILD embassy-hmmer-2.3.2-r4.ebuild 438 RMD160 687dc9e50b82233fa54fe00a201b669c4a9ce039 SHA1 1dce6dec2ad24058158a7ba25e239f64b3bae28a SHA256 4a4e3517749e22a9391a522e4c179dc267d3f8ce312af968a91be8d0c5bbb441 -MISC ChangeLog 5028 RMD160 e55d0237d1181f01a505a27f65034e05bdd65e43 SHA1 1a6f1389f199afdf4741d26e923c940340944b33 SHA256 5dad8124424a0617675d57285fc2a389894da746fab85dc4a2f57b06da465912 +EBUILD embassy-hmmer-2.3.2-r4.ebuild 433 RMD160 3d098505f659369304d1dce8dca1475e5b195659 SHA1 307187135386efbe5bd3c8616f399bf5d87dbaa6 SHA256 ad44710230173dc05223ebc54caf3570ed4eb0e453510d8243594e4310466c8e +MISC ChangeLog 5176 RMD160 e046cd5b3cfdd827839187a496869161edb50dfb SHA1 4622688dcdcaec5b716c6144b87201b60aa1d147 SHA256 86ccd8f23cf30d2bb34cd694b2042f25f5753cfc3ae77ddf1ffaa6103dc4e557 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F4+4ACgkQgAnW8HDreRabeACglncH/YihlwLPOuQj9WyqYb4r -/hUAniEEoL3cwAnF4uAtYE+Vt9itufGQ -=fuCH +iEYEAREIAAYFAk4GApMACgkQgAnW8HDreRauAQCeJHSZh6ySOVS0aq8FMjVfZhM9 +8B0An1Evv0Em8C8XgwOw8CgBBJ5ggSUZ +=x0WC -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild index 6bbdf10e9..21de3d660 100644 --- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild +++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild @@ -8,6 +8,6 @@ EBO_DESCRIPTION="wrappers for HMMER - Biological sequence analysis with profile inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" RDEPEND+=" ~sci-biology/hmmer-${PV}" diff --git a/sci-biology/embassy-iprscan/ChangeLog b/sci-biology/embassy-iprscan/ChangeLog index 5a00be37c..4bf1c83ff 100644 --- a/sci-biology/embassy-iprscan/ChangeLog +++ b/sci-biology/embassy-iprscan/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.5 2010/01/15 22:45:28 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-iprscan-4.3.1-r2.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-iprscan-4.3.1-r2.ebuild, files/embassy-iprscan-4.3.1-r2.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest index 16e26b40f..d2399b2b3 100644 --- a/sci-biology/embassy-iprscan/Manifest +++ b/sci-biology/embassy-iprscan/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-iprscan-4.3.1-r2.patch 9581 RMD160 18a520e521ab8b71cf00085bcb98c4ecb7831da0 SHA1 91b9390317f08f92106c6d22b1d0928ff9d9f3f4 SHA256 b0a36e2aeaef63533b51ef04ca5837fbeb21a4a98b7918495ee9915d2a1012a7 DIST embassy-iprscan-4.3.1.tar.gz 350791 RMD160 d92db63278c489cab73e47634021f057437b89d7 SHA1 e69e55d296b518bab97de21c4dcc10e113dc6ada SHA256 07b1fcfba00af74387312ceaadd890e4ad1af0fdeba4055c88d3d02dc64ee9ca -EBUILD embassy-iprscan-4.3.1-r2.ebuild 393 RMD160 c76fa1ffee5ba0af4fc224ebce59340dafde43b6 SHA1 9e2df1f415d065b5c386f8cc6adbbc99cff5848a SHA256 74a7a65ddc2593788ae1ba53e4f741bfce82a8f1da6d0927572f64b9c4293447 -MISC ChangeLog 1290 RMD160 aca04cd3cd6daee9873104a7bd7d96f967af71cb SHA1 0de1c10fc6ef68b0fc7b24bc987ca7d66de299c1 SHA256 545403fd49e98854da59f8ce52155a80da3a6d9d3989b752618e3b0aae5fd665 +EBUILD embassy-iprscan-4.3.1-r2.ebuild 388 RMD160 326aefc3b8b4b99bdfd27b5f21f42fc53b2f495c SHA1 71879e420064ee8e254e69f12b2ba223cb396de4 SHA256 a30a1ebad4eda4c68ae5bbb6ef31efd715907324dde38581e2437b1965cdde14 +MISC ChangeLog 1440 RMD160 95d8c31977f5018f02daf493896ece827ccc26e2 SHA1 2ec5225cb22266d3061859f750e7ad4fa28981e8 SHA256 30a2f848abb8d7aae9984412ba0d4c38dc62e5d10cb13cac0c862fe8d2017a7c MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F9D0ACgkQgAnW8HDreRbzsgCgw1Gt3VHE8mbtLmpw8744iUEr -sNkAnjbD1vxqf+kaT8vAoutaDeso0POG -=+azL +iEYEAREIAAYFAk4GArkACgkQgAnW8HDreRbNmACfcZdkfUT73Zf7+HFe4uzWpkCb +ejQAn1QO0sjxSlCm9UnQYV/+0dM4uEFa +=pE3G -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild index c69c12518..90b800037 100644 --- a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild +++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="InterProScan motif detection add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-memenew/ChangeLog b/sci-biology/embassy-memenew/ChangeLog index ed3b3d9a7..aabfabe81 100644 --- a/sci-biology/embassy-memenew/ChangeLog +++ b/sci-biology/embassy-memenew/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-memenew/ChangeLog,v 1.11 2010/01/01 22:03:00 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-memenew-4.0.0-r1.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-memenew-4.0.0-r1.ebuild, files/embassy-memenew-4.0.0-r1.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-memenew/Manifest b/sci-biology/embassy-memenew/Manifest index 03273a037..ee13424ad 100644 --- a/sci-biology/embassy-memenew/Manifest +++ b/sci-biology/embassy-memenew/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-memenew-4.0.0-r1.patch 9463 RMD160 20ff4a767e97e953877f9d37f99dee1eac9d45cc SHA1 df9e617534516f5718cbde59e410335949a18925 SHA256 1146c80e4ca91ef9c245b8f7a40be18b399e7c3d84a5cc8573c930832b4083ab DIST embassy-memenew-4.0.0.tar.gz 513418 RMD160 7072d182479a726e568b0bc2a4c7757ed1c6c087 SHA1 d382f39d1302f1b0799d5b6cb02cd9cfbecee972 SHA256 2192d33b5ee1147742f51416b0504812dfeb13b3b8ec0bfb62fd729e703a19c3 -EBUILD embassy-memenew-4.0.0-r1.ebuild 374 RMD160 62df7bc95f5c641cbed4c4974204850d0d50b8e4 SHA1 0e92818381e83cabf6c1aee7a6ce03c5c6e054e3 SHA256 f866cb71fff542644feef2ee276178cc8f6525087d6e34c92734d74a5e48cec2 -MISC ChangeLog 2082 RMD160 e72ab8d451eef69164411a24d3f9c038f710b3bf SHA1 bb0e0adb92139641df2657519c3d98267ae1256b SHA256 475b7025ccf640ed4d55647657ac28d8f92d55feb87266b6ea9a042d5cd8cdad +EBUILD embassy-memenew-4.0.0-r1.ebuild 369 RMD160 d54ebb68ddb2c73b8d79f11a9975e17a02876aeb SHA1 9638bb3bd6d16f48c8347581691a1efd69b7e2da SHA256 c437d23c97bca6ed61d02a9694d23c3e96d39f2701b50efcd4a75f2832f1e1fe +MISC ChangeLog 2232 RMD160 600b4b0585825d38dd1d8f1ee7650e59a200b657 SHA1 ac1be46f939ecd1b3df9e399226ca880779815eb SHA256 a95ade39fbda61bdcf24ba3736e80d95b053cda4bd9787cb8c8adc76b6ca9446 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F9aEACgkQgAnW8HDreRYC7QCeJGvbS5ghAizYSzH0sX4BqCDb -opgAn2ypusu9HZWVtMlibmd04yvcdIwV -=wUKc +iEYEAREIAAYFAk4GAt4ACgkQgAnW8HDreRYIzQCeMASsMM/k4TrLsaYIGCaIsc7O +lhEAoNMHBdobQy5oiLVJCYMR1gwU8qQF +=CJlw -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.ebuild b/sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.ebuild index 1bb7a8f21..caa114b63 100644 --- a/sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.ebuild +++ b/sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="MEME - Multiple Em for Motif Elicitation" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-mira/ChangeLog b/sci-biology/embassy-mira/ChangeLog index 3376be216..18606d7b2 100644 --- a/sci-biology/embassy-mira/ChangeLog +++ b/sci-biology/embassy-mira/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mira/ChangeLog,v 1.5 2010/01/15 22:46:25 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-mira-2.8.2-r2.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-mira-2.8.2-r2.ebuild, files/embassy-mira-2.8.2-r2.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-mira/Manifest b/sci-biology/embassy-mira/Manifest index 8313029b6..a27a55b0d 100644 --- a/sci-biology/embassy-mira/Manifest +++ b/sci-biology/embassy-mira/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-mira-2.8.2-r2.patch 9423 RMD160 b9365ecedfc60214dd28e30ea18fe26c425ae011 SHA1 590e8e0c693a0323e9817bd4542f442a01047b63 SHA256 246850c658980eb99ace5525d0f1ebcefd78b1a4f0f40d7b1c44d14502b50f57 DIST embassy-mira-2.8.2.tar.gz 823636 RMD160 2df2b3102671bc74db93602d7c8ecaaf4f83435a SHA1 a87f51f1ad31d419b634a9e04e985a42f7cae4c2 SHA256 82a57cd526a4348a7456947e5ffc225fc42684bc21b5ec6996d99100f86d31ec -EBUILD embassy-mira-2.8.2-r2.ebuild 377 RMD160 ed50a51cc36d286adfb69c80240ad66d3a0977d0 SHA1 98fe62b9e2e650b7cf22d18e8aaab8fcfdae7b7f SHA256 ca7df07746c0120871cd3622384c257088c1ef5325b0d8cb8375e43dbdbe3de4 -MISC ChangeLog 1456 RMD160 1fc5bc800ea82e7422fa361221d93e80e9166859 SHA1 ba885827be8d691446989cdb5336d24d3e6c24fa SHA256 d47c1e2717426c48c3aea633325a675fd0fa7b91a01a673096aef516fc912e29 +EBUILD embassy-mira-2.8.2-r2.ebuild 372 RMD160 eb6f2b4c0e8cbb2e55af13abcf1e15937b87628f SHA1 685e20d4db697420a8b543e0447daabde5b5c8d1 SHA256 ba38a67f3fb106e571e65a0daf878034acc8daba7e51273f90a1230ac4995339 +MISC ChangeLog 1603 RMD160 0999a452469a08de19c034de11a26dd55116dbb1 SHA1 aee5f16ea3bacda045fc745dac963af12ccea19c SHA256 6c14bde979e50dcc293a643b1bfb6ee6d1ff8016c035fb8cc62091b7e136e1d2 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F9n0ACgkQgAnW8HDreRZb0gCgktn50/6fkfzIDoxuuZAfWTnj -6FQAn092q1Xz09WZ9R5S2MfQ8BY7JcOX -=NXPa +iEYEAREIAAYFAk4GAvAACgkQgAnW8HDreRbOPQCgpjSxLn/J5uk2m/FHLNBFosmX +79sAoLbRJN9H7GPg8Hr1S1ocfz9vWmRR +=ji/h -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-mira/embassy-mira-2.8.2-r2.ebuild b/sci-biology/embassy-mira/embassy-mira-2.8.2-r2.ebuild index 30fb46cb3..2ed8a9fe9 100644 --- a/sci-biology/embassy-mira/embassy-mira-2.8.2-r2.ebuild +++ b/sci-biology/embassy-mira/embassy-mira-2.8.2-r2.ebuild @@ -8,4 +8,4 @@ EBOV_DESCRIPTION="Fragment assembly add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog index 986307764..0d60fafd8 100644 --- a/sci-biology/embassy-mse/ChangeLog +++ b/sci-biology/embassy-mse/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.35 2010/01/01 22:05:28 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.ebuild, files/embassy-mse-3.0.0.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest index ae991627e..c47861b82 100644 --- a/sci-biology/embassy-mse/Manifest +++ b/sci-biology/embassy-mse/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-mse-3.0.0.patch 10900 RMD160 171a943e032522e6de380e699c9a917c634d7fc7 SHA1 28d39621f0b0924bf4c5982a5b50376453d6410f SHA256 1d900f8fb9d6d45f160a33faeb41ba5dc10413c5034d0ee0dcb020a5414bb5ce DIST embassy-mse-3.0.0.tar.gz 435315 RMD160 9e94bdc1cbff5b684a6d7f33a7a95de33c1b910e SHA1 bae84ef0154f444037653df322fb605d013dca0c SHA256 f3bb205b197d4cc4ad7d6ee8e3696eb59d84a8b60a8369d4a645871d0c9619c3 -EBUILD embassy-mse-3.0.0.ebuild 547 RMD160 5949b0db7f8addc9dafca3b3f08b5eda51824e18 SHA1 da9045e9c1c5cf5a0d5e805613c2a0243cb99bc8 SHA256 236230400b07988f6a06de2c73e4913612fc6934339120a79d9fad1cf18ee4b9 -MISC ChangeLog 5598 RMD160 cd7c8a60b5413e0bbb0b12a2f80b8f70082ea099 SHA1 f4076a406c8e947ce68f53a751b5d3dede0da448 SHA256 b27312004ed0af85916da8c9708b3174da48f0a0055d23c493b533f423477932 +EBUILD embassy-mse-3.0.0.ebuild 542 RMD160 f519ac8277e5100da25dae0d36786977f67768f4 SHA1 78d82b15444c953b6ed3c75f612bf8a1dde3c82b SHA256 93bd99eecc5d4b1d9f8032067e664785217729bc107bbc6d37a80bfd421d0161 +MISC ChangeLog 5741 RMD160 a71180e4544aa4d85fbecedd927b905b0aeb9070 SHA1 90c869530f6fcec35ec1359d9b4894b1b1699aaa SHA256 8bd4a2e45a88ef282c2975ef1b8ba0f94ab9700127865e770d2c05ceda041f90 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F+L4ACgkQgAnW8HDreRYFjQCdHmwyYJP/PHR0fJ1l1YZvvsrh -gtEAn3p6LUF1syBnnokCmBkqPPU0HYiy -=BiI2 +iEYEAREIAAYFAk4GAwQACgkQgAnW8HDreRYgEACgyKU8ESvF1rlyKi0Gk4EdwgYW +yOUAn3i6RJmUPE/3Pzir3sgbn4zRsMn/ +=eGWh -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild index dd6a473f0..e8bf5541f 100644 --- a/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild +++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild @@ -8,7 +8,7 @@ EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" IUSE+=" ncurses" diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog index 048d0bd1f..4053bf0b3 100644 --- a/sci-biology/embassy-phylipnew/ChangeLog +++ b/sci-biology/embassy-phylipnew/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.12 2010/01/01 22:02:06 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-phylipnew-3.69.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-phylipnew-3.69.ebuild, files/embassy-phylipnew-3.69.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest index 12722791a..1dd10e35e 100644 --- a/sci-biology/embassy-phylipnew/Manifest +++ b/sci-biology/embassy-phylipnew/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-phylipnew-3.69.patch 9615 RMD160 3933c0479d9bee7b725c7783e652334c1d634d9b SHA1 a8ad42aea033cc3949972a7a5299e551617a9587 SHA256 8b918547f1916c4c8d9127a349714388cfe923c0fa5f65994011c44246bff4d0 DIST embassy-phylipnew-3.69.tar.gz 1667760 RMD160 8cb425f8e7af99d0081d2014403de74ad8e84feb SHA1 65e265190873b14c7449f6d53cc017ea90b612b6 SHA256 2e74ce4f70ad5421ea81e84c199a08bfb4a236e2cf2769be4f309c4badd1302b -EBUILD embassy-phylipnew-3.69.ebuild 390 RMD160 f234e4a08a8ee873f1fca5c2a71d8a685c04959c SHA1 673343e393d6eac17de1cad71184290030cf8b81 SHA256 4ed839a310d8d029858e67aab6aa23ba9d9f9a8756e6881011c834250ec209e8 -MISC ChangeLog 2376 RMD160 e25cdc29505bb478e7b20f76559a5674e481fee1 SHA1 9f73f185f2c2aabcd5208ab919bbdb8f2d51598e SHA256 befa96d493e676d006232875c710abccc88e7a55f958a5dea886e89cd81818f8 +EBUILD embassy-phylipnew-3.69.ebuild 385 RMD160 99fe0e4c52cf4c2aa52f54bace2e3a41b1ed2172 SHA1 85471ce1481cd41592b925833e87eb1055b7b018 SHA256 1c75892670b87492e53e6b3004cebefb21c4a2b52d5c0be0995755cb9ba29542 +MISC ChangeLog 2524 RMD160 45961c99f77705ac0af8d8833ba2f23c7d46feb2 SHA1 e50c3ba423e3675086d63056833150bdb1a44dba SHA256 888f40b1dc771f9e4d0bd7fae9da8e2a538454ca13ef011044f7c963d2e02bf9 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F+joACgkQgAnW8HDreRaRGgCfd3+F9IEe7f120C+q0EmPVY43 -hwAAoKzU7TnMVj8gw5X8XHYVayXX/xmD -=kuSG +iEYEAREIAAYFAk4GAyUACgkQgAnW8HDreRb+9wCeMWpXq2DOLHuGXsCEwLIHyEIV +8eUAoK4HYQ9U/KiJkhb06FIMRBh3cgmF +=ZZ/w -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild index 6767ae7bf..34691a5ef 100644 --- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild @@ -10,4 +10,4 @@ inherit emboss LICENSE+=" freedist" -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-signature/ChangeLog b/sci-biology/embassy-signature/ChangeLog index b541cb909..9bfed99ea 100644 --- a/sci-biology/embassy-signature/ChangeLog +++ b/sci-biology/embassy-signature/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/ChangeLog,v 1.19 2010/01/01 21:59:44 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-signature-0.1.0-r5.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-signature-0.1.0-r5.ebuild, files/embassy-signature-0.1.0-r5.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest index aee7759ba..1cbf4bde6 100644 --- a/sci-biology/embassy-signature/Manifest +++ b/sci-biology/embassy-signature/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-signature-0.1.0-r5.patch 9515 RMD160 d49cc11f72e7538feeb2326846a30cc902c789d8 SHA1 a208e5469d61c77a10b2e729e729782ba08cd97b SHA256 2a6d31d71cc2b3206e88fd21ff69714d2fa97695285f69a6033c9416eb7da4cf DIST embassy-signature-0.1.0.tar.gz 571008 RMD160 d69cbdeb8461d4f5596546dad9d1b7afc14df672 SHA1 bd9834fe0aeb7b6f6fd1a46550adc6be06d74566 SHA256 feaec1c3d3a8a2b98bb691137aa5ac099f7cef6579150fdb1429fcfc5db01024 -EBUILD embassy-signature-0.1.0-r5.ebuild 373 RMD160 239bf7f85b665e3e673768af1a93241e2786ec5c SHA1 3b23acc995d315a71192ec99512112a4f6067759 SHA256 14410def1ecf2e1c48dfaf0fd7124f9af64555c62f216a8e551e7eda67e8084f -MISC ChangeLog 3461 RMD160 ac4a7335f4d3e829ae7a0873dc6ceb191c53bfbc SHA1 f7066903c1ff313981f088665d7c602df5848f9a SHA256 e5ee2628e7fc82f59374369d9eb72090f555e6181345456d5e6cb6dbd13beb1c +EBUILD embassy-signature-0.1.0-r5.ebuild 368 RMD160 d189d471bf91102c82e851c88d7958258513fe9d SHA1 4f9cb575a53614c50eb02f2b5f6e31d09562010a SHA256 9bb72ba36fa13d2bdd427afbcc875f399f93f498c13da7209fe6cea3bf2235c4 +MISC ChangeLog 3615 RMD160 a7579b01318721b2d095af930f710436562bc49f SHA1 4fc57225fca7d622545a6851c844dd4989adc22c SHA256 be033c1257bb9284fd768df472301b9ffa51983c36ea9f8ab48aa3970bd4db78 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F+8oACgkQgAnW8HDreRbvSwCfXEik12rFDZ7o2XrbWi/44jCA -eMIAn0sBel1PQpltnAH+iwwgh+uZx0VD -=Ec7L +iEYEAREIAAYFAk4GA18ACgkQgAnW8HDreRZggACgrFL9oLCRLQplQkq7dZiG16oS +XekAoI9u0kMvGam+ETBTM/StG0qhj9ly +=NIgo -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.0-r5.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.0-r5.ebuild index de1c6abcf..77aefb434 100644 --- a/sci-biology/embassy-signature/embassy-signature-0.1.0-r5.ebuild +++ b/sci-biology/embassy-signature/embassy-signature-0.1.0-r5.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Protein signature add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-structure/ChangeLog b/sci-biology/embassy-structure/ChangeLog index 4fe54066c..7afd64dc4 100644 --- a/sci-biology/embassy-structure/ChangeLog +++ b/sci-biology/embassy-structure/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.19 2010/01/01 21:57:51 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-structure-0.1.0-r5.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-structure-0.1.0-r5.ebuild, files/embassy-structure-0.1.0-r5.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest index db9211988..4da8e216c 100644 --- a/sci-biology/embassy-structure/Manifest +++ b/sci-biology/embassy-structure/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-structure-0.1.0-r5.patch 9522 RMD160 e89d1f49221585e6e25f60aa625ca50727c61da4 SHA1 bf3cc5df2e00f76acfd38fdb555330022b87098f SHA256 106dec75227d9708ec61c0ef9ed5d453e0b1b22dbe3df8443f1c3c27961a6a88 DIST embassy-structure-0.1.0.tar.gz 531604 RMD160 33d351f0b107637d59c1623a9cbd6e97e1f3f17a SHA1 ec19fd6c69e7ed3be894c588fecdd77b98bcb0b8 SHA256 df2dc789544e61f695438e3117921ecef78739963169672e80c3394659720afa -EBUILD embassy-structure-0.1.0-r5.ebuild 373 RMD160 739d25d4a3e8cda97ace59a335a03e72e426b50f SHA1 dfe56ad9090bde5cac1cb06ebfd011236c631845 SHA256 7823fb3b96a2cbf4d55a7061a13e07c187a941640d155ba36d19012e02d3b264 -MISC ChangeLog 3461 RMD160 8515547b3d7b6a2c69387a7f85ecd7120b3911ed SHA1 5057daf1ba8c69a89a55d1d8eb9863373f0d7052 SHA256 2317c7e53ff660fcc4edaf3e8813c9a61e97cf1d952d8fd87492175fdb9396e9 +EBUILD embassy-structure-0.1.0-r5.ebuild 368 RMD160 82400a4204df48c7626351eb58e4f7fd649d123e SHA1 31d3ea026687f378534138b5bd2937671d5a9a1f SHA256 8a8f9eea06d4c795ee65be4bf19224bbdf05dcff6a9410dea2e614d7649f9c3a +MISC ChangeLog 3615 RMD160 20a720b90a2f6f12cb1c2adc90427d06bfe3c8cc SHA1 ee8c349ec0dce53279316fe40511097f2fedcd92 SHA256 99fe3e9e66b374ae2916a5ea372caedaba92bf698efa217eec78d78b577e37ee MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F/DIACgkQgAnW8HDreRYFpACfciQyXDUM2jBuWVCNX+J8vcSz -cjsAoMFM5gfZF/jx7dJBxqHA9weRfqa4 -=6ipH +iEYEAREIAAYFAk4GA3oACgkQgAnW8HDreRZnyQCfTSTEatJJCkBw8KhZVkeQfbAm +AjsAoLlJFz161oJYtulYWE3yqZfhb6Ql +=Z80J -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.0-r5.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.0-r5.ebuild index 4af39271b..ac6658955 100644 --- a/sci-biology/embassy-structure/embassy-structure-0.1.0-r5.ebuild +++ b/sci-biology/embassy-structure/embassy-structure-0.1.0-r5.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Protein structure add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-topo/ChangeLog b/sci-biology/embassy-topo/ChangeLog index bc25e4ebd..5ad2bc721 100644 --- a/sci-biology/embassy-topo/ChangeLog +++ b/sci-biology/embassy-topo/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.29 2010/01/01 21:54:52 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-topo-2.0.0.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-topo-2.0.0.ebuild, files/embassy-topo-2.0.0.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest index cd50c3164..6bce89048 100644 --- a/sci-biology/embassy-topo/Manifest +++ b/sci-biology/embassy-topo/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-topo-2.0.0.patch 9416 RMD160 fdaed3604e8a8d041a189291067332358ed9d349 SHA1 26768d5f14221a40e315b2ed99bc2cd73bc219b2 SHA256 d6c7b9bfd31487b14a608f758e38698a2ace3cad57b8c321fd8d69c1f5d75672 DIST embassy-topo-2.0.0.tar.gz 386287 RMD160 d25cdde9ea76253c088754f1633389ce87e79866 SHA1 c6373211ed36866497ad54a6f8bf9bc0aa4733bc SHA256 023e1f1e92e0372c4029c9e19043af0416d0e294440bb368d30126c5ed330691 -EBUILD embassy-topo-2.0.0.ebuild 373 RMD160 6c3eb53aa44a640807cf562541a574749223da63 SHA1 737062a13b260b7cf1123526aad06112e7f4d20f SHA256 654f9f4ff5929f2ab6f94b1a3fd7c3f6fea696a80be610fccb84e78f8fa73d79 -MISC ChangeLog 4778 RMD160 dc4832b8a5a100c6034a1dc8e6e9b821334a7524 SHA1 d3301ecf66f677a5dd408e61c43135172da5f8df SHA256 8ac4f880d19be2a42e48325c3994391a7cab3a84d231b9a8a0d5976469b3245f +EBUILD embassy-topo-2.0.0.ebuild 368 RMD160 26cc07ab59586b39677492099bc8a5765eb2ade0 SHA1 c6ca98799deb4db707234a2bed49762bc0186ebd SHA256 4d4ab09f8f138533669553a1890a0bbcc025f2c1d3c58e6bb3785997c2b30ecd +MISC ChangeLog 4922 RMD160 8eb2223000309a5e863c613fe4604fcf26870aa3 SHA1 679e45de2387f0abe20536da5e4f94228cb09b21 SHA256 f2baeba6ee08d2dd039329c196b6f64ca4c3ece5b06e175b02aa128ed7533698 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F/PsACgkQgAnW8HDreRZDhgCfSaIUXc8dw4Funmc3tlTtlHZ5 -LiMAoKeN9DAY7CRN1N06tGiYXXwtDO6D -=XtB0 +iEYEAREIAAYFAk4GA5MACgkQgAnW8HDreRZcUQCfXEESoX45eJJV0tbSXobJvHPc +hcIAnAtw8YGpdrVOOVpzHpl7iMf6p6Ec +=2kVI -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.0.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.0.ebuild index 3090d47a6..02244e6f4 100644 --- a/sci-biology/embassy-topo/embassy-topo-2.0.0.ebuild +++ b/sci-biology/embassy-topo/embassy-topo-2.0.0.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Transmembrane protein display" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-vienna/ChangeLog b/sci-biology/embassy-vienna/ChangeLog index 7df53c061..3d15b99f9 100644 --- a/sci-biology/embassy-vienna/ChangeLog +++ b/sci-biology/embassy-vienna/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.8 2010/01/15 22:47:16 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-vienna-1.7.2-r2.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-vienna-1.7.2-r2.ebuild, files/embassy-vienna-1.7.2-r2.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest index 1d018c5d5..066106a0a 100644 --- a/sci-biology/embassy-vienna/Manifest +++ b/sci-biology/embassy-vienna/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-vienna-1.7.2-r2.patch 9731 RMD160 5cda4d8a04c252051a8affb85706648de8fa91a5 SHA1 e7a6d11b6ab4c8f353a530c42d6c677457e15389 SHA256 c5de170aaf19f0339780120132f97a5f26a48b26d739a5bdb772fdb6d26e3bce DIST embassy-vienna-1.7.2.tar.gz 652433 RMD160 753b37bfaa8f362ebc46fb96955537fd82c627c4 SHA1 4eb8f80c9579a96b198c35ec3dba4b93821789f8 SHA256 61c60e4335a716cbc80e6fab47268de64c6c377c0a052686cd98822cf7270d7c -EBUILD embassy-vienna-1.7.2-r2.ebuild 380 RMD160 9105a9723b81e1dce6ccfde70784b4e31970795e SHA1 b44cb11627eca23df2ddcaa922f03f3ff0913808 SHA256 0d56b3ca1f4015a0649eccc94e8ca3ba12a7000036156d537e0ec8a24794bea1 -MISC ChangeLog 1873 RMD160 3633f62b4770438afc5afe6f3171f2f05778bbbb SHA1 a3cd44496536a20d1138c4bd80edaa11605fb48a SHA256 c3ff48d00893aac7fa9fd323eaf58a8a86d8379db26aef358151bf5212fdbce2 +EBUILD embassy-vienna-1.7.2-r2.ebuild 375 RMD160 ce51a1e63695d6286034c08d3cbf2a8d02f61b2f SHA1 3052730952a478de52507eb3dd327a8b0fd9d710 SHA256 fbe5d6d1d1743f1a35f249856e07058d3188dec495ce225479888c202f547b8f +MISC ChangeLog 2022 RMD160 98a74e8684854f45e144475f5ff89d4e443f72be SHA1 e858b3aff5806edfec90760e7e8dea8f24e28b21 SHA256 f7dbc9853c89e650518217552092bad9aa20c27ab8e343db50ebde31bb1c85fa MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F/poACgkQgAnW8HDreRYkigCeJpDVnreI/Rv26tHmb9NbhXq8 -AtkAnR5NrTa5En7RKtyNQK+QIM9hWbRj -=gOG8 +iEYEAREIAAYFAk4GA6QACgkQgAnW8HDreRa+ZwCcC+aDA2QRFokUmI+h52ofAMCe +WegAn1aNcFddrtJ2wh1SJVoZ7UKqdBBx +=iToN -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r2.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r2.ebuild index 9a7b8e53c..594278f81 100644 --- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r2.ebuild +++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r2.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Vienna RNA package - RNA folding" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy/ChangeLog b/sci-biology/embassy/ChangeLog index a08d9efbe..445246a8e 100644 --- a/sci-biology/embassy/ChangeLog +++ b/sci-biology/embassy/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/ChangeLog,v 1.33 2010/01/01 21:35:29 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-6.3.1.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 21 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-6.3.1.ebuild: Fixed for reviewed eclass diff --git a/sci-biology/embassy/Manifest b/sci-biology/embassy/Manifest index 0ee4f05b5..6432e5073 100644 --- a/sci-biology/embassy/Manifest +++ b/sci-biology/embassy/Manifest @@ -1,13 +1,13 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 -EBUILD embassy-6.3.1.ebuild 1104 RMD160 e1332acc8a61e2be31c5bf1957caa983b63e011c SHA1 ba3effa2b9c800f9d29d001e6c4c537f4eae2b7b SHA256 d7a587d1110d29faa63903106edf31faa067dc075d38de5fccb2664207f56dd6 -MISC ChangeLog 5213 RMD160 77f058ea7c5e40d5e101eeaae41e1c93f3b96f4e SHA1 82af9df083283693de75a856497f4bdbce85aba1 SHA256 1fdaa89b82ca06e9c892c9e003f565e4d1a5cd8f4fdf8ecc2a5392e20c2ac834 +EBUILD embassy-6.3.1.ebuild 1099 RMD160 dba540412b7ce2f9b0266facfc37e4ef95e28b58 SHA1 efabf268999265a10e37a7103887bd376c181a7d SHA256 4e30ae47578b0016d495816bb6ebb83bdd8e388b291feaa621214b1580cd8135 +MISC ChangeLog 5352 RMD160 3630f8fee437d95096271e1add960c3ae900b9a1 SHA1 861164d561f325c35e0b0db79892780e1eda3a80 SHA256 6afc7b4a2b9be3b73c648b5e1a2d00c604a39efd3813df7c4a2c0a1ec0f3eae3 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2HQLUACgkQgAnW8HDreRb48ACeNzOEItkFGpd2DSSlkqjUw8iq -FLEAnRD2A6r4lrH0ikbZFJTkrIr1jcPx -=0Chi +iEYEAREIAAYFAk4GAZgACgkQgAnW8HDreRbDwACfVEAGTczIYp6yJQ1dVJKxsdpg +wZMAoJicRtMe/NclSS+wz5SLObdgUjH1 +=S7it -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy/embassy-6.3.1.ebuild b/sci-biology/embassy/embassy-6.3.1.ebuild index 0cceb185c..38ad021a2 100644 --- a/sci-biology/embassy/embassy-6.3.1.ebuild +++ b/sci-biology/embassy/embassy-6.3.1.ebuild @@ -10,7 +10,7 @@ DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons) SRC_URI="" LICENSE+=" freedist" -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" RDEPEND+=" =sci-biology/embassy-cbstools-1.0.0-r2 diff --git a/sci-biology/est2uni/Manifest b/sci-biology/est2uni/Manifest index 29191fd2c..211a599bd 100644 --- a/sci-biology/est2uni/Manifest +++ b/sci-biology/est2uni/Manifest @@ -1,5 +1,6 @@ -AUX 9999-est_clustering.pm.patch 1276 RMD160 4a54b28c9a67ae8476255a4063768a1c7b466357 SHA1 1d255394dad2f608bd91f6064232a3cd431e368d SHA256 c289866a862a18a9385db9931c3c0c9175334e829819f075cc7fbf7e8bbd83ce -AUX 9999-pipe_db.pm.patch 534 RMD160 8b2a5ef4de3a2c65eb65476cbb4decdad3eb8a74 SHA1 46509d05f01ae53764b4947ddb663edbb3bfee9d SHA256 11aa489e406bceabdd3b7d532fbca69ede1c0a116cc7a38ae9ea32dafc41f54c +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX 99est2uni 82 RMD160 4171612511e63f41fa57aa743a435e4e5ca811d1 SHA1 a51b17f763855cda65e3bf5f401dccab231e1593 SHA256 4317ba1309d2506682d5146f7fb52f388b368bfd2ab33b4a2cf95ec8b117341e AUX est2uni 82 RMD160 4171612511e63f41fa57aa743a435e4e5ca811d1 SHA1 a51b17f763855cda65e3bf5f401dccab231e1593 SHA256 4317ba1309d2506682d5146f7fb52f388b368bfd2ab33b4a2cf95ec8b117341e AUX est_annot.pm.patch 19656 RMD160 83c75544edf45b7dffe92b97ec1935ec4774241d SHA1 f6051670594093ba89cb259cb0427222bf4a3f02 SHA256 fdfb19e711a05b02016ffbe57f5d68f5d7b8746690445aafa2cab6ebf8ddd058 @@ -16,9 +17,14 @@ AUX tgicl_files.patch 865 RMD160 cc782fcdf0ae723b69e2b9d7135ad7236a960dc7 SHA1 0 DIST GO.terms_and_ids 1773108 RMD160 6df24848cedea76de66bbebf7eaa5eadd58e016c SHA1 e73465e4c1606245be723417adf9bcdc5c454965 SHA256 8a6d670f4ecdfa81a609abdd959d13fb9f695132eb08a2b412a8d80b50fd7e64 DIST UniVec 1062966 RMD160 ef634cd9e8996d8e3dc6e5fdbabb09ee4f5df2c3 SHA1 c599178ef9e6c6865fd531018145ed43851e5e01 SHA256 6fc0e3644a2ecb59705801416d76d7d74aa8fa5788e955a024b2d9614376f425 DIST UniVec_Core 542650 RMD160 a8cf42b9015622a8ac52839c7b794bbad4c1f92a SHA1 6ebaa99115661302125bd5b15a7caace264f2cda SHA256 7456353d072da508538052286c82ff5fec740a6ceac5621f68fd4eb35bdff9ef -DIST est2uni.tar.gz 10251279 RMD160 a208295065d68e4d68804b0b5c840f877111c0d6 SHA1 f10adac451f739f0ef97aea153eb4ea2066c8229 SHA256 347f668d8a18bedafe8644fe2bcd7d184dd77f1c98aabfbfab70767ceb819874 DIST est2uni_0.27.tar.gz 4616613 RMD160 06ec260f79fe11f7779b75aad825e665f421d4eb SHA1 5ee9b5dc51f4829c5ed0d4ddd47bb68e7f3c43ee SHA256 33d2f2981ca70fa6707d3a2f310c0492cd12a430b6bb9b7ad8697a8fc3305cd4 DIST gene_ontology.obo 19990996 RMD160 b3584271ab0a05909cde9a92e6eb635b08fe23be SHA1 bdb9d396d4320bf639be310cf6f93b08b25ef0e9 SHA256 7f70c7a1dd4b75f6055f05c5e5445a49ecf20fed8172d54ec2d04722842ff19b -EBUILD est2uni-0.27.ebuild 3258 RMD160 4cb0a29cfaaef9573f4e35dbcc649233b7f15563 SHA1 1b9d7ef1df4164e48f7d1dc0fce6367e29049f68 SHA256 0e9fb1acb658babb5de052910db4f86ae1dcd7108ca6aa11a03d150ad0f90838 -EBUILD est2uni-9999.ebuild 3351 RMD160 2a5eb12cb460e76c2bdea8f011e40b67e4a1a62a SHA1 8a422f75cf307669056b947a70126b8bacd9e46c SHA256 9816a7d559440e3cee5dd1e6c8cd423be330f32c9aa700d1d674d1d303277ad6 +EBUILD est2uni-0.27.ebuild 3292 RMD160 d676915e49ef8f3ec04da0391945441fd47028f1 SHA1 a349fbd92f6ec096f5cad8dbabb2769594531111 SHA256 e47c997ced2b2b01e4abc509349e389e9f1e3b272e696c606aa9d010984f2821 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EiSQACgkQgAnW8HDreRaZuwCfYMccT5NROdxtN7jg0sFQZ4vh +QE4AoLcFDH3moqCaBR2DMkuxrBu4i9NL +=ZlWM +-----END PGP SIGNATURE----- diff --git a/sci-biology/est2uni/est2uni-0.27.ebuild b/sci-biology/est2uni/est2uni-0.27.ebuild index 45eaf4290..7252b2f8a 100644 --- a/sci-biology/est2uni/est2uni-0.27.ebuild +++ b/sci-biology/est2uni/est2uni-0.27.ebuild @@ -4,16 +4,18 @@ EAPI=3 -inherit webapp eutils perl-module +inherit eutils perl-module webapp DESCRIPTION="EST assembly+annotation: a perl-based analysis pipeline including php-based web interface" HOMEPAGE="http://cichlid.umd.edu/est2uni/download.php" -SRC_URI="http://cichlid.umd.edu/est2uni/est2uni_0.27.tar.gz - ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec - ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core - http://www.geneontology.org/ontology/gene_ontology.obo - http://www.geneontology.org/doc/GO.terms_and_ids" - +SRC_URI=" + http://cichlid.umd.edu/est2uni/est2uni_0.27.tar.gz + ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec + ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core + http://www.geneontology.org/ontology/gene_ontology.obo + http://www.geneontology.org/doc/GO.terms_and_ids" + +SLOT="0" LICENSE="GPL-3" KEYWORDS="~amd64 ~x86" IUSE="" @@ -31,10 +33,10 @@ RDEPEND="${DEPEND} sci-biology/ncbi-tools sci-biology/bioperl sci-biology/exonerate - perl-gcpan/go-perl www-servers/apache >=dev-db/mysql-4.1 <dev-lang/php-5.3" +# perl-gcpan/go-perl S="${WORKDIR}"/est2uni @@ -45,7 +47,7 @@ src_prepare(){ } src_compile(){ - "$(tc-getCC)" external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik + $(tc-getCC) ${CFLAGS} ${LDFLAGS} external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik || die } src_install(){ diff --git a/sci-biology/estscan/ChangeLog b/sci-biology/estscan/ChangeLog new file mode 100644 index 000000000..ff0f2e4b0 --- /dev/null +++ b/sci-biology/estscan/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/estscan +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> estscan-3.0.3.ebuild, + metadata.xml: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> estscan-3.0.3.ebuild, + metadata.xml: + Added fortran-2.eclass support + diff --git a/sci-biology/estscan/Manifest b/sci-biology/estscan/Manifest index 843cd8426..e41936f81 100644 --- a/sci-biology/estscan/Manifest +++ b/sci-biology/estscan/Manifest @@ -1,3 +1,6 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST At.smat.gz 32314 RMD160 5c66e467d20e1ce43dce35cf20540649bbcf2879 SHA1 bd3e2d87be468e7d9c46557bce68e94bdd3f1aa2 SHA256 7f41329858b19ea13809becf58c7262b48dd8070dc38894b8ad7c55adcdd4c2a DIST BTLib-0.19.tar.gz 36283 RMD160 14ae4a24c81a381e9a75ddcde7552a1f9dc301b8 SHA1 7a0545cb64976ee61e76a80a9ee1a87eb1747078 SHA256 0acd6446031222b8fd5bd11eb3ec6c3164bc50491feef765c052689d9c3ee302 DIST Dm.smat.gz 31711 RMD160 1e77b7f743ea9198108dff3dec2e8fd64ba8751c SHA1 6dd589a2dac0d4ea51ad085a835a5100b5eab8e1 SHA256 1f741836aa2b4ed96ab9ea6adb883eaa4d8d95610bd7a1ac484193ab30afca1d @@ -7,5 +10,13 @@ DIST Mm.smat.gz 62711 RMD160 30cf8dd0d944afcae7dd05b30bc08820e303c7c4 SHA1 2d0d5 DIST Rn.smat.gz 32388 RMD160 4ff99c8502aa914c85aeaf19f98bc7362ab70cb0 SHA1 060e66141a19302e805323322ab219d990cf4592 SHA256 2e0a9b3347a8d216a026f98e38243d207e683bc50ac5be35c4c24f5ee1803cb8 DIST estscan-3.0.3.tar.gz 46412 RMD160 dc5e12e8196837585c405163f643e2da0c84bd79 SHA1 8af2128aaa02c50d1d3cfa75188fac038381975c SHA256 037dc8770681ed12406a789ea292462a4ce5d89b0e906a1a3340aa4debc71e2f DIST user_guide_fev_07.pdf 327005 RMD160 99f838a2c61c82a5078fb49e06ab8c8a7a8c1509 SHA1 335b3bacf0af8947db57324a702d335e72d58abd SHA256 416998f9fc282a53679fd56585b468ccebc4463e61ee5e989d9b426ed6f725fd -EBUILD estscan-3.0.3.ebuild 3959 RMD160 1e0db12b467d3d7cece9b5c3247214c702d783ce SHA1 aac4d9d5d39a9b239bf1d3b16567b9aa2469f5c5 SHA256 14e60176ea0493ec0e28ebca0e8b7165363b70e1165357c29ea6a49d804cb886 -MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +EBUILD estscan-3.0.3.ebuild 3627 RMD160 04e489ba6db85e382a3d55adbab168e46f09e791 SHA1 3412b7e3aa90ee4392a48b59fc3cd5712f0c3a1e SHA256 64c25c435fdaa15c814707ed13d3ad42ca7cac6f5cbb29d1d52ff432359aa4cc +MISC ChangeLog 362 RMD160 fd6d014788fd1c68fd8e1e58b37c2ac0585fdb4d SHA1 5079e398e369900824f8b7f4d3ed176df88a1fd2 SHA256 96f00043d927fffa618ad23bc67589ce75caff6294afd1f4e16795cb47b09082 +MISC metadata.xml 326 RMD160 cdc20d05766f861cff6889339611ca1c22579631 SHA1 dddeeb441b46d5437d1883f7c44ea26ad704344e SHA256 530e03907f86440fdc52832f744b709dde2ee85492cad7b8a263544a93ea0bea +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4DAxcACgkQgAnW8HDreRYbrQCfRdlKYlwAQQu22Y741J7tR7t6 +jp0AoIpbBVtLAlueTxY2BLymUs2wbbGz +=zCkB +-----END PGP SIGNATURE----- diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild index ed573427a..d2828605a 100644 --- a/sci-biology/estscan/estscan-3.0.3.ebuild +++ b/sci-biology/estscan/estscan-3.0.3.ebuild @@ -1,49 +1,54 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 -inherit eutils toolchain-funcs perl-module +inherit eutils fortran-2 perl-module toolchain-funcs -DESCRIPTION="Predict coding regions in DNA/RNA sequences even in low-quality reads with frameshift-causing errors (supersedes ESTscan and ESTscan2)" +DESCRIPTION="Prediction of coding regions in DNA/RNA sequences" HOMEPAGE="http://sourceforge.net/projects/estscan/" -SRC_URI="http://downloads.sourceforge.net/estscan/estscan-3.0.3.tar.gz - http://downloads.sourceforge.net/estscan/At.smat.gz - http://downloads.sourceforge.net/estscan/Dm.smat.gz - http://downloads.sourceforge.net/estscan/Dr.smat.gz - http://downloads.sourceforge.net/estscan/Hs.smat.gz - http://downloads.sourceforge.net/estscan/Mm.smat.gz - http://downloads.sourceforge.net/estscan/Rn.smat.gz - http://downloads.sourceforge.net/estscan/user_guide_fev_07.pdf - http://downloads.sourceforge.net/estscan/BTLib-0.19.tar.gz" +SRC_URI=" + http://downloads.sourceforge.net/estscan/estscan-3.0.3.tar.gz + http://downloads.sourceforge.net/estscan/At.smat.gz + http://downloads.sourceforge.net/estscan/Dm.smat.gz + http://downloads.sourceforge.net/estscan/Dr.smat.gz + http://downloads.sourceforge.net/estscan/Hs.smat.gz + http://downloads.sourceforge.net/estscan/Mm.smat.gz + http://downloads.sourceforge.net/estscan/Rn.smat.gz + http://downloads.sourceforge.net/estscan/user_guide_fev_07.pdf + http://downloads.sourceforge.net/estscan/BTLib-0.19.tar.gz" -LICENSE="estscan" SLOT="0" +LICENSE="estscan" KEYWORDS="~x86 ~amd64" -IUSE="icc ifc" +IUSE="intel" -DEPEND="icc? ( dev-lang/icc ) - ifc? ( dev-lang/ifc )" - -RDEPEND="" +DEPEND=" + virtual/fortran + intel? ( + dev-lang/icc + dev-lang/ifc )" +RDEPEND="${DEPEND}" S="${WORKDIR}" -src_compile() { - # - sed -e 's/\\rm -f/rm -rf/' \ - -e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' -i "${P}"/Makefile || die "failed to edit Makefile" +src_prepare() { + sed \ + -e 's/\\rm -f/rm -rf/' \ + -e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' \ + -i "${P}"/Makefile || die "failed to edit Makefile" # fix hard-coded paths sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/estscan.c || die sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/estscan.spec || die if ! use icc; then - sed -e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' \ + sed \ + -e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' \ -e 's/^ FFLAGS = -O2/#FFLAGS = ${FFLAGS}/' \ -e "s/^ F77 = g77/F77 = $(tc-getF77)/" -i "${P}"/Makefile \ - || die "blah" + || die else # FIXME: I would use $(tc-getCC) instead of hard-coded icc but it gives # me gcc instead, same for $(tc-getF77) @@ -54,49 +59,55 @@ src_compile() { # FIXME: below as a dirty hack I force gfortran instead of ifort for # my testing purposes. Didn't ebuild contain "PROVIDES" line? # Same for FFLAGS. - sed -e "s:^# CC = icc:CC = icc:" \ - -e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \ + sed \ + -e "s:^# CC = icc:CC = icc:" \ + -e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \ -e "s:^# FFLAGS = -O3 -ipo -axP:#FFLAGS = -O3 -ipo -axP:" \ -e "s/^ CFLAGS = -O2/#CFLAGS = -O2/" \ -e "s/^# F77 = ifort/F77 = gfortran/" \ -e "s/^ FFLAGS = -O2/#FFLAGS = -O2/" \ -e "s/^ CC = gcc/# CC = gcc/" \ - -e "s/^ F77 = g77/# F77 = g77/" -i "${P}"/Makefile || die "sed failed to fix CFLAGS, FFLAGS, CC, F77" + -e "s/^ F77 = g77/# F77 = g77/" \ + -i "${P}"/Makefile || die "sed failed to fix CFLAGS, FFLAGS, CC, F77" fi - cd "${P}" || die "chdir "${P}" failed" - emake || die "emake failed" +} + +src_compile() { + emake -C ${P} - cd ../BTLib-0.19 || die "cd ../BTLib-0.19 failed" + cd ../BTLib-0.19 perl Makefile.PL || die "perl Makefile.PL failed" } src_install() { # FIXME: Some kind of documentation is in {P}/estscan.spec - cd "${P}" - dobin build_model estscan evaluate_model extract_EST extract_UG_EST extract_mRNA makesmat maskred prepare_data winsegshuffle || die "dobin failed" + cd ${P} + dobin \ + build_model estscan evaluate_model extract_EST extract_UG_EST \ + extract_mRNA makesmat maskred prepare_data winsegshuffle # the file build_model_utils.pl should go into some PERL site-packages dir # see {P}/estscan.spec # install the doc (but is not in ${WORKDIR} because src_UNPACK() failed on it - cd "${WORKDIR}" || die + cd "${WORKDIR}" insinto /usr/share/doc/ESTscan # grab the file directly from ../distdir/ - doins ../distdir/user_guide_fev_07.pdf || die "failed to install user_guide_fev_07.pdf" + doins ../distdir/user_guide_fev_07.pdf # install the default precomputed matrices - cd "${WORKDIR}" || die + cd "${WORKDIR}" insinto /usr/share/ESTscan - doins *.smat || die "Failed to install matrices" + doins *.smat # install BTlib (in perl) cd BTLib-0.19 || die - dobin fetch indexer netfetch || die "dobin failed" + dobin fetch indexer netfetch insinto /usr/share/ESTscan/ - doins fetch.conf || die "Failed to install fetch.conf" + doins fetch.conf # FIXME: install the *.pm files from BTLib-0.19 myinst="DESTDIR=${D}" - perl-module_src_install || die "perl-module_src_install failed" + perl-module_src_install einfo "Please edit /usr/share/ESTscan/fetch.conf to fit your local database layout." einfo "Also create your own scoring matrices and place them into /usr/share/ESTscan/." diff --git a/sci-biology/estscan/metadata.xml b/sci-biology/estscan/metadata.xml index 07b525505..a68ccd86c 100644 --- a/sci-biology/estscan/metadata.xml +++ b/sci-biology/estscan/metadata.xml @@ -6,4 +6,5 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> +<use><flag name='intel'> Use intel compiler</flag></use> </pkgmetadata> diff --git a/sci-biology/gap2caf/Manifest b/sci-biology/gap2caf/Manifest index 20729601e..124d0831e 100644 --- a/sci-biology/gap2caf/Manifest +++ b/sci-biology/gap2caf/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST gap2caf-2.1.0.tar.gz 92905 RMD160 8b19963ca9e845d9bae2e7fb8253cb77bae78857 SHA1 fdbffcd159caf75d95207e54cab3c8b8270cc8e8 SHA256 1fd237cf1e83c3c4c3b67d2d35c9f059cc7eda9f6ac7886fab994e2386283b9a DIST staden-2.0.0b8.tar.gz 4312143 RMD160 68b91a80fae29e0bf8f7e6ca1c0781591113684c SHA1 742092ff7bfb5acd3376ac85d5ab50507d1dd02f SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d -EBUILD gap2caf-2.1.0.ebuild 2821 RMD160 adbdb532f4294ffe925b3aa11a56d0d0665d24c6 SHA1 63295defe7ff7529e7227e06177bc11045399d91 SHA256 e1ed6dd95796da36e4dca7c6128646685fca722093f7125ca4ebcbf7746ef27d +EBUILD gap2caf-2.1.0.ebuild 2821 RMD160 ed85b15b7b8ed22673cedc4cd152e7ee1f849a37 SHA1 3f4f14dc652a405f84c505f60257328dd7a93c5b SHA256 0879da8f69fc4f0b5edcd0f8d8f34541f91dc47f824e2963e40a553fb6f17e53 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EiSkACgkQgAnW8HDreRZ76wCeJr8TpFUJ0uDHlsOp7OWTId7f +qDoAnRKBm+3GzKuz/fgyA2iDPVwcKS2K +=7T4s +-----END PGP SIGNATURE----- diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild index 5aae263fd..861bbc8f0 100644 --- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild +++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit eutils autotools +inherit autotools eutils DESCRIPTION="GAP4 file format to CAF v2 format converter for genomic assembly data" HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/" diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog index 8024f81e1..e36ad4701 100644 --- a/sci-biology/gbrowse/ChangeLog +++ b/sci-biology/gbrowse/ChangeLog @@ -1,7 +1,20 @@ -# ChangeLog for sci-biology/generic-genome-browser -# Copyright 2000-2010 Gentoo Foundation; Distributed under the GPL v2 +# ChangeLog for sci-biology/gbrowse +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $ +*gbrowse-2.38 (26 Jun 2011) + + 26 Jun 2011; Justin Lecher <jlec@gentoo.org> -gbrowse-2.26.ebuild, + -files/GBrowseInstall.pm-2.26.patch, + -files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch, + -gbrowse-2.33.ebuild, -files/GBrowseInstall.pm-2.33.patch, + +gbrowse-2.38.ebuild, +files/GBrowseInstall.pm-2.38.patch: + Version Bump + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -gbrowse-1.70.ebuild, + -gbrowse-2.00.ebuild, gbrowse-2.26.ebuild, gbrowse-2.33.ebuild: + Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors + 05 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: Version bump diff --git a/sci-biology/gbrowse/Manifest b/sci-biology/gbrowse/Manifest index 96f87cdb3..101b58a14 100644 --- a/sci-biology/gbrowse/Manifest +++ b/sci-biology/gbrowse/Manifest @@ -1,13 +1,11 @@ -AUX GBrowseInstall.pm-2.26.patch 2647 RMD160 5acd26d95bf0c26edb0f816e840b43ef99a88ea3 SHA1 39362a38cff41097ead8c49de5eaf94d77c59f02 SHA256 1aee7359bc1b036f5d214975a5ea2395a507f04b0ee839ed3a1543a0ab4fb3c6 -AUX GBrowseInstall.pm-2.33.patch 1278 RMD160 96c7f2c66537c6e01cf2619018f608607c0927dc SHA1 a3cb874018d2c7a5acf34381971cc09d83a13f73 SHA256 5a1018f582c2e0ffca034d04ce73f678dd879d90932e4e89ea664c7c113f4b7c -AUX GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch 1001 RMD160 6784a8d01714be237247d56df13de96681f3aea5 SHA1 55c3eac7eb1e11c766b8d430c7dd36336347ef50 SHA256 a25f49dba6609a25c799d0290713038b608f8aef1a4275eff5f1f12e5225a19a +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX GBrowseInstall.pm-2.38.patch 1278 RMD160 96c7f2c66537c6e01cf2619018f608607c0927dc SHA1 a3cb874018d2c7a5acf34381971cc09d83a13f73 SHA256 5a1018f582c2e0ffca034d04ce73f678dd879d90932e4e89ea664c7c113f4b7c AUX gbrowse-slave.default 210 RMD160 77245190ab0d3a543f3103bb6f21864f73ea1cde SHA1 a19d60edd3fdc1f059ed8fa58f7e91fc47ec92dc SHA256 e4e6d68ade29681f442b2e1c7f8abbc7ff3255b3b8db3c59ed6368ba561d7d66 AUX gbrowse-slave.init.d 2196 RMD160 8b565d1be23c89cbae0f9fd5cd2201f47a564b94 SHA1 738bc8f06486a0e6caa72642f79f9b7dbb356524 SHA256 de511a92757153ee648eb6cd39e3c69c1e30fa2c2ed406f24c08571c72609219 AUX gbrowse.conf.vhosts.d 740 RMD160 e24f5132e37a84dd0bb9a39e2de99cd11d260844 SHA1 2c44fdcf04bef92eb6210d4e6667b994e5643a13 SHA256 8acd5a067ab3dd42cff0ab7cb0d783b2409ccb872590eba32ea55d4929f65f21 -DIST GBrowse-2.00.tar.gz 3844690 RMD160 f3856ca620d8adc10172d8dfb644dfbbd25cbf88 SHA1 9d78393ca21d2569a975cfff7588cb7fe62d1082 SHA256 62c96ae1c6c1494ff67fbea1fde0d80d5051705c22167a55db317a0d33b1b8ea -DIST GBrowse-2.26.tar.gz 11937473 RMD160 c2c9d988e3183637b0a97f00e8de1387ad107eab SHA1 3153afc0ef7e6ea8ca6879343028673fdb062501 SHA256 4ac5c0fd87c5ab64b3c52ebb51f51433cb8c6062fd80a56d3de91f24594d3a3f -DIST GBrowse-2.33.tar.gz 11915644 RMD160 0e2f054b4bcc2748895a856620af7e50f5e15038 SHA1 f31cbe960904b5a2ea4b7eae7a9d78baaf29fce0 SHA256 063114b844776a9500528437fb3dbc60f47a8ac380d910bd6b3148ec7cc0cc4b -DIST Generic-Genome-Browser-1.70.tar.gz 3331393 RMD160 056f72fc17bdbf803fce7e6bdde406566a80c204 SHA1 7a83abaedc4d2b061e1247972036025a713a845f SHA256 e08ef0d1ffff8186bffd30177808ad3dd7991a99abf3ea6350c8d487ba835486 +DIST GBrowse-2.38.tar.gz 11966992 RMD160 dde50d49ee1b228103dffc9701e450ac9e3be3cd SHA1 4228a4938cbdbc409ddb23f81cd3186cdf15391d SHA256 acf7d3d0f32d0138640b2773ed580572ff63d646d4538f354dec8986607aa275 DIST README-gff-files 5309 RMD160 8ba184fa8a6b921f925143cf53de06e3da353023 SHA1 ad2d2b3133c73a05ace4a0107ff1a3a4221bc8f8 SHA256 21f4f026b212698c5aac0e82045670f8397ab50fdfe74b938fcbc71a1d36c82a DIST Refseq_Genome_TBLASTX.tar.gz 56482234 RMD160 e188d9dfe12bed3fd299be4625f7e658f54bb8c4 SHA1 72ec3de9b9ca0e10c2dd8dcda24f9be74f98cf09 SHA256 7036bdd9aefbf44e384df83f4c1e973c1ab3eac8fe74b37499c4a3f1c55a18af DIST fly.fasta.gz 37349852 RMD160 4bedfcc5d0ea3d325f3d3e446713251a8ce34ca3 SHA1 8f2c7a2f24dbab0f27c73009fe51efb8f41d6769 SHA256 892ed03e17edd3469f1ed00cb9967fb905bbac57c1cb7858667381f34a6bfeea @@ -18,9 +16,13 @@ DIST worm.fasta.gz 30593662 RMD160 674ef3d09cdfaa5d748f18c0e769f0a5ca3d48cf SHA1 DIST worm.gff.gz 65789458 RMD160 ddced7c965963ce41a10bdecae949731ed305121 SHA1 ccfb0f287e27ff7849b099c81d811f468a7e617c SHA256 afd63c65c3fdb0ba8a1cf455bd4477a2d5d27d5b0e88c6a5a10d156d0567374f DIST yeast.fasta.gz 3801757 RMD160 5545054cf6ffa5381c7992141144107076fdf62e SHA1 c36fddc5fd2c79e01292f66644088654304bc438 SHA256 bf51cbced31aa6a30bca43cc72fdb53194fbb403407e2ebb9d70c901ab072e6d DIST yeast.gff.gz 249814 RMD160 64538d18de23d930915938bd00ae4a94a52f3960 SHA1 ec753b1ae409e1377f568531a53be8985a7bfa2e SHA256 20c93e6ba9457896a693d13e8fd8fa00d77acbb55aee9b19a31c2b29c4b7e9b1 -EBUILD gbrowse-1.70.ebuild 1670 RMD160 e9bf6980abebabc6ff807ea3c682a3988d0a5f14 SHA1 0413b93216348184e79b3feea36cd68618bed688 SHA256 ecb0b9290e48b82a0d29520d8418593db7baa564bb3731ed7ed808f1b4b5ff3f -EBUILD gbrowse-2.00.ebuild 1932 RMD160 5a0d15a10c2f6f9e4ac1f60ce048efcd2311cdb4 SHA1 186d5a91fbae9b6894091ac376addb84784d6a03 SHA256 21b035ef921900bc893a4de0fe123b6192860265e0594b73723c24b03dd5a23c -EBUILD gbrowse-2.26.ebuild 6959 RMD160 a3b966bad08410ea7e619b4cb6497a78836c6094 SHA1 ec109df87df0cfc0d72c35a1c662b2c85f495a10 SHA256 3020b2c5953e7bc02ed1e1e98a8b63bb69feda55101725d019201e748394e5b6 -EBUILD gbrowse-2.33.ebuild 6207 RMD160 20e3780fe421c5b83add7a52d4629a9e169994f0 SHA1 cb5c80a5e6f558f41b71a832e4384501a846271d SHA256 1dfe2823194c4ac30ffd2530d96c04c4a533592fbd1a6931584c0af74422cca3 -MISC ChangeLog 1985 RMD160 9695d7522c6165b842087b67938629377f9cc82b SHA1 3edd2e74f9b26289d95ad7609b838edb3ccb9561 SHA256 76c1d0553f09390397af4354dc653677f25d06828e42e57a60b2f35a869222ac +EBUILD gbrowse-2.38.ebuild 6136 RMD160 9da72299772f44f80f9a653840fa167d04c1d3e5 SHA1 9a65efd853905e653b5a781128e45cc0e00e611a SHA256 db0cc819ad165d509c935e4cef5be3ee1f47d0e0a0a1ecb697ef6290b7259ad5 +MISC ChangeLog 2531 RMD160 a666bbe4d2aa432f678eb56d321db77686990b45 SHA1 d4950185a71e503373f25af3466fd876d2996249 SHA256 2c805b6e02263dfaf7b2c87ed68e8da2a8cbc1d23409968c36037105338038da MISC metadata.xml 572 RMD160 bc941571413238acb3d77e61d49b959737ed4f5a SHA1 0c05303509c0e2dd21b37fc93c936809db49e530 SHA256 89b9964a9404a95dbb622a91735348da8e66d34d7dd7e7f144ed8c0159c43e31 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4G56MACgkQgAnW8HDreRaXVQCgwiv8qpUdbIu7rc522SjTi/lq +cQ4AoMbh/D6qOR+v7qwowOCzPKmTktJb +=+CVr +-----END PGP SIGNATURE----- diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch deleted file mode 100644 index 4c17f8d9a..000000000 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch +++ /dev/null @@ -1,72 +0,0 @@ ---- install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.000000000 +0100 -+++ install_util/GBrowseInstall.pm 2010-11-27 12:02:15.000000000 +0100 -@@ -436,8 +436,8 @@ - $self->ownership_warning($databases,$user); - } - -- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); -- $self->fix_selinux; -+ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); -+ # $self->fix_selinux; - - my $base = basename($self->install_path->{htdocs}); - ---- install_util/GBrowseInstall.pm.ori 2011-02-14 13:39:46.000000000 +0100 -+++ install_util/GBrowseInstall.pm 2011-02-14 13:41:50.000000000 +0100 -@@ -438,25 +438,25 @@ - $gid =~ /^(\d+)$/; - $gid = $1; - -- unless (chown $uid,$gid,$tmp) { -- $self->ownership_warning($tmp,$user); -- } -+# unless (chown $uid,$gid,$tmp) { -+# $self->ownership_warning($tmp,$user); -+# } - - my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i'); - my $images = File::Spec->catfile($tmp,'images'); - my $htdocs = $self->install_path->{htdocs}; -- chown $uid,-1,$htdocs; -- { -- local $> = $uid; -- symlink($images,$htdocs_i); # so symlinkifowner match works! -- } -- chown $>,-1,$self->install_path->{htdocs}; -+# chown $uid,-1,$htdocs; -+# { -+# local $> = $uid; -+# symlink($images,$htdocs_i); # so symlinkifowner match works! -+# } -+# chown $>,-1,$self->install_path->{htdocs}; - - my $databases = $self->install_path->{'databases'}; - -- unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { -- $self->ownership_warning($databases,$user); -- } -+# unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { -+# $self->ownership_warning($databases,$user); -+# } - - # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); - # $self->fix_selinux; ---- install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.000000000 +0100 -+++ install_util/GBrowseInstall.pm 2011-02-14 13:51:46.000000000 +0100 -@@ -470,11 +470,11 @@ - my @inc = map{"-I$_"} split ':',$self->added_to_INC; - system $perl,@inc,$metadb_script; - -- if (Module::Build->y_n( -- "It is recommended that you restart Apache. Shall I try this for you?",'y' -- )) { -- system "sudo /etc/init.d/apache2 restart"; -- } -+# if (Module::Build->y_n( -+# "It is recommended that you restart Apache. Shall I try this for you?",'y' -+# )) { -+# system "sudo /etc/init.d/apache2 restart"; -+# } - - print STDERR "\n***INSTALLATION COMPLETE***\n"; - print STDERR "Load http://localhost/$base for demo and documentation.\n"; diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch index e91fe1634..e91fe1634 100644 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch +++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch deleted file mode 100644 index 0dde70406..000000000 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch +++ /dev/null @@ -1,21 +0,0 @@ ---- install_util/GBrowseInstall.pm.ori 2011-05-11 04:10:08.000000000 +0200 -+++ install_util/GBrowseInstall.pm 2011-05-11 04:10:26.000000000 +0200 -@@ -463,12 +463,12 @@ - - my $base = basename($self->install_path->{htdocs}); - -- # Configure the databases, if needed. -- print STDERR "Updating user account database...\n"; -- my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); -- my $perl = $self->perl; -- my @inc = map{"-I$_"} split ':',$self->added_to_INC; -- system $perl,@inc,$metadb_script; -+# # Configure the databases, if needed. -+# print STDERR "Updating user account database...\n"; -+# my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); -+# my $perl = $self->perl; -+# my @inc = map{"-I$_"} split ':',$self->added_to_INC; -+# system $perl,@inc,$metadb_script; - - # if (Module::Build->y_n( - # "It is recommended that you restart Apache. Shall I try this for you?",'y' diff --git a/sci-biology/gbrowse/gbrowse-1.70.ebuild b/sci-biology/gbrowse/gbrowse-1.70.ebuild deleted file mode 100644 index 9bf0f47ce..000000000 --- a/sci-biology/gbrowse/gbrowse-1.70.ebuild +++ /dev/null @@ -1,68 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/generic-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $ - -EAPI="2" - -inherit perl-module webapp - -MY_P="Generic-Genome-Browser-${PV}" - -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://gmod.org" -SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz" - -LICENSE="Artistic" -# webapp ebuilds do not set SLOT -KEYWORDS="~x86 ~amd64" -IUSE="-minimal" # lwp moby scf - -S="${WORKDIR}/${MY_P}" - -# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/libwww-perl, LWP -DEPEND=">=dev-lang/perl-5.8.8 - >=sci-biology/bioperl-1.6 - >=dev-perl/GD-2.07 - dev-perl/IO-String - virtual/perl-Digest-MD5 - >=dev-perl/CGI-Session-4.03 - dev-perl/Statistics-Descriptive - >=dev-perl/Bio-Graphics-1.97" -RDEPEND="${DEPEND} - >=www-servers/apache-2.0.47 - >=virtual/perl-CGI-2.56 - dev-perl/DBI - dev-perl/DBD-mysql - dev-perl/Class-Base - dev-perl/Text-Shellwords - !minimal? ( - dev-perl/XML-Parser - dev-perl/XML-Writer - dev-perl/XML-Twig - dev-perl/XML-DOM - dev-perl/GD-SVG - dev-perl/Bio-Das - )" - -src_configure() { - webapp_src_preinst - perl Makefile.PL \ - HTDOCS="${D}/${MY_HTDOCSDIR}" \ - CGIBIN="${D}/${MY_HTDOCSDIR}/cgi-bin" \ - CONF="${D}/etc" \ - PREFIX="${D}/usr" \ - PACKAGE_DIR="${D}" \ - INSTALLDIRS=vendor \ - GBROWSE_ROOT=gbrowse \ - DESTDIR="${ROOT}" \ - || die -} - -src_install() { - mydoc="Changes README TODO INSTALL" - perl-module_src_install - - # TODO: write our own readme - webapp_postinst_txt en "${S}/INSTALL" - webapp_src_install -} diff --git a/sci-biology/gbrowse/gbrowse-2.00.ebuild b/sci-biology/gbrowse/gbrowse-2.00.ebuild deleted file mode 100644 index cce42a39b..000000000 --- a/sci-biology/gbrowse/gbrowse-2.00.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/generic-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $ - -EAPI="2" - -inherit perl-module webapp - -MY_P="GBrowse-${PV}" - -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://gmod.org" -SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz" - -LICENSE="Artistic" -# webapp ebuilds do not set SLOT -KEYWORDS="~x86 ~amd64" -IUSE="-minimal" # lwp moby scf - -S="${WORKDIR}/${MY_P}" - -# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10) -DEPEND=">=dev-lang/perl-5.8.8 - >=sci-biology/bioperl-1.6 - >=dev-perl/GD-2.07 - dev-perl/IO-String - virtual/perl-Digest-MD5 - >=dev-perl/CGI-Session-4.03 - dev-perl/Statistics-Descriptive - >=dev-perl/Bio-Graphics-1.97 - dev-perl/JSON - dev-perl/libwww-perl" -RDEPEND="${DEPEND} - >=www-servers/apache-2.0.47 - dev-perl/DBI - || ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) - !minimal? ( - dev-perl/File-NFSLock - dev-perl/FCGI - perl-core/Math-BigInt - dev-perl/Digest-SHA1 - dev-perl/Crypt-SSLeay - dev-perl/Net-SMTP-SSL - dev-perl/GD-SVG - dev-perl/Net-OpenID-Consumer - virtual/perl-DB_File - dev-perl/DB_File-Lock - )" - -src_prepare() { - sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die -} - -src_configure() { - webapp_src_preinst - perl Makefile.PL \ - HTDOCS="${D}/${MY_HTDOCSDIR}" \ - CGIBIN="${D}/${MY_HTDOCSDIR}/cgi-bin" \ - CONF="${D}/etc" \ - PREFIX="${D}/usr" \ - PACKAGE_DIR="${D}" \ - INSTALLDIRS=vendor \ - GBROWSE_ROOT=gbrowse \ - DESTDIR="${ROOT}" \ - || die -} - -src_install() { - mydoc="Changes README TODO INSTALL" - perl-module_src_install - - # TODO: write our own readme - webapp_postinst_txt en "${S}/INSTALL" - webapp_src_install -# find "${D}" -type f | xargs sed -i "s|${D}||" || die -} diff --git a/sci-biology/gbrowse/gbrowse-2.26.ebuild b/sci-biology/gbrowse/gbrowse-2.26.ebuild deleted file mode 100644 index 89000cfd4..000000000 --- a/sci-biology/gbrowse/gbrowse-2.26.ebuild +++ /dev/null @@ -1,167 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ -EAPI="2" - -inherit perl-module webapp - -MY_P="GBrowse-${PV}" - -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://gmod.org" -SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz - test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" - -LICENSE="Artistic" -# webapp ebuilds do not set SLOT -KEYWORDS="~x86 ~amd64" -IUSE="-minimal svg test" # lwp moby scf - -S="${WORKDIR}/${MY_P}" - -# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10) -# TODO: make sure www-servers/apache +cgi -DEPEND=">=dev-lang/perl-5.8.8 - dev-perl/Capture-Tiny - >=sci-biology/bioperl-1.6 - >=dev-perl/GD-2.07 - dev-perl/IO-String - virtual/perl-Digest-MD5 - >=dev-perl/CGI-Session-4.03 - dev-perl/Statistics-Descriptive - >=dev-perl/Bio-Graphics-1.97 - dev-perl/JSON - dev-perl/libwww-perl - svg? ( dev-perl/GD-SVG )" - -# TODO: based on the following message in apache/error_log the list of deps should be longer -# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase - -# * Bio::DB::BigFile is not installed -# * Bio::DB::Sam is not installed -# * DBD::Pg is not installed - -RDEPEND="${DEPEND} - >=www-servers/apache-2.0.47 - www-apache/mod_fastcgi - dev-perl/DBI - || ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) - !minimal? ( - dev-perl/File-NFSLock - dev-perl/FCGI - perl-core/Math-BigInt - perl-core/Math-BigInt-FastCalc - dev-perl/Math-BigInt-GMP - dev-perl/Digest-SHA1 - dev-perl/Crypt-SSLeay - dev-perl/Net-SMTP-SSL - dev-perl/Net-OpenID-Consumer - virtual/perl-DB_File - dev-perl/DB_File-Lock - dev-perl/GD-SVG - dev-perl/Text-Shellwords - dev-perl/XML-Twig - dev-perl/XML-DOM - dev-perl/XML-Writer - dev-perl/XML-Parser - dev-perl/Bio-Das - dev-perl/Text-Shellwords - )" - -src_prepare() { - sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die - sed -i 's/process_/bp_process_/g' INSTALL || die - epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to patch" - epatch "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl"${PV}".pm.patch || die "Failed to patch" -} - -src_configure() { - # GBROWSE_ROOT is the root path in SRC_URI to be prepended - # /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf - - # if we use CONF="${D}${MY_HTDOCSDIR}"/etc/gbrowse the the install process - # will not find currently installed config files and therefore place *.conf - # files into "{$S}"/blib/conf/*.conf instead of creating "{$S}"/blib/conf/*.conf.new - webapp_src_preinst - perl Makefile.PL \ - HTDOCS="${MY_HTDOCSDIR}" \ - CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \ - CONF="${MY_HTDOCSDIR}"/etc/gbrowse \ - PACKAGE_DIR="${D}" \ - INSTALLDIRS=vendor \ - GBROWSE_ROOT="gbrowse" \ - DESTDIR="${D}" \ - DATABASES="/var/www/gbrowse2/databases/" \ - TMP="/var/tmp/gbrowse2" \ - INSTALLETC="n" \ - INSTALLCONF="n" \ - WWWUSER="apache" \ - DO_XS=1 \ - NONROOT=1 \ - || die - - #sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/install_util/GBrowseInstall.pm || die - #sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/conf/GBrowse.conf || die - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/build_params - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/config_data - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/runtime_params -} - -src_install() { - mydoc="Changes README TODO INSTALL" - perl-module_src_install - - # TODO: write our own readme - webapp_src_preinst - webapp_postinst_txt en "${S}"/INSTALL || die - webapp_src_install - - # should create a /etc/init.d/ startup script based on this - # /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave - - # pre-create the directory so we can force its owner later on - mkdir -p "${D}"/var/www/gbrowse2/databases || die - chown -R apache.apache "${D}"/var/www/gbrowse2/databases || die - mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die - - ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/var/www/localhost/htdocs/gbrowse/i || die - - einfo "Probably you want to install a cron job to remove the generated temporary images:" - einfo "find /var/tmp/gbrowse2/images -type f -atime +20 -print -exec rm {}" - - einfo "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/" - - sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die - sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf* - sed -i 's#DBI:SQLite:'${D}'/var/www/gbrowse2/databases/#DBI:SQLite:/var/www/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die -} - -pkg_postinst() { - webapp_pkg_postinst || die "webapp_pkg_postinst failed" - - einfo "Please run gbrowse_metadb_config.pl to upate SQlite flatfiles or the live database" - einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm.patch" -} - -src_test() { - mysql -uroot -p password -e 'create database yeast' - mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse@localhost' - mysql -uroot -p password -e 'grant file on *.* to gbrowse@localhost' - mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhost' - - cd /usr/portage/distfiles || die - gzip -d yeast.fasta.gz || die - gzip -d yeast.gff.gz || die - #gzip -d fly.fasta.gz - #gzip -d fly.gff.gz - bp_bulk_load_gff.pl -d yeast -fasta yeast.fasta yeast.gff || die -} diff --git a/sci-biology/gbrowse/gbrowse-2.33.ebuild b/sci-biology/gbrowse/gbrowse-2.38.ebuild index e2bcfc3be..9cc3ce479 100644 --- a/sci-biology/gbrowse/gbrowse-2.33.ebuild +++ b/sci-biology/gbrowse/gbrowse-2.38.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI="2" @@ -7,21 +7,23 @@ inherit perl-module webapp MY_P="GBrowse-${PV}" -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://gmod.org" +DESCRIPTION="Display of genomic annotations on interactive web pages" +HOMEPAGE="http://gmod.org/" # mirror://sourceforge/gmod/${MY_P}.tar.gz -# http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz -SRC_URI="http://search.cpan.org/CPAN/authors/id/L/LD/LDS/${MY_P}.tar.gz - test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" +# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz +SRC_URI=" + mirror://cpan/authors/id/L/LD/LDS/${MY_P}.tar.gz + test? ( + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" LICENSE="Artistic" # webapp ebuilds do not set SLOT @@ -54,7 +56,6 @@ DEPEND=" # * Bio::DB::Sam is not installed # * DBD::Pg is not installed - RDEPEND="${DEPEND} >=www-servers/apache-2.0.47 www-apache/mod_fastcgi diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest index f0061cf81..18b89f258 100644 --- a/sci-biology/mira/Manifest +++ b/sci-biology/mira/Manifest @@ -1,8 +1,11 @@ +AUX libtool.m4.patch 355 RMD160 3c6386ced352747fa274c1a6f70e5cff9969a050 SHA1 dddbed5cd51bb86209e6108d542fdb13c0481341 SHA256 58065ce386008c4843ea42e30d406257e25656ae7870c6e6f65735f1a84326ed AUX mira-3.0.0-asneeded.patch 1468 RMD160 5ad66bd3a1861ef984af4fb2b527755fd8901440 SHA1 f17e537e98f77eeaaf7502894f8383dd96c588bc SHA256 17dec784921baccf2c515f7c269209b5cdeb23143b3412e8ad967e74682ee71f AUX mira_left_clip.readpool.C.patch 1036 RMD160 ed1fb66fb936958df8fb5ffe830bd367e2a68a19 SHA1 8a3f0cd92c86adf6131dc5a8e52ab9de5bbbb6e0 SHA256 63e027658e7ce7418641477294af473a7c9253c20374e6918254f8e2404d1212 DIST mira-3.2.1.17.tar.bz2 9611305 RMD160 b9a124c572763fa8923c1b1ee5b12e54b881b67c SHA1 a2731ba4da5af9f0c575ff355a481ea0190dd898 SHA256 2d79ebbbfc6801ff500cabd79cd63358e50296fbdcd1aed4028ea52503d76f8c +DIST mira-3.2.1.18.tar.bz2 9614978 RMD160 39e7afc6dfe1b97b5b7b2201b7b970ca9eb3222a SHA1 07d8c98c7234919411f55e915d1f8f483eb1e883 SHA256 9e05870da7828981a265fa79b717858959538593b4985cd4244fe4b16ebf709a DIST mira-3.2.1.tar.bz2 9626154 RMD160 b998226fe4ea0efbe6023dac8b073af1782167b9 SHA1 432d1ecd2acb62a8584f29a10b55943165cd0586 SHA256 86a2c00d182573008ef41f7725aec72ea69756ea9f3dc7e798a7d253a47f8bd7 DIST mira_3rdparty_17-04-2010.tar.bz2 31296 RMD160 888a38f865963b3109d3a331604e079010b55d81 SHA1 5f2fbe3e2e1bb5c5de44d414963e57b8dbcf760c SHA256 ec2c77508d75b7c28d3d26137ab69648b1ed653af93d486245ad0e4624e332b2 -EBUILD mira-3.2.1-r2.ebuild 1625 RMD160 0cbe968caf227b01a11d1c96ffb5f4706d47a542 SHA1 446130eb9a3a900147ae4d01cbe821f007987814 SHA256 659a3a9c1a9d60c64c990e9899e8d571676dd3aafc648867d49846fe04fe43e2 -EBUILD mira-3.2.1.17-r1.ebuild 1985 RMD160 58d00d38cee873a88779206cf6813a0be759756e SHA1 7649c28cd3f21b5eca0233686efbc9833268ef04 SHA256 dc47d01298cc48d80698869fade197462f2e7ed319d7fe70c5e932838288acc8 +EBUILD mira-3.2.1-r2.ebuild 1664 RMD160 be0cc98203c14df172ceeaa8594ba81a9dda8040 SHA1 2742271c780c73dd05e0549486e63bea1683631c SHA256 fbd24bad5133e64bc38055b038ae6093b2fcc024d66c04dffa2ca2f5d067d39c +EBUILD mira-3.2.1.17-r1.ebuild 1751 RMD160 02c62d754aac7173934f587ffe3bb005c893b5cd SHA1 269b9c4dd37e4568b9c3506c2e12fdb3d56dd12b SHA256 f80038926310bb16f9f9d6bf99e662b96a0f53195462bd59ea6130b76393ae06 +EBUILD mira-3.2.1.18.ebuild 1788 RMD160 ab3617a08c3daf04ccb737588856952dec8ee593 SHA1 bdecda83ee1cf7185b1b98c38fd8497a3dbfa1ce SHA256 535493e9bf59476570cd979176d58a2a03d25b5776459ad61eaa82113415efaa MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/sci-biology/mira/files/libtool.m4.patch b/sci-biology/mira/files/libtool.m4.patch new file mode 100644 index 000000000..9cfaeef09 --- /dev/null +++ b/sci-biology/mira/files/libtool.m4.patch @@ -0,0 +1,13 @@ +--- config/m4/libtool.m4.ori 2011-06-22 12:28:14.000000000 +0200 ++++ config/m4/libtool.m4 2011-06-22 12:28:39.000000000 +0200 +@@ -88,10 +88,6 @@ + # This can be used to rebuild libtool when needed + LIBTOOL_DEPS="$ltmain" + +-# Always use our own libtool. +-LIBTOOL='$(SHELL) $(top_builddir)/libtool' +-AC_SUBST(LIBTOOL)dnl +- + _LT_SETUP + + # Only expand once: diff --git a/sci-biology/mira/mira-3.2.1-r2.ebuild b/sci-biology/mira/mira-3.2.1-r2.ebuild index a4de8cce4..c110959eb 100644 --- a/sci-biology/mira/mira-3.2.1-r2.ebuild +++ b/sci-biology/mira/mira-3.2.1-r2.ebuild @@ -31,6 +31,7 @@ src_prepare() { epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch # http://sourceforge.net/apps/trac/mira-assembler/ticket/47 epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch + epatch "${FILESDIR}"/libtool.m4.patch AT_M4DIR="config/m4" eautoreconf } diff --git a/sci-biology/mira/mira-3.2.1.17-r1.ebuild b/sci-biology/mira/mira-3.2.1.17-r1.ebuild index 9fe96ff69..04b37674c 100644 --- a/sci-biology/mira/mira-3.2.1.17-r1.ebuild +++ b/sci-biology/mira/mira-3.2.1.17-r1.ebuild @@ -16,9 +16,7 @@ SRC_URI="mirror://sourceforge/mira-assembler/${P}.tar.bz2 LICENSE="GPL-2" SLOT="0" IUSE="" -KEYWORDS="" -# masked because of 'libtool: Version mismatch error. This is libtool 2.4, but the definition of this LT_INIT comes from libtool 2.2.6b. You should recreate aclocal.m4 with macros from libtool 2.4 and run autoconf again.', dyeing at src/examples_programming/ -#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" CDEPEND=">=dev-libs/boost-1.41.0-r3 dev-util/google-perftools" @@ -33,6 +31,7 @@ src_prepare() { epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch # http://sourceforge.net/apps/trac/mira-assembler/ticket/47 epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch + epatch "${FILESDIR}"/libtool.m4.patch AT_M4DIR="config/m4" eautoreconf } diff --git a/sci-biology/mira/mira-3.2.1.18.ebuild b/sci-biology/mira/mira-3.2.1.18.ebuild new file mode 100644 index 000000000..3ea8ce177 --- /dev/null +++ b/sci-biology/mira/mira-3.2.1.18.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +MIRA_3RDPARTY_PV="17-04-2010" + +inherit autotools base multilib + +DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" +HOMEPAGE="http://www.chevreux.org/projects_mira.html" +SRC_URI="mirror://sourceforge/mira-assembler/${P}.tar.bz2 + mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" + +CDEPEND=">=dev-libs/boost-1.41.0-r3 + dev-util/google-perftools" +DEPEND="${CDEPEND} + dev-libs/expat" +RDEPEND="${CDEPEND} + sci-biology/smalt-bin + sci-biology/ssaha2-bin" + +src_prepare() { + find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die + epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch + # http://sourceforge.net/apps/trac/mira-assembler/ticket/47 + epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch + epatch "${FILESDIR}"/libtool.m4.patch + AT_M4DIR="config/m4" eautoreconf + #epatch "${FILESDIR}"/libtool.patch +} + +src_configure() { + econf \ + --with-boost="${EPREFIX}"/usr/$(get_libdir) \ + --with-boost-libdir="${EPREFIX}"/usr/$(get_libdir) \ + --with-boost-thread=boost_thread-mt +} + +src_compile() { + base_src_compile + # TODO: resolve docbook incompatibility for building docs + if use doc; then emake -C doc clean docs || die "This will probably die because upstream did not imrove re-genartion of the docs yet."; fi +} + +src_install() { + einstall || die + dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL + find doc/docs/man -type f | xargs doman + find doc/docs/texinfo -type f | xargs doinfo + dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} +} diff --git a/sci-biology/mrbayes/ChangeLog b/sci-biology/mrbayes/ChangeLog index f2ce30569..7c54e60cf 100644 --- a/sci-biology/mrbayes/ChangeLog +++ b/sci-biology/mrbayes/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/mrbayes -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/ChangeLog,v 1.19 2008/06/11 18:10:48 ken69267 Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> mrbayes-3.1.2-r1.ebuild, + metadata.xml: + RDEPEND is not explicitly assigned -> fixed + 27 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> mrbayes-3.1.2-r1.ebuild: QA fixes diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest index 96782ec95..96dcbdf8a 100644 --- a/sci-biology/mrbayes/Manifest +++ b/sci-biology/mrbayes/Manifest @@ -1,25 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX mb_readline_312.patch 1108 RMD160 5901513567ef2198b4c9c1baeb1ecc295af3eee8 SHA1 c5526cf58fe15cb22c401de19de7056a66c37414 SHA256 6d7566cbe59eee9881b41a21ea561fd610816df768bb8fda42ef4435c84f5f22 DIST mrbayes-3.1.2.tar.gz 545968 RMD160 b90b9406f34806bcd18bc49dc998b7ed444e93c3 SHA1 db73f53361688e1451ec155ccbdd130c3f889817 SHA256 c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4 -EBUILD mrbayes-3.1.2-r1.ebuild 1290 RMD160 ea28415fb61052376cb5f969d45fbf6f02e629a8 SHA1 95c96987a36c751e9e71d7c75409df4d3ca85586 SHA256 37fe5ed6d86c80bf35a54fe930166b0710625e3336d52421ad9acd3f5a6a46f9 -MISC ChangeLog 2968 RMD160 09b289d34cd8679cbee91b06804825d0af85d41b SHA1 0a04a57f0930a2813d3c423a38a7d65c994a4504 SHA256 a5a75909a551d9064baa39f8417fab021d253947715d9bac92d1a491cd3ea8fb -MISC metadata.xml 730 RMD160 46eda6e69c53a0e301343cfc645c343c5aa9fdd6 SHA1 06e33f8fa877635c7e771e74e3edeb8cba146fb3 SHA256 fe9b9273c53a7c502d6688d63557fe603f63a47c8ff17355b9db7cdc0b78f446 +EBUILD mrbayes-3.1.2-r1.ebuild 1316 RMD160 ded04cf025556ded7cd1c34f18c283dde70ae5d4 SHA1 a660680775448d9f313e7040eed5436eab172fba SHA256 fd3653ddccf4faa0dddfb502b8d0ea59cfcf7a2788dc1906b58607638de716c6 +MISC ChangeLog 3103 RMD160 46686758663971c63f4504b3f6765112da662bee SHA1 fd287ecf0d712fd76267cf73d9a96bd554acff40 SHA256 644b6d880b1e332e61ba896a2e86347b42f18ced23f83922f3cdd674df2f786b +MISC metadata.xml 732 RMD160 c9c73ca971a4c88f5054245bde9585b694924fe8 SHA1 7d2195b53ba6e6a30f6a3c84072d62a0822faf06 SHA256 b1d3e5fd22ec3c1cd73e0a1de97d994690145894dbe024cf66e91e56ee3925eb -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMJ67+AAoJENwGBM22xffezFoP/0wwMAdnLe3KZUO7TNg4rc+X -l8Ll2kWUJ64krvyMucKDqQ9ZCK9XR4R7q97p+pOaFjno0sVqk9kBpRzvMewMryxH -HeKV/7CrCkCKVjNdSxH0G2ZT7pPfCEM394rrFMucVqZvyb76azhT1VDizGWQJkDj -2e3WPAuiULklW4kHaD6R0TDSGhpnptLyu7UQLIsiF3anReMS/QSX7XwM5rAejfkw -hoa6+iiQYe2+sI9RWmj9KvjQNwv5tEt8FlMqTA26S4RL6ceTb8QPRWFE6AZWPCid -HCj0oWIQIBAptkhCKKoqE423u9EIGfN9r1zRgVX+gLr+2gC0aA9Ag1kB9ZF384jp -MmxgDwVjKZqT4qw5HRXMMLGPqL2RxsaGb9ZD50ucE0Eb6zaWHexCXEOiS0Ik4lXV -/Idl1KUCl7wQpewZO0HPniaVDz/waKVlcawCSNFzAX/1mLtthtvwyFoN4hCn/mth -6CTY7itGOneSZmoxabbOOXb2aKMNsrkvRxL+kVWzn+375Cibc2tAZF5VgTDucq4D -XE09M/0qNRdThzvIyBW1wpEWLZynIpCqjoA53JwaMF8wBiF61NNL0JPYCGQD5v+r -SOvYIOceuMb1ifmuZjcZMNV8dGmleGel5/4YCvYjARjHxBa/QtQnUDHJ1tMhi5nN -W+b5ci6syZqZ8VMLuXIL -=Toc4 +iEYEAREIAAYFAk4F5kUACgkQgAnW8HDreRbrcQCgwaM3QhDgQSOnyM7DN3nNw1Bt +tkoAn0eVMkH/raPdh1MAcoQEK0QFsI3d +=OD3v -----END PGP SIGNATURE----- diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml index d33282dbb..102b1ec80 100644 --- a/sci-biology/mrbayes/metadata.xml +++ b/sci-biology/mrbayes/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-biology</herd> -<longdescription> + <herd>sci-biology</herd> + <longdescription> MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild index 4c65db786..f29856adf 100644 --- a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild +++ b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild @@ -1,25 +1,28 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2.ebuild,v 1.7 2008/06/11 18:10:48 ken69267 Exp $ -inherit eutils toolchain-funcs mpi +inherit eutils mpi toolchain-funcs DESCRIPTION="Bayesian Inference of Phylogeny" -LICENSE="GPL-2" HOMEPAGE="http://mrbayes.csit.fsu.edu/" SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" SLOT="0" -IUSE="mpi readline" +LICENSE="GPL-2" KEYWORDS="~amd64 ~x86" +IUSE="mpi readline" -DEPEND="mpi? ( $(mpi_pkg_deplist) ) +DEPEND=" + mpi? ( $(mpi_pkg_deplist) ) readline? ( sys-libs/readline )" +RDEPEND="${DEPEND}" src_unpack() { unpack ${A} cd "${S}" - sed -e "s:OPTFLAGS ?= -O3:CFLAGS = ${CFLAGS}:" \ + sed \ + -e "s:OPTFLAGS ?= -O3:CFLAGS = ${CFLAGS}:" \ -e "s:CC = gcc:CC = $(tc-getCC):" \ -e "s:CC = mpicc:CC = $(mpi_pkg_cc):" \ -e "s:LDFLAGS =:LDFLAGS ?=:" \ diff --git a/sci-biology/newbler/ChangeLog b/sci-biology/newbler/ChangeLog deleted file mode 100644 index d651a0680..000000000 --- a/sci-biology/newbler/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ -# ChangeLog for sci-biology/newbler -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 01 May 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by me - diff --git a/sci-biology/newbler/Manifest b/sci-biology/newbler/Manifest deleted file mode 100644 index f96dc4334..000000000 --- a/sci-biology/newbler/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST offInstrumentApps_2.0.01.10-64.tar.gz 80613372 RMD160 2d638e058a11117dbe23d27902eb28fd60f4a1aa SHA1 eec7a881ed2f8dbf277233660f38d7ab72a0ccc6 SHA256 349b8065a323526fce6394c9cdc3959f68d2a6690cdcbbd3aca6a08729ff5bd0 -EBUILD newbler-2.0.01.10.ebuild 965 RMD160 65c9abe5b1ad755a0fbf150382bc51f34d1ecdef SHA1 2328164d1387fd2a0813745946ee9ba1bce65ec7 SHA256 0c1aec58f151d423c9b8176204c1e3d1c0f50e3c893eddcab9174aff3af02dfb -MISC ChangeLog 218 RMD160 a71508054d9bb459a17ec6888fe33656bcdf296c SHA1 46f02a60127224aaa3f3722b650bb4a7fc6d8f8b SHA256 c2b76d95cbde1128dc5b36fc466ccfd1c08179ac6b28d6b897fbd10fe974221a -MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 diff --git a/sci-biology/newbler/newbler-2.0.01.10.ebuild b/sci-biology/newbler/newbler-2.0.01.10.ebuild deleted file mode 100644 index a044ea826..000000000 --- a/sci-biology/newbler/newbler-2.0.01.10.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-2.0.8.ebuild,v 1.2 2009/03/15 17:58:50 maekke Exp $ - -EAPI="2" - -DESCRIPTION="Roche 454 pyrosequencing assembler" -HOMEPAGE="http://www.454.com/products-solutions/analysis-tools/index.asp" -SRC_URI="offInstrumentApps_2.0.01.10-64.tar.gz" - -LICENSE="newbler" -SLOT="0" -IUSE="" -KEYWORDS="~amd64" - -DEPEND="app-arch/rpm" -RDEPEND=">=virtual/jre-1.6" - -RESTRICT="fetch" - -S="${WORKDIR}/offInstrumentApps_${PV}-64" - -pkg_nofetch() { - einfo "Please visit ftp://ftp.454.com/ and obtain the file" - einfo "\"${SRC_URI}\", then place it in ${DISTDIR}" -} - -src_prepare() { - sed -i -e "s|/etc/profile.d|${D}/etc/profile.d|" "${S}/INSTALL" || die -} - -src_install() { - echo -e "\n\n${D}/opt/454\nno\n" | "${S}"/INSTALL || die - rm -rf "${D}/opt/454/jre" || die - echo "PATH=/opt/454/bin" > "${S}/99${PN}" - doenvd "${S}/99${PN}" -} diff --git a/sci-biology/nrcl/ChangeLog b/sci-biology/nrcl/ChangeLog new file mode 100644 index 000000000..86d3e89ec --- /dev/null +++ b/sci-biology/nrcl/ChangeLog @@ -0,0 +1,14 @@ +# ChangeLog for sci-biology/nrcl +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/110625-build.patch, + -files/0.1-build.patch: + mv 0.1-build.patch 110625-build.patch + +*nrcl-110625 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/0.1-build.patch, + -nrcl-0.1.ebuild, +nrcl-110625.ebuild: + Cleaned ebuild + diff --git a/sci-biology/nrcl/Manifest b/sci-biology/nrcl/Manifest index 41cd6ca97..ca68de31d 100644 --- a/sci-biology/nrcl/Manifest +++ b/sci-biology/nrcl/Manifest @@ -1,4 +1,16 @@ -DIST cdbfasta.tar.gz 59735 RMD160 c90e0ede03a01bf2da77f9beaa3c97fa7e46ff2a SHA1 2419421ab1d753d3bb8778c92236da74fee30526 SHA256 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c -DIST nrcl.tar.gz 14782 RMD160 c3e122ccd1d30e25c278e9f0a7928ab6d1a1e451 SHA1 8650388bbf27640f5b2c261e1eafe286e34adcb4 SHA256 8795728d60416d1329a352479335b084d3627af8e6ba5e4ba043041970886f46 -EBUILD nrcl-0.1.ebuild 1223 RMD160 163f2e14872074fb445b8941038e417d22d1193a SHA1 c842fdc757a6b984a724981155d122ce5d178cb7 SHA256 cbb0f36d07ede9150b1b8b37558f83a7c4a3692fcaf0344f58db61ef85c7efda +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX 110625-build.patch 1184 RMD160 adbdf53d27d41f8095492ed28a437d6b64191886 SHA1 09bbb5e77185ecc7cde825d395a908600bda794d SHA256 eee62d137ca6359c2a2f614054d55afb711291dffc239c62a5cc07f01b9f293e +DIST gclib.tar.gz 82727 RMD160 f12395354b47980577e9d83cc100a6bf6568bd33 SHA1 4c433e6a87663211dc00e2d855a11a058e5b6b48 SHA256 0c7f21fc92b033cd442b672e9014e3ffb9f2de97769ca525715692ed9359439b +DIST nrcl-110625.tar.gz 14782 RMD160 c3e122ccd1d30e25c278e9f0a7928ab6d1a1e451 SHA1 8650388bbf27640f5b2c261e1eafe286e34adcb4 SHA256 8795728d60416d1329a352479335b084d3627af8e6ba5e4ba043041970886f46 +EBUILD nrcl-110625.ebuild 695 RMD160 0fc3eaa7b2e44a6f75a02338c0cdb46c40e746f4 SHA1 9abbc7a63ee83d05d6b4a0beda87a5d49a2805dd SHA256 c26a2521b93facdb258ddafd778cff41e77dfe7fcc8807c36e678ba01ee13846 +MISC ChangeLog 416 RMD160 3fefc5209cdc0714d17cc9185ccded1f231ca510 SHA1 437674e0eb6356d52606daff5b8059ba5afe95e8 SHA256 2e65db83ad0ada4de4aab7272adeb63ead6a90ced9a2447502797153ede09b58 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F+ssACgkQgAnW8HDreRaX4gCfe65l6YTL5Wxo5Q5l8PPYUpQS +qlMAnib37W1cGwHoiSaqMRe4yhukXkhW +=ShI9 +-----END PGP SIGNATURE----- diff --git a/sci-biology/nrcl/files/110625-build.patch b/sci-biology/nrcl/files/110625-build.patch new file mode 100644 index 000000000..64fa893a4 --- /dev/null +++ b/sci-biology/nrcl/files/110625-build.patch @@ -0,0 +1,48 @@ + Makefile | 18 +++++++++--------- + 1 files changed, 9 insertions(+), 9 deletions(-) + +diff --git a/Makefile b/Makefile +index 6d5d68f..30a1019 100644 +--- a/Makefile ++++ b/Makefile +@@ -11,23 +11,23 @@ SYSTYPE := $(shell uname) + + # C compiler + +-CC := g++ +-CFLAGS = -O2 -Wall ${SEARCHDIRS} -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT ++CXX ?= g++ ++CXXFLAGS += -Wall ${SEARCHDIRS} -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT + + %.o : %.c +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + +-%.o : %.cc +- ${CC} ${CFLAGS} -c $< -o $@ ++%.o : %.CXX ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.C +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cxx +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + # C/C++ linker + +@@ -39,7 +39,7 @@ LOADLIBES := + all: nrcl + + nrcl: ./nrcl.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o +- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} ++ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} + + # target for removing all object files + diff --git a/sci-biology/nrcl/nrcl-0.1.ebuild b/sci-biology/nrcl/nrcl-0.1.ebuild deleted file mode 100644 index 6f44a0b17..000000000 --- a/sci-biology/nrcl/nrcl-0.1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -DESCRIPTION="Containment clustering and layout utility for processing pairwise alignments from TIGR Gene Indices project tools" -HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" -SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_prepare() { - # we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h - sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed" - sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die - cd ${PN} || die - ln -s ../cdbfasta/gcl . || die "Cannot make a softlink" -} - -src_compile() { - cd ${PN} || die - emake || die "emake failed in "${S}"/${PN}" -} - -src_install() { - cd ${PN} || die - dobin ${PN} || die "Failed to install ${PN} binary" - newdoc README README.${PN} -} diff --git a/sci-biology/nrcl/nrcl-110625.ebuild b/sci-biology/nrcl/nrcl-110625.ebuild new file mode 100644 index 000000000..1a599dd4c --- /dev/null +++ b/sci-biology/nrcl/nrcl-110625.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Containment clustering and layout utility for processing pairwise alignments" +HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" +SRC_URI=" + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz -> gclib.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +S="${WORKDIR}"/${PN} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-build.patch + tc-export CXX +} + +src_install() { + dobin ${PN} + dodoc README +} diff --git a/sci-biology/proda/ChangeLog b/sci-biology/proda/ChangeLog index 7ca249fa6..46cc65f5c 100644 --- a/sci-biology/proda/ChangeLog +++ b/sci-biology/proda/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/proda -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +proda-1.0.ebuild: Mass import from sunrise diff --git a/sci-biology/proda/Manifest b/sci-biology/proda/Manifest index a08c08aed..22b6dfbbc 100644 --- a/sci-biology/proda/Manifest +++ b/sci-biology/proda/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST proda_1_0.tar.gz 38868 RMD160 b024496c935cebb74d50479d8cdeacce820358b1 SHA1 44303e1639b5c52278758d23d149ef1c434593a4 SHA256 439a93bf35e1a29ac1d5dde51e61f2cb174618596afaaaaa27d33a8ea1868a08 EBUILD proda-1.0.ebuild 703 RMD160 46c755309e2925f3ebcc6ede718cd7b3d38c8469 SHA1 e9c55e5782f00660795cb8749c5373f4c1124bbd SHA256 8c454b35cafb73ca9c77662f922cff590498d39dafca97bbf2a4803e8d8c6524 -MISC ChangeLog 335 RMD160 913d0c1816d44d2b575580909498c0ab71a2d16c SHA1 0d4cb7d8379e35695dc9f76df4d6120bd1d7cbbc SHA256 c9a0ed83283201f9dc4e644e83668eb162f6be98cf08e9b55c3df4748355c85d -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 +MISC ChangeLog 432 RMD160 3c15b5841844c425a4bed5010bed995e637c9916 SHA1 63f329133582b2ea3d9e5e801e876090d831142a SHA256 4c837b94fcb8b4fd0725d7c8a7ed3acb821aa566e8da1ba8013d6bca1844cef0 +MISC metadata.xml 158 RMD160 9b441c987a00c5a66c06850c0d587a2abd70893c SHA1 7a8997eb2fc55fda167d3e95cdffb43c8f817fdf SHA256 dae7918daac89b300804812d32584889aa1c4e8b9edeced06006900494457a6d +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Fkb0ACgkQgAnW8HDreRbkZgCgk8Gs1Q0Tp6imzxlr2e85PGAf +iHsAn34iEA5K4GDFRQ/F33g8Uo4pXePG +=iiaD +-----END PGP SIGNATURE----- diff --git a/sci-biology/proda/metadata.xml b/sci-biology/proda/metadata.xml index 7e3286984..897aa2e6b 100644 --- a/sci-biology/proda/metadata.xml +++ b/sci-biology/proda/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>maintainer-wanted</herd> + <herd>sci</herd> </pkgmetadata> diff --git a/sci-biology/seqclean/ChangeLog b/sci-biology/seqclean/ChangeLog new file mode 100644 index 000000000..b03c585ea --- /dev/null +++ b/sci-biology/seqclean/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/seqclean +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*seqclean-110625 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -seqclean-0.1.ebuild, + +seqclean-110625.ebuild, +files/seqclean-110625-build.patch: + Cleaned ebuild + diff --git a/sci-biology/seqclean/Manifest b/sci-biology/seqclean/Manifest index bd0c55a33..4249af699 100644 --- a/sci-biology/seqclean/Manifest +++ b/sci-biology/seqclean/Manifest @@ -1,5 +1,17 @@ -DIST mdust.tar.gz 7526 RMD160 c04a6ba5a56724bfee70b8fe31f0bf4132b74885 SHA1 8885f206d61a76c6623c4115af02793bb52911c4 SHA256 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d -DIST seqcl_scripts.tar.gz 14840 RMD160 5e97c43b1e6b77aef48366d7802e04c9ec0b8054 SHA1 cf487d2321f21894014f361a2a6839bef6e85f24 SHA256 bc8bba4fcff5e012a3eafe48fc5d5f843e9689aad5f063c595bede9ac5b27e43 -DIST trimpoly.tar.gz 12747 RMD160 a3b22f501a8291a015a0a85efc4afa812a1d1439 SHA1 bde5b24e1cbc522609ae660343bbe4084da330f0 SHA256 e6dfb3cb6b8e205a5627d20029207cd0a87be5095b4c556b6b3f716fba287666 -EBUILD seqclean-0.1.ebuild 1842 RMD160 48be3cec69ecede8e90ccd2297ca279ccca51937 SHA1 2b54b2ec16b1689429a5e7638a9a753574c3d5b8 SHA256 449489cce79b04376fc5a27010eb2c9a4cd07cc372b3937a127b422d8078beb3 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX seqclean-110625-build.patch 2984 RMD160 cdce63f091a24cdad8452969e8ae7304ec783fcc SHA1 3daf1144a675bb228584389dbc9be2865ada4947 SHA256 443bd8ae25894bf1d63c72370caaf48fb2ebff825a26f4fff313ee0f181f832a +DIST mdust-110625.tar.gz 7526 RMD160 c04a6ba5a56724bfee70b8fe31f0bf4132b74885 SHA1 8885f206d61a76c6623c4115af02793bb52911c4 SHA256 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d +DIST seqcl_scripts-110625.tar.gz 14840 RMD160 5e97c43b1e6b77aef48366d7802e04c9ec0b8054 SHA1 cf487d2321f21894014f361a2a6839bef6e85f24 SHA256 bc8bba4fcff5e012a3eafe48fc5d5f843e9689aad5f063c595bede9ac5b27e43 +DIST trimpoly-110625.tar.gz 12747 RMD160 a3b22f501a8291a015a0a85efc4afa812a1d1439 SHA1 bde5b24e1cbc522609ae660343bbe4084da330f0 SHA256 e6dfb3cb6b8e205a5627d20029207cd0a87be5095b4c556b6b3f716fba287666 +EBUILD seqclean-110625.ebuild 1373 RMD160 0c84d786c58625deea76f46789a71c22ebd0f44f SHA1 80afe2eb6f076926be19fa2343a2542f18e86913 SHA256 f27cf254f1a03650024d617f4678f3339505da19f268369ec9428577857db4e7 +MISC ChangeLog 303 RMD160 a33093fdf475cfa7a02a48646f05fd9446067cb9 SHA1 554321e80db0da43ee4f1e6740fc019e30a1e88b SHA256 98ec118f2981a85729c45bba185175374120c6caecb5af3f460711edc653fc86 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F+98ACgkQgAnW8HDreRa7/QCeOpQW46JXR8Me2PxOWFPXNA/7 +AMMAnAofQaaVdRqV1GtUgp2q/NR8WM+d +=XQtZ +-----END PGP SIGNATURE----- diff --git a/sci-biology/seqclean/files/seqclean-110625-build.patch b/sci-biology/seqclean/files/seqclean-110625-build.patch new file mode 100644 index 000000000..b5797618f --- /dev/null +++ b/sci-biology/seqclean/files/seqclean-110625-build.patch @@ -0,0 +1,135 @@ + mdust/Makefile | 18 +++++++++--------- + mdust/fastafile.c | 3 ++- + mdust/mdust.c | 1 + + trimpoly/Makefile | 16 ++++++++-------- + 4 files changed, 20 insertions(+), 18 deletions(-) + +diff --git a/mdust/Makefile b/mdust/Makefile +index 81bf4e9..0c75e69 100644 +--- a/mdust/Makefile ++++ b/mdust/Makefile +@@ -1,40 +1,40 @@ + # Useful directories + + # Directories to search for header files +-SEARCHDIRS := -I. -I- ++SEARCHDIRS := -I. -iquote + + + #SYSTYPE := $(shell uname) + +-CC := gcc +-CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT ++CC ?= gcc ++CFLAGS += ${SEARCHDIRS} -D_REENTRANT ++CXXFLAGS += ${SEARCHDIRS} -D_REENTRANT + + %.o : %.c + ${CC} ${CFLAGS} -c $< -o $@ + + %.o : %.cc +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.C +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cxx +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + # C/C++ linker + + LINKER := gcc +-LDFLAGS = + LOADLIBES := + + .PHONY : all + all: mdust + + mdust: ./mdust.o ./dust.o ./fastafile.o +- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} ++ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} + + # target for removing all object files + +diff --git a/mdust/fastafile.c b/mdust/fastafile.c +index 6c14b99..5f70f14 100644 +--- a/mdust/fastafile.c ++++ b/mdust/fastafile.c +@@ -1,7 +1,8 @@ + #include <stdio.h> + #include <ctype.h> + #include <malloc.h> +- ++#include <string.h> ++#include <stdlib.h> + #include "fastafile.h" + + +diff --git a/mdust/mdust.c b/mdust/mdust.c +index f2bae99..c3ee686 100644 +--- a/mdust/mdust.c ++++ b/mdust/mdust.c +@@ -1,6 +1,7 @@ + #include <stdlib.h> + #include <stdio.h> + #include <ctype.h> ++#include <string.h> + #include "dust.h" + #include "fastafile.h" + +diff --git a/trimpoly/Makefile b/trimpoly/Makefile +index 84db22d..71145c2 100644 +--- a/trimpoly/Makefile ++++ b/trimpoly/Makefile +@@ -3,28 +3,28 @@ + # Directories to search for header files + SEARCHDIRS := -I. + +-CC := gcc +-CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT ++CC ?= gcc ++CFLAGS += ${SEARCHDIRS} -D_REENTRANT ++CXXFLAGS += ${SEARCHDIRS} -D_REENTRANT + + %.o : %.c + ${CC} ${CFLAGS} -c $< -o $@ + + %.o : %.cc +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.C +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cxx +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + # C/C++ linker + + LINKER := gcc +-LDFLAGS = + LOADLIBES = + SYSTYPE := $(shell uname) + #ifeq ($(SYSTYPE), Linux) +@@ -37,7 +37,7 @@ SYSTYPE := $(shell uname) + all: trimpoly + + trimpoly: ./trimpoly.o color_c.o +- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} ++ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} + + # target for removing all object files + diff --git a/sci-biology/seqclean/seqclean-0.1.ebuild b/sci-biology/seqclean/seqclean-0.1.ebuild deleted file mode 100644 index eae3ef686..000000000 --- a/sci-biology/seqclean/seqclean-0.1.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA sequences, low quality and low-complexity sequences with two binaries" -HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software" -for i in seqclean/{seqcl_scripts,mdust,trimpoly}; do - SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz" -done - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="dev-lang/perl - sci-biology/ncbi-tools" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_unpack() { - unpack {seqcl_scripts,mdust,trimpoly}.tar.gz -} - -src_prepare() { - # disable the necessity to install Mailer.pm with this tool - einfo "Disabling mailer feature within seqclean" - sed -i 's/use Mailer;/#use Mailer;/' "${S}"/"${PN}"/"${PN}" || die - - for i in mdust trimpoly; do - sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${i}/Makefile || die "Failed to run sed" - sed -i "s#-I-#-iquote#" "${S}"/${i}/Makefile || die "Failed to run sed" - done -} - -src_compile() { - # seqclean/ contains just perl scripts, no need to compile - for i in mdust trimpoly; do - cd "${S}"/${i} || die "Failed to cd "${S}"/${i}" - emake || die "emake failed in "${S}"/${i}" - done -} - -src_install() { - dobin seqclean/{seqclean,cln2qual,bin/seqclean.psx} || die "Failed to install the perl-based scripts" - newdoc seqclean/README README.seqclean - for i in mdust trimpoly; do - dobin ${i}/${i} || die "Failed to install ${i} binary" - done - - einfo "Optionally, you might want to download UniVec from NCBI if you do not have your own" - einfo "fasta file with vector sequences you want to remove from sequencing" - einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html" -} diff --git a/sci-biology/seqclean/seqclean-110625.ebuild b/sci-biology/seqclean/seqclean-110625.ebuild new file mode 100644 index 000000000..45085b137 --- /dev/null +++ b/sci-biology/seqclean/seqclean-110625.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA sequences" +HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" +for i in seqcl_scripts mdust trimpoly; do + SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/${i}.tar.gz -> ${i}-${PV}.tar.gz" +done + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + dev-lang/perl + sci-biology/ncbi-tools" +RDEPEND="${DEPEND}" + +S=${WORKDIR} + +src_prepare() { + # disable the necessity to install Mailer.pm with this tool + einfo "Disabling mailer feature within seqclean" + sed -i 's/use Mailer;/#use Mailer;/' "${S}"/"${PN}"/"${PN}" || die + + epatch "${FILESDIR}"/${P}-build.patch + + tc-export CC CXX +} + +src_compile() { + for i in mdust trimpoly; do + LDLFAGS="${LDFLAGS}" \ + emake -C "${S}"/${i} + done +} + +src_install() { + dobin seqclean/{seqclean,cln2qual,bin/seqclean.psx} + newdoc seqclean/README README.seqclean + for i in mdust trimpoly; do + dobin ${i}/${i} + done + + einfo "Optionally, you might want to download UniVec from NCBI if you do not have your own" + einfo "fasta file with vector sequences you want to remove from sequencing" + einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html" +} diff --git a/sci-biology/sequin/ChangeLog b/sci-biology/sequin/ChangeLog index 7b5a10528..ca9c2b059 100644 --- a/sci-biology/sequin/ChangeLog +++ b/sci-biology/sequin/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/sequin -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + 19 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: New package, ebuild written by me diff --git a/sci-biology/sequin/Manifest b/sci-biology/sequin/Manifest index d606d2794..6d4f5ce54 100644 --- a/sci-biology/sequin/Manifest +++ b/sci-biology/sequin/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST sequin-20090722-x86.tar.gz 5999782 RMD160 44ce5da6cebdc0cbf385982dc721acf5c0ab982d SHA1 80804ec6fe8beac91f3b56f4ca8dcdee43dddb16 SHA256 f12fe7fa084a1d19a75e67cfcb4027cefb91c819b7c6219499072a87f00bdc51 DIST sequin-20090722-x86_64.tar.gz 6911415 RMD160 69da84f677231a5f98ae80de87681355810f31da SHA1 84b4bb6e5a93534fcb580c2e92050885f3a72c69 SHA256 338de057edf9c14e911f69c372c9480675c2b5a4b24efed605dcbdf7e8e4d486 EBUILD sequin-20090722.ebuild 918 RMD160 61377e7367be0ef84a8d56fa6759dd4d796083dd SHA1 1de1bbc623f981a9f6e7915110f8b1de4e20fbc9 SHA256 a8e7d9d4e52be5e5662a8f67f515368610dcf0b3879f1e015b3ab80ed8f83c45 -MISC ChangeLog 217 RMD160 f99bc54f2f294bf99eb980b779503328d14dc9bf SHA1 84777dfb9a8770ee62cb07508be4d7f1c1f0f2e8 SHA256 ae0d741bd69f675ac6fbc8b45fe81d4fbeb770a4ff4ffabf2d85969e8a70592e -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 +MISC ChangeLog 314 RMD160 eedb349e22d5bdbda160c8847026f629e0c2dd8e SHA1 a827628c2054151ba73a37a8d958e64e3defb371 SHA256 a0177570f06b4c8482c41c213ef9284a5c7feb9008c0b0871be168c1eae2fc78 +MISC metadata.xml 158 RMD160 9b441c987a00c5a66c06850c0d587a2abd70893c SHA1 7a8997eb2fc55fda167d3e95cdffb43c8f817fdf SHA256 dae7918daac89b300804812d32584889aa1c4e8b9edeced06006900494457a6d +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4FkdsACgkQgAnW8HDreRZrxACgu4X2EJXZJ2q+eZM0Sa0m+mT4 +oxAAnjsZD1+LIAWcqg2CaTnRBUy2BNwa +=iDtV +-----END PGP SIGNATURE----- diff --git a/sci-biology/sequin/metadata.xml b/sci-biology/sequin/metadata.xml index 7e3286984..897aa2e6b 100644 --- a/sci-biology/sequin/metadata.xml +++ b/sci-biology/sequin/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>maintainer-wanted</herd> + <herd>sci</herd> </pkgmetadata> diff --git a/sci-biology/sff_dump/ChangeLog b/sci-biology/sff_dump/ChangeLog new file mode 100644 index 000000000..a9d53a380 --- /dev/null +++ b/sci-biology/sff_dump/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/sff_dump +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> sff_dump-1.04.ebuild: + Some ebuild cleaning + diff --git a/sci-biology/sff_dump/Manifest b/sci-biology/sff_dump/Manifest index b0cb07b6a..f38058e05 100644 --- a/sci-biology/sff_dump/Manifest +++ b/sci-biology/sff_dump/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST sff_dump-1.04.tgz 55640 RMD160 4a83c4dd8427e101d15e28987434638408a6eb83 SHA1 ad2854724029ad476fe1719d6953cc9a58338f5f SHA256 94bfeb55bc146f2e0183a0b85622e3fa19772d4d2fb324332d72f4cc5a4104ba -EBUILD sff_dump-1.04.ebuild 726 RMD160 38282c68b9ad8d2cee6a231ce2e1588c21821457 SHA1 b08fdad83744f79b57f42eed3c81284dcbe61866 SHA256 1284a3166910f60acb0b9632151b321335a6007e85e06359f9260b0e5c333e62 -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +EBUILD sff_dump-1.04.ebuild 647 RMD160 feb6f52b46dca5dd4cdb197d169e697c746f24ec SHA1 e679e8d5a0139cf70bc096f9e10850d85f7aa0cb SHA256 4ad2b394ec9bb964d23e5cfb73f6900b4b0a5f6d3c5f52bc9f775d43f78c5af8 +MISC ChangeLog 214 RMD160 dfffb7d56e057849bb97f3123e34689f4cc6cc92 SHA1 2ff87865fce952cc2733a9da6fcf0588cc82122b SHA256 64ffd81ec69e04e05f9c7ae23d0e8dd6b4ab1d358d8714a80c5dc0f37c9377e7 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EzfwACgkQgAnW8HDreRaHkwCfVH92rc6/kopE+JHXd/80Tefl +IvgAnRaD/+vCOGHzdVV1aKPkVpSkzpQ1 +=plyn +-----END PGP SIGNATURE----- diff --git a/sci-biology/sff_dump/sff_dump-1.04.ebuild b/sci-biology/sff_dump/sff_dump-1.04.ebuild index 136e7276b..b0942764d 100644 --- a/sci-biology/sff_dump/sff_dump-1.04.ebuild +++ b/sci-biology/sff_dump/sff_dump-1.04.ebuild @@ -1,28 +1,30 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 -DESCRIPTION="Convert Roche SFF files to FASTA file format (alternative to sffdump from Roche and sff_extract from mira)" +inherit toolchain-funcs + +DESCRIPTION="Convert Roche SFF files to FASTA file format" HOMEPAGE="http://genome.imb-jena.de/software/roche454ace2caf" -SRC_URI="http://genome.imb-jena.de/software/roche454ace2caf/download/src/sff_dump-1.04.tgz" +SRC_URI="http://genome.imb-jena.de/software/roche454ace2caf/download/src/${P}.tgz" LICENSE="FLI-Jena" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - src_prepare(){ - sed -i 's:^CC :#CC :' Makefile - sed -i 's:^LD :#LD :' Makefile - sed -i 's:^CFLAGS.*:CFLAGS+= -D__LINUX__ -Wcast-align:' Makefile - sed -i 's:^LDFLAGS=:#LDFLAGS=:' Makefile + sed \ + -e 's:^CC :#CC :' \ + -e 's:^LD :#LD :' \ + -e 's:^CFLAGS.*:CFLAGS+= -D__LINUX__ -Wcast-align:' \ + -e 's:^LDFLAGS=:#LDFLAGS=:' \ + -i Makefile || die + tc-export CC LD } src_install(){ - dobin sff_dump || die + dobin sff_dump } diff --git a/sci-biology/smalt-bin/ChangeLog b/sci-biology/smalt-bin/ChangeLog new file mode 100644 index 000000000..f3268fd32 --- /dev/null +++ b/sci-biology/smalt-bin/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/smalt-bin +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> smalt-bin-0.5.1.ebuild: + Cleaned ebuild and fixed LICENSE + diff --git a/sci-biology/smalt-bin/Manifest b/sci-biology/smalt-bin/Manifest index ff06d7e11..22371e482 100644 --- a/sci-biology/smalt-bin/Manifest +++ b/sci-biology/smalt-bin/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST smalt-0.5.1.tgz 534824 RMD160 4c0a26256784f3eae2d3e9e62142faacb67c8e68 SHA1 070e548905306c8d41a5cf02e63287318e80e892 SHA256 c8bca18a7ded7ad4b7070be7478bd046cf2d6a0a81054dfd96ebdba65c0a49d0 -EBUILD smalt-bin-0.5.1.ebuild 731 RMD160 31c6e6d423edd8e3d4a0d34d71644dd86271a134 SHA1 8dcd74a972a0c41145dea31287918892a1459bf4 SHA256 f97a797c4191b588f66a16800d651ed37e60509b92a9e3b3fcd32b5d163fd4ac +EBUILD smalt-bin-0.5.1.ebuild 631 RMD160 da666c04658f52c2b682ab9d4b2d791a7121f5cb SHA1 4d5ab3db32936e0795f16385523ed94e1f18ff63 SHA256 aa1370a8a78759d3fe186537c86ac156a119371e8e4972b3becd11f37812b802 +MISC ChangeLog 229 RMD160 187bb30cd58954da377d4d8d45b7103eb234b489 SHA1 4c82cafe0d7b70539d9ce7d07ff3531ba213ab71 SHA256 b9e0b03040eeb118ec6b1423dd7a67125378b391bc75f96d9a1d91a69fe5ac8a MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F28EACgkQgAnW8HDreRZ1BQCgqgk9ZcB25V3lwOO9yfSKQW+X +Zs0AnRlU96l4nxvPH63mkqggHMAzBcMZ +=DNRi +-----END PGP SIGNATURE----- diff --git a/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild b/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild index 9124a6cbb..7566c2097 100644 --- a/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild +++ b/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild @@ -2,32 +2,24 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 -DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2." +DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2" HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/" SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-"${PV}".tgz" -LICENSE="GRL" +LICENSE="as-is" SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - S="${WORKDIR}"/smalt-"${PV}" src_install(){ - if use x86; then - newbin smalt_i386 smalt || die - fi - if use amd64; then - newbin smalt_x86_64 smalt || die - fi - if use ia64; then - newbin smalt_ia64 || die - fi - dodoc NEWS smalt_manual.pdf || die - doman smalt.1 || die + use x86 && newbin smalt_i386 smalt + use amd64 && newbin smalt_x86_64 smalt + use ia64 && newbin smalt_ia64 + + dodoc NEWS smalt_manual.pdf + doman smalt.1 } diff --git a/sci-biology/ssaha2-bin/ChangeLog b/sci-biology/ssaha2-bin/ChangeLog new file mode 100644 index 000000000..914725e6e --- /dev/null +++ b/sci-biology/ssaha2-bin/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/ssaha2-bin +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> ssaha2-bin-2.5.3.ebuild: + Cleaned ebuild and fixed LICENSE + diff --git a/sci-biology/ssaha2-bin/Manifest b/sci-biology/ssaha2-bin/Manifest index 148bbd392..548ad7100 100644 --- a/sci-biology/ssaha2-bin/Manifest +++ b/sci-biology/ssaha2-bin/Manifest @@ -1,7 +1,18 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST samflag.c 2424 RMD160 a338182d756bdcd1214861d6273c0149df5e3177 SHA1 631282cc7fe88bac4f43011a0db09d9a1494859a SHA256 945958214ef1adc40029a6b3c323c37338e095e9e2bcbff5e5ec05aadbdb67d0 DIST ssaha2-manual.pdf 163188 RMD160 903bc1dc7f7bf89966f957c9df3c82128e233a53 SHA1 8e332b01628a3b64ea3dcc86d654a99d59277934 SHA256 1a0529168b71ac55e13b34264a854daa6a5dac9468f81ccb5b63bd5e1baafdbf DIST ssaha2_i686.tgz 288481 RMD160 0c493b917f40f5f259b6a6fe564ebc6a9e4409ec SHA1 b042e36c57f5e89098b6c5f07a2d646c02e76110 SHA256 7d173d763d9f685ef3d0075124bf8b763c6d2d3ed1a1f823bc66d6b6b029abed DIST ssaha2_ia64.tgz 458507 RMD160 8c3c821d292db94036f8d93342357ff0a8773bbe SHA1 a7ac847a64240f85eca3aff0df21bf9d339eed8f SHA256 3eb2a31559911f3ee87e11f3b977962da31b60c25ea0c9a064edfd1165b6b5dd DIST ssaha2_x86_64.tgz 287790 RMD160 93938da9898f30cf77f020329316228fd47ebe41 SHA1 d16d38e3bdab97994b4a70e4c0fc737a09b94d3a SHA256 0135ab2e285a898d450744b7c9d643efbeb6048783169a6647f310ce2e7b8138 -EBUILD ssaha2-bin-2.5.3.ebuild 1262 RMD160 316d8a8bfa9141159ce98215ee2a8ef121dfcb65 SHA1 7e4f63058267190dea68478ef20935bda63b848a SHA256 0929206dc3c0376c038507a234a2f54e5ad581514030e1131867c78cd2ddd07a +EBUILD ssaha2-bin-2.5.3.ebuild 1116 RMD160 af0f196ba6ce959ebf6d81115db2e9baa0190554 SHA1 79e1c04e3325d05dc0f914c14070955a1056cb4f SHA256 2c48c5fb6a7206930af612e88f52a1d5ce2537fb413fcb764060e4e9a2dcf68d +MISC ChangeLog 231 RMD160 5145398f2bfa105a4bdd2d361e32f7c51d15279e SHA1 0039c81fb8cfb17b60fbce912e03e9908042bdec SHA256 5aaf2c3745044bb045b9d1fc38249f74e135d690c9af921e030cf7a3606be2ef MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F3IUACgkQgAnW8HDreRbi3ACcCcSa7OHDWpL9VypnMDUMXsY+ +9CkAoJdyh2VAAqvtLbRkQ1PyZbAo3qNk +=hNec +-----END PGP SIGNATURE----- diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild index eaf02be74..34b63dd43 100644 --- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild +++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild @@ -1,43 +1,34 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 inherit toolchain-funcs DESCRIPTION="SSAHA2: Sequence Search and Alignment by Hashing Algorithm" HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2" -SRC_URI="x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_i686.tgz ) - amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_x86_64.tgz ) - ia64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_ia64.tgz ) - ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c - ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf" - -LICENSE="GRL" +SRC_URI=" + x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_i686.tgz ) + amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_x86_64.tgz ) + ia64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_ia64.tgz ) + ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c + ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf" + +LICENSE="as-is" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - -if use x86; then - S="${WORKDIR}"/ssaha2_v"${PV}"_i686 -fi -if use amd64; then - S="${WORKDIR}"/ssaha2_v"${PV}"_x86_64 -fi -if use ia64; then - S="${WORKDIR}"/ssaha2_v"${PV}"_ia64 -fi +use x86 && S="${WORKDIR}"/ssaha2_v"${PV}"_i686 +use amd64 && S="${WORKDIR}"/ssaha2_v"${PV}"_x86_64 +use ia64 && S="${WORKDIR}"/ssaha2_v"${PV}"_ia64 src_compile() { - $(tc-getCC) ${CFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags" + $(tc-getCC) ${CFLAGS} ${LDFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags" } src_install() { - dobin samflag ssaha2 ssaha2Build ssahaSNP || die "dobin failed" - dodoc README || die "dodoc failed" - dodoc "${DISTDIR}"/ssaha2-manual.pdf || die "Failed to install ssaha2-manual.pdf" + dobin samflag ssaha2 ssaha2Build ssahaSNP + dodoc README "${DISTDIR}"/ssaha2-manual.pdf } diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog new file mode 100644 index 000000000..1bf6d72fe --- /dev/null +++ b/sci-biology/staden/ChangeLog @@ -0,0 +1,16 @@ +# ChangeLog for sci-biology/staden +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild, + staden-9999.ebuild: + Streamlined fortran-2 eclass usage + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild, + staden-9999.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild, + staden-9999.ebuild: + Added fortran-2.eclass support + diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest index cc5fcf2b3..29d068a26 100644 --- a/sci-biology/staden/Manifest +++ b/sci-biology/staden/Manifest @@ -1,6 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX rpath.patch 4178 RMD160 0d2c8778ff81bc122a9a8eb0b28e8a423172075d SHA1 1360f9cfaa02c15a8e7a9535ae1a02099501d1f5 SHA256 126be8f08307ebefb9312d4c1a63e8ee00ed4976440248fe1fe4d0ab7f2b4736 DIST staden-2.0.0b8.tar.gz 4312143 RMD160 68b91a80fae29e0bf8f7e6ca1c0781591113684c SHA1 742092ff7bfb5acd3376ac85d5ab50507d1dd02f SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d DIST staden_doc-2.0.0b8-src.tar.gz 3068758 RMD160 4844c3b5acc1ef16c438f66313e1a8b3c182edc2 SHA1 daa6f0702fa250817fbdd07f932cdf0ed993c6c2 SHA256 77dbf83ef674affb5ee21b6ac7875e8c36446092e076e4d99cffbc4b2220c65f -EBUILD staden-2.0.0_beta8.ebuild 2284 RMD160 0ca58b683a3d314035c6d2f122f071fdca2ee3df SHA1 7a9ddee9c21e17a2a2349038f5ca834a08a86e21 SHA256 1c745cff13c22949aaba0bbd6a389365d48474b3ae4415b91b272d755ad2accb -EBUILD staden-9999.ebuild 2287 RMD160 dcdc6a912ea5eb074241f5483e9ac1f5160ef280 SHA1 db4440eb263d1b692e8187e021b4e0bad95b6b74 SHA256 258092dc0cfe3fd1f3a01e0c48b930d101f86936aab7853a9dda9cdec3a599bf +EBUILD staden-2.0.0_beta8.ebuild 2171 RMD160 d081b577c1c77700864c0b52d2353a7446160345 SHA1 cd017670a4eccbd81e8cc36a228947d02c023ea7 SHA256 4ab13673c38cb2571a86f2e0db65cb82032298a5f04b4b2a330b81178987a8f4 +EBUILD staden-9999.ebuild 2033 RMD160 d420d1e7f1ba242e3d70f6e912c040648c02dd29 SHA1 f694feec606602f93b23f3dc2735b2e0794e003b SHA256 b917fc7dc9fe88ae3929032dc0509531c82ae6a9f2e2180fdd9e822678049205 +MISC ChangeLog 517 RMD160 57f23b63c7feec53fbfc53b50d72d9152522bdb0 SHA1 70db18c65e33bc2d20d80ea71c709fd2c576b8b5 SHA256 c2e03544f72470ecfd4b6f3e5e9de9375b64a159fd3ea81972b9cb849254b6d4 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4DBiAACgkQgAnW8HDreRbZJwCfdd5Q1Y9W83ZzZx1PRSZfsVFP +goUAoNBW6lxxgve9xYwfaCvRsRrt7NiY +=Nos6 +-----END PGP SIGNATURE----- diff --git a/sci-biology/staden/staden-2.0.0_beta8.ebuild b/sci-biology/staden/staden-2.0.0_beta8.ebuild index a4e1e4737..f4f2411c3 100644 --- a/sci-biology/staden/staden-2.0.0_beta8.ebuild +++ b/sci-biology/staden/staden-2.0.0_beta8.ebuild @@ -4,40 +4,39 @@ EAPI=3 -inherit eutils flag-o-matic base +inherit base eutils flag-o-matic fortran-2 multilib -DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)." -HOMEPAGE="http://sourceforge.net/projects/staden" -SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz - http://sourceforge.net/projects/staden/files/staden/2.0.0b8/staden_doc-2.0.0b8-src.tar.gz" +DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" +HOMEPAGE="http://sourceforge.net/projects/staden/" +SRC_URI=" + http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz + http://sourceforge.net/projects/staden/files/staden/2.0.0b8/staden_doc-2.0.0b8-src.tar.gz" LICENSE="staden" SLOT="0" KEYWORDS="~x86 ~amd64" -IUSE="debug fortran X png curl tcl tk zlib" +IUSE="curl debug fortran png tcl tk X zlib" # either g77 or gfortran must be available # edit src/mk/linux.mk accordingly - # # this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058 # -# # -DEPEND=">=dev-lang/tk-8.4 - >=dev-lang/tcl-8.4 - dev-tcltk/tklib - >=sci-libs/io_lib-1.12.2 - >=sys-libs/zlib-1.2 - >=media-libs/libpng-1.2 - sci-biology/samtools - >=app-arch/xz-utils-4.999" - -# maybe we should depend on app-arch/lzma or app-arch/xz-utils? - -RDEPEND="tcl? ( >=dev-tcltk/itcl-3.2 ) - tk? ( >=dev-tcltk/itk-3.2 ) - >=dev-tcltk/iwidgets-4.0" +# +DEPEND=" + app-arch/xz-utils + dev-lang/tk + dev-tcltk/tklib + >=media-libs/libpng-1.2 + sci-biology/samtools + >=sci-libs/io_lib-1.12.2 + >=sys-libs/zlib-1.2 + virtual/fortran" +RDEPEND="${DEPEND} + >=dev-tcltk/iwidgets-4.0 + tcl? ( >=dev-tcltk/itcl-3.2 ) + tk? ( >=dev-tcltk/itk-3.2 )" S="${WORKDIR}"/staden-2.0.0b8-src @@ -54,11 +53,7 @@ src_configure(){ myconf=" --with-tklib=/usr/lib/tklib0.5" # HACK use amd64 && myconf="${myconf} --enable-64bit" use debug && append-cflags "-DCACHE_REF_DEBUG" - econf ${myconf} || die "configure failed" -} - -src_compile() { - emake || die "emake failed" + econf ${myconf} } src_install() { @@ -70,6 +65,8 @@ src_install() { # subsequently, apps linked against /usr/lib/staden can be run because # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden' # somehow for gap2caf, for example - echo 'LDPATH=/usr/lib/staden' > 99staden || die + cat >> "${T}"/99staden <<- EOF + LDPATH=/usr/$(get_libdir)/staden + EOF doenvd 99staden } diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild index fa67b6f96..47f7694ab 100644 --- a/sci-biology/staden/staden-9999.ebuild +++ b/sci-biology/staden/staden-9999.ebuild @@ -1,26 +1,24 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=3 -inherit eutils flag-o-matic base subversion # autotools +inherit base eutils flag-o-matic fortran-2 multilib subversion -DESCRIPTION="A fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin)." -HOMEPAGE="http://sourceforge.net/projects/staden" +DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" +HOMEPAGE="http://sourceforge.net/projects/staden/" # https://staden.svn.sourceforge.net/svnroot/staden staden if [ "$PV" == "9999" ]; then ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk" - #KEYWORDS="~amd64 ~x86" else SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b7-src.tar.gz" - #KEYWORDS="~amd64 ~x86" fi LICENSE="staden" SLOT="0" KEYWORDS="" -IUSE="debug fortran X png curl tcl tk zlib" +IUSE="curl debug fortran png tcl tk X zlib" # either g77 or gfortran must be available # edit src/mk/linux.mk accordingly @@ -28,23 +26,20 @@ IUSE="debug fortran X png curl tcl tk zlib" # # this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058 # -# # -DEPEND="dev-vcs/subversion - >=dev-lang/tk-8.4 - >=dev-lang/tcl-8.4 - dev-tcltk/tklib - >=sci-libs/io_lib-1.12.2 - >=sys-libs/zlib-1.2 - >=media-libs/libpng-1.2 - sci-biology/samtools - >=app-arch/xz-utils-4.999" - -# maybe we should depend on app-arch/lzma or app-arch/xz-utils? - -RDEPEND="tcl? ( >=dev-tcltk/itcl-3.2 ) - tk? ( >=dev-tcltk/itk-3.2 ) - >=dev-tcltk/iwidgets-4.0" +DEPEND=" + app-arch/xz-utils + dev-lang/tk + dev-tcltk/tklib + >=media-libs/libpng-1.2 + sci-biology/samtools + >=sci-libs/io_lib-1.12.2 + >=sys-libs/zlib-1.2 + virtual/fortran" +RDEPEND="${DEPEND} + >=dev-tcltk/iwidgets-4.0 + tcl? ( >=dev-tcltk/itcl-3.2 ) + tk? ( >=dev-tcltk/itk-3.2 )" src_unpack() { if [ "$PV" == "9999" ]; then @@ -67,16 +62,15 @@ src_configure() { use amd64 && myconf="${myconf} --enable-64bit" use debug && append-cflags "-DCACHE_REF_DEBUG" use debug && append-cxxflags "-DCACHE_REF_DEBUG" - econf ${myconf} || die "configure failed" - emake || die "emake failed" -} - -src_compile() { - emake || die "emake failed" + econf ${myconf} } src_install() { emake install DESTDIR="${D}" || die "make install failed" - echo "STADENROOT="${EPREFIX}"/usr/share/staden" > "${S}"/99staden + + cat >> "${S}"/99staden <<- EOF + STADENROOT="${EPREFIX}"/usr/share/staden + EOF + doenvd "${S}"/99staden || die } diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest index f9e28ae52..d47503418 100644 --- a/sci-biology/tablet-bin/Manifest +++ b/sci-biology/tablet-bin/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX response.varfile 645 RMD160 4662694266ac6104b5829923e5b6099ff68552f3 SHA1 971f052ae515bb630d166651adbf06005762b0a0 SHA256 29c9e65e81636b977ec0439f650d83b3cbfc3d23aef600339e4c8949fcd5369f DIST coveragestats.py 4800 RMD160 a45ef0ef293d08c62f79d4921c810554cea5cc44 SHA1 87b2e3432919c8cd2eb673bd8cf4a59f34d4a58e SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc DIST tablet_linux_x86_1_11_05_03.sh 24035425 RMD160 1d36db184cb79b93bd8460e9be293514d7db93d6 SHA1 42580d61f3c725fd357776538484ecc442c2c797 SHA256 3c7de5f0e5d37019485612723dfd3b17fd34e24df8986eb535fcb0335f8b2e99 -EBUILD tablet-bin-1.11.05.03.ebuild 3145 RMD160 6b74a2d66d74893a22380b0bc40853ba2bdb316e SHA1 8bf49eb7bf048d37942c6762125c7ab8ec9ab296 SHA256 fb6bc253d4ad10b5c5ab26f62394e46427b69b37c3f7ec0d03631b1ff372d24b +EBUILD tablet-bin-1.11.05.03.ebuild 3145 RMD160 3b9ac0279bd286fdf48801d5c1e54a028853f770 SHA1 fa826a6f22c1c3e6e2dacd42b538302d4c4a25c3 SHA256 24d671f4f0be32a3989d00b7ef545f6ead12bb1819f90539e833f2bca01c5759 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EiTQACgkQgAnW8HDreRYRTwCfTWaPyk1yHX+1i3YIkuh7+C38 +NVQAnj2ZKs20U5bdiPnxgg5bQL6tOobe +=aZHh +-----END PGP SIGNATURE----- diff --git a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild b/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild index 5f066d618..49983e32a 100644 --- a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild +++ b/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit python java-pkg-2 +inherit java-pkg-2 python DESCRIPTION="Graphical viewer for next generation sequence assemblies and alignments." HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" diff --git a/sci-biology/tclust/ChangeLog b/sci-biology/tclust/ChangeLog new file mode 100644 index 000000000..049bd0800 --- /dev/null +++ b/sci-biology/tclust/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/tclust +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*tclust-110625 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -tclust-0.1.ebuild, + +tclust-110625.ebuild, +files/tclust-110625-build.patch: + Cleaned ebuild + diff --git a/sci-biology/tclust/Manifest b/sci-biology/tclust/Manifest index 1298508f3..492f9b251 100644 --- a/sci-biology/tclust/Manifest +++ b/sci-biology/tclust/Manifest @@ -1,4 +1,16 @@ -DIST cdbfasta.tar.gz 59735 RMD160 c90e0ede03a01bf2da77f9beaa3c97fa7e46ff2a SHA1 2419421ab1d753d3bb8778c92236da74fee30526 SHA256 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c -DIST tclust.tar.gz 9521 RMD160 380e9811be58a2ab9659d25ade0b2a89d705c60f SHA1 42dec7cb63b895730babff5522b257c45001b016 SHA256 d222a7109ec135d5e80767046c47aa6d4201ae779e5d516771b377dbbd261798 -EBUILD tclust-0.1.ebuild 1219 RMD160 f5fb3902935005c2bcf61b12d36fc7bc36b9285a SHA1 305e0d1f49181e7a4ddb95395750e1c8e39fc982 SHA256 d0f33ac7b2b10d1295cd303bca041464849d59174aebb31e9877f964f8d24f97 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX tclust-110625-build.patch 1292 RMD160 4d97931504dba7b9a1c2d72430b2a63417cc9ea6 SHA1 0db6225234b85cc81fc744b0650e0108eed024f7 SHA256 70134ca266c8903da42b19e432e7b6c1840fe29f8139cf7f8c6e3742a4a43a56 +DIST gclib-110625.tar.gz 82727 RMD160 f12395354b47980577e9d83cc100a6bf6568bd33 SHA1 4c433e6a87663211dc00e2d855a11a058e5b6b48 SHA256 0c7f21fc92b033cd442b672e9014e3ffb9f2de97769ca525715692ed9359439b +DIST tclust-110625.tar.gz 9521 RMD160 380e9811be58a2ab9659d25ade0b2a89d705c60f SHA1 42dec7cb63b895730babff5522b257c45001b016 SHA256 d222a7109ec135d5e80767046c47aa6d4201ae779e5d516771b377dbbd261798 +EBUILD tclust-110625.ebuild 690 RMD160 844b13e2acc2e7aed99b5be134dbe2113077638f SHA1 f2adcfcc2803411baf02dadb0ea9db2f31328851 SHA256 b9fdd5b6e2844165b3d1862ba8a0fdf5cdced5403faacddec7d33c38dcf6ac04 +MISC ChangeLog 293 RMD160 0ef9d9f4df6e14863342c316a3d2911a9bb7d315 SHA1 d777b3cf178b10a4f15b0194fbdbd074e41926b7 SHA256 048c8e8d3667f6d087100b9f84fa0a36f058d60b8e99dc7e7c7d8ca39870ed10 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F/gMACgkQgAnW8HDreRYIlACfbxspQ6szup9+y0u/154r+iAM +IfkAoIQDAlCRsGAkjROODFzIu0eNtnI3 +=VNJs +-----END PGP SIGNATURE----- diff --git a/sci-biology/tclust/files/tclust-110625-build.patch b/sci-biology/tclust/files/tclust-110625-build.patch new file mode 100644 index 000000000..9474916af --- /dev/null +++ b/sci-biology/tclust/files/tclust-110625-build.patch @@ -0,0 +1,43 @@ + Makefile | 9 ++++----- + 1 files changed, 4 insertions(+), 5 deletions(-) + +diff --git a/Makefile b/Makefile +index f4f69f1..30ba16e 100644 +--- a/Makefile ++++ b/Makefile +@@ -11,8 +11,8 @@ SYSTYPE := $(shell uname) + + # C compiler + +-CC := g++ +-CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-exceptions -fno-rtti -fno-strict-aliasing ++CC ?= g++ ++CXXFLAGS += -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-exceptions -fno-rtti -fno-strict-aliasing + + %.o : %.c + ${CC} ${CFLAGS} -c $< -o $@ +@@ -24,7 +24,7 @@ CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_ + ${CC} ${CFLAGS} -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cxx + ${CC} ${CFLAGS} -c $< -o $@ +@@ -32,14 +32,13 @@ CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_ + # C/C++ linker + + LINKER := g++ +-LDFLAGS = + LOADLIBES := + + .PHONY : all + all: tclust + + tclust: ./tclust.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o +- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} ++ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} + + # target for removing all object files + diff --git a/sci-biology/tclust/tclust-0.1.ebuild b/sci-biology/tclust/tclust-0.1.ebuild deleted file mode 100644 index e41de0785..000000000 --- a/sci-biology/tclust/tclust-0.1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -DESCRIPTION="transitive closure clustering tool with overlap filtering options from TIGR Gene Indices project tools" -HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" -SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_prepare() { - # we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h - sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed" - sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die - cd ${PN} || die - ln -s ../cdbfasta/gcl . || die "Cannot make a softlink" -} - -src_compile() { - cd ${PN} || die - emake || die "emake failed in "${S}"/${PN}" -} - -src_install() { - cd ${PN} || die - dobin ${PN} || die "Failed to install ${PN} binary" - newdoc README README.${PN} || die -} diff --git a/sci-biology/tclust/tclust-110625.ebuild b/sci-biology/tclust/tclust-110625.ebuild new file mode 100644 index 000000000..563cdabfb --- /dev/null +++ b/sci-biology/tclust/tclust-110625.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Transitive closure clustering tool with overlap filtering options" +HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" +SRC_URI=" + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz -> gclib-${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +S=${WORKDIR}/${PN} + +src_prepare() { + epatch "${FILESDIR}"/${P}-build.patch + tc-export CC CXX +} + +src_install() { + dobin ${PN} + dodoc README +} diff --git a/sci-biology/tigr-assembler/ChangeLog b/sci-biology/tigr-assembler/ChangeLog index 8ac88cca5..adc4f70cf 100644 --- a/sci-biology/tigr-assembler/ChangeLog +++ b/sci-biology/tigr-assembler/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/tigr-assembler -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> tigr-assembler-2.0.ebuild: + Some ebuild cleaning + 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +tigr-assembler-2.0.ebuild: Mass import from sunrise diff --git a/sci-biology/tigr-assembler/Manifest b/sci-biology/tigr-assembler/Manifest index 826770d5c..0df073a6d 100644 --- a/sci-biology/tigr-assembler/Manifest +++ b/sci-biology/tigr-assembler/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX run_TA 1114 RMD160 a4889d91040e823a8caee8fc2eca6b8a7b38e97c SHA1 b69635740623566bf1658716958cb7a00afb5bbd SHA256 4b3ba31d7308932db000f66dbc4f5b12689efef2a125606ca7336c054770240a DIST TIGR_Assembler_v2.tar.gz 3252950 RMD160 5b7eaeebf8791acb3b53ab864f6e9c6571c70877 SHA1 8bd1886eb33d203598ac03decc7798a1fa0d85d7 SHA256 b5b660db388788173f7bd9778fe9b1e904bed7f6a464ab6cc92cd4608e70fd42 -EBUILD tigr-assembler-2.0.ebuild 1302 RMD160 abb59c33ee5f843f91cbb46cebda010560b7d0c0 SHA1 9b34eb85a125e774b9d772509c8725be7ac1663a SHA256 dd12539261adda1cc0311d036a2acbb4d81c91b9f14b541c2de6917665460b1a -MISC ChangeLog 366 RMD160 456390461b0286ece0f75002dcd49f90bd42e754 SHA1 a6d057fde4a594d8fb2d127bbb443d85ea039d9a SHA256 9b8273b2bfb0bd78ef4656523a6edd6e4fc4d4467c90fdc34995c1f95662c288 -MISC metadata.xml 312 RMD160 ba3ddd549c5d72f3c8872d00fb4c7c3131c5e9f5 SHA1 48b455ee7b2d56564438e66b1d81f72532cf3668 SHA256 02c1f9ac5ad24abc92c3a40e0340c9b2cb8874c00399013d20320141ecb43981 +EBUILD tigr-assembler-2.0.ebuild 1271 RMD160 3af030d6e00632bbd8819795732a2f6fea201df1 SHA1 d7a84e1a500a34b0c40cae5895be2897f7fdca16 SHA256 2953ddfc984238a12248fb19a51b28530f2dd28ff7e08c1d83857e6968968f96 +MISC ChangeLog 464 RMD160 923d85af2185c47f596cfdcb8390efa452d27930 SHA1 078287d84a8545710ac3e1b0022b1c87eff7249f SHA256 ea1e2b2acda2a1de1e3f7448e2a8abe71f4060a0d4590765a457eb1526c4793b +MISC metadata.xml 320 RMD160 4be5330790446398bad0fdababbe2ae8d5369ce3 SHA1 24457ce23ce8facf3852f9c3c35e574b9ee0785e SHA256 338be70c2ea8c0c6f5601311f86117f727fbd96e3b4908784a14683acd7c6601 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EznQACgkQgAnW8HDreRZU7wCfcWTJgYTrEZ33/hUANGkXdJPM +AgIAn3hu50aM69GZMk6OtQuO/cOs7jvS +=tMO2 +-----END PGP SIGNATURE----- diff --git a/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild b/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild index 0247b44a0..a55c067ff 100644 --- a/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild +++ b/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -13,9 +13,6 @@ SLOT="0" IUSE="" KEYWORDS="~amd64 ~x86" -DEPEND="" -RDEPEND="${DEPEND}" - S="${WORKDIR}/TIGR_Assembler_v2" src_prepare() { diff --git a/sci-biology/tigr-foundation-libs/ChangeLog b/sci-biology/tigr-foundation-libs/ChangeLog new file mode 100644 index 000000000..583614555 --- /dev/null +++ b/sci-biology/tigr-foundation-libs/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for sci-biology/tigr-foundation-libs +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> + tigr-foundation-libs-2.0-r1.ebuild: + Some ebuild cleaning + diff --git a/sci-biology/tigr-foundation-libs/Manifest b/sci-biology/tigr-foundation-libs/Manifest index 92f8cbbad..3e0ae1f33 100644 --- a/sci-biology/tigr-foundation-libs/Manifest +++ b/sci-biology/tigr-foundation-libs/Manifest @@ -1,4 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX TigrFoundation-all-patches.patch 2071 RMD160 ce194684d054613b254fa5f41fd31e520fe1cf5b SHA1 4a3f0d061b8024abb21178feeef3b1256e4117ac SHA256 e13f6136ef336e54ecc24d0e34e65e1ab827cfb7365b2d2686541ceed3cd6ac5 DIST autoEditor-1.20.tar.gz 2438903 RMD160 598ac977eb424959fc052b4c857ef4487b7e13f9 SHA1 985b5e880148a904b157295053945f9530718d30 SHA256 c0c399eda52a10deb0e0362b4caf909014768a4d08e90c900392cdf712cefd66 -EBUILD tigr-foundation-libs-2.0-r1.ebuild 901 RMD160 21432c20a478821460f5023f3f04d790656d0478 SHA1 79628e3286811af4cd3e97899ee77430f7c1a642 SHA256 5ceb776c2c45b9e105e6d0382be97f5a4e070504c1af674a2c0737e36552f7e8 -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +EBUILD tigr-foundation-libs-2.0-r1.ebuild 870 RMD160 330a00f7479fc33127ad2843045e47c35b09cdcf SHA1 533dc4ae3a82c2b9f8727f4acde9b5d41ffcdf1b SHA256 674553bbc205a83b2070a8cca1806bf44e50a687ea6e67d0c799b210f87fa0a3 +MISC ChangeLog 242 RMD160 fbaa9a69394a8f13e55c33a03460f547d35ff58f SHA1 597023def99a74e8772d980836a88a320392cc8a SHA256 e4d3c69604699333eec2b02fe46afe50432f3ee17104612adff3c4a99f912c7d +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EzqAACgkQgAnW8HDreRavZwCeJHLxV+A4K3Q5mFy2qjBnn5cA +p9gAnio/NdUn1JiPJuhmi2iL4sQrqcfi +=DrAT +-----END PGP SIGNATURE----- diff --git a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild index 18df09e4b..61068e4d5 100644 --- a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild +++ b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -18,9 +18,6 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - S="${WORKDIR}"/autoEditor-1.20/TigrFoundation-2.0 src_prepare(){ diff --git a/sci-biology/wcd/ChangeLog b/sci-biology/wcd/ChangeLog new file mode 100644 index 000000000..19bb05dc9 --- /dev/null +++ b/sci-biology/wcd/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/wcd +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*wcd-0.6.0 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -wcd-0.6.0_beta.ebuild, + +wcd-0.6.0.ebuild: + Cleaned ebuild + diff --git a/sci-biology/wcd/Manifest b/sci-biology/wcd/Manifest index 8f7fc7749..4fc1c885b 100644 --- a/sci-biology/wcd/Manifest +++ b/sci-biology/wcd/Manifest @@ -1,3 +1,14 @@ -DIST wcd-0.6.0B.tar.gz 595214 RMD160 eda5edf8215f0b723c5d1e970f36cb3e97b09e6f SHA1 988f944d4a6cd0894a864fa990f0f6eaab3b94bd SHA256 58a02677a0d89f9c2ff89f6f0ef9f5ce9caa487ff3f85a0a73fb9da0ec138509 -EBUILD wcd-0.6.0_beta.ebuild 1071 RMD160 ed692f6030456ff3f05c74e949c5e638ede04f64 SHA1 4d49e12d08a438222df4a6333c040ec614abb32e SHA256 3b84ec384dd12ecb97372b8959703375a422a4a4959af9a954769c3b18bef3ff -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +DIST wcd-0.6.0.tar.gz 595214 RMD160 eda5edf8215f0b723c5d1e970f36cb3e97b09e6f SHA1 988f944d4a6cd0894a864fa990f0f6eaab3b94bd SHA256 58a02677a0d89f9c2ff89f6f0ef9f5ce9caa487ff3f85a0a73fb9da0ec138509 +EBUILD wcd-0.6.0.ebuild 973 RMD160 3d00bc12ea340547f4fdf0a89eb2f1fb31392747 SHA1 28958b7829c5cc0235e0466586ffe46f9fdc5bb8 SHA256 23e8405f1cc13e1757e9d2dc6c977d0aa49f8b3f289e74cc2742cd5eb08b3f3d +MISC ChangeLog 252 RMD160 81599f287c3039cbe19f123d6d1d84497d64069f SHA1 49342a48f0625cbd073ef422c4b3c9ad8023b6e7 SHA256 66b8f77a881dfaacbd55af73ff2babfcd98df06c82271233b08adadc9cdb01e3 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F8ewACgkQgAnW8HDreRbOIgCgszlZYbNNJke5eKkilI0GC4eQ +s4gAoMes0BTxyr3lJKNv7FVO3MGwKR5Q +=dC9T +-----END PGP SIGNATURE----- diff --git a/sci-biology/wcd/wcd-0.6.0.ebuild b/sci-biology/wcd/wcd-0.6.0.ebuild new file mode 100644 index 000000000..3367cc404 --- /dev/null +++ b/sci-biology/wcd/wcd-0.6.0.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils flag-o-matic + +DESCRIPTION="Sequence clustering by either of: d2 function, edit distance, common word heuristics" +HOMEPAGE="http://code.google.com/p/wcdest/" +SRC_URI="http://wcdest.googlecode.com/files/${P}B.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="doc mpi threads" + +DEPEND="mpi? ( sys-cluster/mpich2 )" +RDEPEND="" + +S="${WORKDIR}"/wcd-0.6.0 + +src_configure(){ + local myconf="" + if use mpi; then + myconf="${myconf} --enable-mpi" + fi + + if use threads; then + myconf="${myconf} --enable-pthreads" + fi + + econf ${myconf} +} + +src_compile() { + emake + if use doc; then + emake pdf info html + fi +} + +src_install() { + local f + emake PREFIX=/usr DESTDIR="${D}" LIBDIR="${D}"usr/$(get_libdir) install + + if use doc; then + for f in README doc/wcd.html doc/wcd.pdf doc/wcd.texi; do + dodoc ${f} + done + fi +} diff --git a/sci-biology/wcd/wcd-0.6.0_beta.ebuild b/sci-biology/wcd/wcd-0.6.0_beta.ebuild deleted file mode 100644 index f7fbd7558..000000000 --- a/sci-biology/wcd/wcd-0.6.0_beta.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit flag-o-matic eutils - -DESCRIPTION="wcd clusters sequences (typically ESTs) by either of: d2 function, edit distance, common word heuristics." -HOMEPAGE="http://code.google.com/p/wcdest" -SRC_URI="http://wcdest.googlecode.com/files/wcd-0.6.0B.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="mpi threads" - -DEPEND="mpi? ( sys-cluster/mpich2 )" -RDEPEND="" - -S="${WORKDIR}"/wcd-0.6.0 - -src_prepare(){ - mv "${DESTDIR}"/wcd-0.6.0B.tar.gz "${DESTDIR}"/wcd-0.6.0.tar.gz || die -} - -src_compile(){ - local myconf="" - if use mpi; then - myconf="${myconf} --enable-mpi" - fi - - if use threads; then - myconf="${myconf} --enable-pthreads" - fi - - econf ${myconf} || die - - emake || die - emake pdf || die - emake info || die - emake html || die -} - -src_install() { - emake PREFIX=/usr DESTDIR="${D}" LIBDIR="${D}"usr/$(get_libdir) install \ - || die "make install failed" - for f in README doc/wcd.html doc/wcd.pdf doc/wcd.texi; do dodoc ${f} || die; done -} diff --git a/sci-biology/zmsort/ChangeLog b/sci-biology/zmsort/ChangeLog new file mode 100644 index 000000000..7e45e0a2c --- /dev/null +++ b/sci-biology/zmsort/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/zmsort +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*zmsort-110625 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -zmsort-0.1.ebuild, + +zmsort-110625.ebuild, +files/zmsort-110625-build.patch: + Cleaned ebuild + diff --git a/sci-biology/zmsort/Manifest b/sci-biology/zmsort/Manifest index 52cdae403..6fa0e1f31 100644 --- a/sci-biology/zmsort/Manifest +++ b/sci-biology/zmsort/Manifest @@ -1,4 +1,16 @@ -DIST cdbfasta.tar.gz 59735 RMD160 c90e0ede03a01bf2da77f9beaa3c97fa7e46ff2a SHA1 2419421ab1d753d3bb8778c92236da74fee30526 SHA256 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c -DIST zmsort.tar.gz 6192 RMD160 ccd1996ac194ee9b34044f585b3a82b94e07b7d5 SHA1 d0f0adca786f33329c5be93740ba9910c09c64d6 SHA256 8267592ec5ddb070a5feb07fcf475ce13ec28cdda33d685a218098bd6bc2962f -EBUILD zmsort-0.1.ebuild 1310 RMD160 f59ce932feb35dcc054fe86ce8c66b768967e1d5 SHA1 d5e6a043d362d22dfb2dea3c1c5e2bb2ae2c4dd3 SHA256 ce2fd5d34bc8a39285ce71308b646b469491b9efcf79404be0f2d18d6561ef47 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX zmsort-110625-build.patch 1188 RMD160 c9cafc93f2b64a47f29ae0b847913fe829973dfb SHA1 020f892aae2090f7149f7566d9b3b9cd45167b22 SHA256 6d5a8fb86bba20b92a526dcf7f9db893668e21f569fe6af78c5cfc8b9bf66b7e +DIST gclib-110625.tar.gz 82727 RMD160 f12395354b47980577e9d83cc100a6bf6568bd33 SHA1 4c433e6a87663211dc00e2d855a11a058e5b6b48 SHA256 0c7f21fc92b033cd442b672e9014e3ffb9f2de97769ca525715692ed9359439b +DIST zmsort-110625.tar.gz 6192 RMD160 ccd1996ac194ee9b34044f585b3a82b94e07b7d5 SHA1 d0f0adca786f33329c5be93740ba9910c09c64d6 SHA256 8267592ec5ddb070a5feb07fcf475ce13ec28cdda33d685a218098bd6bc2962f +EBUILD zmsort-110625.ebuild 698 RMD160 d4a6036541b04b17060b105830ff229d6379cf31 SHA1 3e5166d7afc2fd12ba880e71273fda39194aed32 SHA256 3393c1030128e87fefec376411923748c18698c641381b232c1e2e6e6d454c31 +MISC ChangeLog 293 RMD160 f961b1d43e475cd93fd62c98be34521770d284c7 SHA1 5dfbee5d688c55dc9a58f6359e83420d4e86db16 SHA256 c62d31ed38b317b278a9d026cd5eb78fb154418c1327893ee970e005d81ea84a MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F/tcACgkQgAnW8HDreRaDzgCgtvLzI/SDlJtObDEWHN5L+h2j +kAAAoKTXfitPox+bygIBTnazLcOfr0+S +=OOC7 +-----END PGP SIGNATURE----- diff --git a/sci-biology/zmsort/files/zmsort-110625-build.patch b/sci-biology/zmsort/files/zmsort-110625-build.patch new file mode 100644 index 000000000..3c6fe8a40 --- /dev/null +++ b/sci-biology/zmsort/files/zmsort-110625-build.patch @@ -0,0 +1,41 @@ + Makefile | 7 +++---- + 1 files changed, 3 insertions(+), 4 deletions(-) + +diff --git a/Makefile b/Makefile +index 82e16a0..f9505e0 100644 +--- a/Makefile ++++ b/Makefile +@@ -12,7 +12,7 @@ SYSTYPE := $(shell uname) + # C compiler + + CC := g++ +-CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 \ ++CXXFLAGS += -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 \ + -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT + + %.o : %.c +@@ -25,7 +25,7 @@ CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 \ + ${CC} ${CFLAGS} -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cxx + ${CC} ${CFLAGS} -c $< -o $@ +@@ -33,14 +33,13 @@ CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 \ + # C/C++ linker + + LINKER := g++ +-LDFLAGS = + LOADLIBES := + + .PHONY : all + all: zmsort + + zmsort: ./zmsort.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o +- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} ++ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} + + # target for removing all object files + diff --git a/sci-biology/zmsort/zmsort-0.1.ebuild b/sci-biology/zmsort/zmsort-0.1.ebuild deleted file mode 100644 index 2cec398e8..000000000 --- a/sci-biology/zmsort/zmsort-0.1.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -DESCRIPTION="merge-sort utility for compressed alignment files, with multi-file output option from TIGR Gene Indices project tools" -HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" -SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_prepare() { - # we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h - sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed" - sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die - sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' "${S}"/"${PN}"/zmsort.cpp || die - cd ${PN} || die - ln -s ../cdbfasta/gcl . || die "Cannot make a softlink" -} - -src_compile() { - cd ${PN} || die - emake || die "emake failed in "${S}"/${PN}" -} - -src_install() { - cd ${PN} || die - dobin ${PN} || die "Failed to install ${PN} binary" - newdoc README README.${PN} || die -} diff --git a/sci-biology/zmsort/zmsort-110625.ebuild b/sci-biology/zmsort/zmsort-110625.ebuild new file mode 100644 index 000000000..7d2920411 --- /dev/null +++ b/sci-biology/zmsort/zmsort-110625.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Merge-sort utility for compressed alignment files, with multi-file output" +HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" +SRC_URI=" + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz -> gclib-${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +S=${WORKDIR}/${PN} + +src_prepare() { + epatch "${FILESDIR}"/${P}-build.patch + tc-export CC CXX +} + +src_install() { + dobin ${PN} + dodoc README +} diff --git a/sci-chemistry/almost/Manifest b/sci-chemistry/almost/Manifest index 1bdb6de9f..dddcdd156 100644 --- a/sci-chemistry/almost/Manifest +++ b/sci-chemistry/almost/Manifest @@ -6,13 +6,13 @@ AUX configure.patch 10729 RMD160 da67da5102879a65bdf3afd4da721f68f20508db SHA1 d AUX configure2.patch 10918 RMD160 903207a4bdf34a73d78b344993c81640bf01f471 SHA1 2c39cb0f4e96c6e1351d74ff6282c6a8f31f9ba0 SHA256 dd31b4d155a7b0fb05b509a7f923d61e422524cdd857b1eb29d8debc171b2b54 AUX gcc-4.3.patch 2086 RMD160 58ef54dee42e6f44d90fb32f0fc0fb5d4b81152e SHA1 ceaf2e304b8f332c579f9888f5401400b77f3c2c SHA256 3210e88cc2bb6516b707d55ff1ea569a557ef34c6b6db9e41206743111d8a06f DIST almost-1.0.3-090822.tar.gz 10973194 RMD160 e1aaa736cc063275ecca347e4f483d5787bc2db3 SHA1 b8565ff71fb65e9f7e615050f1995b9cdd3087d0 SHA256 1e6351cc9de342c2d1ce64b4c44b66b482f7c2267dc0eca39ca2452e7b33422a -EBUILD almost-1.0.3-r2.ebuild 1868 RMD160 f7ec32bcb1dcfb7c99f575bc4909d0bbc686a6cf SHA1 d9669d140fd46a5699d14c05c28f52db6d4922e7 SHA256 25baae9d212f6e59f7a18c7617d1c51860b130ea23554064058be2a5ab2a2391 +EBUILD almost-1.0.3-r2.ebuild 1868 RMD160 9ef75acc4be02f8a89878687f5c1e64178629b1e SHA1 f877a20813d942806da53d72810e83d636bfa495 SHA256 bc54478d0387dae61f5f5142b77df241e17c3fdc6f3ff5560fb3453efc35b9aa MISC ChangeLog 514 RMD160 9f56e4d70dc7773c122a9af56c7e473e2f5dd3a6 SHA1 bd4b98558738b91c912754344ec49bd982563a95 SHA256 8f29f46a6f400801dc6d7ddd5df55248b99ca00286c4245290c2f950d5a00fa1 -MISC metadata.xml 268 RMD160 adbf63d25b16c6d9199c20ab0092b9a75a851605 SHA1 ffc9c0fba9a923d9ba5326283b60c31573888cf3 SHA256 6a8f1e47a14b8730b4a7ba9e0f0055ab4d6071ebcaf12bb601e8b949223c0c7f +MISC metadata.xml 255 RMD160 a86d48ddbccb0fabe237d68dcc9989b53cb0550b SHA1 91fd2c69d256979c92ac85401420c2760fb80c44 SHA256 d39da63d4038ef783fada0c4970d172c9620ae6727b88cd8406ee2d6afc9770a -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.11 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkqWNZMACgkQ5BmOA85PVLjTwwCeKdr3omrJP4sMrry+T41xQXW2 -OGoAoJwHUG6tU8WSK5+Dst2KVGxFZNeM -=JmlH +iEYEARECAAYFAk4EiXMACgkQgAnW8HDreRYicACfW4J2ld3+ROoa0bDEBIHydjKB +oiUAoKOFPjS+kiw6KD5rrxfEBKPcrgFj +=8sFV -----END PGP SIGNATURE----- diff --git a/sci-chemistry/almost/almost-1.0.3-r2.ebuild b/sci-chemistry/almost/almost-1.0.3-r2.ebuild index f91b72300..4ba5707b1 100644 --- a/sci-chemistry/almost/almost-1.0.3-r2.ebuild +++ b/sci-chemistry/almost/almost-1.0.3-r2.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit eutils flag-o-matic autotools +inherit autotools eutils flag-o-matic DATE="090822" diff --git a/sci-chemistry/almost/metadata.xml b/sci-chemistry/almost/metadata.xml index 27e626a3f..59d99c304 100644 --- a/sci-chemistry/almost/metadata.xml +++ b/sci-chemistry/almost/metadata.xml @@ -1,10 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>maintainer-wanted</herd> - <maintainer> - <email>jlec@gentoo.org</email> - <name>Justin Lecher</name> - </maintainer> + <herd>sci</herd> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher</name> + </maintainer> </pkgmetadata> - diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog index 26101af84..d51fa1a46 100644 --- a/sci-chemistry/ambertools/ChangeLog +++ b/sci-chemistry/ambertools/ChangeLog @@ -2,6 +2,19 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild, + -files/ambertools-1.4-bugfix_1-18.patch, ambertools-1.5.ebuild, + -files/ambertools-1.5-bugfix_1-3.patch: + Cleaned ebuild + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild, + ambertools-1.5.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild, + ambertools-1.5.ebuild: + Added fortran-2.eclass support + *ambertools-1.5 (04 Jun 2011) 04 Jun 2011; Reinis Danne <rei4dan@gmail.com> +ambertools-1.5.ebuild, diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest index 8e1849394..98d79e2e3 100644 --- a/sci-chemistry/ambertools/Manifest +++ b/sci-chemistry/ambertools/Manifest @@ -1,10 +1,20 @@ -AUX ambertools-1.4-bugfix_1-18.patch 365430 RMD160 09bf7da6a1d386af8fc5cb70269442ed82c81866 SHA1 11c8aa73dc11dd2b4794a25fe8bf8c26813024f3 SHA256 9b4e310e02039e07f4b063af13ba360afc88b92912f2e283210be26a89245bfa +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX ambertools-1.4-gentoo.patch 9926 RMD160 d84b121e1fa940cbf949855de3a5f0bee7566330 SHA1 08ea41b969bed5320230420d047e71a28333f76c SHA256 8f520c01146a704173ca31c68dc9440e2938263416f6d0c95de22d138426e01f -AUX ambertools-1.5-bugfix_1-3.patch 142997 RMD160 db9360ec6fca0be4582380bf99e5b981dae9ee77 SHA1 49be38f7650959705516948e5b0c9d27b6f3775f SHA256 f0bb5a30fb9bff698dcbcddd27c5412377a43577a883f7bbf8488c8fffdfbab3 AUX ambertools-1.5-gentoo.patch 14083 RMD160 762c52626c4eda51839caf74c001bb660052706a SHA1 ab0afa1f5b73569539515dba4cf6638a594c7d6e SHA256 82a83f660701c192272e79f5bab17a8a8be945d78fdab454ade3918281749922 DIST AmberTools-1.4.tar.bz2 67331137 RMD160 b499e18b583a0b454dd3a554986c19c111822e6a SHA1 ef0f9a44c8767ed35f942fd41afc636b67da0389 SHA256 af61da2f3643b4ec7f41620242b734a3cb4a79c5d422100fbd1fd1c402fecfc1 DIST AmberTools-1.5.tar.bz2 121062582 RMD160 4a086b42c378f0904f7bf0b16adb042f1677be55 SHA1 92e47e7337fb4901a5a145d808c5ffd42c82d08d SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c -EBUILD ambertools-1.4.ebuild 3359 RMD160 a0b078a57fd80f2d0df8fc26d5688d298d82ac5d SHA1 da867732e9c4fa91de6f604548d8fb321aa6e246 SHA256 2825415aabbf92511697aab8ee8904979e9f82e2d4445189f0b99adebe947740 -EBUILD ambertools-1.5.ebuild 3495 RMD160 6ef1dbeeb35c73b1287d7110e517c6fa41e3dad9 SHA1 abf6794ee04f9b6781d90f4b19ca7f56677cb373 SHA256 30764e6655577d2a4e8d979ac31bb3ad7b8ec2922f0ae6045acdcb6dcb5e49a2 -MISC ChangeLog 521 RMD160 d5011b16b7a96cbe8fcde381d04f81c0abdcc428 SHA1 36ef13374ebd6710d65ec40ffacbe43b8d6b519a SHA256 99338ed1207f6925eb8f5af0f088acef63a347da7e12c9e3628dc93208f719f7 +DIST ambertools-1.4-bugfix_1-18.patch.xz 48136 RMD160 83fe98ef2f4620cd4c85fc72147f830ddfa47b51 SHA1 7a5a2cba9172d017d83aed16ece06d6fed6a5196 SHA256 7ea936442ce1b29943e867adaeb69932d297ae50e0a63b0e03cfb18953e9f7c2 +DIST ambertools-1.5-bugfix_1-3.patch.xz 27268 RMD160 18a74e2e84e81d39417f656ef93e8ee4d4d4583d SHA1 bc52c0776d151a8db005bb7bfb40bf9e963bdeba SHA256 edec6ccc275ee0a70b2ecc9316c031249c4f32d89b1aa145cee32c862516049a +EBUILD ambertools-1.4.ebuild 3201 RMD160 b2f4331166bafc5093f04c4e7ad9bf2eee9ee0e5 SHA1 4033d6225f7e86d42292eed5ddecd7edeb6742ec SHA256 e3a77f1a006832c46117a5c6a6a641685965f8dfe0c949c0ec1e2f7e57f73835 +EBUILD ambertools-1.5.ebuild 3336 RMD160 d97fc7eade8bcf0d12596d42a512560671751d18 SHA1 0427a45349e95be91e274d0e12eb2eb484da6dd3 SHA256 8f8f33770cb12253fef10e9b651a567de36a2863d674b82ca3b1959ab8684353 +MISC ChangeLog 979 RMD160 02da25807e2c08495e5e6ed5803c8db37b6f0630 SHA1 086394d21356fb100929d5f86e86a098d34abe43 SHA256 c3cf8fabe0c249e1b500319df8296405392fa976fb599d941544af342d292aec MISC metadata.xml 263 RMD160 9484584cc295931e963dc785e211261f68e48c82 SHA1 a2c5af57c8eb879a4249fc0240432a4fc5b91ca5 SHA256 0e94df6d8502bc41ccd18ec4d570490e245c08595e837fd116a255458939e69b +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4E9DkACgkQgAnW8HDreRa8NwCg0fxLgoMsWuqoreVAAV0tzOgb +Bp4An3RO97c8j9rzfFLDjx6ix2ySY7kE +=zAXR +-----END PGP SIGNATURE----- diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild index 9e0e96b48..5e75cdb63 100644 --- a/sci-chemistry/ambertools/ambertools-1.4.ebuild +++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild @@ -2,18 +2,21 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="4" +EAPI=4 -inherit toolchain-funcs eutils +inherit eutils fortran-2 toolchain-funcs -DESCRIPTION="A suite of programs for carrying out complete molecular mechanics investigations" +DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" HOMEPAGE="http://ambermd.org/#AmberTools" -SRC_URI="AmberTools-${PV}.tar.bz2" +SRC_URI=" + AmberTools-${PV}.tar.bz2 + mirror://gentoo/${P}-bugfix_1-18.patch.xz" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="mpi openmp X" + RESTRICT="fetch" RDEPEND=" @@ -23,7 +26,8 @@ RDEPEND=" sci-libs/cifparse-obj sci-chemistry/mopac7 sci-libs/netcdf - sci-chemistry/reduce" + sci-chemistry/reduce + virtual/fortran" DEPEND="${RDEPEND} dev-util/byacc dev-libs/libf2c @@ -36,21 +40,18 @@ pkg_nofetch() { } pkg_setup() { - if use openmp && - [[ $(tc-getCC)$ == *gcc* ]] && - ( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] || - ! has_version sys-devel/gcc[openmp] ) - then - ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 " - ewarn "If you want to build ${PN} with OpenMP, abort now," - ewarn "and switch CC to an OpenMP capable compiler" + fortran-2_pkg_setup + if use openmp; then + tc-has-openmp || \ + die "Please select an openmp capable compiler like gcc[openmp]" fi AMBERHOME="${S}" } src_prepare() { - epatch "${FILESDIR}/${P}-bugfix_1-18.patch" - epatch "${FILESDIR}/${P}-gentoo.patch" + epatch \ + "${WORKDIR}/${P}-bugfix_1-18.patch" \ + "${FILESDIR}/${P}-gentoo.patch" cd AmberTools/src rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die } diff --git a/sci-chemistry/ambertools/ambertools-1.5.ebuild b/sci-chemistry/ambertools/ambertools-1.5.ebuild index 776a56f5b..9ac9755e7 100644 --- a/sci-chemistry/ambertools/ambertools-1.5.ebuild +++ b/sci-chemistry/ambertools/ambertools-1.5.ebuild @@ -2,18 +2,21 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="4" +EAPI=4 -inherit toolchain-funcs eutils +inherit eutils fortran-2 toolchain-funcs -DESCRIPTION="A suite of programs for carrying out complete molecular mechanics investigations" +DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" HOMEPAGE="http://ambermd.org/#AmberTools" -SRC_URI="AmberTools-${PV}.tar.bz2" +SRC_URI=" + AmberTools-${PV}.tar.bz2 + mirror://gentoo/${P}-bugfix_1-3.patch.xz" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="mpi openmp X" + RESTRICT="fetch" RDEPEND=" @@ -25,7 +28,8 @@ RDEPEND=" sci-chemistry/mopac7 sci-libs/netcdf sci-libs/fftw:2.1 - sci-chemistry/reduce" + sci-chemistry/reduce + virtual/fortran" DEPEND="${RDEPEND} dev-util/byacc dev-libs/libf2c @@ -38,21 +42,18 @@ pkg_nofetch() { } pkg_setup() { - if use openmp && - [[ $(tc-getCC)$ == *gcc* ]] && - ( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] || - ! has_version sys-devel/gcc[openmp] ) - then - ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 " - ewarn "If you want to build ${PN} with OpenMP, abort now," - ewarn "and switch CC to an OpenMP capable compiler" + fortran-2_pkg_setup + if use openmp; then + tc-has-openmp || \ + die "Please select an openmp capable compiler like gcc[openmp]" fi AMBERHOME="${S}" } src_prepare() { - epatch "${FILESDIR}/${P}-bugfix_1-3.patch" - epatch "${FILESDIR}/${P}-gentoo.patch" + epatch \ + "${WORKDIR}/${P}-bugfix_1-3.patch" \ + "${FILESDIR}/${P}-gentoo.patch" cd AmberTools/src rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die } diff --git a/sci-chemistry/ambertools/files/ambertools-1.4-bugfix_1-18.patch b/sci-chemistry/ambertools/files/ambertools-1.4-bugfix_1-18.patch deleted file mode 100644 index 2bc899b3c..000000000 --- a/sci-chemistry/ambertools/files/ambertools-1.4-bugfix_1-18.patch +++ /dev/null @@ -1,9025 +0,0 @@ -diff -urN amber11.orig/AmberTools/src/gleap/leapsrc/plugins.cpp amber11/AmberTools/src/gleap/leapsrc/plugins.cpp ---- amber11.orig/AmberTools/src/gleap/leapsrc/plugins.cpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/leapsrc/plugins.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -37,7 +37,7 @@ - - amber::help_command g_help_command; - amber::add_command g_add_command2; --amber::addions_command g_addions_command2; -+amber::addions_command g_addions_command2( "addions" ); - amber::addmap_command g_addpdbatommap_command2( "addpdbatommap" ); - amber::addmap_command g_addpdbresmap_command2( "addpdbresmap" ); - amber::null_command g_addatomtypes_command2( "addatomtypes" ); -diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/ambfmt/parm.cpp amber11/AmberTools/src/gleap/mortsrc/ambfmt/parm.cpp ---- amber11.orig/AmberTools/src/gleap/mortsrc/ambfmt/parm.cpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/mortsrc/ambfmt/parm.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -110,7 +110,7 @@ - assert( tmp.size() == 3 ); - atmvec as(tmp); - -- angl_t an = angl_t::create( as[0], as[1], as[2] ); -+ angl_t an = angl_t::frcget( as[0], as[1], as[2] ); - set_les( an ); - - atom_t pa1( *pff, as[0].get_i(TYPEID)-1 ); -@@ -277,6 +277,15 @@ - copy_dparm(pdihs[i], SCEE, di); - copy_dparm(pdihs[i], SCNB, di); - set_les( di ); -+ -+ /* -+ std::cout << as[0].get_s(NAME) << "-"; -+ std::cout << as[1].get_s(NAME) << "-"; -+ std::cout << as[2].get_s(NAME) << "-"; -+ std::cout << as[3].get_s(NAME) << " SCEE=" << di.get_d(SCEE) << std::endl; -+ */ -+ -+ - } - } - } -@@ -434,6 +443,8 @@ - parm_gbsa( *ai, gbtype ); - } - -+ //std::cout << " atom parameter assigned." << std::endl; -+ - bonditer_t bi = mol.bond_begin(); - bonditer_t be = mol.bond_end(); - for( ; bi != be; ++bi ) -@@ -441,6 +452,8 @@ - parm_bond( &ff, *bi ); - } - -+ //std::cout << " bond parameter assigned." << std::endl; -+ - bool fw = fixed_water(); - ai = mol.atom_begin(); - ae = mol.atom_end(); -diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/ambfmt/prep.cpp amber11/AmberTools/src/gleap/mortsrc/ambfmt/prep.cpp ---- amber11.orig/AmberTools/src/gleap/mortsrc/ambfmt/prep.cpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/mortsrc/ambfmt/prep.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -39,7 +39,7 @@ - resd_t r = resd_t::create( m ); - r.set_s(NAME, name); - r.set_s(TYPE, name.length()<3?name:name.substr(0,3)); -- -+ //std::cout << "Loading model " << name << std::endl; - // CORR/CHANGE, if CHANGE then sort line according - // the first column, no supported any more. - string use_first_column; -@@ -55,9 +55,13 @@ - is >> cutoff; - is.ignore(MAX_LINE_WIDTH, '\n'); - -+ vector<numvec> crdlst; -+ vector<int> nbrmap; -+ -+ // stacks - vector<atom_t> atoms; -- vector<numvec> crds; - vector<int> nunfills; -+ vector<int> idxstack; - - int head = 0; - int tail = 0; -@@ -71,7 +75,7 @@ - string name, type, chain; - ls >> name >> type >> chain; - -- -+ //std::cout << " processing atom " << name << std::endl; - string curt; - vector<string> terms; - while(ls >> curt) -@@ -96,22 +100,31 @@ - double angl = atof( terms[4].c_str() ); - double tors = atof( terms[5].c_str() ); - pchg = (terms.size()==7) ? atof( terms[6].c_str() ) : 0.0; -- int len = crds.size(); -- if(len==0) -+ if( idxstack.size()==0 ) - { - pos = makevec(0.0, 0.0, 0.0); -- } -- else if(len==1) -- { -- pos = zmatrix(crds[len-1], dist); -- } -- else if(len==2) -- { -- pos = zmatrix(crds[len-1], dist, crds[len-2], angl); -+ crdlst.push_back( pos ); -+ nbrmap.push_back( -1 ); - } - else -- { -- pos = zmatrix(crds[len-1], dist, crds[len-2], angl, crds[len-3], tors); -+ { -+ int nbr1 = idxstack.back(); -+ int nbr2 = nbrmap[nbr1]; -+ int nbr3 = (nbr2==-1) ? -1 : nbrmap[nbr2]; -+ if(nbr2==-1) -+ { -+ pos = zmatrix(crdlst[nbr1], dist); -+ } -+ else if(nbr3==-1) -+ { -+ pos = zmatrix(crdlst[nbr1], dist, crdlst[nbr2], angl); -+ } -+ else -+ { -+ pos = zmatrix(crdlst[nbr1], dist, crdlst[nbr2], angl, crdlst[nbr3], tors); -+ } -+ crdlst.push_back( pos ); -+ nbrmap.push_back( nbr1 ); - } - } - -@@ -127,7 +140,7 @@ - - if(atoms.size() > 0) - { -- assert( nunfills.size()==crds.size() ); -+ assert( nunfills.size()==idxstack.size() ); - bond_t::create(atom, atoms.back() ).set_i(ORDER, 1); - nunfills.back() -= 1; - } -@@ -145,7 +158,7 @@ - - if( nunfills.size()>0 && nunfills.back()==0 ) - { -- crds.pop_back(); -+ idxstack.pop_back(); - atoms.pop_back(); - nunfills.pop_back(); - } -@@ -153,7 +166,7 @@ - int nunfill = get_nunfill(chain); - if(nunfill > 0) - { -- crds.push_back(pos); -+ idxstack.push_back(crdlst.size()-1); - if(type != "DU") - atoms.push_back(atom); - nunfills.push_back(nunfill); -diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/capbox/addions.cpp amber11/AmberTools/src/gleap/mortsrc/capbox/addions.cpp ---- amber11.orig/AmberTools/src/gleap/mortsrc/capbox/addions.cpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/mortsrc/capbox/addions.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -83,11 +83,82 @@ - - void addions( molecule_t& m, const molecule_t& ion, int num_ion, double shlext, double resolution ) - { -+ vector<molecule_t> ionlst(num_ion, ion); - mort_ionee ionee(m); -- addions_core( ionee, ion, num_ion, shlext, resolution ); -+ addions_core( ionee, ionlst, shlext, resolution ); -+ m.cleanup(); - } - -- void addions_core( ionee_i& ionee, const molecule_t& ion, int num_ion, double shlext, double resolution ) -+ void addions( molecule_t& m, const molecule_t& ion1, int numion1, const molecule_t& ion2, int numion2, double shlext, double resolution ) -+ { -+ vector<molecule_t> ionlst; -+ int minnumion = std::min( numion1, numion2 ); -+ for( int i=0; i < minnumion; ++i ) -+ { -+ ionlst.push_back( ion1 ); -+ ionlst.push_back( ion2 ); -+ } -+ -+ int moreadd = std::max( numion1, numion2 ) - minnumion; -+ if( moreadd > 0 ) -+ { -+ const molecule_t* padd = (minnumion==numion1) ? &ion2 : &ion1; -+ for( int i=0; i < moreadd; ++i ) -+ { -+ ionlst.push_back( *padd ); -+ } -+ } -+ -+ mort_ionee ionee(m); -+ addions_core( ionee, ionlst, shlext, resolution ); -+ m.cleanup(); -+ } -+ -+ double get_ionvdwr( const molecule_t& ion ) -+ { -+ double r = get_vdwr( ion.atom_begin()->get_s(TYPE) ); -+ if( ion.natom() > 1 ) -+ { -+ std::cout << "Info: polyatomic ion, radius set to " << r*2.5 << " (2.5 times first atom)" << std::endl; -+ r *= 2.5; -+ } -+ return r; -+ } -+ -+ double get_minvdwr( const vector<molecule_t>& ionlst ) -+ { -+ double minr = 1000.0; -+ int numion = ionlst.size(); -+ for( int i=0; i < numion; ++i ) -+ { -+ double r = get_ionvdwr( ionlst[i] ); -+ minr = std::min( r, minr ); -+ } -+ -+ if( numion > 5 ) -+ { -+ double f = exp( log(numion+1.0)/3.0 ); -+ if( f > 1.0 ) minr *= f; -+ } -+ -+ return minr; -+ } -+ -+ double get_maxvdwr( const vector<molecule_t>& ionlst ) -+ { -+ double maxr = 0.0; -+ int numion = ionlst.size(); -+ for( int i=0; i < numion; ++i ) -+ { -+ double r = get_ionvdwr( ionlst[i] ); -+ maxr = std::max( r, maxr ); -+ } -+ -+ return maxr; -+ } -+ -+ -+ void addions_core( ionee_i& ionee, const vector<molecule_t>& ionlst, double shlext, double resolution ) - { - int natom = ionee.natom(); - int nresd = ionee.nresd(); -@@ -98,8 +169,8 @@ - - if( solute_natom != ionee.natom() ) - { -- std::cout << "Info: solute natom, total natom: " << solute_natom << " " << natom << std::endl; -- std::cout << " solute nresd, total nresd: " << solute_nresd << " " << nresd << std::endl; -+ std::cout << "Info: Number of solute atoms: " << solute_natom << ", total number of atoms: " << natom << std::endl; -+ std::cout << " Number of solute residues: " << solute_nresd << ", total number of residues: " << nresd << std::endl; - } - - vector<double>& pcord = ionee.getcord(); -@@ -111,23 +182,12 @@ - minmaxpos( pcord, pmin, pmax, solute_natom ); - - double max_radius = *std::max_element( pvdwr.begin(), pvdwr.end() ); -- double ion_radius = get_vdwr( ion.atom_begin()->get_s(TYPE) ); -- if( ion.natom() > 1 ) -- { -- std::cout << "Info: polyatomic ion, radius set to " << ion_radius*2.5 << " (2.5 times first atom)" << std::endl; -- ion_radius *= 2.5; -- } -- -- if( std::abs( charge(ion) ) < 0.1 ) -- { -- throw std::runtime_error( "Error: the ion you chose is in fact netural, thus add ion won't work" ); -- } -+ double ion_radius = get_maxvdwr( ionlst ); - - double buffer = ion_radius + max_radius + shlext; - std::cout << "Info: rmax, rion, shell: " << max_radius << " " << ion_radius << " " << shlext << std::endl; -- -- std::cout << "Info: pmin: " << pmin[0] << " " << pmin[1] << " " << pmin[2] << std::endl; -- std::cout << "Info: pmax: " << pmax[0] << " " << pmax[1] << " " << pmax[2] << std::endl; -+ //std::cout << "Info: pmin: " << pmin[0] << " " << pmin[1] << " " << pmin[2] << std::endl; -+ //std::cout << "Info: pmax: " << pmax[0] << " " << pmax[1] << " " << pmax[2] << std::endl; - - - pmin -= makevec(buffer, buffer, buffer); -@@ -151,9 +211,20 @@ - std::pair<double, numvec> max = make_pair(-1e20, numvec(3)); - tree.calculate( capbox::elepot_t(&pcord[0], &pchrg[0], solute_natom), min, max ); - -- for( int i=0; i < num_ion; ++i ) -+ int numion = ionlst.size(); -+ for( int i=0; i < numion; ++i ) - { -- numvec pos = charge(ion)>0 ? min.second : max.second; -+ if( std::abs( charge(ionlst[i]) ) < 0.1 ) -+ { -+ throw std::runtime_error( "Error: the ion you chose is in fact netural, thus add ion won't work" ); -+ } -+ -+ std::cout << "min potential: " << min.first << " x,y,z: " << min.second[0] << " " << min.second[1] << " " << min.second[2] << std::endl; -+ std::cout << "max potential: " << max.first << " x,y,z: " << max.second[0] << " " << max.second[1] << " " << max.second[2] << std::endl; -+ -+ -+ -+ numvec pos = charge(ionlst[i])>0 ? min.second : max.second; - - if( nosolvent ) - { -@@ -161,8 +232,8 @@ - std::cout << "Info: new ion will be placed at: "; - std::cout << pos[0] << " " << pos[1] << " " << pos[2] << " " << std::endl; - -- numvec sft = pos - center(ion); -- ionee.insert_resd( ion, sft, -1 ); -+ numvec sft = pos - center(ionlst[i]); -+ ionee.insert_resd( ionlst[i], sft, -1 ); - } - else - { -@@ -171,19 +242,19 @@ - { - // solvent present, find the nearest solvent residue, use ion to replace it. - // besides the ion must be before solvent, after the solute -- numvec sft = pos - center(ion); -- ionee.insert_resd( ion, sft, solute_nresd+i ); -+ numvec sft = pos - center(ionlst[i]); -+ ionee.insert_resd( ionlst[i], sft, solute_nresd+i ); - ionee.remove_resd( rid ); - } - else - { - // no bump atom: insert residue directly, no need to delete solvent residue -- numvec sft = pos - center(ion); -- ionee.insert_resd( ion, sft, solute_nresd+i ); -+ numvec sft = pos - center(ionlst[i]); -+ ionee.insert_resd( ionlst[i], sft, solute_nresd+i ); - } - } - -- if( i < num_ion-1 ) -+ if( i < numion-1 ) - { - // more ions to add: cut a sphere from the tree, make sure no overlapping - // the radius is 2*ion_radius, to avoid in the future ion -@@ -193,7 +264,7 @@ - - min.first = 1e20; - max.first =-1e20; -- tree.calculate(elepot_t(pos, charge(ion)), min, max); -+ tree.calculate(elepot_t(pos, charge(ionlst[i])), min, max); - } - } - -diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/capbox/addions.hpp amber11/AmberTools/src/gleap/mortsrc/capbox/addions.hpp ---- amber11.orig/AmberTools/src/gleap/mortsrc/capbox/addions.hpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/mortsrc/capbox/addions.hpp 2011-03-08 16:38:44.000000000 +0300 -@@ -91,7 +91,7 @@ - - if( i != m_natom ) - { -- throw std::runtime_error( "Error: there are atoms do not belong to any residue" ); -+ throw std::runtime_error( "Error: Atoms are present that are part of no residue!" ); - } - - m_pcord = &m_cord; -@@ -178,9 +178,11 @@ - vector<string> m_type; - }; - -- void addions_core( ionee_i& ionee, const molecule_t& ion, int nion, double shlext, double resolution ); -- -+ void addions_core( ionee_i& ionee, const vector<molecule_t>& ionlst, double shlext, double resolution ); -+ - void addions( molecule_t& m, const molecule_t& ion, int nion, double shlext, double res ); -+ -+ void addions( molecule_t& m, const molecule_t& ion1, int numion1, const molecule_t& ion2, int numion2, double shlext, double res ); - } - - -diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/capbox/solvate.cpp amber11/AmberTools/src/gleap/mortsrc/capbox/solvate.cpp ---- amber11.orig/AmberTools/src/gleap/mortsrc/capbox/solvate.cpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/mortsrc/capbox/solvate.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -126,13 +126,23 @@ - return cap.extent(); - } - -- numvec solvatebox_core( solute_i& solute, const molecule_t& m, double buffer, double closeness ) -+ numvec solvatebox_core( solute_i& solute, const molecule_t& m, double buffer, double closeness, bool iso ) - { - funstack_t::push( "solvatebox" ); - - numvec extent = regionlize( solute, true ); - extent += scalar_numvec(extent.size(), 2*buffer); - -+ if( iso ) -+ { -+ double extmax = std::max( extent[0], std::max(extent[1], extent[2]) ); -+ extent[0] = extmax; -+ extent[1] = extmax; -+ extent[2] = extmax; -+ } -+ -+ -+ - box_region box( extent ); - out_solute inn( solute, closeness ); - solvate( solute, m, and_region(box, inn) ); -@@ -180,10 +190,10 @@ - mol.set_v( CAP, makevec(capcnt[0],capcnt[1],capcnt[2],caprad) ); - } - -- void solvatebox(molecule_t& mol, const molecule_t& svt, double buffer, double closeness) -+ void solvatebox(molecule_t& mol, const molecule_t& svt, double buffer, double closeness, bool iso) - { - mort_solute solute(mol); -- numvec extent = solvatebox_core( solute, svt, buffer, closeness ); -+ numvec extent = solvatebox_core( solute, svt, buffer, closeness, iso ); - - mol.set_i( SOLUTE, BOX ); - mol.set_v( BOX, makevec(extent[0], extent[1], extent[2], 90.0) ); -diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/capbox/solvate.hpp amber11/AmberTools/src/gleap/mortsrc/capbox/solvate.hpp ---- amber11.orig/AmberTools/src/gleap/mortsrc/capbox/solvate.hpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/mortsrc/capbox/solvate.hpp 2011-03-08 16:38:44.000000000 +0300 -@@ -10,7 +10,7 @@ - - numvec solvatecap_core( solute_i& solute, const molecule_t& m, const numvec& capcnt, double caprad, double closeness ); - -- numvec solvatebox_core( solute_i& solute, const molecule_t& m, double buffer, double closeness ); -+ numvec solvatebox_core( solute_i& solute, const molecule_t& m, double buffer, double closeness, bool iso ); - - double solvateoct_core( solute_i& solute, const molecule_t& m, double buffer, double closeness ); - -@@ -18,7 +18,7 @@ - - void solvatecap( molecule_t& mol, const molecule_t& svt, const numvec& capcnt, double caprad, double closeness ); - -- void solvatebox( molecule_t& mol, const molecule_t& svt, double buffer, double closeness ); -+ void solvatebox( molecule_t& mol, const molecule_t& svt, double buffer, double closeness, bool iso ); - - void solvateoct( molecule_t& mol, const molecule_t& svt, double buffer, double closeness ); - -diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/pdbent/atom.cpp amber11/AmberTools/src/gleap/mortsrc/pdbent/atom.cpp ---- amber11.orig/AmberTools/src/gleap/mortsrc/pdbent/atom.cpp 2010-04-06 04:38:00.000000000 +0400 -+++ amber11/AmberTools/src/gleap/mortsrc/pdbent/atom.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -57,9 +57,9 @@ - { - funstack_t::push( "pdbent::write_atom" ); - -- os << "ATOM "; -+ os << "ATOM "; - -- write_iparm( os, atom, ID, "%5d" ); -+ write_iparm( os, atom, ID, "%6d" ); - - write_atom_name( os, atom ); - -@@ -102,7 +102,15 @@ - os << ' '; - } - -- os << format( "%4d " ) % (atom.resd().relid()+1); -+ int rid = atom.resd().relid() + 1; -+ if( rid < 10000 ) -+ { -+ os << format( "%4d " ) % rid; -+ } -+ else -+ { -+ os << format( "%5d " ) % rid; -+ } - } - - } // namespace pdbent -diff -urN amber11.orig/AmberTools/src/gleap/plugins/addions.cpp amber11/AmberTools/src/gleap/plugins/addions.cpp ---- amber11.orig/AmberTools/src/gleap/plugins/addions.cpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/plugins/addions.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -4,15 +4,33 @@ - - namespace amber - { -+ int get_numion( double dstchg, double ionchg ) -+ { -+ if( dstchg * ionchg >= 0 ) -+ { -+ throw std::runtime_error( "Error: molecule and ion are both positive (or negative), can not make neutral" ); -+ } -+ -+ return int( -dstchg/ionchg+0.5); -+ } -+ -+ - -- addions_command::addions_command( ) -- :command_i( "addions" ) -+ addions_command::addions_command( const char* cmd ) -+ :command_i( cmd ) - { - } - -- addions_command::addions_command( const string& dest, const string& ion, int number ) -- :m_dest( dest ), m_ion( ion ), m_number( number ) -+ addions_command::addions_command( const string& dest, const string& ion1, int numion1 ) -+ :m_dest( dest ), m_ion1( ion1 ), m_numion1( numion1 ) - { -+ m_runtyp = 1; -+ } -+ -+ addions_command::addions_command( const string& dest, const string& ion1, int numion1, const string& ion2, int numion2 ) -+ :m_dest( dest ), m_ion1( ion1 ), m_numion1( numion1 ), m_ion2(ion2), m_numion2(numion2) -+ { -+ m_runtyp = 2; - } - - addions_command::~addions_command() -@@ -21,28 +39,42 @@ - - bool addions_command::exec() - { -+ double shell_extent = 4.0; -+ double resolution = 1.0; - molecule_ptr pdst = content().get_mol( m_dest ); -- molecule_ptr pion = content().get_mol( m_ion ); - -- if( m_number==0 ) -+ if( m_runtyp==1 ) - { -- double dstchg = charge( *pdst ); -- double ionchg = charge( *pion ); -- if( dstchg * ionchg >= 0 ) -+ molecule_ptr pion = content().get_mol( m_ion1 ); -+ if( m_numion1==0 ) - { -- throw std::runtime_error( "Error: molecule and ion are both positive (or negative), can not make neutral" ); -+ m_numion1 = get_numion( charge(*pdst), charge(*pion) ); - } -- -- m_number = int( -dstchg/ionchg+0.5); -+ -+ assert( pdst != NULL && pion != NULL ); -+ addions( *pdst, *pion, m_numion1, shell_extent, resolution); - } -- -- -- assert( pdst != NULL && pion != NULL ); -+ else if( m_runtyp==2 ) -+ { -+ molecule_ptr pion1 = content().get_mol( m_ion1 ); -+ molecule_ptr pion2 = content().get_mol( m_ion2 ); -+ if( m_numion1==0 && m_numion2==0 ) -+ { -+ throw std::runtime_error( "Error: while addions2, numion1 and numion2 cannot both be zero" ); -+ } - -- double shell_extent = 4.0; -- double resolution = 1.0; -+ if( m_numion1==0 ) -+ { -+ m_numion1 = get_numion( charge(*pdst)+m_numion2*charge(*pion2), charge(*pion1) ); -+ } -+ else if( m_numion2==0 ) -+ { -+ m_numion2 = get_numion( charge(*pdst)+m_numion1*charge(*pion1), charge(*pion2) ); -+ } -+ -+ addions( *pdst, *pion1, m_numion1, *pion2, m_numion2, shell_extent, resolution ); -+ } - -- addions( *pdst, *pion, m_number, shell_extent, resolution); - return true; - } - -@@ -53,22 +85,29 @@ - - const char* addions_command::info( ) const - { -- return " usage: addion mol ion1 numIon1 "; -+ return " usage: addions mol ion1 numIon1 "; - } - - shared_ptr< command_i > addions_command::clone( const vector< string >& args ) const - { -- if( args.size()!=3 && args.size()!=4 ) -+ if( args.size()==3 || args.size()==4 ) - { -- throw std::runtime_error( "Error: wrong number of arguments " ); -+ int numb = args.size()==3 ? 0 : atoi(args[3].c_str()); -+ return shared_ptr< command_i >( new addions_command(args[1], args[2], numb) ); - } - -- int numb = args.size()==3 ? 0 : atoi(args[3].c_str()); -- -- return shared_ptr< command_i >( new addions_command(args[1], args[2], numb) ); -+ if( args.size()==6 ) -+ { -+ int nion1 = atoi( args[3].c_str() ); -+ int nion2 = atoi( args[5].c_str() ); -+ return shared_ptr< command_i >( new addions_command(args[1], args[2], nion1, args[4], nion2 ) ); -+ } -+ -+ throw std::runtime_error( "Error: Wrong number of arguments!" ); - } - -- addions_command g_addions_command; -+ addions_command g_addions_command( "addions" ); -+ addions_command g_addions2_command( "addions2" ); - - } // namespace amber - -diff -urN amber11.orig/AmberTools/src/gleap/plugins/addions.hpp amber11/AmberTools/src/gleap/plugins/addions.hpp ---- amber11.orig/AmberTools/src/gleap/plugins/addions.hpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/plugins/addions.hpp 2011-03-08 16:38:44.000000000 +0300 -@@ -11,10 +11,12 @@ - { - public: - -- addions_command(); -+ addions_command( const char* cmdnam ); - - addions_command( const string& dest, const string& ion, int number ); -- -+ -+ addions_command( const string& dest, const string& ion1, int numion1, const string& ion2, int numion2 ); -+ - virtual ~addions_command(); - - virtual bool exec(); -@@ -28,10 +30,12 @@ - private: - - string m_dest; -+ string m_ion1; -+ int m_numion1; -+ string m_ion2; -+ int m_numion2; - -- string m_ion; -- -- int m_number; -+ int m_runtyp; - }; - - } // namespace amber -diff -urN amber11.orig/AmberTools/src/gleap/plugins/check.cpp amber11/AmberTools/src/gleap/plugins/check.cpp ---- amber11.orig/AmberTools/src/gleap/plugins/check.cpp 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/src/gleap/plugins/check.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,415 @@ -+#include <object.hpp> -+#include "check.hpp" -+ -+namespace amber -+{ -+ void check_charge( const molecule_t& m ) -+ { -+ std::cout << "Checking charge: "; -+ double chg = charge( m ); -+ double dif = std::abs( chg - int(chg) ); -+ if( dif > 0.01 && dif < 0.99 ) -+ { -+ std::cout << std::endl; -+ std::cout << "Warning: non-integral total charge: " << chg << std::endl; -+ } -+ else -+ { -+ std::cout << chg << ", OK!" << std::endl; -+ } -+ } -+ -+ void check_bond_length( const molecule_t& m, double lowcutoff, double hghcutoff ) -+ { -+ std::cout << "Checking bond lengths: "; -+ bool ok = true; -+ bonditer_t bi = m.bond_begin(); -+ for( ; bi != m.bond_end(); ++bi ) -+ { -+ atom_t a1 = atom_1st( *bi ); -+ atom_t a2 = atom_2nd( *bi ); -+ double ln = dist( a1, a2 ); -+ if( ln < lowcutoff || ln > hghcutoff ) -+ { -+ resd_t r1 = a1.resd(); -+ resd_t r2 = a2.resd(); -+ ok = false; -+ std::cout << std::endl; -+ std::cout << format("Warning: There is a bond of %4.2f angstroms between: ") % ln; -+ std::cout << r1.get_s(NAME) << "." << a1.get_s(NAME) << " and "; -+ std::cout << r2.get_s(NAME) << "." << a2.get_s(NAME); -+ } -+ } -+ -+ if( ok ) -+ { -+ std::cout << "OK!" << std::endl; -+ } -+ else -+ { -+ std::cout << std::endl; -+ } -+ } -+ -+ void check_atom_distance( const molecule_t& m, double cutoff ) -+ { -+ std::cout << "Checking nonbonded atom contacts: "; -+ bool ok = true; -+ atomiter_t ai = m.atom_begin(); -+ for( ; ai != m.atom_end(); ++ai ) -+ { -+ atomiter_t aj = ai + 1; -+ for( ; aj != m.atom_end(); ++aj ) -+ { -+ if( bond_t::has(*ai, *aj) ) -+ { -+ continue; -+ } -+ -+ double d = dist( *ai, *aj ); -+ if( d < cutoff ) -+ { -+ ok = false; -+ resd_t r1 = ai->resd(); -+ resd_t r2 = aj->resd(); -+ std::cout << std::endl; -+ std::cout << format( "Warning: Close contact of %4.2f Angstroms between atoms ") % d; -+ std::cout << r1.get_s(NAME) << "." << ai->name() << " and "; -+ std::cout << r2.get_s(NAME) << "." << aj->name(); -+ } -+ } -+ } -+ -+ if( ok ) -+ { -+ std::cout << "OK!" << std::endl; -+ } -+ else -+ { -+ std::cout << std::endl; -+ } -+ } -+ -+ void check_atom_params( const molecule_t& m, const molecule_t& ff ) -+ { -+ std::cout << "Checking atom parameters: "; -+ bool ok = true; -+ atomiter_t ai = m.atom_begin(); -+ for( ; ai != m.atom_end(); ++ai ) -+ { -+ string t = ai->type(); -+ if( !atom_t::has(ff, t) ) -+ { -+ ok = false; -+ std::cout << "Warning: could not find parameters for atom: " << t << std::endl; -+ } -+ } -+ -+ if( ok ) -+ { -+ std::cout << "OK!" << std::endl; -+ } -+ else -+ { -+ std::cout << std::endl; -+ } -+ } -+ -+ void check_bond_params( const molecule_t& m, const molecule_t& ff ) -+ { -+ std::cout << "Checking bond parameters: "; -+ bool ok = true; -+ bonditer_t bi = m.bond_begin(); -+ for( ; bi != m.bond_end(); ++bi ) -+ { -+ atom_t a1 = atom_1st( *bi ); -+ atom_t a2 = atom_2nd( *bi ); -+ string t1 = a1.type(); -+ string t2 = a2.type(); -+ -+ atom_t pa1(ff, -1), pa2(ff, -1); -+ -+ if( atom_t::get(ff, t1, pa1) && atom_t::get(ff, t2, pa2) ) -+ { -+ if( bond_t::has(pa1, pa2) ) -+ { -+ continue; -+ } -+ } -+ -+ ok = false; -+ std::cout << std::endl; -+ std::cout << "Warning: could not find parameters for bond " << t1 << "-" << t2 << std::endl; -+ } -+ -+ if( ok ) -+ { -+ std::cout << "OK!" << std::endl; -+ } -+ else -+ { -+ std::cout << std::endl; -+ } -+ } -+ -+ void check_angl_params( const molecule_t& m, const molecule_t& ff ) -+ { -+ std::cout << "Checking angle parameters: "; -+ bool ok = true; -+ atomiter_t ai = m.atom_begin(); -+ for( ; ai != m.atom_end(); ++ai ) -+ { -+ atomiter_t aj = ai->atom_begin(); -+ for( ; aj != ai->atom_end(); ++aj ) -+ { -+ atomiter_t ak = aj + 1; -+ for( ; ak != ai->atom_end(); ++ak ) -+ { -+ string t1 = ai->type(); -+ string t2 = aj->type(); -+ string t3 = ak->type(); -+ atom_t pa1(ff, -1); -+ atom_t pa2(ff, -1); -+ atom_t pa3(ff, -1); -+ if( atom_t::get(ff, t1, pa1) && atom_t::get(ff, t2, pa2) && atom_t::get(ff, t3, pa3) ) -+ { -+ if( angl_t::has(pa2, pa1, pa3) ) -+ { -+ continue; -+ } -+ } -+ -+ ok = false; -+ std::cout << std::endl; -+ std::cout << "Warning: could not find parameters for angle " << t2 << "-" << t1 << "-" << t3; -+ } -+ } -+ } -+ -+ if( ok ) -+ { -+ std::cout << "OK!" << std::endl; -+ } -+ else -+ { -+ std::cout << std::endl; -+ } -+ } -+ -+ check_command::check_command() -+ : command_i( "check" ) -+ { -+ } -+ -+ check_command::check_command( bool checkmolcharge, bool checkatomparams, -+ bool checkbondparams, bool checkangleparams, -+ bool checkbondlength, bool checkatomclashes, -+ const string& molnam ) -+ : m_checkmolcharge(checkmolcharge), m_checkatomparams(checkatomparams), -+ m_checkbondparams(checkbondparams), m_checkangleparams(checkangleparams), -+ m_checkbondlength(checkbondlength), m_checkatomclashes(checkatomclashes), -+ m_molnam( molnam ) -+ { -+ } -+ -+ check_command::~check_command( ) -+ { -+ } -+ -+ bool check_command::exec( ) -+ { -+ int ndot = std::count( m_molnam.begin(), m_molnam.end(), '.' ); -+ if( ndot != 0 ) -+ { -+ throw std::runtime_error( "Error: Arguments, other than flags, must be units!" ); -+ } -+ -+ std::cout << "Checking unit \"" << m_molnam << "\"" << std::endl; -+ -+ molecule_ptr pmol = content().get_mol( m_molnam ); -+ molecule_ptr parm = content().get_mol( "_amberffp" ); -+ -+ if (m_checkmolcharge == true) -+ { -+ check_charge( *pmol ); -+ } -+ -+ if (m_checkatomparams == true) -+ { -+ check_atom_params( *pmol, *parm ); -+ } -+ -+ if (m_checkbondparams == true) -+ { -+ check_bond_params( *pmol, *parm ); -+ } -+ -+ if (m_checkangleparams == true) -+ { -+ check_angl_params( *pmol, *parm ); -+ } -+ -+ if (m_checkbondlength == true) -+ { -+ check_bond_length( *pmol, 0.5, 3.0 ); -+ } -+ -+ if (m_checkatomclashes == true) -+ { -+ check_atom_distance( *pmol, 1.5 ); -+ } -+ -+ return true; -+ } -+ -+ void check_command::undo() -+ { -+ } -+ -+ const char* check_command::info() const -+ { -+ return "check unit"; -+ } -+ -+ command_ptr check_command::clone( const vector< string >& args ) const -+ { -+ bool checkall = false; -+ bool checkmolcharge = false; -+ bool checkatomparams = false; -+ bool checkbondparams = false; -+ bool checkangleparams = false; -+ bool checkbondlength = false; -+ bool checkatomclashes = false; -+ bool nocheckatomclashes = false; -+ -+ std::string unit = ""; -+ -+ int i; -+ -+ //if( args.size()!=2 ) -+ //{ -+ // throw std::runtime_error( "Error: Wrong number of arguments!" ); -+ //} -+ -+ for (i = 1; i < args.size(); i++) -+ { -+ if (args[i] == "-charge") -+ { -+ checkmolcharge = true; -+ std::cout << "charge check requested" << std::endl; -+ } -+ else if (args[i] == "-atomparams") -+ { -+ checkatomparams = true; -+ std::cout << "atom parameter check requested" << std::endl; -+ } -+ else if (args[i] == "-bondparams") -+ { -+ checkbondparams = true; -+ std::cout << "bond parameter check requested" << std::endl; -+ } -+ else if (args[i] == "-angleparams") -+ { -+ checkangleparams = true; -+ std::cout << "angle parameter check requested" << std::endl; -+ } -+ else if (args[i] == "-bondlength") -+ { -+ checkbondlength = true; -+ std::cout << "bond length check requested" << std::endl; -+ } -+ else if (args[i] == "-clashes") -+ { -+ if (nocheckatomclashes == true) -+ { -+ throw std::runtime_error("Error: can't use -clashes and -noclashes together!"); -+ } -+ -+ checkatomclashes = true; -+ std::cout << "atom proximity (clash) check requested" << std::endl; -+ } -+ else if (args[i] == "-noclashes") -+ { -+ if (checkatomclashes == true) -+ { -+ throw std::runtime_error("Error: can't use -clashes and -noclashes together!"); -+ } -+ if (checkall == true) -+ { -+ throw std::runtime_error("Error: can't use -all and -noclashes together!"); -+ } -+ -+ nocheckatomclashes = true; -+ // Set everything else, too -+ checkmolcharge = true; -+ checkatomparams = true; -+ checkbondparams = true; -+ checkangleparams = true; -+ checkbondlength = true; -+ checkatomclashes = false; -+ checkall = false; -+ std::cout << "all except atom proximity (clash) check requested" << std::endl; -+ } -+ else if (args[i] == "-all") -+ { -+ if (nocheckatomclashes == true) -+ { -+ throw std::runtime_error("Error: can't use -all and -noclashes together!"); -+ } -+ -+ checkall = true; -+ } -+ else if (args[i].substr(0,1) == "-") -+ { -+ throw std::runtime_error("Error: in check, unrecognised flag: " + args[i] + "\n" -+ + " Allowed flags:" + "\n" -+ + " -charge" + "\n" -+ + " -atomparams" + "\n" -+ + " -bondparams" + "\n" -+ + " -angleparams" + "\n" -+ + " -bondlength" + "\n" -+ + " -clashes" + "\n" -+ + " -noclashes" + "\n" -+ + " -all" ); -+ } -+ else if (unit == "") -+ { -+ unit = args[i]; -+ } -+ else -+ { -+ throw std::runtime_error("Error: Too many arguments!"); -+ } -+ } -+ -+ if (unit == "") -+ { -+ throw std::runtime_error("Error: A unit must be supplied as an argument!"); -+ } -+ -+ // If everything is false except possibly checkall (whose truth -+ // or falsity is irrelevant), we want to check everything -+ if (checkmolcharge == false && checkatomparams == false -+ && checkbondparams == false && checkangleparams == false -+ && checkbondlength == false && checkatomclashes == false -+ && nocheckatomclashes == false) -+ { -+ checkmolcharge = true; -+ checkatomparams = true; -+ checkbondparams = true; -+ checkangleparams = true; -+ checkbondlength = true; -+ checkatomclashes = true; -+ std::cout << "all checks requested" << std::endl; -+ } -+ -+ return shared_ptr< command_i >( new check_command(checkmolcharge, checkatomparams, -+ checkbondparams, checkangleparams, -+ checkbondlength, checkatomclashes, -+ unit ) ); -+ } -+ -+} // namespace amber -+ -+amber::check_command g_check_command; -+ -diff -urN amber11.orig/AmberTools/src/gleap/plugins/check.hpp amber11/AmberTools/src/gleap/plugins/check.hpp ---- amber11.orig/AmberTools/src/gleap/plugins/check.hpp 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/src/gleap/plugins/check.hpp 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,49 @@ -+#ifndef GLEAP_PLUGINS_CHECK_HPP -+#define GLEAP_PLUGINS_CHECK_HPP -+ -+#include <guilib.hpp> -+ -+namespace amber -+{ -+ -+ using namespace mort; -+ -+ class check_command : public command_i -+ { -+ public: -+ -+ check_command(); -+ -+ check_command( bool checkmolcharge, bool checkatomparams, -+ bool checkbondparams, bool checkangleparams, -+ bool checkbondlength, bool checkatomclashes, -+ const string& molnam ); -+ -+ virtual ~check_command(); -+ -+ virtual bool exec(); -+ -+ virtual void undo(); -+ -+ virtual const char* info( ) const; -+ -+ virtual shared_ptr< command_i > clone( const vector<string>& args ) const; -+ -+ private: -+ -+ bool m_checkmolcharge; -+ bool m_checkatomparams; -+ bool m_checkbondparams; -+ bool m_checkangleparams; -+ bool m_checkbondlength; -+ bool m_checkatomclashes; -+ string m_molnam; -+ -+ }; -+ -+} // namespace amber -+ -+ -+ -+#endif -+ -diff -urN amber11.orig/AmberTools/src/gleap/plugins/loadpdb.cpp amber11/AmberTools/src/gleap/plugins/loadpdb.cpp ---- amber11.orig/AmberTools/src/gleap/plugins/loadpdb.cpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/plugins/loadpdb.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -31,28 +31,29 @@ - throw std::runtime_error( "Error: file " + m_file + " doesn't exist" ); - } - -- - molecule_ptr pmol( new molecule_t() ); - - read_pdb( is, *pmol ); - - string disulf = "auto"; - mortenv().get_s("disulfide", disulf); -- console_t* pcon = (disulf=="auto") ? NULL : console().get(); -+ if( disulf!="off" ) -+ { -+ console_t* pcon = (disulf=="auto") ? NULL : console().get(); - -- double disulfcut = 2.1; -- string tmp; -- if( mortenv().get_s("disulfcut", tmp) ) -- { -- disulfcut = atof( tmp.c_str() ); -- } -+ double disulfcut = 2.1; -+ string tmp; -+ if( mortenv().get_s("disulfcut", tmp) ) -+ { -+ disulfcut = atof( tmp.c_str() ); -+ } - -- disulfide( *pmol, disulfcut, pcon ); -+ disulfide( *pmol, disulfcut, pcon ); -+ } - - namemap_ptr nmap = content().get_nmap( "_namemap" ); - if( nmap != NULL ) - { -- - if( m_action=="loadpdb" ) - { - mdlize_mdb( *pmol, content() ); -diff -urN amber11.orig/AmberTools/src/gleap/plugins/merge.cpp amber11/AmberTools/src/gleap/plugins/merge.cpp ---- amber11.orig/AmberTools/src/gleap/plugins/merge.cpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/plugins/merge.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -241,6 +241,12 @@ - - - morf_t resd = merge(*pmol, *pseg, -1); -+ if( i==1 ) -+ { -+ // for the first residue. the head atom need to be unset for counting nunit in topology. -+ resd.set_i(HEAD, 0); -+ } -+ - resd.get_i(HEAD, head); - - if( m_action == "sequence" && i > 1) -diff -urN amber11.orig/AmberTools/src/gleap/plugins/set.cpp amber11/AmberTools/src/gleap/plugins/set.cpp ---- amber11.orig/AmberTools/src/gleap/plugins/set.cpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/plugins/set.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -4,6 +4,29 @@ - - namespace amber - { -+ vector<string> split( const string& a ) -+ { -+ size_t bgn = a.find( '{' ); -+ if( bgn==string::npos ) bgn = 0; -+ else bgn = bgn + 1; -+ -+ size_t end = a.rfind( '}' ); -+ if( end==string::npos ) end = a.length(); -+ -+ vector<string> result; -+ std::istringstream is( a.substr(bgn, end - bgn) ); -+ string s; -+ while( is >> s ) -+ { -+ result.push_back( s ); -+ } -+ -+ return result; -+ } -+ -+ -+ -+ - numvec atov(const string& a, int len) - { - std::istringstream is(a); -@@ -98,9 +121,23 @@ - } - else if( parm == "box" ) - { -+ numvec box(4); - obj.set_i(SOLUTE, BOX); -- obj.set_v(BOX, atov4d(value) ); -- return true; -+ vector<string> itmlst = split( value ); -+ if( itmlst.size()==3 || itmlst.size()==4 ) -+ { -+ box[0] = atof( itmlst[0].c_str() ); -+ box[1] = atof( itmlst[1].c_str() ); -+ box[2] = atof( itmlst[2].c_str() ); -+ box[3] = (itmlst.size()==4) ? atof(itmlst[3].c_str()) : 90.0; -+ obj.set_v(BOX, box); -+ return true; -+ } -+ else -+ { -+ std::cout << "Error: cannot understand box value: " << value << std::endl; -+ return false; -+ } - } - else if( parm == "cap" ) - { -diff -urN amber11.orig/AmberTools/src/gleap/plugins/solvate.cpp amber11/AmberTools/src/gleap/plugins/solvate.cpp ---- amber11.orig/AmberTools/src/gleap/plugins/solvate.cpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/plugins/solvate.cpp 2011-03-08 16:38:44.000000000 +0300 -@@ -11,9 +11,9 @@ - } - - solvate_command::solvate_command( const string& action, const string& solute, const string& solvent, -- const string& center, const string& extent, double closeness ) -+ const string& center, const string& extent, double closeness, bool iso ) - : m_action( action ), m_solute( solute ), m_center( center ), m_solvent( solvent ), -- m_extent( extent ), m_closeness( closeness ) -+ m_extent( extent ), m_closeness( closeness ), m_iso(iso) - { - } - -@@ -33,7 +33,7 @@ - { - double length = atof( m_extent.c_str() ); - -- solvatebox( *psolute, *psolvent, length, m_closeness ); -+ solvatebox( *psolute, *psolvent, length, m_closeness, m_iso ); - - return true; - } -@@ -103,7 +103,48 @@ - - shared_ptr< command_i > solvate_command::clone( const vector< string >& args ) const - { -- if( args[0]=="solvatebox" || args[0]=="solvateshell" || args[0]=="solvateoct" ) -+ if( args[0]=="solvatebox" ) -+ { -+ bool iso = false; -+ double closeness = 1.0; -+ if( args.size()==4 ) -+ { -+ iso = false; -+ closeness = 1.0; -+ } -+ else if( args.size()==5 ) -+ { -+ if( args[4]=="iso" ) -+ { -+ iso = true; -+ closeness = 1.0; -+ } -+ else -+ { -+ iso = false; -+ closeness = atof( args[4].c_str() ); -+ } -+ } -+ else if( args.size()==6 ) -+ { -+ if( args[5] != "iso" ) -+ { -+ throw std::runtime_error( "Error: cannot understand argument: " + args[5] ); -+ } -+ -+ iso = true; -+ closeness = atof( args[4].c_str() ); -+ } -+ else -+ { -+ throw std::runtime_error( "Error: wrong number of argument." ); -+ } -+ -+ return shared_ptr<command_i>( new solvate_command(args[0], args[1], args[2], "", args[3], closeness, iso) ); -+ } -+ -+ -+ if( args[0]=="solvateshell" || args[0]=="solvateoct" ) - { - if( args.size()!=4 && args.size()!=5 ) - { -@@ -111,7 +152,7 @@ - } - - double closeness = (args.size()==4) ? 1.0 : atof( args[4].c_str() ); -- return shared_ptr< command_i >( new solvate_command( args[0], args[1], args[2], "", args[3], closeness ) ); -+ return shared_ptr<command_i>( new solvate_command(args[0], args[1], args[2], "", args[3], closeness, false) ); - } - - assert( args[0] == "solvatecap" ); -@@ -122,7 +163,7 @@ - } - - double closeness = (args.size()==5) ? 1.0 : atof( args[5].c_str() ); -- return shared_ptr< command_i >( new solvate_command( args[0], args[1], args[2], args[3], args[4], closeness ) ); -+ return shared_ptr< command_i >( new solvate_command( args[0], args[1], args[2], args[3], args[4], closeness,false) ); - } - - } // namespace amber -diff -urN amber11.orig/AmberTools/src/gleap/plugins/solvate.hpp amber11/AmberTools/src/gleap/plugins/solvate.hpp ---- amber11.orig/AmberTools/src/gleap/plugins/solvate.hpp 2010-03-31 07:05:14.000000000 +0400 -+++ amber11/AmberTools/src/gleap/plugins/solvate.hpp 2011-03-08 16:38:44.000000000 +0300 -@@ -13,7 +13,7 @@ - - solvate_command( const string& type ); - -- solvate_command( const string& action, const string& solute, const string& solvent, const string& center, const string& extent, double closeness ); -+ solvate_command( const string& action, const string& solute, const string& solvent, const string& center, const string& extent, double closeness, bool iso ); - - virtual ~solvate_command( ); - -@@ -38,6 +38,8 @@ - string m_extent; - - double m_closeness; -+ -+ bool m_iso; - }; - - } // namespace amber -diff -urN amber11.orig/AmberTools/src/leap/src/leap/basics.c amber11/AmberTools/src/leap/src/leap/basics.c ---- amber11.orig/AmberTools/src/leap/src/leap/basics.c 2010-03-31 07:05:15.000000000 +0400 -+++ amber11/AmberTools/src/leap/src/leap/basics.c 2011-03-08 16:38:44.000000000 +0300 -@@ -462,7 +462,7 @@ - SmPMallocList = mPMem; - - sTrailer = ((char*)mPMem)+sizeof(MEMHEADER)+lSize; -- memcpy( sTrailer, mPMem->sCheck, TRAILERLEN ); -+ memmove( sTrailer, mPMem->sCheck, TRAILERLEN ); - - return ((char*)mPMem) + sizeof(MEMHEADER); - } -@@ -528,7 +528,7 @@ - if ( mPMem == NULL ) { - DFATAL(( "Could not malloc in REALLOC: %s\n", strerror(errno) )); - } -- memcpy( mPMem, mPPrevious, -+ memmove( mPMem, mPPrevious, - MIN( lSize, mPPrevious->lSize) + sizeof(MEMHEADER)+TRAILERLEN ); - - strcpy( mPPrevious->sCheck, FREESTR ); -@@ -540,7 +540,8 @@ - /* Fill the trailer */ - - sTrailer = ((char*)mPMem)+sizeof(MEMHEADER)+lSize; -- strcpy( sTrailer, mPMem->sCheck ); -+ memmove( sTrailer, mPMem->sCheck, strlen(mPMem->sCheck) ); -+ sTrailer[strlen(mPMem->sCheck)]='\0'; - - return ((char*)mPMem) + sizeof(MEMHEADER); - } -diff -urN amber11.orig/AmberTools/src/leap/src/leap/database.c amber11/AmberTools/src/leap/src/leap/database.c ---- amber11.orig/AmberTools/src/leap/src/leap/database.c 2010-03-31 07:05:15.000000000 +0400 -+++ amber11/AmberTools/src/leap/src/leap/database.c 2011-03-08 16:38:44.000000000 +0300 -@@ -594,6 +594,7 @@ - sStripString( char *sLine, char *sStr ) - { - char c, *sCur, *sStart; -+int mylength; - - sCur = sLine; - sStart = sStr; -@@ -615,8 +616,10 @@ - (*sStr++) = c; - } while ( (*sCur) != '\0' ); - *sStr = '\0'; -- strcpy( sLine, sCur ); -- -+ mylength=strlen(sCur); -+ //strcpy( sLine, sCur ); -+ memmove(sLine, sCur, mylength); -+ sLine[mylength]='\0'; - return(sStart); - } - -diff -urN amber11.orig/AmberTools/src/leap/src/leap/sort.c amber11/AmberTools/src/leap/src/leap/sort.c ---- amber11.orig/AmberTools/src/leap/src/leap/sort.c 2010-03-31 07:05:15.000000000 +0400 -+++ amber11/AmberTools/src/leap/src/leap/sort.c 2011-03-08 16:38:44.000000000 +0300 -@@ -217,9 +217,9 @@ - /* If false then swap it with the bottom of the false */ - /* group, and leave the current pointer where it is */ - -- memcpy( PSwapBuffer, PCur, iElementSize ); -- memcpy( PCur, PTop, iElementSize ); -- memcpy( PTop, PSwapBuffer, iElementSize ); -+ memmove( PSwapBuffer, PCur, iElementSize ); -+ memmove( PCur, PTop, iElementSize ); -+ memmove( PTop, PSwapBuffer, iElementSize ); - - PTop = (char*)PTop - iElementSize; - iBottomFalse--; -diff -urN amber11.orig/AmberTools/src/leap/src/leap/stringExtra.c amber11/AmberTools/src/leap/src/leap/stringExtra.c ---- amber11.orig/AmberTools/src/leap/src/leap/stringExtra.c 2010-03-31 07:05:15.000000000 +0400 -+++ amber11/AmberTools/src/leap/src/leap/stringExtra.c 2011-03-08 16:38:44.000000000 +0300 -@@ -130,10 +130,13 @@ - sRemoveLeadingSpaces( char *sLine ) - { - char *sTemp; -- -+int mylength; - sTemp = sLine; - while ( (*sTemp==' ') && ( *sTemp!='\0' )) sTemp++; -- strcpy( sLine, sTemp ); -+ mylength=strlen(sTemp); -+ //strcpy( sLine, sTemp ); -+ memmove(sLine, sTemp, mylength); -+ sLine[mylength]='\0'; - return(sLine); - } - -@@ -152,6 +155,7 @@ - sRemoveFirstString( char *sLine, char *sHead ) - { - char *sTemp; -+int mylength; - - sTemp = sLine; - while ( (*sTemp!=' ') && ( *sTemp!='\0' )) sTemp++; -@@ -163,7 +167,11 @@ - *sTemp = '\0'; - strcpy( sHead, sLine ); - sTemp++; -- strcpy( sLine, sTemp ); -+ mylength=strlen(sTemp); -+ //strcpy( sLine, sTemp ); -+ memmove(sLine, sTemp, mylength); -+ sLine[mylength]='\0'; -+ - } - - -diff -urN amber11.orig/AmberTools/src/leap/src/leap/xaCommand.c amber11/AmberTools/src/leap/src/leap/xaCommand.c ---- amber11.orig/AmberTools/src/leap/src/leap/xaCommand.c 2010-03-31 07:05:15.000000000 +0400 -+++ amber11/AmberTools/src/leap/src/leap/xaCommand.c 2011-03-08 16:38:44.000000000 +0300 -@@ -837,7 +837,7 @@ - * at the top of the list - */ - qsort( saPNames, iNumber, sizeof(STRING), -- (int (*) (void *, void *) )ziXACCompareTwoDirectoryEntries ); -+ (int (*) (const void *, const void *) )ziXACCompareTwoDirectoryEntries ); - - /* - * Reformulate as an array of pointers to char -diff -urN amber11.orig/AmberTools/src/pbsa/pb_init.f amber11/AmberTools/src/pbsa/pb_init.f ---- amber11.orig/AmberTools/src/pbsa/pb_init.f 2010-03-31 07:05:15.000000000 +0400 -+++ amber11/AmberTools/src/pbsa/pb_init.f 2011-03-08 16:38:44.000000000 +0300 -@@ -153,6 +153,7 @@ - - integer ires, iatm, jatm, maxmax, ic, i, j, jp, idum - integer alloc_err(64) -+ _REAL_ maxnbr_l, maxnba_l - _REAL_ rinchk - _REAL_ ucrgh(natom), ucrga(natom) - character (len=4) :: residue, resid(natom) -@@ -207,16 +208,24 @@ - - ! allocate pb nblists - -- maxnba = natom * ( sqrt( max(cutnb,cutsa,cutfd) ) )**3 / 3.0d0 -- maxnbr = natom * ( sqrt( cutres ) + 3.0d0 )**3 / 3.0d0 -+ maxnba_l = dble(natom) * ( sqrt( max(cutnb,cutsa,cutfd) ) )**3 / 3.0d0 -+ maxnbr_l = dble(natom) * ( sqrt( cutres ) + 3.0d0 )**3 / 3.0d0 - if ( natom >= 65536 ) then - write(6,'(a)') "PB Warnning: natom**2 exceeds integer limit (2147483647)." - maxmax = 2147483647 - else - maxmax = ceiling(dble(natom)/2*dble(natom)) -- endif -- if ( maxnba > maxmax ) maxnba = maxmax -- if ( maxnbr > maxmax ) maxnbr = maxmax -+ end if -+ if ( maxnbr_l > maxmax ) then -+ maxnbr = maxmax -+ else -+ maxnbr = int(maxnbr_l) -+ end if -+ if ( maxnba_l > maxmax ) then -+ maxnba = maxmax -+ else -+ maxnba = int(maxnba_l) -+ end if - - allocate( iar1pb (6,0:natom), stat = alloc_err(24) ) - allocate( iprshrt( maxnba ), stat = alloc_err(25) ) -diff -urN amber11.orig/AmberTools/src/ptraj/actions.c amber11/AmberTools/src/ptraj/actions.c ---- amber11.orig/AmberTools/src/ptraj/actions.c 2010-03-31 07:05:16.000000000 +0400 -+++ amber11/AmberTools/src/ptraj/actions.c 2011-03-08 16:38:44.000000000 +0300 -@@ -3655,6 +3655,8 @@ - { - action->mask = processAtomMask("*", action->state); - } -+ if (action->mask==NULL) -+ return INVALID_ARGUMENTS_RETURN_CODE; - /* Create a new "substate" trajInfo->state containing only some atoms: */ - modifyStateByMask(&trajInfo->state, &action->state, action->mask, 0); - trajInfo->atoms = trajInfo->state->atoms; -@@ -16406,6 +16408,10 @@ - residues[i].antiparallelSheetProb = 0; - residues[i].turnProb = 0; - residues[i].isActive = 0; -+ residues[i].H=-1; -+ residues[i].C=-1; -+ residues[i].N=-1; -+ residues[i].O=-1; - } - actRes = 0; - for (i = 0; i < action->state->atoms; i++) { -diff -urN amber11.orig/AmberTools/src/ptraj/cluster.c amber11/AmberTools/src/ptraj/cluster.c ---- amber11.orig/AmberTools/src/ptraj/cluster.c 2010-03-31 07:05:16.000000000 +0400 -+++ amber11/AmberTools/src/ptraj/cluster.c 2011-03-08 16:38:44.000000000 +0300 -@@ -4041,7 +4041,7 @@ - OutputTrajInfo = (trajectoryInfo*)action->carg2; - } - -- if (!FirstOutputFlag) -+ if (FirstOutputFlag==NULL) - { - FirstOutputFlag = (int*)SafeMalloc(__FILE__, __LINE__, sizeof(int) * This->ClusterCount); - memset(FirstOutputFlag, 1, sizeof(int) * This->ClusterCount); -@@ -4089,7 +4089,7 @@ - * to avoid crashing out if we hit the OS-level file-size limit: - */ - FileNumber[ClusterIndex] = FileNumber[ClusterIndex] + 1; -- fclose(OutputFiles[ClusterIndex]); -+ safe_fclose(OutputFiles[ClusterIndex]); - FirstOutputFlag[ClusterIndex] = 1; - FirstFlag = 1; - } -diff -urN amber11.orig/AmberTools/src/ptraj/io.c amber11/AmberTools/src/ptraj/io.c ---- amber11.orig/AmberTools/src/ptraj/io.c 2010-03-31 07:05:16.000000000 +0400 -+++ amber11/AmberTools/src/ptraj/io.c 2011-03-08 16:38:44.000000000 +0300 -@@ -673,6 +673,107 @@ - } - } - -+/* gzipFileSize() -+ * DRR: Return the uncompressed size in bytes of gzipped file by peeking -+ * at the last 4 bytes. -+ * NOTE: long long int should be equivalent to off_t. -+ */ -+long long int gzipFileSize(char *filename) { -+ FILE *infile; -+ unsigned char b1,b2,b3,b4; -+ long long int val,temp; -+ -+ if (filename==NULL) return -1; -+ if ( (infile = fopen(filename,"rb"))==NULL ) { -+ fprintf(stdout,"Error: gzipFileSize: Could not open %s for reading.\n",filename); -+ return -1; -+ } -+ -+ // Place 4 bytes from the end -+ fseek(infile, -4, SEEK_END); -+ -+ b1=0; b2=0; b3=0; b4=0; -+ fread(&b4,1,1,infile); -+ fread(&b3,1,1,infile); -+ fread(&b2,1,1,infile); -+ fread(&b1,1,1,infile); -+ -+ val = 0; -+ temp = (long long int) b1; -+ temp <<= 24; -+ val = val | temp; -+ temp = (long long int) b2; -+ temp <<= 16; -+ val = val | temp; -+ temp = (long long int) b3; -+ temp <<= 8; -+ val = val | temp; -+ temp = (long long int) b4; -+ val = val | temp; -+ -+ //val = (b1 << 24) | (b2 << 16) + (b3 << 8) + b4; -+ -+ fclose(infile); -+ -+ if (prnlev>0) fprintf(stdout,"gzipFileSize: Uncompressed size of %s: %lli\n",filename,val); -+ -+ return val; -+} -+ -+/* -+ * bzip2FileSize() -+ * DRR: Return the uncompressed size of bzip2 file in bytes by counting -+ * all characters using bzcat and wc. -+ */ -+long long int bzip2FileSize(char *filename) { -+ long long int val; -+ char *command; -+ FILE *pipe; -+ -+ if (filename==NULL) return -1; -+ // Use bzcat <file> | wc -c to calc file size -+ command=(char*) malloc( (15 + strlen(filename)) * sizeof(char)); -+ sprintf(command,"bzcat %s | wc -c",filename); -+ if ((pipe=popen(command,"r"))==NULL) { -+ fprintf(stdout,"Error: bzip2FileSize: Could not open %s for reading.\n",filename); -+ fprintf(stdout," Check that bzcat and wc are present on your system.\n"); -+ return -1; -+ } -+ fscanf(pipe,"%lli",&val); -+ pclose(pipe); -+ -+ if (prnlev>0) fprintf(stdout,"bzip2FileSize: Uncompressed size of %s: %lli\n",filename,val); -+ -+ return val; -+} -+ -+/* -+ * zipFileSize() -+ * DRR: Return the uncompressed size of zip file in bytes by counting -+ * all characters using unzip and wc. -+ */ -+long long int zipFileSize(char *filename) { -+ long long int val; -+ char *command; -+ FILE *pipe; -+ -+ if (filename==NULL) return -1; -+ // Use unzip -p <file> | wc -c to calc file size -+ command=(char*) malloc( (18 + strlen(filename)) * sizeof(char)); -+ sprintf(command,"unzip -p %s | wc -c",filename); -+ if ((pipe=popen(command,"r"))==NULL) { -+ fprintf(stdout,"Error: zipFileSize: Could not open %s for reading.\n",filename); -+ fprintf(stdout," Check that unzip and wc are present on your system.\n"); -+ return -1; -+ } -+ fscanf(pipe,"%lli",&val); -+ pclose(pipe); -+ -+ if (prnlev>0) fprintf(stdout,"zipFileSize: Uncompressed size of %s: %lli\n",filename,val); -+ -+ return val; -+} -+ - /* DAN ROE: - * id_Filesig(): Attempt to identify the file type by first 3 hex vals. - * A filename or an open stream should be supplied. -@@ -689,7 +790,7 @@ - * -2: Internal error - */ - int id_Filesig(char *filename, FILE *infile) { -- int *h; -+ unsigned char *h; - int i, type; - - /* Check that either filename or infile is specified, but not both */ -@@ -712,7 +813,7 @@ - rewind(infile); - - /* Read first 3 bytes from file */ -- h=(int*) calloc(3,sizeof(int)); -+ h=(unsigned char*) calloc(3,sizeof(unsigned char)); - fread(h,1,1,infile); - fread(h+1,1,1,infile); - fread(h+2,1,1,infile); -diff -urN amber11.orig/AmberTools/src/ptraj/io.h amber11/AmberTools/src/ptraj/io.h ---- amber11.orig/AmberTools/src/ptraj/io.h 2010-03-31 07:05:16.000000000 +0400 -+++ amber11/AmberTools/src/ptraj/io.h 2011-03-08 16:38:44.000000000 +0300 -@@ -76,6 +76,9 @@ - - extern void doSystem(char *); - extern char * promptToOpenFile( FILE **, char *, char *, char *); -+extern long long int gzipFileSize(char *); -+extern long long int bzip2FileSize(char *); -+extern long long int zipFileSize(char *); - extern int id_Filesig(char *,FILE *); - extern int openFile( FILE **, char *, char *); - extern int promptUserResponse(FILE *, FILE *, char *, char *, int); -@@ -94,6 +97,9 @@ - - extern void doSystem(); - extern char * promptToOpenFile(); -+extern long long int gzipFileSize(); -+extern long long int bzip2FileSize(); -+extern long long int zipFileSize(); - extern int id_Filesig(); - extern int openFile(); - extern int promptUserResponse(); -diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.c amber11/AmberTools/src/ptraj/ptraj.c ---- amber11.orig/AmberTools/src/ptraj/ptraj.c 2010-04-23 18:17:17.000000000 +0400 -+++ amber11/AmberTools/src/ptraj/ptraj.c 2011-03-08 16:38:44.000000000 +0300 -@@ -2058,7 +2058,8 @@ - int lines_per_set; - int start = 1; - int stop = 1; -- int frame_lines, frame_size, title_size, seekable; -+ int frame_lines, title_size, seekable; -+ long long int file_size, frame_size; - long int endoffset; - float *binposScratch; - FILE *fp; -@@ -2414,12 +2415,34 @@ - fprintf(stderr, "WARNING in %s: Could not find file status for %s\n", ROUTINE, filename); - return NULL; - } -+ -+ // Determine Uncompressed File Size for Nframes calculation -+ file_size=0; -+ if (trajInfo->compressType==1) // Gzip -+ file_size=gzipFileSize(filename); -+ else if (trajInfo->compressType==2) // Bzip2 -+ file_size=bzip2FileSize(filename); -+ else if (trajInfo->compressType==3) // Zip -+ file_size=zipFileSize(filename); -+ if (file_size<0) { -+ fprintf(stdout, -+ "ERROR in %s: Could not calculate uncompressed file size for %s\n", -+ ROUTINE, filename); -+ return NULL; -+ } -+ if (file_size==0) file_size=frame_stat.st_size; -+ - if (prnlev>0) -- fprintf(stdout,"[%i] Title offset %u Frame Size %u File size %lu\n", -- worldrank,trajInfo->titleSize,trajInfo->frameSize,frame_stat.st_size); -- if (((frame_stat.st_size - trajInfo->titleSize) % (trajInfo->frameSize)) == 0) { -+ fprintf(stdout,"[%i] Title offset %u Frame Size %u File size %lli\n", -+ worldrank,trajInfo->titleSize,trajInfo->frameSize,file_size); -+ frame_size = (long long int) trajInfo->titleSize; -+ file_size = file_size - frame_size; // Subtract title size from file total size. -+ frame_size = (long long int) trajInfo->frameSize; -+ trajInfo->Nframes = (int) (file_size / frame_size); -+ if (prnlev>0) fprintf(stdout," File has %i frames.\n",trajInfo->Nframes); -+ if ( (file_size % frame_size) == 0 ) { - seekable = 1; -- stop = (int) ((frame_stat.st_size - trajInfo->titleSize) / trajInfo->frameSize); -+ stop = trajInfo->Nframes; - } else { - stop = -1; - seekable = 0; -@@ -2538,7 +2561,8 @@ - printfone(" With this version of the code, this will likely lead to program failure!!!\n"); - } - -- -+ // Set number of frames. Amber trajectory sets Nframes above -+ if (trajInfo->Nframes==0 && stop>0) trajInfo->Nframes=stop; - trajInfo->start = start; - trajInfo->stop = stop; - trajInfo->offset = 1; -@@ -4182,7 +4206,7 @@ - fprintf(stderr,"Could not get replica temperature from file# %i\n",i); - break; - } -- fprintf(stdout," Replica %i mytemp=%lf ",i,repTemp); //DEBUG -+ if (prnlev>0) fprintf(stdout," Replica %i mytemp=%lf ",i,repTemp); //DEBUG - if (repTemp==currentCoordinateInfo->remdtrajtemp) { - if (prnlev>0) fprintf(stdout, - " REMD target temperature (%lf) found (%lf) at replica index %i\n", -@@ -7078,6 +7102,7 @@ - stackType *sp, *argumentStack; - ptrajState *startingState, *currentState, **statep; - char *continuation; -+ int totalFrames; - - int readCoordinates; - int processCoordinates; -@@ -7140,8 +7165,8 @@ - */ - - argumentStack = NULL; -- while ( (bufferp = fgets(buffer, BUFFER_SIZE, infile)) != NULL && -- strcmp(bufferp, "go\n") != 0 ) { -+ while ( (bufferp = fgets(buffer, BUFFER_SIZE, infile)) != NULL ) { -+ if ( strncmp(bufferp, "go", 2) == 0 ) break; - - continuation = bufferp; - while ( continuation != NULL ) { -@@ -7218,18 +7243,25 @@ - */ - - startingState->maxFrames = 0; -+ totalFrames=0; - for (sp = transformFileStack; sp != NULL; sp = sp->next) { - currentCoordinateInfo = (coordinateInfo *) sp->entry; - -+ fprintf(stdout," %s: %i frames.\n",currentCoordinateInfo->filename,currentCoordinateInfo->Nframes); -+ - startingState->maxFrames += (currentCoordinateInfo->stop - - currentCoordinateInfo->start) / - currentCoordinateInfo->offset + 1; -+ // In case we dont know how many frames will be processed, use total number of frames -+ totalFrames += currentCoordinateInfo->Nframes; - } - - printfone("\nPTRAJ: Successfully read the input file.\n"); -- if (startingState->maxFrames == -1) -+ if (startingState->maxFrames == -1) { - printfone(" Coordinate processing will occur until EOF (unknown number of frames).\n"); -- else -+ // Use total frames for action memory alloc. -+ startingState->maxFrames = totalFrames; -+ } else - printfone(" Coordinate processing will occur on %i frames.\n", - startingState->maxFrames); - printfone(" Summary of I/O and actions follows:\n\n"); -diff -urN amber11.orig/AmberTools/src/ptraj/trajectory.c amber11/AmberTools/src/ptraj/trajectory.c ---- amber11.orig/AmberTools/src/ptraj/trajectory.c 2010-03-31 07:05:16.000000000 +0400 -+++ amber11/AmberTools/src/ptraj/trajectory.c 2011-03-08 16:38:44.000000000 +0300 -@@ -2341,15 +2341,22 @@ - - /* trajFile_fseek() - * Wrapper for fseek. Seek to a given frame. -+ * fseeko is used for better compatibility with large files. To avoid -+ * losing bits each variable is explicitly converted to off_t in offset -+ * calculation. - */ - int trajFile_fseek(coordinateInfo *C, int frame) { - int err; -+ off_t offset; - - if (C==NULL) return -1; - -- if (C->isMPI==0) -- err=fseek(C->file, C->titleSize+(frame*C->frameSize), SEEK_SET); -- else -+ if (C->isMPI==0) { -+ offset = (off_t) frame; -+ offset *= (off_t) C->frameSize; -+ offset += (off_t) C->titleSize; -+ err=fseeko(C->file, offset, SEEK_SET); -+ } else - err=parallel_fseek(C,frame); - - return err; -diff -urN amber11.orig/AmberTools/src/ptraj/trajectory.h amber11/AmberTools/src/ptraj/trajectory.h ---- amber11.orig/AmberTools/src/ptraj/trajectory.h 2010-03-31 07:05:16.000000000 +0400 -+++ amber11/AmberTools/src/ptraj/trajectory.h 2011-03-08 16:38:44.000000000 +0300 -@@ -168,6 +168,7 @@ - char *filename; // File name - int start; // Frame to start processing - int stop; // Frame to end processing -+ int Nframes; // Total number of frames in the file. - int offset; // # of frames to skip - int append; // File will be appended to - int isBox; // File has box information -@@ -230,6 +231,7 @@ - _p_->filename = NULL; \ - _p_->start = 1; \ - _p_->stop = -1; \ -+ _p_->Nframes = 0; \ - _p_->offset = 1; \ - _p_->append = 0; \ - _p_->isBox = 0; \ -diff -urN amber11.orig/AmberTools/src/rism/amber_rism_interface.f amber11/AmberTools/src/rism/amber_rism_interface.f ---- amber11.orig/AmberTools/src/rism/amber_rism_interface.f 2010-04-07 16:55:55.000000000 +0400 -+++ amber11/AmberTools/src/rism/amber_rism_interface.f 2011-03-08 16:38:44.000000000 +0300 -@@ -501,7 +501,8 @@ - call timer_stop(TIME_REORIENT) - !linproj predict - call timer_start(TIME_CRDINTERP) -- call fce_force(fce_o,ff,rism_3d%solu%ratu) -+ if(rismprm%apply_rism_force==1)& -+ call fce_force(fce_o,ff,rism_3d%solu%ratu) - call timer_stop(TIME_CRDINTERP) - - call timer_start(TIME_REORIENT) -@@ -537,16 +538,17 @@ - end if - #else /*SANDER*/ - #endif /*SANDER*/ -- call rism3d_force(rism_3d,ff) -- if(rismprm%zerofrc==1)then -+ if(rismprm%apply_rism_force==1)then -+ call rism3d_force(rism_3d,ff) -+ if(rismprm%zerofrc==1)then - #ifdef MPI -- call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom,& -- mpirank,mpisize,mpicomm) -+ call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom,& -+ mpirank,mpisize,mpicomm) - #else -- call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom) -+ call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom) - #endif /*MPI*/ -+ end if - end if -- - !get the excess chemical potential - call timer_start(TIME_EXCHEM) - if(rismprm%gauss_fluct == 0)then -@@ -563,12 +565,12 @@ - #endif /*defined(MPI)*/ - end if - call timer_stop(TIME_EXCHEM) -- -+ - #ifdef RISM_CRDINTERP - call timer_start(TIME_REORIENT) - call orient(rism_3d,ff,qback) - call timer_stop(TIME_REORIENT) -- if(rismprm%fcestride >0)then -+ if(rismprm%fcestride >0 .and. rismprm%apply_rism_force==1)then - call timer_start(TIME_SAVECRDINTERP) - call fce_update(fce_o,ff,rism_3d%solu%ratu) - call timer_stop(TIME_SAVECRDINTERP) -@@ -586,7 +588,6 @@ - - end if - if(rismprm%apply_rism_force==1) frc = frc+ff -- call flush(6) - return - end subroutine rism_force - -@@ -1087,6 +1088,7 @@ - subroutine rism_writeSolvDistF(this,step) - use amber_rism_interface - use rism3d_opendx -+ use safemem - implicit none - #if defined(MPI) - include 'mpif.h' -@@ -1097,9 +1099,18 @@ - character(len=16) :: cstep - character(len=64) :: suffix - integer :: unit = 99,iostat=0 -+#ifdef MPI -+ integer :: err -+ _REAL_, pointer::work(:,:,:)=>NULL() -+#endif /*MPI*/ - #ifdef RISM_DEBUG - write(6,*) "printrism" - #endif -+#ifdef MPI -+ if(len_trim(guvfile) /= 0 .or. len_trim(huvfile) /= 0)then -+ work => reallocate_pointer(work, this%ng3(1), this%ng3(2), this%nz_local) -+ end if -+#endif /*MPI*/ - !................... outputting Guv and Cuv profiles ................... - do iv=1,this%solv%natom - write(cstep,'(i16)') step -@@ -1112,9 +1123,15 @@ - call mexit(6,1) - end if - # if defined(MPI) -+ do k=1,this%nz_local -+ do j=1,this%ng3(2) -+ do i=1,this%ng3(1) -+ work(i,j,k) = this%guv(i+(j-1)*(this%ng3(1)+2)+(k-1)*(this%ng3(1)+2)*this%ng3(2),iv) -+ end do -+ end do -+ end do - call writeDX(unit,& -- (/(((this%guv(i+(j-1)*(this%ng3(1)+2)+(k-1)*(this%ng3(1)+2)*this%ng3(2),iv)& -- ,i=1,this%ng3(1)),j=1,this%ng3(2)),k=1,this%nz_local)/),& -+ work,& - this%boxlen,this%ng3_local,this%ng3(3),this%ratucm,& - mpirank,mpisize,mpicomm) - # else -@@ -1131,9 +1148,16 @@ - call mexit(6,1) - end if - # if defined(MPI) -+ -+ do k=1,this%nz_local -+ do j=1,this%ng3(2) -+ do i=1,this%ng3(1) -+ work(i,j,k) =this%huv(i+(j-1)*(this%ng3(1)+2)+(k-1)*(this%ng3(1)+2)*this%ng3(2),iv) -+ end do -+ end do -+ end do - call writeDX(unit,& -- (/(((this%huv(i+(j-1)*(this%ng3(1)+2)+(k-1)*(this%ng3(1)+2)*this%ng3(2),iv)& -- ,i=1,this%ng3(1)),j=1,this%ng3(2)),k=1,this%nz_local)/),& -+ work,& - this%boxlen,this%ng3_local,this%ng3(3),this%ratucm,& - mpirank,mpisize,mpicomm) - # else -@@ -1160,6 +1184,9 @@ - if(mpirank==0)close(unit) - endif - end do -+#ifdef MPI -+ err = safe_deallocate(work) -+#endif /*MPI*/ - end subroutine rism_writeSolvDistF - - !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -diff -urN amber11.orig/AmberTools/src/rism/rism3d_c.f amber11/AmberTools/src/rism/rism3d_c.f ---- amber11.orig/AmberTools/src/rism/rism3d_c.f 2010-04-07 16:55:55.000000000 +0400 -+++ amber11/AmberTools/src/rism/rism3d_c.f 2011-03-08 16:38:44.000000000 +0300 -@@ -911,7 +911,7 @@ - !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - subroutine rism3d_aexchem_sp (this,xmu0,xmu0sp,egf) - use constants, only : PI,KB,AMBER_ELECTROSTATIC2 -- use rism_util, only : gaussquad_legendre -+ use rism_util, only : gaussquad_legendre, checksum - implicit none - #if defined(MPI) - include 'mpif.h' -@@ -947,132 +947,130 @@ - call flush(6) - #endif /*RISM_DEBUG*/ - -+ !.....total charge of solute -+ qut = sum(this%solu%charge) - !.....getting the numerical long-range contribution - egf = 0 -- eqkt = AMBER_ELECTROSTATIC2/KB/this%solv%temperature -- -- Nintmx = 200 -- if(Nintmx > ntvlmx)then -- write(6,'(1X,"Nintmx gt ntvlmx",I10)')ntvlmx -- call mexit(6,1) -- endif -- -- !.....initialize gauss-legendre integration -- call gaussquad_legendre (0d0,1d0,argum,weight,Nintmx) -- sumhc = 0.d0 -- sumh2 = 0.d0 -- -- !.....k loop -- do ik = 1, Nintmx -- -- k = argum(ik)/(1.d0-argum(ik)) -- -- !.....Bessel part -- sumb = 0.d0 -- -- do i=2,this%solu%natom -- do j=1,i-1 -- -- !......... site separation .......... -- dx = this%solu%ratu(1,i) - this%solu%ratu(1,j) -- dy = this%solu%ratu(2,i) - this%solu%ratu(2,j) -- dz = this%solu%ratu(3,i) - this%solu%ratu(3,j) -- -- r2 = dx*dx + dy*dy + dz*dz -- -- xarg = this%solv%xappa*k*sqrt(r2) -- if(xarg == 0.d0) & -- sumb = sumb + 1.d0*this%solu%charge(i)*this%solu%charge(j) -- if(xarg /= 0.d0) & -- sumb = sumb + sin(xarg)/xarg *this%solu%charge(i)*this%solu%charge(j) - -+ if(this%mpirank==0)then -+ eqkt = AMBER_ELECTROSTATIC2/KB/this%solv%temperature -+ Nintmx = 200 -+ if(Nintmx > ntvlmx)then -+ write(6,'(1X,"Nintmx gt ntvlmx",I10)')ntvlmx -+ call mexit(6,1) -+ endif -+ -+ !.....initialize gauss-legendre integration -+ call gaussquad_legendre (0d0,1d0,argum,weight,Nintmx) -+ sumhc = 0.d0 -+ sumh2 = 0.d0 -+ -+ !.....k loop -+ do ik = 1, Nintmx -+ -+ k = argum(ik)/(1.d0-argum(ik)) -+ -+ !.....Bessel part -+ sumb = 0.d0 -+ -+ do i=2,this%solu%natom -+ do j=1,i-1 -+ -+ !......... site separation .......... -+ dx = this%solu%ratu(1,i) - this%solu%ratu(1,j) -+ dy = this%solu%ratu(2,i) - this%solu%ratu(2,j) -+ dz = this%solu%ratu(3,i) - this%solu%ratu(3,j) -+ -+ r2 = dx*dx + dy*dy + dz*dz -+ -+ xarg = this%solv%xappa*k*sqrt(r2) -+ if(xarg == 0.d0) & -+ sumb = sumb + 1.d0*this%solu%charge(i)*this%solu%charge(j) -+ if(xarg /= 0.d0) & -+ sumb = sumb + sin(xarg)/xarg *this%solu%charge(i)*this%solu%charge(j) -+ -+ enddo - enddo -- enddo -- -- sumb = sumb*2.d0 -- -- do i=1,this%solu%natom -- sumb = sumb + 1.d0*this%solu%charge(i)*this%solu%charge(i) -- enddo -- -- !.....end of Bessel part -- -- x2arg = (k*this%solv%xappa*this%solv%smear)**2 -- k2 = k**2 -- -- denom = argum(ik)**2+(1.0d0-argum(ik))**2 -- -- sumhc = sumhc + & -- exp(-x2arg/2.d0)/denom*sumb*weight(ik) -- sumh2 = sumh2 + & -- exp(-x2arg/2.d0)*argum(ik)**2/(denom**2)*sumb*weight(ik) -- -- enddo -- -- !.....end of k-loop -- -- !.....total charge of solute -- qut = 0.d0 -- do i = 1,this%solu%natom -- qut = qut + this%solu%charge(i) -- enddo -- !.....site xappa -- if (this%closure == KH) then -+ -+ sumb = sumb*2.d0 -+ -+ do i=1,this%solu%natom -+ sumb = sumb + 1.d0*this%solu%charge(i)*this%solu%charge(i) -+ enddo -+ -+ !.....end of Bessel part -+ -+ x2arg = (k*this%solv%xappa*this%solv%smear)**2 -+ k2 = k**2 -+ -+ denom = argum(ik)**2+(1.0d0-argum(ik))**2 -+ -+ sumhc = sumhc + & -+ exp(-x2arg/2.d0)/denom*sumb*weight(ik) -+ sumh2 = sumh2 + & -+ exp(-x2arg/2.d0)*argum(ik)**2/(denom**2)*sumb*weight(ik) -+ -+ enddo -+ -+ !.....end of k-loop -+ -+ !.....site xappa -+ if (this%closure == KH) then -+ do iv = 1,this%solv%natom -+ if(qut*this%solv%charge_sp(iv) <= 0.d0) & -+ xmuh2lr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge_sp(iv)**2 -+ if(qut*this%solv%charge_sp(iv) > 0.d0) & -+ xmuh2lr(iv) = 0.d0 -+ xmuhclr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv) -+ enddo -+ else -+ do iv = 1,this%solv%natom -+ xmuh2lr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge_sp(iv)**2 -+ xmuhclr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv) -+ enddo -+ endif -+ -+ !.....unit for xappa - do iv = 1,this%solv%natom -- if(qut*this%solv%charge_sp(iv) <= 0.d0) & -- xmuh2lr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge_sp(iv)**2 -- if(qut*this%solv%charge_sp(iv) > 0.d0) & -- xmuh2lr(iv) = 0.d0 -- xmuhclr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv) -+ xmuh2lr(iv) = xmuh2lr(iv) * eqkt -+ xmuhclr(iv) = xmuhclr(iv) * eqkt - enddo -- else -+ -+ !.....divided by total xappa -+ if(this%solv%xappa /= 0.d0)then -+ do iv = 1,this%solv%natom -+ xmuh2lr(iv) = xmuh2lr(iv) / this%solv%xappa -+ xmuhclr(iv) = xmuhclr(iv) / this%solv%xappa -+ enddo -+ else -+ do iv = 1,this%solv%natom -+ xmuh2lr(iv) = 0.d0 -+ xmuhclr(iv) = 0.d0 -+ enddo -+ endif -+ -+ !.....multiplying xmulr by integral - do iv = 1,this%solv%natom -- xmuh2lr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge_sp(iv)**2 -- xmuhclr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv) -+ xmuh2lr(iv) = xmuh2lr(iv)*sumh2 -+ xmuhclr(iv) = - xmuhclr(iv)*sumhc - enddo -- endif -- -- !.....unit for xappa -- do iv = 1,this%solv%natom -- xmuh2lr(iv) = xmuh2lr(iv) * eqkt -- xmuhclr(iv) = xmuhclr(iv) * eqkt -- enddo -- -- !.....divided by total xappa -- if(this%solv%xappa /= 0.d0)then -+ -+ sumh2 = 0.d0 -+ sumhc = 0.d0 - do iv = 1,this%solv%natom -- xmuh2lr(iv) = xmuh2lr(iv) / this%solv%xappa -- xmuhclr(iv) = xmuhclr(iv) / this%solv%xappa -+ sumh2 = sumh2 + xmuh2lr(iv) -+ sumhc = sumhc + xmuhclr(iv) - enddo -- else -+ -+ !.....J devided by KT -+ sumh2 = sumh2 / (PI*this%solv%dielconst) * eqkt -+ sumhc = sumhc / PI * eqkt - do iv = 1,this%solv%natom -- xmuh2lr(iv) = 0.d0 -- xmuhclr(iv) = 0.d0 -+ xmuh2lr(iv) = xmuh2lr(iv) / (PI*this%solv%dielconst) * eqkt -+ xmuhclr(iv) = xmuhclr(iv) / PI * eqkt - enddo -- endif -- -- !.....multiplying xmulr by integral -- do iv = 1,this%solv%natom -- xmuh2lr(iv) = xmuh2lr(iv)*sumh2 -- xmuhclr(iv) = - xmuhclr(iv)*sumhc -- enddo -- -- sumh2 = 0.d0 -- sumhc = 0.d0 -- do iv = 1,this%solv%natom -- sumh2 = sumh2 + xmuh2lr(iv) -- sumhc = sumhc + xmuhclr(iv) -- enddo -- -- !.....J devided by KT -- sumh2 = sumh2 / (PI*this%solv%dielconst) * eqkt -- sumhc = sumhc / PI * eqkt -- do iv = 1,this%solv%natom -- xmuh2lr(iv) = xmuh2lr(iv) / (PI*this%solv%dielconst) * eqkt -- xmuhclr(iv) = xmuhclr(iv) / PI * eqkt -- enddo -- xmulr = sumh2 + sumhc -- -+ xmulr = sumh2 + sumhc -+ end if - !.................. calculating xMu0 by PLHNC closure .................. - if (this%closure == KH) then - dxmu = 0.d0 -@@ -1232,13 +1230,20 @@ - xmu0sp(iv) = xmu0sp(iv) * (this%boxvol/this%ngr) - enddo - -- !.....add long-range part -- xmu0 = xmu0 + (xmulr) -- egf = egf + (xmulr) -- do iv=1,this%solv%natom -- xmu0sp(iv) = xmu0sp(iv) + xmuh2lr(iv) + xmuhclr(iv) -- enddo -- -+ !.....add long-range part but only on the master process so we don't over count -+ !.....this contribution. -+!!$ write(0,*) "pre lr", this%mpirank, xmu0 -+!!$ write(0,*) checksum(this%huv,product(shape(this%huv)),this%mpicomm), & -+!!$ checksum(this%cuv,product(shape(this%cuv)),this%mpicomm), & -+!!$ checksum(this%uuv,product(shape(this%uuv)),this%mpicomm) -+ if(this%mpirank==0)then -+ xmu0 = xmu0 + (xmulr) -+ egf = egf + (xmulr) -+ do iv=1,this%solv%natom -+ xmu0sp(iv) = xmu0sp(iv) + xmuh2lr(iv) + xmuhclr(iv) -+ enddo -+ end if -+!!$ write(0,*) "post lr", this%mpirank, xmu0 - return - end subroutine rism3d_aexchem_sp - -@@ -2322,6 +2327,7 @@ - subroutine asympch(this,huvk0) - use constants, only : PI, FOURPI,& - AMBER_ELECTROSTATIC2,KB -+ use rism_util, only : checksum - implicit none - #if defined(MPI) - include 'mpif.h' -@@ -2339,9 +2345,7 @@ - _REAL_ :: xappa2,smear2_4 - _REAL_ :: asymhr_coeff - _REAL_,save :: asymhr_coeff_at_cut=0,asymcr_coeff_at_cut=0 -- _REAL_,save :: erfcAtCut=0,erfcAtNegCut=0,cut=15.5d0 --!! _REAL_,save :: erfcAtCut=0,erfcAtNegCut=0,cut=999d0 --! !linear spacing of the grid -+ _REAL_,save :: erfcAtCut=0,erfcAtNegCut=0,cut=4d0,maxcut - !offset :: z-axis offset (important for spatially distributed MPI) - _REAL_ :: offset - ! !number of gridpoints in each direction to use -@@ -2351,7 +2355,7 @@ - _REAL_ :: erfc - external erfc - integer :: irank,ierr,i -- _REAL_:: checksum,mpitmp -+ _REAL_:: mpitmp - - half_smear_root_pi=sqrt(PI)*this%solv%smear/2d0 - half_xappa_smear=this%solv%xappa*this%solv%smear/2d0 -@@ -2361,7 +2365,9 @@ - asymhr_coeff=exp(-(this%solv%xappa**2)*(this%solv%smear**2)/4d0)* & - (2d0*exp(-(this%solv%smear*this%solv%xappa/2d0)**2)/(sqrt(PI)*this%solv%smear) & - - this%solv%xappa * erfc(this%solv%xappa*this%solv%smear/2d0)) -- do while(exp(-quarter_xappa2_smear2)-asymhr_coeff_at_cut > 1d-7 .and. 1d0-asymcr_coeff_at_cut > 1d-7) -+ maxcut = sqrt(sum(this%boxlen**2)) -+ do while((exp(-quarter_xappa2_smear2)-asymhr_coeff_at_cut > 1d-7 .or. 1d0-asymcr_coeff_at_cut > 1d-7)& -+ .and. cut < maxcut) - erfcAtCut = erfc(cut) - erfcAtNegCut = erfc(-cut) - asymhr_coeff_at_cut=exp(-quarter_xappa2_smear2) & -@@ -2370,10 +2376,10 @@ - !(erfcAtNegCut - erfcAtCut)/2d0 - asymcr_coeff_at_cut=(1d0-erfc(cut/this%solv%smear)) - cut = cut+.1d0 -- ! write(6,*)'cut coeff',asymhr_coeff_at_cut,asymcr_coeff_at_cut -+! write(0,*)'cut coeff',this%mpirank,asymhr_coeff_at_cut,asymcr_coeff_at_cut - end do - #ifdef RISM_DEBUG -- write(6,*)'cut coeff',cut,asymhr_coeff_at_cut,asymcr_coeff_at_cut -+ write(0,*)'cut coeff',cut,exp(-quarter_xappa2_smear2)-asymhr_coeff_at_cut,asymcr_coeff_at_cut - #endif /*RISM_DEBUG*/ - !.....initialize - this%asymcr=0d0 -@@ -2569,7 +2575,7 @@ - this%asymcr = this%asymcr * factor - this%asymhr = this%asymhr * factor - this%asymck = this%asymck * (factor / this%boxvol) -- this%asymhk = this%asymhk * (factor / this%boxvol)/2d0/PI**2 -+ this%asymhk = this%asymhk * (factor / this%boxvol) - - !?WHY IS THIS ONLY FOR ny_start==0?! - if(this%ny_start==0)then -@@ -2591,35 +2597,22 @@ - end if - #ifdef RISM_DEBUG - # ifdef MPI -- checksum = sum(this%asymck) --# ifdef USE_MPI_IN_PLACE -- call mpi_allreduce(MPI_IN_PLACE,checksum,1,MPI_DOUBLE_PRECISION,mpi_sum,this%mpicomm,ierr) --# else -- call mpi_allreduce(checksum,mpitmp,1,MPI_DOUBLE_PRECISION,mpi_sum,this%mpicomm,ierr) -- checksum = mpitmp --# endif /*USE_MPI_IN_PLACE*/ -- if(this%mpirank == 0)then -- write(6,*) "SUM this%asymck", this%mpirank, checksum -+ write(6,*) "SUM this%asymhr", this%mpirank, & -+ checksum(this%asymhr,product(shape(this%asymhr)), this%mpicomm), sum(this%asymhr) -+ write(6,*) "SUM this%asymcr", this%mpirank, & -+ checksum(this%asymcr,product(shape(this%asymcr)), this%mpicomm), sum(this%asymcr) - call flush(6) -- end if -- checksum = sum(this%asymhk) --# ifdef USE_MPI_IN_PLACE -- call mpi_allreduce(MPI_IN_PLACE,checksum,1,MPI_DOUBLE_PRECISION,mpi_sum,this%mpicomm,ierr) --# else -- call mpi_allreduce(checksum,mpitmp,1,MPI_DOUBLE_PRECISION,mpi_sum,this%mpicomm,ierr) -- checksum = mpitmp --# endif /*USE_MPI_IN_PLACE*/ -- if(this%mpirank == 0)then -- write(6,*) "SUM this%asymhk", this%mpirank, checksum -- call flush(6) -- end if - # else -- write(6,*)"SUM this%asymcr ",size(this%asymcr),sum(this%asymcr),& -- sum(this%asymcr(1:this%ngr_local/2)),sum(this%asymcr(this%ngr_local/2+1:this%ngr_local)) -- write(6,*)"SUM this%asymhr ",size(this%asymhr),sum(this%asymhr),& -- sum(this%asymhr(1:this%ngr_local/2)),sum(this%asymhr(this%ngr_local/2+1:this%ngr_local)) -+ write(6,*) cut, asymhr_coeff_at_cut, asymcr_coeff_at_cut -+ write(6,*)"SUM this%asymcr ",size(this%asymcr),sum(this%asymcr),& -+ sum(this%asymcr(1:this%ngr_local/2)),sum(this%asymcr(this%ngr_local/2+1:this%ngr_local)) -+ write(6,*)"SUM this%asymhr ",size(this%asymhr),sum(this%asymhr),& -+ sum(this%asymhr(1:this%ngr_local/2)),sum(this%asymhr(this%ngr_local/2+1:this%ngr_local)) -+ stop -+# endif /*MPI */ - #endif /*RISM_DEBUG*/ - #ifdef RISM_DEBUG -+# ifdef MPI - write(6,*) "RANK",this%mpirank,factor,this%boxvol - write(6,'(a,i4,f15.10,f15.10)') "SUM this%asymck",this%ngk,sum(this%asymck),sum(this%asymck(3:)) - write(6,'(a,i4,f15.10,f15.10)') "SUM this%asymhk",this%ngk,sum(this%asymhk),sum(this%asymhk(3:)) -diff -urN amber11.orig/AmberTools/src/rism/rism3d_opendx.f amber11/AmberTools/src/rism/rism3d_opendx.f ---- amber11.orig/AmberTools/src/rism/rism3d_opendx.f 2010-04-07 16:55:55.000000000 +0400 -+++ amber11/AmberTools/src/rism/rism3d_opendx.f 2011-03-08 16:38:44.000000000 +0300 -@@ -55,28 +55,37 @@ - contains - subroutine writeDX (unit, data, rism_box, n,nz_total,ratucm & - #ifdef MPI -- ,rank,size,comm & -+ ,rank,nproc,comm & - #endif /*MPI*/ - ) -+ use safemem - implicit none - #if defined(MPI) - include 'mpif.h' -- integer, intent(in) :: rank,size,comm -+ integer, intent(in) :: rank,nproc,comm - #else -- integer,parameter :: rank = 0, size=1 -+ integer,parameter :: rank = 0, nproc=1 - #endif /*defined(MPI)*/ - integer, intent(in) :: nz_total - integer,intent(in) :: unit, n(3) - _REAL_,intent(in) :: data(n(1),n(2),n(3)), rism_box(3),ratucm(3) - integer :: i,j,k, irank, ierr,count,icount -- integer :: nz_offset(size),nz_local(size) -+ integer :: nz_offset(nproc),nz_local(nproc) - integer, parameter :: dataperline=3 -- _REAL_ :: z_data(nz_total) -+#ifdef MPI -+ integer :: err -+ _REAL_,pointer :: z_data(:)=>NULL() -+#endif /*MPI*/ - #ifdef RISM_DEBUG -+ - write(6,*) "writeDX",rism_box,ratucm - call flush(6) - #endif /*RISM_DEBUG*/ -- -+!!$ do i = 1,nproc -+!!$ if(rank==i)& -+!!$ write(0,*) "DX",rank,sum(data)/(rank+1),n(3) -+!!$ call mpi_barrier(comm,ierr) -+!!$ end do - if(rank==0)then - write(unit,"(a,i8,i8,i8)") "object 1 class gridpositions counts",n(1),n(2),nz_total - write(unit,"(a,3(f15.8))") "origin ",ratucm(1)-rism_box(1)/2,ratucm(2)-rism_box(2)/2,ratucm(3)-rism_box(3)/2 -@@ -89,9 +98,14 @@ - end if - count = 0 - #if defined(MPI) -+ z_data =>reallocate_pointer(z_data,nz_total) - call mpi_gather(n(3),1,mpi_integer,nz_local,1,mpi_integer,0,comm,ierr) - nz_offset(1) = 0 -- nz_offset(2:) = nz_local(1:size-1) -+ do i = 2, nproc -+ nz_offset(i) =sum( nz_local(1:i-1)) -+ end do -+!!$ if(rank==0)& -+!!$ write(0,*) "NZ",rank,nz_offset, nz_local - #endif /*defined(MPI)*/ - do i=1,n(1) - do j=1,n(2) -@@ -122,5 +136,8 @@ - end if - write(unit,"(a)") 'object "Untitled" call field' - end if -+#ifdef MPI -+ err = safe_deallocate(z_data) -+#endif /*MPI*/ - end subroutine writeDX - end module rism3d_opendx -diff -urN amber11.orig/AmberTools/src/rism/rism_fft.f amber11/AmberTools/src/rism/rism_fft.f ---- amber11.orig/AmberTools/src/rism/rism_fft.f 2010-04-07 16:55:55.000000000 +0400 -+++ amber11/AmberTools/src/rism/rism_fft.f 2011-03-08 16:38:44.000000000 +0300 -@@ -205,19 +205,23 @@ - ! Normalizing while Forward FFT (KEY=1) * - !*********************************************************************** - subroutine rlft3i (data, ng3, key,n_local,plan) -+ use safemem - implicit none - integer :: ng3(3), key - integer :: n_local - integer*8,intent(in) :: plan -- _REAL_ :: data((ng3(1)+2)*ng3(2)*n_local) -- _REAL_ :: work((ng3(1)+2)*ng3(2)*n_local) -+! _REAL_ :: data((ng3(1)+2)*ng3(2)*n_local) -+! _REAL_ :: work((ng3(1)+2)*ng3(2)*n_local) -+ _REAL_ :: data(:) -+ _REAL_,pointer :: work(:) - integer :: ngr, ngr_local,ngk_local, ig, ierr - integer, parameter :: FFTW_TRANSPOSED_ORDER=1, FFTW_NORMAL_ORDER=0 - !....................... R-space data array size ....................... - # ifdef RISM_DEBUG -- write(6,*) "rlft3i",n_local -- call flush(6) -+ write(0,*) "rlft3i",n_local -+ call flush(0) - # endif /*RISM_DEBUG*/ -+ work=>reallocate_pointer(work,size(data)) - ngr = ng3(1)*ng3(2)*ng3(3) - ngr_local = ng3(1)*ng3(2)*n_local - ngk_local = (ng3(1)+2)*ng3(2)*n_local -@@ -230,6 +234,7 @@ - call rfftwnd_f77_mpi( plan,1,data,work,1, & - FFTW_TRANSPOSED_ORDER) - end if -+ ierr = safe_deallocate(work) - end subroutine rlft3i - - #else /*defined(MPI)*/ -diff -urN amber11.orig/AmberTools/src/sff/mm_options.l amber11/AmberTools/src/sff/mm_options.l ---- amber11.orig/AmberTools/src/sff/mm_options.l 2010-03-31 07:05:17.000000000 +0400 -+++ amber11/AmberTools/src/sff/mm_options.l 2011-03-08 16:38:44.000000000 +0300 -@@ -75,7 +75,7 @@ - dynamic_loops[=\ ][01] { ECHO; dynamic_loops = atoi( &yytext[14] ); } - static_arrays[=\ ][01] { ECHO; static_arrays = atoi( &yytext[14] ); } - blocksize[=\ ][0-9]+ { ECHO; blocksize = atoi( &yytext[10] ); } --gbsa[=\ ][0-5] { ECHO; gbsa = atoi( &yytext[5] ); } -+gbsa[=\ ][01] { ECHO; gbsa = atoi( &yytext[5] ); } - dim[=\ ][34] { ECHO; dim = atoi( &yytext[4] ); } - - rism[=\ ][01] { ECHO; rismData.rism = atoi( &yytext[5] ); } -diff -urN amber11.orig/AmberTools/src/sff/sff2.c amber11/AmberTools/src/sff/sff2.c ---- amber11.orig/AmberTools/src/sff/sff2.c 2010-03-31 07:05:17.000000000 +0400 -+++ amber11/AmberTools/src/sff/sff2.c 2011-03-08 16:38:44.000000000 +0300 -@@ -1384,6 +1384,7 @@ - e = ct2 * (ct2 * (ct2 * 32.0 - 48.0) + 18.0) - 1.0; - df = ct * (ct2 * (ct2 * 192.0 - 192.0) + 36.0); - ddf = ct2 * (ct2 * 960.0 - 576.0) + 36.0; -+ break; - - default: - fprintf(stderr, "bad periodicity: %d\n", iper); -@@ -4557,7 +4558,7 @@ - qi2h = 0.5 * qi * qi; - qid2h = qi2h * dielfac; - -- if ((gbsa == 1) || (gbsa == 4) || (gbsa == 5)) { -+ if ((gbsa == 4) || (gbsa == 5)) { - vdwdenom = 1.0 / (ri + rwater); - vdwterm = - alphanp * (prm->Gvdw[i]) * vdwdenom * vdwdenom * -diff -urN amber11.orig/AmberTools/src/sqm/qm2_load_params_and_allocate.f amber11/AmberTools/src/sqm/qm2_load_params_and_allocate.f ---- amber11.orig/AmberTools/src/sqm/qm2_load_params_and_allocate.f 2010-04-14 16:13:28.000000000 +0400 -+++ amber11/AmberTools/src/sqm/qm2_load_params_and_allocate.f 2011-03-08 16:38:44.000000000 +0300 -@@ -136,9 +136,12 @@ - n_atomic_orb=natomic_orbs(iqm_atomic) - if (n_atomic_orb>1) nheavy_atoms=nheavy_atoms+1 - ! Check we don't bust any static arrays -- if (n_atomic_orb > MAX_VALENCE_ORBITALS) then -- write (6,*) 'n_atomic_orb of ',n_atomic_orb,' exceeds max_valence_orbitals of MAX_VALENCE_ORBITALS' -- call sander_bomb('qm2_load_params.f','exceeded max','Check qmmm_module.f and parameters.h') -+ ! DFTB is independent of this and checks are done in qm2_dftb_load_params -+ if ( .not. qmmm_nml%qmtheory%DFTB ) then -+ if (n_atomic_orb > MAX_VALENCE_ORBITALS) then -+ write (6,*) 'n_atomic_orb of ',n_atomic_orb,' exceeds max_valence_orbitals of MAX_VALENCE_ORBITALS' -+ call sander_bomb('qm2_load_params.f','exceeded max','Check qmmm_module.f and parameters.h') -+ end if - end if - qm2_params%natomic_orbs(i)=n_atomic_orb - qm2_params%orb_loc(1,i)=qm2_struct%norbs+1 -diff -urN amber11.orig/AmberTools/src/sqm/qm2_scf.f amber11/AmberTools/src/sqm/qm2_scf.f ---- amber11.orig/AmberTools/src/sqm/qm2_scf.f 2010-03-31 07:05:17.000000000 +0400 -+++ amber11/AmberTools/src/sqm/qm2_scf.f 2011-03-08 16:38:44.000000000 +0300 -@@ -33,9 +33,9 @@ - qm_gb, qmmm_mpi, qmmm_scratch - use constants, only : EV_TO_KCAL, zero, two - -- use qm2_iterator_mod, only : scf_iterator_value -- use qm2_iterator_mod, only : diis_iterator_value -- use qm2_iterator_mod, only : remaining_diis_tokens -+ use qm2_iterator_mod, only : scf_iterator_value ! this is an integer function -+ use qm2_iterator_mod, only : diis_iterator_value ! this is an integer function -+ use qm2_iterator_mod, only : remaining_diis_tokens ! this is an integer function - - - implicit none -@@ -75,21 +75,24 @@ - !again. This is used to force the last few SCF steps to be full diagonalisations. - logical fock_predict_active !Set to true if we are attempting to predict the fock matrix on this QMMM call. - -- logical diis_is_off, errmat_is_converged - character(len=1) :: fock_extrap_flag -- logical dont_turn_off_diis - -+ ! DIIS -+ ! While DIIS will accelerate SCF convergence it will do so at a very high cost -+ ! since Fock matrix builds and diagonalizations for semiempirical methods are -+ ! cheaper than the overhead generated by the matrix multiplications required for DIIS -+ ! Thus switch DIIS only on if we have difficulty in converging the SCF -+ ! switch DIIS on after SCF step 100 if user turns on DIIS by setting ndiis_attempts > 0 -+ integer, parameter :: switch_on_diis = 100 ! don't set this to values lower than 3!!! -+ ! switch DIIS on as a last resort if SCF did not converge until iteration 800 -+ integer, parameter :: switch_on_diis_last_resort = 800 -+ logical diis_is_off, errmat_is_converged, errmat_is_on -+ logical dont_turn_off_diis - _REAL_ :: errval - --! scf_iterator_value is a function --! integer :: scf_iterator_value -- - ! current_scf_errval is a function - _REAL_ :: current_scf_errval - --! remaining_diis_tokens is a function --! integer :: remaining_diis_tokens -- - !qm2_Helect is a function - _REAL_ qm2_HELECT - -@@ -141,12 +144,13 @@ - ! i = remaining_diis_tokens( qmmm_nml%ndiis_attempts ) - i = remaining_diis_tokens( 0 ) - dont_turn_off_diis = .FALSE. -+ diis_is_off = qmmm_nml%ndiis_attempts < 1 .OR. qmmm_nml%ndiis_matrices < 2 -+ errmat_is_on = qmmm_nml%errconv < 1.0D-02 -+ errval = -1.0D0 ! initialize errval to unrealistic value - - fock_extrap_flag = " " - - -- -- - if (qmmm_nml%verbosity > 2 .and. qmmm_mpi%commqmmm_master) then - write(6,'("QMMM: ")') - write(6,'("QMMM: SCF Convergence Information")') -@@ -214,8 +218,18 @@ - energy_diff = scf_energy - eold - - if (qmmm_mpi%commqmmm_master) then -- CALL pack_diis(SIZE(fock_matrix),fock_matrix,den_matrix) -- errval = current_scf_errval() -+ ! do this only if we need it, this seriously affects performance -+ if ( .not. errmat_is_on ) then -+ ! check if we shall switch calculation of the error matrix on for diis -+ if ( ( ( .not. diis_is_off ) .and. (scf_iteration+qmmm_nml%ndiis_matrices >= switch_on_diis) ) & -+ .or. (scf_iteration+qmmm_nml%ndiis_matrices >= switch_on_diis_last_resort) ) then -+ errmat_is_on = .true. -+ end if -+ end if -+ if ( errmat_is_on ) then -+ CALL pack_diis(SIZE(fock_matrix),fock_matrix,den_matrix) -+ errval = current_scf_errval() -+ end if - end if - - -@@ -290,7 +304,7 @@ - ! IF THE USER REQUESTED US TO!! The default value of - ! qmmm_nml%ndiis_attempts is 0, so this requires a form - ! of human intervention -- if ( scf_iteration == 100 ) then -+ if ( scf_iteration == switch_on_diis ) then - i = remaining_diis_tokens( qmmm_nml%ndiis_attempts ) - dont_turn_off_diis = .TRUE. - -@@ -306,7 +320,7 @@ - ! turn the (default OFF) diis parameters on. - ! I guess we should turn diis ON for the user. - ! I mean, we're at iteration #800. What else can we do? -- if ( scf_iteration == 800 ) then -+ if ( scf_iteration == switch_on_diis_last_resort ) then - i = remaining_diis_tokens( 100 ) - dont_turn_off_diis = .TRUE. - -@@ -329,8 +343,8 @@ - ! end if - - -- diis_is_off = qmmm_nml%ndiis_attempts < 1 .OR. qmmm_nml%ndiis_matrices < 2 -- errmat_is_converged = errval < qmmm_nml%errconv !.OR. diis_is_off -+ ! Is the error matrix converged? Set to true if we don't check for the error matrix -+ errmat_is_converged = errval < qmmm_nml%errconv .OR. ( .not. errmat_is_on ) - - - if (abs(energy_diff) < qmmm_nml%scfconv .AND. & -@@ -379,7 +393,7 @@ - ! We have decided that we have not converged - ! We must diagonalize a fock matrix so that the next iteration can form a new guess - ! density matrix, provided a set of trial orbitals -- if (qmmm_mpi%commqmmm_master) then -+ if (qmmm_mpi%commqmmm_master .and. (.not. diis_is_off) .and. ( scf_iteration >= switch_on_diis ) ) then - CALL diis_extrap( qm2_struct%matsize, fock_matrix , fock_extrap_flag ) - end if - -@@ -1941,10 +1955,6 @@ - _REAL_,intent(out) :: pf(npf) ! packed fock matrix - character(len=1),intent(out) :: extrap_flag - --! integer :: scf_iterator_value --! integer :: diis_iterator_value --! integer :: diis_iterator_prev_value --! integer :: remaining_diis_tokens - _REAL_ :: current_scf_errval - - logical :: HAVE_DIIS_DATA -@@ -1975,7 +1985,6 @@ - ERR_IS_SMALL = current_scf_errval() < 0.5d0 - HAVE_DIIS_TOKENS = remaining_diis_tokens() > 0 - EXTRAPOLATE = HAVE_DIIS_DATA .AND. ERR_IS_SMALL .AND. HAVE_DIIS_TOKENS -- - IF ( .NOT. EXTRAPOLATE ) THEN - pf = qm2_struct%diis_fock( : , diis_idx ) - RETURN -diff -urN amber11.orig/AmberTools/src/sqm/qmmm_module.f amber11/AmberTools/src/sqm/qmmm_module.f ---- amber11.orig/AmberTools/src/sqm/qmmm_module.f 2010-04-14 16:13:28.000000000 +0400 -+++ amber11/AmberTools/src/sqm/qmmm_module.f 2011-03-08 16:38:44.000000000 +0300 -@@ -84,7 +84,7 @@ - !--------- SIZE / ARRAY LIMITATIONS ----------------------- - - ! Locks maximum valence orbitals at 4 = S,P (no D or F - code is not present) -- integer, parameter :: MAX_VALENCE_ORBITALS =4 -+ integer, parameter :: MAX_VALENCE_ORBITALS = 4 - integer, parameter :: MAX_VALENCE_DIMENSION = MAX_VALENCE_ORBITALS*(MAX_VALENCE_ORBITALS+1)/2 - - !---------------------------------------------------------- -diff -urN amber11.orig/AmberTools/src/sqm/sqm.f amber11/AmberTools/src/sqm/sqm.f ---- amber11.orig/AmberTools/src/sqm/sqm.f 2010-04-14 16:13:28.000000000 +0400 -+++ amber11/AmberTools/src/sqm/sqm.f 2011-03-08 16:38:44.000000000 +0300 -@@ -13,7 +13,7 @@ - - implicit none - -- _REAL_ x(3000), f(3000), escf, reff(1000), onereff(1000), work(18000), scf_mchg(1000) -+ _REAL_ x(3000), f(3000), escf, reff(1000), onereff(1000), work(18000) - character(len=8) atnam(1000) - _REAL_ born_radii(1000), one_born_radii(1000) - _REAL_ intdiel, extdiel, Arad -@@ -104,20 +104,23 @@ - call allocate_qmgb(qmmm_struct%nquant_nlink) - - allocate( qmmm_struct%dxyzqm(3, qmmm_struct%nquant_nlink), stat = ier ) -- REQUIRE(ier == 0) !Deallocated in deallocate qmmm -+ REQUIRE(ier == 0) -+ -+ allocate ( qm2_struct%scf_mchg(qmmm_struct%nquant_nlink), stat = ier ) -+ REQUIRE(ier == 0) - - if (maxcyc < 1) then - ! ------------------------ - ! Single point calculation - ! ------------------------ - call sqm_energy(natom, x, escf, born_radii, one_born_radii, & -- intdiel, extdiel, Arad, scf_mchg ) -+ intdiel, extdiel, Arad, qm2_struct%scf_mchg ) - else - ! --------------------- - ! Geometry optimization - ! --------------------- - call xmin(natom, x, f, escf, xmin_iter, maxcyc, born_radii, & -- one_born_radii, intdiel, extdiel, Arad, scf_mchg, grms_tol, ntpr) -+ one_born_radii, intdiel, extdiel, Arad, qm2_struct%scf_mchg, grms_tol, ntpr) - end if - - ! ---------------- -@@ -140,7 +143,7 @@ - - write(6,*) '' - call qm2_print_charges(1,qmmm_nml%dftb_chg,qmmm_struct%nquant_nlink, & -- scf_mchg,qmmm_struct%iqm_atomic_numbers) -+ qm2_struct%scf_mchg,qmmm_struct%iqm_atomic_numbers) - - write(6,*) '' - write(6,*) 'Final Structure' -@@ -150,6 +153,12 @@ - write(6,*) ' --------- Calculation Completed ----------' - write(6,*) - -+ deallocate( qmmm_struct%dxyzqm, stat = ier ) -+ REQUIRE(ier == 0) -+ -+ deallocate ( qm2_struct%scf_mchg, stat = ier ) -+ REQUIRE(ier == 0) -+ - call mexit(6,0) - - end program sqm -diff -urN amber11.orig/AmberTools/test/check_slko_files.x amber11/AmberTools/test/check_slko_files.x ---- amber11.orig/AmberTools/test/check_slko_files.x 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/test/check_slko_files.x 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,14 @@ -+#!/bin/csh -f -+#checks if cc.spl file exists - if it does then it -+#assumes that all slko files are installed. -+ -+if( -r $AMBERHOME/dat/slko/C-C.skf ) then -+ #Exists -+ exit(0) -+else -+ echo "DFTB SLKO files not found - Skipping DFTB tests..." -+ echo "" -+ exit(1) -+endif -+ -+ -diff -urN amber11.orig/AmberTools/test/nab/cuv.H1.4.dx.check amber11/AmberTools/test/nab/cuv.H1.4.dx.check ---- amber11.orig/AmberTools/test/nab/cuv.H1.4.dx.check 2010-04-07 16:55:55.000000000 +0400 -+++ amber11/AmberTools/test/nab/cuv.H1.4.dx.check 2011-03-08 16:38:44.000000000 +0300 -@@ -344,7 +344,7 @@ - 0.70282E-001 0.80739E-001 0.91198E-001 - 0.94417E-001 0.91703E-001 0.77197E-001 - 0.50502E-001 0.19853E-001 -0.36599E-003 -- 0.22738E-005 0.16691E-001 0.36195E-001 -+ 0.22736E-005 0.16691E-001 0.36195E-001 - 0.49401E-001 0.53981E-001 0.53966E-001 - 0.47335E-001 0.56527E-001 0.67703E-001 - 0.78860E-001 0.90368E-001 0.10008E+000 -diff -urN amber11.orig/AmberTools/test/nab/huv.H1.4.dx.check amber11/AmberTools/test/nab/huv.H1.4.dx.check ---- amber11.orig/AmberTools/test/nab/huv.H1.4.dx.check 2010-04-07 16:55:55.000000000 +0400 -+++ amber11/AmberTools/test/nab/huv.H1.4.dx.check 2011-03-08 16:38:44.000000000 +0300 -@@ -37,7 +37,7 @@ - -0.39322E-002 -0.18784E-002 -0.58137E-002 - 0.10207E-002 0.62249E-003 -0.98638E-003 - 0.37094E-003 -0.28752E-003 0.22042E-004 -- -0.99891E-004 0.15368E-003 -0.19634E-004 -+ -0.99891E-004 0.15368E-003 -0.19635E-004 - 0.35824E-003 -0.40488E-003 0.40397E-003 - 0.14213E-003 0.61945E-002 -0.76858E-002 - 0.81862E-002 -0.54091E-002 0.13352E-002 -@@ -58,7 +58,7 @@ - 0.22994E-002 -0.34751E-002 -0.37733E-001 - -0.16433E-001 -0.59317E-002 0.71093E-002 - -0.46373E-002 0.32238E-002 -0.25894E-002 -- 0.22145E-002 -0.65291E-004 -0.12695E-003 -+ 0.22145E-002 -0.65292E-004 -0.12695E-003 - -0.16873E-003 0.45506E-003 -0.14159E-002 - 0.16342E-002 -0.79582E-002 0.56556E-002 - -0.43786E-001 -0.46923E-002 -0.27685E-002 -@@ -96,11 +96,11 @@ - 0.34445E-003 0.33513E-002 0.63723E-003 - -0.45516E-003 0.16641E-004 -0.90223E-004 - 0.10300E-003 -0.99252E-004 0.15249E-004 -- -0.10662E-004 -0.19945E-004 -0.63404E-006 -+ -0.10662E-004 -0.19945E-004 -0.63406E-006 - 0.11124E-004 -0.28230E-004 -0.31534E-003 - -0.33642E-002 -0.57217E-003 -0.27793E-002 - -0.74846E-003 0.29526E-003 -0.94696E-004 -- 0.64217E-004 -0.66025E-004 -0.40449E-005 -+ 0.64216E-004 -0.66025E-004 -0.40449E-005 - -0.30799E-004 -0.16361E-004 -0.62269E-004 - -0.51020E-005 -0.16001E-003 0.92448E-004 - -0.57830E-003 -0.21012E-002 -0.69590E-003 -@@ -117,7 +117,7 @@ - -0.21378E-002 -0.44258E-003 -0.15111E-002 - -0.13934E-002 0.53131E-003 -0.22947E-003 - -0.74937E-005 -0.46655E-004 -0.61371E-004 -- 0.61593E-004 0.13955E-004 0.16010E-003 -+ 0.61594E-004 0.13955E-004 0.16010E-003 - -0.17966E-003 0.34275E-003 -0.36108E-003 - 0.76113E-003 0.23418E-002 0.29182E-003 - 0.19046E-002 0.12879E-002 -0.85274E-003 -@@ -131,7 +131,7 @@ - -0.24936E-003 0.43593E-003 -0.38975E-003 - 0.48502E-003 -0.28550E-003 0.94466E-003 - 0.27789E-002 0.71808E-003 0.38223E-002 -- -0.14124E-004 -0.13567E-002 0.12326E-002 -+ -0.14125E-004 -0.13567E-002 0.12326E-002 - -0.66934E-003 0.45864E-003 -0.28062E-003 - -0.43706E-003 0.34374E-003 -0.56160E-003 - 0.23427E-003 -0.19776E-003 -0.12917E-003 -@@ -182,7 +182,7 @@ - -0.11703E-002 0.14706E-002 -0.40144E-003 - 0.10286E-003 0.45475E-004 -0.49081E-004 - -0.47357E-004 0.54489E-006 -0.61082E-004 -- 0.65984E-004 -0.69587E-004 -0.10541E-003 -+ 0.65984E-004 -0.69588E-004 -0.10541E-003 - 0.64247E-003 0.25698E-002 0.28005E-002 - 0.27413E-002 0.12876E-002 -0.75471E-003 - 0.57492E-004 0.66448E-004 -0.42928E-004 -@@ -229,7 +229,7 @@ - -0.40783E-002 0.30972E-002 -0.35632E-002 - -0.14974E-004 0.13258E-002 -0.10864E-002 - 0.34485E-003 -0.16911E-003 -0.62126E-004 -- 0.72158E-004 -0.22208E-004 0.77266E-004 -+ 0.72158E-004 -0.22208E-004 0.77265E-004 - 0.24040E-003 -0.72533E-003 0.13593E-002 - -0.16119E-002 0.10078E-001 -0.20050E-001 - 0.72175E-002 -0.45419E-002 0.45478E-003 -@@ -292,7 +292,7 @@ - 0.33230E-003 -0.62327E-003 0.36713E-003 - -0.30819E-002 -0.32037E-003 -0.17162E-002 - -0.14580E-002 0.46999E-003 -0.97290E-004 -- -0.73333E-004 0.14729E-006 -0.11485E-003 -+ -0.73333E-004 0.14727E-006 -0.11485E-003 - -0.10058E-003 0.62528E-004 -0.17489E-003 - 0.15221E-003 -0.46879E-003 0.25396E-003 - -0.52915E-003 -0.27851E-002 0.22929E-002 -@@ -318,7 +318,7 @@ - -0.68610E-003 0.64051E-003 -0.81356E-003 - 0.24281E-003 -0.94464E-003 -0.31260E-002 - 0.48815E-002 -0.32512E-002 -0.12194E-002 -- 0.15282E-002 -0.10747E-002 0.37017E-003 -+ 0.15282E-002 -0.10747E-002 0.37016E-003 - -0.43401E-003 0.37194E-003 0.90390E-003 - -0.87376E-003 0.10045E-002 -0.10100E-002 - 0.89048E-003 -0.53634E-003 0.18096E-002 -@@ -355,14 +355,14 @@ - 0.26923E-003 -0.62333E-003 0.92867E-003 - -0.23947E-002 0.40142E-002 -0.86299E-002 - 0.45605E-002 -0.33767E-001 0.48411E-002 -- -0.86790E-002 0.13146E-002 -0.92538E-004 -+ -0.86790E-002 0.13146E-002 -0.92539E-004 - -0.33552E-003 -0.15197E-003 0.54828E-004 - -0.61954E-003 0.61334E-003 -0.71350E-003 - 0.88754E-003 -0.46185E-003 -0.11825E-002 - 0.49261E-002 -0.92336E-002 0.11674E-001 - -0.57510E-002 0.61122E-002 0.39077E-003 - -0.16127E-002 0.13002E-002 -0.76188E-003 -- 0.68127E-003 0.46393E-003 -0.60936E-003 -+ 0.68127E-003 0.46394E-003 -0.60936E-003 - 0.83803E-003 -0.13684E-002 0.18949E-002 - -0.20507E-002 0.86720E-003 0.55761E-002 - -0.38872E-002 0.87045E-002 0.57034E-003 -@@ -384,7 +384,7 @@ - 0.14459E-002 -0.36764E-002 -0.16466E-002 - 0.78190E-003 -0.21388E-003 -0.13391E-003 - -0.71292E-004 -0.25972E-004 0.81385E-005 -- -0.75784E-005 0.84210E-004 -0.57027E-004 -+ -0.75783E-005 0.84210E-004 -0.57027E-004 - 0.24646E-003 -0.15344E-004 0.44974E-003 - 0.29483E-002 -0.13186E-002 0.30172E-002 - 0.14066E-002 -0.51937E-003 0.13804E-003 -@@ -425,7 +425,7 @@ - 0.15873E-002 -0.26341E-002 0.28432E-002 - 0.49007E-003 0.10263E-001 -0.44098E-001 - 0.25985E-003 -0.50604E-002 0.20816E-002 -- -0.97801E-005 -0.13212E-003 -0.22909E-003 -+ -0.97796E-005 -0.13212E-003 -0.22909E-003 - 0.48134E-003 0.52250E-002 -0.61139E-002 - 0.74868E-002 -0.97022E-002 0.12736E-001 - -0.13924E-001 0.13569E-001 -0.16048E-001 -@@ -442,13 +442,13 @@ - -0.17468E-001 0.24222E-001 -0.13107E+000 - -0.65242E-001 0.19459E-001 -0.38769E-002 - -0.13998E-002 0.28896E-002 -0.44039E-002 -- 0.52052E-002 0.11744E-002 0.25963E-003 -+ 0.52052E-002 0.11744E-002 0.25964E-003 - -0.21866E-002 0.47172E-002 -0.81182E-002 - 0.10154E-001 -0.15684E-001 0.18417E-001 - -0.10597E+000 0.22097E-001 0.78443E-003 - -0.56097E-002 0.55039E-002 -0.44612E-002 - 0.32653E-002 -0.22953E-002 -0.13331E-002 -- 0.91243E-003 -0.94485E-004 -0.12826E-002 -+ 0.91243E-003 -0.94484E-004 -0.12826E-002 - 0.43961E-002 -0.78443E-002 0.13464E-001 - -0.13779E-002 0.40528E-001 -0.22036E-002 - 0.10425E-001 -0.96531E-003 -0.13430E-002 -@@ -512,13 +512,13 @@ - 0.11827E-001 -0.45014E-002 0.27467E-002 - -0.41543E-003 -0.71183E-003 0.52608E-003 - -0.64382E-003 0.45191E-003 0.50605E-003 -- -0.44980E-003 0.37809E-003 -0.38388E-004 -+ -0.44981E-003 0.37809E-003 -0.38389E-004 - -0.49061E-003 -0.81143E-003 0.86459E-002 - -0.45388E-002 -0.19539E-001 -0.35704E-002 -- -0.21204E-002 0.67039E-003 0.70119E-003 -+ -0.21204E-002 0.67038E-003 0.70119E-003 - -0.74427E-003 0.55233E-003 -0.45289E-003 - -0.11702E-002 0.10513E-002 -0.10446E-002 -- 0.48184E-003 -0.52832E-003 0.40688E-002 -+ 0.48184E-003 -0.52833E-003 0.40688E-002 - -0.13663E-001 -0.53287E-002 0.80893E-001 - 0.13554E-001 0.87640E-003 -0.12860E-002 - -0.94409E-003 0.13653E-002 -0.14728E-002 -@@ -570,12 +570,12 @@ - 0.55487E-003 0.57562E-002 -0.85141E-003 - 0.10230E-001 0.16214E-002 -0.31963E-002 - 0.16965E-002 -0.39151E-003 0.11883E-003 -- 0.27054E-005 -0.64436E-004 0.29371E-004 -+ 0.27053E-005 -0.64436E-004 0.29371E-004 - -0.24818E-003 0.15603E-003 -0.36597E-003 - -0.15165E-003 -0.30508E-003 -0.55843E-002 - 0.25615E-002 -0.87369E-002 -0.12896E-002 - 0.21029E-002 -0.12728E-002 0.23925E-003 -- -0.20980E-003 -0.40398E-004 -0.37869E-004 -+ -0.20980E-003 -0.40397E-004 -0.37869E-004 - -0.22762E-004 0.97304E-004 -0.13256E-003 - 0.76121E-004 0.46124E-003 -0.11364E-003 - 0.51685E-002 -0.25639E-002 0.77172E-002 -@@ -627,7 +627,7 @@ - -0.13873E-001 0.13771E-001 -0.15353E-001 - 0.19554E-001 -0.31206E-001 0.64687E-002 - 0.12878E+000 0.43115E+000 0.18311E+000 -- -0.42341E-001 0.49587E-002 0.50176E-002 -+ -0.42341E-001 0.49588E-002 0.50176E-002 - -0.10381E-001 0.12020E-001 -0.13237E-001 - -0.18428E-001 0.21596E-001 -0.25230E-001 - 0.33125E-001 -0.42929E-001 0.59353E-001 -@@ -693,12 +693,12 @@ - -0.13202E-001 -0.15081E-001 0.28654E-002 - 0.45947E-002 -0.39497E-002 0.16991E-002 - -0.85009E-003 0.46037E-003 -0.41389E-003 -- -0.11503E-004 -0.26360E-004 0.13328E-004 -+ -0.11503E-004 -0.26361E-004 0.13328E-004 - 0.44265E-003 -0.10259E-002 -0.89230E-003 - 0.43360E-002 0.12999E-001 0.67878E-002 - -0.14383E-001 -0.53637E-003 0.27114E-002 - -0.14313E-002 0.43554E-003 -0.55232E-004 -- 0.54550E-004 -0.19917E-002 0.19778E-002 -+ 0.54549E-004 -0.19917E-002 0.19778E-002 - -0.22171E-002 0.17858E-002 -0.28501E-002 - 0.81796E-002 -0.15748E-001 -0.97599E-002 - 0.11465E-001 0.41396E-001 -0.12368E-001 -@@ -737,7 +737,7 @@ - 0.33287E-001 -0.21712E-001 0.12598E-001 - -0.78119E-002 0.22442E-002 -0.20161E-001 - 0.21504E-001 -0.24273E-001 0.27271E-001 -- -0.28503E-001 0.16461E-001 -0.41419E-004 -+ -0.28503E-001 0.16461E-001 -0.41414E-004 - -0.12990E+000 0.75360E-001 -0.11560E+000 - -0.19544E-001 0.27969E-001 -0.25346E-001 - 0.21675E-001 -0.20092E-001 0.19462E-001 -@@ -766,7 +766,7 @@ - -0.47737E-003 -0.51835E-004 0.58766E-003 - -0.52596E-003 0.72315E-003 -0.11079E-001 - -0.25431E-001 -0.12595E-001 0.68054E-002 -- -0.18857E-002 0.60829E-004 0.13868E-003 -+ -0.18857E-002 0.60830E-004 0.13868E-003 - -0.55933E-003 0.34562E-003 -0.15041E-003 - 0.80074E-004 -0.32555E-003 0.67842E-003 - -0.15202E-002 0.14050E-002 -0.80795E-003 -@@ -798,7 +798,7 @@ - -0.27721E-002 0.29741E-002 -0.49061E-003 - -0.72566E-002 0.14443E-001 -0.11927E-001 - 0.82051E-001 0.95570E-002 0.10700E-002 -- -0.33922E-004 0.14627E-003 0.88681E-003 -+ -0.33919E-004 0.14627E-003 0.88681E-003 - -0.13081E-002 0.21604E-002 0.33550E-002 - -0.40840E-002 0.36977E-002 -0.35055E-002 - 0.41269E-003 0.67781E-002 0.27814E-002 -@@ -892,9 +892,9 @@ - 0.63672E-002 -0.57904E-002 0.46308E-002 - -0.36396E-002 -0.26400E-002 0.17391E-002 - -0.14131E-002 0.78246E-003 -0.61051E-003 -- 0.63366E-003 0.24693E-001 0.29656E-001 -+ 0.63365E-003 0.24693E-001 0.29656E-001 - 0.13438E+000 0.27901E-001 -0.22954E-001 -- 0.12869E-001 -0.76758E-002 0.58582E-002 -+ 0.12869E-001 -0.76757E-002 0.58582E-002 - -0.46806E-002 0.36183E-002 0.68827E-002 - -0.57133E-002 0.56860E-002 -0.66211E-002 - 0.99125E-002 -0.15797E-001 -0.52503E-002 -@@ -908,7 +908,7 @@ - -0.45900E-001 0.36916E-001 -0.30142E-001 - 0.26465E-001 0.50030E-001 -0.48827E-001 - 0.51561E-001 -0.58944E-001 0.74179E-001 -- -0.94716E-001 0.36687E-001 -0.46168E+000 -+ -0.94715E-001 0.36687E-001 -0.46168E+000 - -0.10000E+001 -0.17472E+000 0.15670E+000 - -0.98122E-001 0.78741E-001 -0.64288E-001 - 0.58448E-001 -0.52472E-001 0.59653E-001 -@@ -931,7 +931,7 @@ - -0.21260E-001 0.26058E-001 -0.35050E-001 - 0.44521E-001 -0.58930E-001 -0.46967E-002 - -0.62950E+000 -0.10000E+001 -0.58023E+000 -- 0.84660E-001 -0.20803E-001 -0.24936E-003 -+ 0.84661E-001 -0.20803E-001 -0.24937E-003 - -0.56711E-002 0.77515E-002 -0.12967E-001 - -0.33634E-001 0.36370E-001 -0.40813E-001 - 0.52730E-001 -0.69416E-001 0.11055E+000 -@@ -940,7 +940,7 @@ - -0.50993E-001 0.42341E-001 -0.35645E-001 - 0.34334E-001 0.13016E-002 -0.18908E-002 - 0.21484E-002 -0.35223E-002 0.43357E-002 -- -0.52692E-002 -0.30889E-001 -0.10458E+000 -+ -0.52692E-002 -0.30890E-001 -0.10458E+000 - 0.59570E-001 -0.10076E+000 -0.14057E-001 - 0.10367E-001 -0.60574E-002 0.13132E-002 - 0.10164E-003 -0.11144E-002 -0.80129E-003 -@@ -1070,7 +1070,7 @@ - -0.27848E-002 0.34661E-002 -0.63123E-002 - 0.10345E-001 -0.10633E-001 -0.26698E-001 - 0.37697E-001 -0.14235E-001 -0.27804E-003 -- -0.11597E-002 0.47695E-005 0.21900E-003 -+ -0.11597E-002 0.47700E-005 0.21900E-003 - -0.12610E-002 0.14246E-002 0.19513E-002 - -0.22230E-002 0.25913E-002 -0.34398E-002 - 0.62826E-002 -0.11033E-001 0.11857E-001 -@@ -1096,7 +1096,7 @@ - 0.17629E-001 -0.16578E-001 0.17704E-001 - -0.21181E-001 0.31547E-001 -0.44986E-001 - 0.53814E-001 0.61709E-001 0.41895E-001 -- -0.58391E-002 0.71644E-001 -0.50130E-001 -+ -0.58392E-002 0.71644E-001 -0.50130E-001 - 0.37052E-001 -0.27166E-001 0.23023E-001 - -0.18847E-001 -0.57070E-002 0.32394E-002 - -0.47133E-002 0.71203E-002 -0.17409E-001 -@@ -1107,7 +1107,7 @@ - 0.49908E-002 0.25980E-002 -0.10390E-001 - 0.32835E-001 -0.45644E-001 0.28388E-001 - 0.32651E+000 0.74550E+000 0.24253E-001 -- 0.23336E-001 -0.11200E-002 -0.67666E-003 -+ 0.23336E-001 -0.11200E-002 -0.67665E-003 - 0.71472E-002 -0.62491E-002 0.83474E-002 - 0.87319E-002 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- 0.12872E+000 -0.22970E+000 0.37029E-001 - -0.71820E-002 -0.61730E-002 0.60023E-002 - -0.62195E-002 0.33179E-002 0.35063E-002 -- -0.15743E-002 0.24932E-003 0.59944E-003 -+ -0.15743E-002 0.24932E-003 0.59943E-003 - 0.50805E-002 -0.22435E-001 0.78080E-001 - -0.11217E+000 0.27769E+000 0.13301E-001 - 0.48142E-001 -0.25712E-001 0.18216E-001 -@@ -1234,8 +1234,8 @@ - -0.37349E-002 0.40923E-002 0.33100E-003 - -0.73044E-003 0.14901E-002 -0.27451E-002 - 0.39569E-002 -0.39194E-002 -0.22396E-002 -- 0.69572E-002 0.15456E-001 0.68766E-003 -- -0.55836E-002 -0.59161E-004 0.28366E-003 -+ 0.69572E-002 0.15456E-001 0.68765E-003 -+ -0.55836E-002 -0.59162E-004 0.28366E-003 - 0.59373E-005 -0.29036E-003 -0.28278E-003 - -0.93105E-004 0.55976E-004 -0.22540E-003 - 0.63416E-003 -0.86325E-003 -0.56872E-003 -@@ -1259,13 +1259,13 @@ - -0.21463E-002 -0.95702E-003 0.16305E-002 - -0.48868E-003 0.37838E-003 -0.98649E-004 - 0.17415E-003 -0.39204E-003 0.40478E-003 -- -0.47636E-003 0.25159E-003 0.32794E-005 -+ -0.47636E-003 0.25159E-003 0.32795E-005 - -0.27191E-003 -0.25541E-002 0.80677E-002 - 0.23348E-001 0.22086E-002 0.10997E-002 - -0.16811E-002 0.61473E-003 -0.17759E-003 - -0.60773E-004 0.91723E-004 0.50744E-003 - -0.63597E-003 0.55533E-003 -0.33123E-003 -- -0.68908E-005 0.25682E-003 0.26735E-002 -+ -0.68909E-005 0.25682E-003 0.26735E-002 - -0.91015E-002 -0.22651E-001 -0.42938E-002 - -0.10604E-002 0.20136E-002 -0.89377E-003 - 0.20609E-003 0.28182E-004 -0.21460E-003 -@@ -1273,7 +1273,7 @@ - 0.63594E-004 0.46567E-003 -0.90712E-003 - -0.31638E-002 0.94292E-002 0.26064E-001 - 0.58926E-002 0.14824E-003 -0.26379E-002 -- 0.13364E-002 -0.27849E-003 0.67584E-007 -+ 0.13364E-002 -0.27849E-003 0.67664E-007 - 0.21329E-003 0.75173E-003 -0.70904E-003 - 0.24518E-003 -0.31473E-003 -0.44500E-003 - -0.26955E-003 0.56039E-002 -0.11484E-001 -@@ -1298,7 +1298,7 @@ - -0.74153E-002 0.51462E-002 -0.85486E-002 - 0.10486E-001 -0.12082E-001 0.13714E-001 - -0.11389E-001 0.19279E-002 0.36232E-001 -- -0.48818E-001 0.17388E+000 -0.35474E-002 -+ -0.48818E-001 0.17388E+000 -0.35475E-002 - -0.97685E-002 0.97677E-002 -0.64763E-002 - 0.62604E-002 -0.67795E-002 0.78175E-002 - 0.18823E-001 -0.16976E-001 0.13255E-001 -@@ -1310,7 +1310,7 @@ - -0.59406E-002 0.53394E-002 -0.13726E-002 - -0.50565E-002 0.17728E-001 0.83748E-001 - -0.37446E-001 0.12400E+000 -0.15472E-001 -- -0.38171E-003 0.54899E-002 -0.24982E-002 -+ -0.38172E-003 0.54899E-002 -0.24982E-002 - -0.85504E-004 0.30624E-002 0.30068E-002 - -0.46418E-002 0.65796E-002 -0.90030E-002 - 0.10723E-001 -0.66793E-002 -0.19808E-001 -@@ -1330,7 +1330,7 @@ - 0.99945E-003 -0.12217E-002 0.75822E-003 - -0.58237E-003 0.70553E-004 0.47287E-004 - -0.92834E-003 0.22845E-002 -0.35398E-003 -- -0.49955E-002 -0.32604E-001 0.29414E-003 -+ -0.49955E-002 -0.32604E-001 0.29415E-003 - 0.26270E-002 0.12013E-003 0.18530E-003 - -0.67394E-003 0.78294E-003 -0.77240E-003 - -0.39514E-003 0.36294E-003 -0.34122E-003 -@@ -1340,7 +1340,7 @@ - -0.43384E-003 0.62665E-003 -0.53140E-003 - 0.35037E-003 0.11598E-003 -0.33590E-004 - 0.77756E-004 -0.11361E-003 0.29272E-004 -- 0.53713E-003 0.24967E-002 -0.95835E-002 -+ 0.53714E-003 0.24967E-002 -0.95835E-002 - -0.23813E-001 -0.28729E-002 0.35840E-003 - 0.75277E-003 0.14870E-003 -0.18813E-003 - 0.13874E-003 0.53665E-005 -0.82118E-004 -@@ -1383,7 +1383,7 @@ - 0.14890E-002 -0.11973E-002 0.75295E-003 - -0.10473E-002 0.10737E-002 -0.99465E-003 - 0.10667E-002 0.18484E-003 -0.15909E-002 -- -0.44370E-003 0.65566E-002 0.16554E-001 -+ -0.44371E-003 0.65566E-002 0.16554E-001 - 0.15235E-001 -0.16429E-001 0.79078E-002 - -0.29231E-002 0.16543E-002 -0.11884E-002 - 0.10008E-002 0.22131E-002 -0.11833E-002 -@@ -1395,7 +1395,7 @@ - -0.34902E-002 0.51729E-002 -0.78836E-002 - 0.96755E-002 -0.80416E-002 -0.15180E-001 - 0.48776E-001 -0.11424E+000 0.12364E-001 -- 0.32693E-002 -0.19227E-002 -0.65699E-004 -+ 0.32693E-002 -0.19227E-002 -0.65698E-004 - 0.16871E-003 0.29036E-004 -0.95792E-003 - -0.31449E-002 0.21159E-002 -0.34442E-003 - 0.30292E-003 0.22482E-002 -0.56246E-002 -@@ -1476,10 +1476,10 @@ - -0.15578E-002 0.14449E-002 -0.13015E-002 - 0.35158E-002 0.18690E-001 0.71087E-002 - -0.33624E-002 -0.86947E-004 0.13615E-002 -- -0.25872E-003 -0.28246E-003 0.49430E-003 -+ -0.25873E-003 -0.28246E-003 0.49430E-003 - 0.20061E-002 -0.22055E-002 0.25174E-002 - -0.32849E-002 0.24711E-002 -0.12430E-002 -- 0.31615E-004 -0.16073E-002 -0.13936E-001 -+ 0.31616E-004 -0.16073E-002 -0.13936E-001 - -0.78198E-002 0.10677E-001 -0.53430E-002 - 0.19467E-002 -0.20078E-002 0.18727E-002 - -0.18399E-002 -0.24069E-002 0.18144E-002 -@@ -1523,13 +1523,13 @@ - -0.57937E-004 0.38925E-004 -0.25529E-003 - -0.80223E-004 0.62244E-003 -0.92409E-003 - -0.50111E-002 -0.15028E-001 -0.48849E-002 -- 0.10809E-002 0.94785E-003 -0.90578E-003 -+ 0.10809E-002 0.94785E-003 -0.90579E-003 - 0.21632E-003 0.48547E-004 -0.10362E-003 - 0.65746E-004 -0.57485E-004 -0.10330E-003 - 0.17296E-003 -0.10843E-003 -0.17317E-003 - 0.24191E-003 0.53215E-002 0.12629E-001 - 0.39700E-002 -0.84627E-004 -0.65947E-003 -- 0.46649E-003 -0.16035E-003 0.28558E-005 -+ 0.46649E-003 -0.16035E-003 0.28557E-005 - -0.74149E-004 -0.74431E-004 0.89221E-004 - 0.14291E-004 -0.10742E-003 0.75570E-004 - 0.32302E-003 -0.45917E-003 -0.47563E-002 -@@ -1555,7 +1555,7 @@ - -0.24567E-003 0.25650E-003 -0.22210E-003 - 0.35310E-003 -0.54501E-003 0.49667E-003 - 0.46922E-002 0.53681E-003 0.53276E-002 -- -0.25038E-004 -0.47621E-003 0.25061E-003 -+ -0.25039E-004 -0.47621E-003 0.25061E-003 - -0.14151E-003 0.25689E-003 -0.23625E-003 - -0.39925E-003 0.24288E-003 -0.45878E-003 - 0.19103E-003 -0.46845E-003 0.39169E-003 -@@ -1602,7 +1602,7 @@ - -0.42312E-002 0.26362E-002 0.71520E-003 - -0.20235E-003 -0.89467E-004 0.11620E-002 - -0.32420E-002 0.52388E-002 0.58477E-003 -- -0.67996E-002 0.56024E-005 0.55241E-003 -+ -0.67996E-002 0.56018E-005 0.55241E-003 - 0.13967E-001 -0.58142E-002 0.37372E-002 - -0.25763E-002 0.19323E-002 -0.10220E-002 - -0.13957E-003 0.89996E-004 -0.29649E-003 -@@ -1726,7 +1726,7 @@ - -0.65025E-004 0.20691E-004 0.20988E-004 - 0.29987E-003 -0.69971E-003 -0.25561E-002 - -0.47408E-002 -0.17716E-002 -0.10624E-002 -- 0.72365E-003 -0.12367E-003 0.91100E-004 -+ 0.72365E-003 -0.12367E-003 0.91099E-004 - -0.11286E-003 0.65700E-004 -0.38225E-004 - -0.18443E-004 -0.10315E-004 -0.41438E-004 - -0.23530E-004 -0.27346E-003 0.79396E-003 -diff -urN amber11.orig/AmberTools/test/nab/huv.O.4.dx.check amber11/AmberTools/test/nab/huv.O.4.dx.check ---- amber11.orig/AmberTools/test/nab/huv.O.4.dx.check 2010-04-07 16:55:55.000000000 +0400 -+++ amber11/AmberTools/test/nab/huv.O.4.dx.check 2011-03-08 16:38:44.000000000 +0300 -@@ -42,10 +42,10 @@ - -0.26664E-002 0.76462E-002 -0.65646E-002 - 0.65013E-002 -0.98756E-002 0.51997E-002 - -0.15412E-002 0.14894E-002 -0.58327E-003 -- 0.74208E-003 -0.46330E-005 0.26925E-003 -+ 0.74208E-003 -0.46331E-005 0.26925E-003 - -0.21081E-003 0.19041E-003 -0.70176E-003 - 0.40604E-002 -0.59967E-002 0.25324E-001 -- -0.58949E-001 0.48671E-001 -0.63192E-002 -+ -0.58949E-001 0.48671E-001 -0.63193E-002 - -0.14555E-002 0.17515E-002 -0.12653E-002 - 0.59124E-003 -0.44081E-004 -0.46024E-003 - -0.33221E-003 0.43262E-003 -0.73462E-003 -@@ -55,10 +55,10 @@ - 0.29042E-002 -0.18964E-002 0.77617E-003 - -0.18302E-003 0.26483E-004 0.13553E-002 - -0.75012E-003 0.17059E-002 -0.70949E-003 -- 0.15620E-001 0.67864E-002 -0.96628E-001 -+ 0.15620E-001 0.67863E-002 -0.96628E-001 - -0.15238E-001 -0.64540E-002 0.11108E-001 - -0.71349E-002 0.42594E-002 -0.24297E-002 -- 0.14742E-002 0.50969E-003 -0.14490E-003 -+ 0.14742E-002 0.50969E-003 -0.14489E-003 - -0.15852E-002 0.26525E-002 -0.54371E-002 - 0.63513E-002 -0.19991E-001 0.88607E-003 - -0.90619E-001 -0.26234E-001 0.54685E-002 -@@ -74,7 +74,7 @@ - -0.67192E-002 0.20436E-002 0.15087E-002 - -0.12351E-001 -0.10538E-001 0.30347E-002 - -0.24133E-002 0.57521E-003 -0.89346E-003 -- -0.19758E-003 0.85846E-004 0.21885E-003 -+ -0.19759E-003 0.85846E-004 0.21885E-003 - 0.59427E-004 0.40476E-003 -0.45294E-003 - 0.17127E-002 0.22700E-002 -0.36055E-002 - -0.94861E-002 -0.31257E-002 0.59927E-002 -@@ -89,13 +89,13 @@ - -0.21190E-003 0.38823E-003 -0.99192E-004 - 0.14844E-002 -0.48467E-002 -0.10472E-001 - -0.56834E-002 0.17312E-002 0.44869E-003 -- 0.59430E-004 -0.99269E-004 0.22702E-003 -+ 0.59429E-004 -0.99269E-004 0.22702E-003 - -0.46728E-004 -0.99733E-004 -0.59632E-005 - -0.15996E-003 0.21334E-003 -0.60938E-003 - 0.46539E-003 -0.16741E-002 0.53916E-002 - 0.73981E-002 0.59857E-002 -0.16663E-002 - 0.12223E-003 -0.48450E-003 0.17812E-003 -- -0.11241E-003 -0.53881E-005 0.24248E-003 -+ -0.11241E-003 -0.53882E-005 0.24248E-003 - -0.20069E-003 0.17999E-003 -0.24877E-003 - 0.30370E-003 -0.44718E-003 0.73307E-003 - -0.42363E-002 -0.80946E-002 -0.48617E-002 -@@ -172,7 +172,7 @@ - 0.18498E-002 -0.73133E-003 0.88568E-003 - -0.14499E-003 -0.13914E-004 -0.23519E-003 - 0.28978E-003 -0.69524E-003 0.99658E-003 -- -0.19354E-002 -0.38389E-003 -0.15309E-003 -+ -0.19354E-002 -0.38389E-003 -0.15308E-003 - 0.11672E-001 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-0.46499E-002 - 0.43349E-002 -0.38558E-002 0.59891E-003 - 0.34349E-003 -0.86951E-003 0.19112E-002 - -0.11810E-002 -0.18282E-002 0.31268E-002 -@@ -1524,7 +1524,7 @@ - 0.12391E-003 -0.17626E-003 0.37440E-002 - -0.73418E-002 -0.43798E-001 0.49519E-002 - 0.14953E-002 0.20774E-002 -0.22890E-002 -- 0.11235E-002 0.53678E-004 0.34160E-004 -+ 0.11235E-002 0.53679E-004 0.34160E-004 - -0.92654E-003 0.75587E-003 -0.15990E-002 - 0.13713E-002 -0.14112E-002 0.18715E-002 - -0.44715E-002 0.85039E-002 0.41635E-001 -@@ -1534,13 +1534,13 @@ - 0.11901E-002 -0.16300E-002 0.17072E-002 - -0.20384E-002 0.41606E-002 -0.83538E-002 - -0.36935E-001 -0.18397E-003 0.75164E-003 -- 0.32749E-004 -0.54313E-004 -0.55384E-003 -+ 0.32749E-004 -0.54314E-004 -0.55384E-003 - 0.59897E-003 -0.55366E-003 -0.85402E-003 - 0.60344E-003 -0.12434E-002 0.99286E-003 - -0.13524E-002 0.82954E-003 -0.21224E-002 - 0.41911E-002 0.38989E-001 -0.21565E-002 - 0.91862E-003 -0.97115E-003 0.27219E-003 -- 0.52312E-005 -0.71291E-003 0.34833E-003 -+ 0.52313E-005 -0.71291E-003 0.34833E-003 - -0.48047E-003 0.23123E-003 -0.44657E-003 - 0.33067E-003 -0.41250E-003 0.10632E-003 - -0.22842E-002 0.73852E-002 0.61030E-002 -@@ -1574,7 +1574,7 @@ - 0.99674E-002 -0.24989E-002 0.30342E-003 - -0.53277E-003 0.79955E-003 -0.21966E-003 - -0.59661E-003 0.35264E-003 -0.65872E-004 -- 0.11436E-002 0.38480E-003 -0.35781E-002 -+ 0.11436E-002 0.38479E-003 -0.35781E-002 - 0.36223E-002 -0.75229E-002 0.15451E-001 - 0.40636E-002 -0.14021E-001 0.68264E-002 - -0.25865E-002 0.28621E-002 -0.14937E-002 -@@ -1607,7 +1607,7 @@ - -0.72048E-002 0.52170E-002 -0.32634E-002 - -0.19081E-002 0.22332E-002 -0.24117E-002 - 0.23217E-002 0.50866E-003 -0.17204E-002 -- -0.75871E-002 0.73309E-002 0.25632E-005 -+ -0.75871E-002 0.73309E-002 0.25651E-005 - -0.21416E-001 -0.12367E-001 0.49953E-002 - -0.41626E-002 0.41883E-002 -0.30311E-002 - 0.19037E-002 0.31388E-003 -0.26396E-003 -@@ -1640,8 +1640,8 @@ - 0.33179E-003 -0.34087E-003 0.23211E-003 - -0.32071E-003 -0.56331E-004 0.14792E-003 - -0.41476E-003 -0.10262E-002 -0.21101E-001 -- -0.94099E-004 -0.10972E-002 0.73413E-003 -- -0.43772E-003 -0.10434E-003 0.72385E-004 -+ -0.94100E-004 -0.10972E-002 0.73413E-003 -+ -0.43772E-003 -0.10434E-003 0.72384E-004 - -0.27691E-003 -0.27499E-003 0.40064E-003 - -0.26074E-003 0.46773E-003 -0.13622E-003 - 0.20913E-003 -0.18338E-003 0.73660E-003 -@@ -1683,7 +1683,7 @@ - 0.38887E-003 -0.10225E-003 -0.35480E-003 - 0.21989E-002 -0.46306E-002 0.27804E-001 - -0.46260E-001 0.99268E-001 -0.12849E-001 -- 0.69339E-002 -0.28353E-002 0.32796E-002 -+ 0.69340E-002 -0.28353E-002 0.32796E-002 - -0.19358E-002 0.10950E-002 -0.18272E-003 - 0.56051E-002 -0.38298E-002 0.13655E-003 - 0.13715E-002 -0.54991E-002 0.85791E-002 -diff -urN amber11.orig/AmberTools/test/nab/Makefile amber11/AmberTools/test/nab/Makefile ---- amber11.orig/AmberTools/test/nab/Makefile 2010-04-01 08:14:34.000000000 +0400 -+++ amber11/AmberTools/test/nab/Makefile 2011-03-08 16:38:44.000000000 +0300 -@@ -12,7 +12,7 @@ - rattle_md_test rembed_test dhfrndpmtx_test asp_test \ - aspnb_test prm_test cif_test xmin_test \ - lmod_test nmode1_test nmode2_test nmode3_test ips_test \ -- pbsa_test rism_test rism_md_test rism_dist rism_hnc -+ pbsa_test rism_test rism_md_test rism_dist rism_hnc rism_ion - - duplex_test:: - @./Run.duplex -@@ -112,3 +112,6 @@ - - rism_dist:: - @./Run.rism_dist -+ -+rism_ion:: -+ @sh ./Run.rism_ion -diff -urN amber11.orig/AmberTools/test/nab/Na+.parm7 amber11/AmberTools/test/nab/Na+.parm7 ---- amber11.orig/AmberTools/test/nab/Na+.parm7 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/test/nab/Na+.parm7 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,124 @@ -+%VERSION VERSION_STAMP = V0001.000 DATE = 06/20/07 15:21:17 -+%FLAG TITLE -+%FORMAT(20a4) -+ -+%FLAG POINTERS -+%FORMAT(10I8) -+ 1 1 0 0 0 0 0 0 0 0 -+ 1 1 0 0 0 0 0 0 1 0 -+ 0 0 0 0 0 0 0 1 1 0 -+ 0 -+%FLAG ATOM_NAME -+%FORMAT(20a4) -+Na+ -+%FLAG CHARGE -+%FORMAT(5E16.8) -+ 1.82223000E+01 -+%FLAG MASS -+%FORMAT(5E16.8) -+ 2.29900000E+01 -+%FLAG ATOM_TYPE_INDEX -+%FORMAT(10I8) -+ 1 -+%FLAG NUMBER_EXCLUDED_ATOMS -+%FORMAT(10I8) -+ 1 -+%FLAG NONBONDED_PARM_INDEX -+%FORMAT(10I8) -+ 1 -+%FLAG RESIDUE_LABEL -+%FORMAT(20a4) -+Na+ -+%FLAG RESIDUE_POINTER -+%FORMAT(10I8) -+ 1 -+%FLAG BOND_FORCE_CONSTANT -+%FORMAT(5E16.8) -+ -+%FLAG BOND_EQUIL_VALUE -+%FORMAT(5E16.8) -+ -+%FLAG ANGLE_FORCE_CONSTANT -+%FORMAT(5E16.8) -+ -+%FLAG ANGLE_EQUIL_VALUE -+%FORMAT(5E16.8) -+ -+%FLAG DIHEDRAL_FORCE_CONSTANT -+%FORMAT(5E16.8) -+ -+%FLAG DIHEDRAL_PERIODICITY -+%FORMAT(5E16.8) -+ -+%FLAG DIHEDRAL_PHASE -+%FORMAT(5E16.8) -+ -+%FLAG SOLTY -+%FORMAT(5E16.8) -+ 0.00000000E+00 -+%FLAG LENNARD_JONES_ACOEF -+%FORMAT(5E16.8) -+ 2.04815198E+04 -+%FLAG LENNARD_JONES_BCOEF -+%FORMAT(5E16.8) -+ 1.50643699E+01 -+%FLAG BONDS_INC_HYDROGEN -+%FORMAT(10I8) -+ -+%FLAG BONDS_WITHOUT_HYDROGEN -+%FORMAT(10I8) -+ -+%FLAG ANGLES_INC_HYDROGEN -+%FORMAT(10I8) -+ -+%FLAG ANGLES_WITHOUT_HYDROGEN -+%FORMAT(10I8) -+ -+%FLAG DIHEDRALS_INC_HYDROGEN -+%FORMAT(10I8) -+ -+%FLAG DIHEDRALS_WITHOUT_HYDROGEN -+%FORMAT(10I8) -+ -+%FLAG EXCLUDED_ATOMS_LIST -+%FORMAT(10I8) -+ 0 -+%FLAG HBOND_ACOEF -+%FORMAT(5E16.8) -+ -+%FLAG HBOND_BCOEF -+%FORMAT(5E16.8) -+ -+%FLAG HBCUT -+%FORMAT(5E16.8) -+ -+%FLAG AMBER_ATOM_TYPE -+%FORMAT(20a4) -+IP -+%FLAG TREE_CHAIN_CLASSIFICATION -+%FORMAT(20a4) -+M -+%FLAG JOIN_ARRAY -+%FORMAT(10I8) -+ 0 -+%FLAG IROTAT -+%FORMAT(10I8) -+ 0 -+%FLAG SOLVENT_POINTERS -+%FORMAT(3I8) -+ 1 1 2 -+%FLAG ATOMS_PER_MOLECULE -+%FORMAT(10I8) -+ 1 -+%FLAG BOX_DIMENSIONS -+%FORMAT(5E16.8) -+ 9.00000000E+01 2.56000000E+01 2.56000000E+01 2.56000000E+01 -+%FLAG RADIUS_SET -+%FORMAT(1a80) -+modified Bondi radii (mbondi) -+%FLAG RADII -+%FORMAT(5E16.8) -+ 1.50000000E+00 -+%FLAG SCREEN -+%FORMAT(5E16.8) -+ 8.00000000E-01 -diff -urN amber11.orig/AmberTools/test/nab/Na+.pdb amber11/AmberTools/test/nab/Na+.pdb ---- amber11.orig/AmberTools/test/nab/Na+.pdb 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/test/nab/Na+.pdb 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,4 @@ -+REMARK -+ATOM 1 Na+ Na+ 1 0.000 0.000 0.000 1.00 0.00 N -+TER -+END -diff -urN amber11.orig/AmberTools/test/nab/rismion.nab amber11/AmberTools/test/nab/rismion.nab ---- amber11.orig/AmberTools/test/nab/rismion.nab 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/test/nab/rismion.nab 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,22 @@ -+molecule m; -+float m_xyz[dynamic], f_xyz[dynamic], v_xyz[dynamic]; -+float dgrad, fret; -+int ier, i; -+ -+m = getpdb("Na+.pdb"); -+readparm(m, "Na+.parm7"); -+allocate m_xyz[3*m.natoms]; -+allocate f_xyz[3*m.natoms]; -+allocate v_xyz[3*m.natoms]; -+mm_options( "e_debug=0, ntpr=1, ntpr_md=1, cut=999.0, dt=0.001, rattle=0, tempi=0, zerov=0"); -+mm_options( "rism=1, apply_rism_force=0"); -+mm_options( "buffer=12, solvcut=999"); -+mm_options( "progress=1, xvvfile=../rism1d/spc/spc-nacl.xvv.save"); -+mme_init( m, NULL, "::Z", m_xyz, NULL); -+ -+setxyz_from_mol( m, NULL, m_xyz ); -+ -+ier = md(3*m.natoms,0,m_xyz,f_xyz,v_xyz, mme ); -+ -+if(mytaskid==0) -+ printf( "md returns %d\n", ier ); -diff -urN amber11.orig/AmberTools/test/nab/rismion.out.check amber11/AmberTools/test/nab/rismion.out.check ---- amber11.orig/AmberTools/test/nab/rismion.out.check 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/test/nab/rismion.out.check 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,24 @@ -+Reading parm file (Na+.parm7) -+title: -+ -+ mm_options: e_debug=0 -+ mm_options: ntpr=1 -+ mm_options: ntpr_md=1 -+ mm_options: cut=999.0 -+ mm_options: dt=0.001 -+ mm_options: rattle=0 -+ mm_options: tempi=0 -+ mm_options: zerov=0 -+ mm_options: rism=1 -+ mm_options: apply_rism_force=0 -+ mm_options: buffer=12 -+ mm_options: solvcut=999 -+ mm_options: progress=1 -+ mm_options: xvvfile=../rism1d/spc/spc-nacl.xvv.save -+| New format PARM file being parsed. -+| Version = 0.001 Date = 04:06:10 Time = 16:41:39 -+ iter Total bad vdW elect nonpolar genBorn frms -+ nblist_box, number of atoms= 1 -+ nblist_box, number of pairs= 0 -+ff: 0 -73.97 0.00 0.00 0.00 0.00 -73.97 0.00e+00 -+md returns 0 -diff -urN amber11.orig/AmberTools/test/nab/Run.rism_ion amber11/AmberTools/test/nab/Run.rism_ion ---- amber11.orig/AmberTools/test/nab/Run.rism_ion 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/test/nab/Run.rism_ion 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,39 @@ -+#!/bin/sh -+ -+toomany() { -+ echo "${0}: This test requires 1, 2, 3, 4, 6, 8, 12 or 24 processes" -+ echo "for meaningful comparison." -+ exit 0 -+} -+ -+if [ -n "${DO_PARALLEL}" ] ; then -+ numprocs=`echo $DO_PARALLEL | awk -f ../numprocs.awk ` -+ if [ ! \( "$numprocs" -eq "12" -o "$numprocs" -eq "24"\ -+ -o "$numprocs" -eq "8" -o "$numprocs" -eq "6"\ -+ -o "$numprocs" -eq "3" -o "$numprocs" -eq "4"\ -+ -o "$numprocs" -eq "2" -o "$numprocs" -le "1" \) ]; then -+ echo " DO_PARALLEL set to $DO_PARALLEL" -+ toomany -+ elif [ -n "${MP_PROCS}" ]; then -+ if [ ! \( "$MP_PROCS" -eq "12" -o "$MP_PROCS" -eq "24"\ -+ -o "$MP_PROCS" -eq "8" -o "$MP_PROCS" -eq "6"\ -+ -o "$MP_PROCS" -eq "3" -o "$MP_PROCS" -eq "4"\ -+ -o "$MP_PROCS" -eq "2" -o "$MP_PROCS" -le "1" \) ]; then -+# --- For IBM AIX --- -+ echo " MP_PROCS set to "$MP_PROCS -+ toomany -+ fi -+ fi -+fi -+. ../program_error.sh -+ -+echo "Running test for ionic solvent and charge solute" -+echo "(this tests the 3D-RISM-KH implementation)" -+echo "" -+../../bin/nab -o sff rismion.nab || error -+$DO_PARALLEL ./sff > rismion.out || error -+ -+../dacdif rismion.out.check rismion.out -+ -+rm -f sff rismion.c -+exit 0 -diff -urN amber11.orig/AmberTools/test/sleap/glycam/n.pdb.save amber11/AmberTools/test/sleap/glycam/n.pdb.save ---- amber11.orig/AmberTools/test/sleap/glycam/n.pdb.save 2010-03-31 07:05:23.000000000 +0400 -+++ amber11/AmberTools/test/sleap/glycam/n.pdb.save 2011-03-08 16:38:44.000000000 +0300 -@@ -8,13 +8,13 @@ - ATOM 8 O4 6LB 1 5.435 3.303 2.147 1.00 0.00 - ATOM 9 H4O 6LB 1 5.122 4.155 1.839 1.00 0.00 - ATOM 10 C3 6LB 1 5.271 3.073 -0.262 1.00 0.00 --ATOM 11 H3 6LB 1 4.894 2.740 -1.242 1.00 0.00 --ATOM 12 O3 6LB 1 6.571 3.630 -0.399 1.00 0.00 --ATOM 13 H3O 6LB 1 7.188 2.917 -0.649 1.00 0.00 --ATOM 14 C2 6LB 1 4.314 4.119 0.310 1.00 0.00 --ATOM 15 H2 6LB 1 3.733 4.482 1.177 1.00 0.00 --ATOM 16 O2 6LB 1 5.419 4.938 -0.016 1.00 0.00 --ATOM 17 H2O 6LB 1 6.213 5.114 -0.520 1.00 0.00 -+ATOM 11 H3 6LB 1 5.706 2.518 -1.108 1.00 0.00 -+ATOM 12 O3 6LB 1 5.591 4.453 -0.363 1.00 0.00 -+ATOM 13 H3O 6LB 1 6.553 4.558 -0.232 1.00 0.00 -+ATOM 14 C2 6LB 1 3.753 2.890 -0.273 1.00 0.00 -+ATOM 15 H2 6LB 1 3.395 3.508 0.570 1.00 0.00 -+ATOM 16 O2 6LB 1 3.239 3.287 -1.528 1.00 0.00 -+ATOM 17 H2O 6LB 1 2.352 3.631 -1.425 1.00 0.00 - ATOM 18 C6 6LB 1 5.842 0.516 2.583 1.00 0.00 - ATOM 19 H61 6LB 1 6.928 0.603 2.654 1.00 0.00 - ATOM 20 H62 6LB 1 5.375 1.096 3.383 1.00 0.00 -@@ -37,7 +37,7 @@ - ATOM 37 C2 VLB 2 4.686 -2.097 4.639 1.00 0.00 - ATOM 38 H2 VLB 2 4.209 -2.878 4.019 1.00 0.00 - ATOM 39 O2 VLB 2 3.816 -1.039 4.992 1.00 0.00 --ATOM 40 H2O VLB 2 2.957 -1.387 4.762 1.00 0.00 -+ATOM 40 H2O VLB 2 4.332 -0.238 5.050 1.00 0.00 - ATOM 41 O3 VLB 2 4.014 -3.472 6.508 1.00 0.00 - ATOM 42 C1 VLB 3 2.893 -2.701 6.920 1.00 0.00 - ATOM 43 H1 VLB 3 3.071 -1.648 6.648 1.00 0.00 -@@ -57,7 +57,7 @@ - ATOM 57 C2 VLB 3 1.614 -3.056 6.171 1.00 0.00 - ATOM 58 H2 VLB 3 1.323 -4.090 6.432 1.00 0.00 - ATOM 59 O2 VLB 3 1.793 -2.849 4.782 1.00 0.00 --ATOM 60 H2O VLB 3 1.405 -3.634 4.401 1.00 0.00 -+ATOM 60 H2O VLB 3 2.476 -2.193 4.666 1.00 0.00 - ATOM 61 O3 VLB 3 -0.763 -2.638 6.079 1.00 0.00 - ATOM 62 C1 3GB 4 -0.905 -2.644 4.665 1.00 0.00 - ATOM 63 H1 3GB 4 0.044 -2.311 4.215 1.00 0.00 -@@ -68,7 +68,7 @@ - ATOM 68 H61 3GB 4 -3.380 -0.533 1.560 1.00 0.00 - ATOM 69 H62 3GB 4 -4.134 -1.031 3.099 1.00 0.00 - ATOM 70 O6 3GB 4 -2.909 0.649 3.114 1.00 0.00 --ATOM 71 H6O 3GB 4 -3.688 0.628 3.666 1.00 0.00 -+ATOM 71 H6O 3GB 4 -2.709 0.580 4.045 1.00 0.00 - ATOM 72 C4 3GB 4 -2.352 -2.990 2.187 1.00 0.00 - ATOM 73 H4 3GB 4 -3.330 -3.384 2.501 1.00 0.00 - ATOM 74 O4 3GB 4 -2.343 -2.789 0.771 1.00 0.00 -@@ -78,7 +78,7 @@ - ATOM 78 C2 3GB 4 -1.106 -4.042 4.090 1.00 0.00 - ATOM 79 H2 3GB 4 -2.075 -4.437 4.446 1.00 0.00 - ATOM 80 O2 3GB 4 -0.002 -4.864 4.416 1.00 0.00 --ATOM 81 H2O 3GB 4 0.874 -5.115 4.125 1.00 0.00 -+ATOM 81 H2O 3GB 4 -0.154 -5.298 5.256 1.00 0.00 - ATOM 82 O3 3GB 4 -1.600 -5.254 2.060 1.00 0.00 - ATOM 83 C1 0GB 5 -0.735 -6.360 2.282 1.00 0.00 - ATOM 84 H1 0GB 5 0.116 -6.024 2.897 1.00 0.00 -@@ -89,7 +89,7 @@ - ATOM 89 H61 0GB 5 1.836 -9.117 -0.171 1.00 0.00 - ATOM 90 H62 0GB 5 0.236 -8.623 -0.788 1.00 0.00 - ATOM 91 O6 0GB 5 1.789 -7.246 -0.898 1.00 0.00 --ATOM 92 H6O 0GB 5 1.142 -7.286 -1.600 1.00 0.00 -+ATOM 92 H6O 0GB 5 1.207 -6.488 -0.919 1.00 0.00 - ATOM 93 C4 0GB 5 0.134 -9.099 1.971 1.00 0.00 - ATOM 94 H4 0GB 5 -0.679 -9.576 1.404 1.00 0.00 - ATOM 95 O4 0GB 5 1.193 -10.038 2.180 1.00 0.00 -@@ -103,49 +103,49 @@ - ATOM 103 O2 0GB 5 -1.753 -6.949 4.385 1.00 0.00 - ATOM 104 H2O 0GB 5 -2.644 -6.603 4.344 1.00 0.00 - TER --ATOM 105 C1 3LB 6 10.501 -4.485 3.172 1.00 0.00 --ATOM 106 H1 3LB 6 10.220 -5.544 3.293 1.00 0.00 --ATOM 107 O5 3LB 6 11.709 -4.218 3.853 1.00 0.00 --ATOM 108 C5 3LB 6 12.798 -5.075 3.481 1.00 0.00 --ATOM 109 H5 3LB 6 12.529 -6.122 3.711 1.00 0.00 --ATOM 110 C6 3LB 6 13.974 -4.687 4.358 1.00 0.00 --ATOM 111 H61 3LB 6 14.831 -5.300 4.073 1.00 0.00 --ATOM 112 H62 3LB 6 14.206 -3.632 4.190 1.00 0.00 --ATOM 113 O6 3LB 6 13.745 -4.955 5.727 1.00 0.00 --ATOM 114 H6O 3LB 6 13.914 -4.037 5.928 1.00 0.00 --ATOM 115 C4 3LB 6 13.095 -4.959 1.987 1.00 0.00 --ATOM 116 H4 3LB 6 13.857 -5.698 1.700 1.00 0.00 --ATOM 117 O4 3LB 6 13.583 -3.638 1.737 1.00 0.00 --ATOM 118 H4O 3LB 6 13.207 -3.313 0.918 1.00 0.00 --ATOM 119 C3 3LB 6 11.834 -5.224 1.182 1.00 0.00 --ATOM 120 H3 3LB 6 11.550 -6.279 1.318 1.00 0.00 --ATOM 121 C2 3LB 6 10.690 -4.332 1.666 1.00 0.00 --ATOM 122 H2 3LB 6 11.034 -3.304 1.454 1.00 0.00 --ATOM 123 O2 3LB 6 9.498 -4.685 0.991 1.00 0.00 --ATOM 124 H2O 3LB 6 9.019 -5.430 0.628 1.00 0.00 --ATOM 125 O3 3LB 6 12.104 -4.961 -0.188 1.00 0.00 --ATOM 126 C1 0GB 7 11.081 -5.133 -1.159 1.00 0.00 --ATOM 127 H1 0GB 7 10.154 -5.434 -0.645 1.00 0.00 --ATOM 128 O5 0GB 7 11.461 -6.115 -2.101 1.00 0.00 --ATOM 129 C5 0GB 7 10.440 -6.444 -3.054 1.00 0.00 --ATOM 130 H5 0GB 7 9.559 -6.842 -2.518 1.00 0.00 --ATOM 131 C6 0GB 7 11.002 -7.552 -3.925 1.00 0.00 --ATOM 132 H61 0GB 7 10.258 -7.800 -4.686 1.00 0.00 --ATOM 133 H62 0GB 7 11.913 -7.191 -4.409 1.00 0.00 --ATOM 134 O6 0GB 7 11.234 -8.746 -3.207 1.00 0.00 --ATOM 135 H6O 0GB 7 12.148 -8.727 -3.483 1.00 0.00 --ATOM 136 C4 0GB 7 10.017 -5.207 -3.846 1.00 0.00 --ATOM 137 H4 0GB 7 10.852 -4.864 -4.475 1.00 0.00 --ATOM 138 O4 0GB 7 8.908 -5.572 -4.672 1.00 0.00 --ATOM 139 H4O 0GB 7 9.006 -5.159 -5.530 1.00 0.00 --ATOM 140 C3 0GB 7 9.603 -4.096 -2.897 1.00 0.00 --ATOM 141 H3 0GB 7 8.685 -4.408 -2.376 1.00 0.00 --ATOM 142 O3 0GB 7 9.362 -2.917 -3.653 1.00 0.00 --ATOM 143 H3O 0GB 7 8.751 -3.136 -4.381 1.00 0.00 --ATOM 144 C2 0GB 7 10.699 -3.835 -1.863 1.00 0.00 --ATOM 145 H2 0GB 7 11.561 -3.486 -2.459 1.00 0.00 --ATOM 146 O2 0GB 7 10.240 -2.889 -0.917 1.00 0.00 --ATOM 147 H2O 0GB 7 10.975 -2.374 -0.585 1.00 0.00 -+ATOM 105 C1 3LB 6 3.394 1.433 0.000 1.00 0.00 -+ATOM 106 H1 3LB 6 3.836 0.891 -0.851 1.00 0.00 -+ATOM 107 O5 3LB 6 3.973 0.998 1.212 1.00 0.00 -+ATOM 108 C5 3LB 6 5.405 1.087 1.247 1.00 0.00 -+ATOM 109 H5 3LB 6 5.826 0.451 0.448 1.00 0.00 -+ATOM 110 C6 3LB 6 5.842 0.516 2.583 1.00 0.00 -+ATOM 111 H61 3LB 6 6.928 0.603 2.654 1.00 0.00 -+ATOM 112 H62 3LB 6 5.375 1.096 3.383 1.00 0.00 -+ATOM 113 O6 3LB 6 5.555 -0.862 2.707 1.00 0.00 -+ATOM 114 H6O 3LB 6 4.615 -0.981 2.592 1.00 0.00 -+ATOM 115 C4 3LB 6 5.865 2.527 1.025 1.00 0.00 -+ATOM 116 H4 3LB 6 6.962 2.560 0.948 1.00 0.00 -+ATOM 117 O4 3LB 6 5.435 3.303 2.147 1.00 0.00 -+ATOM 118 H4O 3LB 6 5.122 4.155 1.839 1.00 0.00 -+ATOM 119 C3 3LB 6 5.271 3.073 -0.262 1.00 0.00 -+ATOM 120 H3 3LB 6 5.706 2.518 -1.108 1.00 0.00 -+ATOM 121 C2 3LB 6 3.753 2.890 -0.273 1.00 0.00 -+ATOM 122 H2 3LB 6 3.395 3.508 0.570 1.00 0.00 -+ATOM 123 O2 3LB 6 3.238 3.288 -1.530 1.00 0.00 -+ATOM 124 H2O 3LB 6 2.351 3.631 -1.427 1.00 0.00 -+ATOM 125 O3 3LB 6 5.591 4.453 -0.363 1.00 0.00 -+ATOM 126 C1 0GB 7 5.149 5.205 -1.484 1.00 0.00 -+ATOM 127 H1 0GB 7 4.548 4.549 -2.133 1.00 0.00 -+ATOM 128 O5 0GB 7 6.255 5.718 -2.197 1.00 0.00 -+ATOM 129 C5 0GB 7 5.911 6.393 -3.416 1.00 0.00 -+ATOM 130 H5 0GB 7 5.402 5.682 -4.091 1.00 0.00 -+ATOM 131 C6 0GB 7 7.218 6.805 -4.066 1.00 0.00 -+ATOM 132 H61 0GB 7 6.987 7.354 -4.981 1.00 0.00 -+ATOM 133 H62 0GB 7 7.764 7.455 -3.378 1.00 0.00 -+ATOM 134 O6 0GB 7 8.002 5.699 -4.466 1.00 0.00 -+ATOM 135 H6O 0GB 7 8.174 5.164 -3.694 1.00 0.00 -+ATOM 136 C4 0GB 7 4.976 7.569 -3.140 1.00 0.00 -+ATOM 137 H4 0GB 7 5.507 8.340 -2.562 1.00 0.00 -+ATOM 138 O4 0GB 7 4.562 8.106 -4.399 1.00 0.00 -+ATOM 139 H4O 0GB 7 4.551 9.062 -4.345 1.00 0.00 -+ATOM 140 C3 0GB 7 3.759 7.096 -2.362 1.00 0.00 -+ATOM 141 H3 0GB 7 3.169 6.430 -3.010 1.00 0.00 -+ATOM 142 O3 0GB 7 2.987 8.230 -1.991 1.00 0.00 -+ATOM 143 H3O 0GB 7 2.828 8.771 -2.788 1.00 0.00 -+ATOM 144 C2 0GB 7 4.185 6.326 -1.112 1.00 0.00 -+ATOM 145 H2 0GB 7 4.726 7.072 -0.501 1.00 0.00 -+ATOM 146 O2 0GB 7 3.042 5.790 -0.474 1.00 0.00 -+ATOM 147 H2O 0GB 7 3.187 5.738 0.470 1.00 0.00 - CONECT 1 2 3 14 - CONECT 2 1 - CONECT 3 1 4 -@@ -173,7 +173,7 @@ - CONECT 25 24 26 27 31 - CONECT 26 25 - CONECT 27 25 28 29 30 --CONECT 28 27 105 -+CONECT 28 27 - CONECT 29 27 - CONECT 30 27 - CONECT 31 25 32 33 35 -@@ -250,7 +250,7 @@ - CONECT 102 101 - CONECT 103 101 104 - CONECT 104 103 --CONECT 105 28 106 107 121 -+CONECT 105 106 107 121 - CONECT 106 105 - CONECT 107 105 108 - CONECT 108 107 109 110 115 -diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_amino91.lib.save amber11/AmberTools/test/sleap/oldleap/ff91/all_amino91.lib.save ---- amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_amino91.lib.save 2010-03-31 07:05:23.000000000 +0400 -+++ amber11/AmberTools/test/sleap/oldleap/ff91/all_amino91.lib.save 2011-03-08 16:38:44.000000000 +0300 -@@ -256,7 +256,7 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.230747 4.925147 1.196914 -- 4.828085 5.500165 0.713033 -+ 3.983296 5.433818 1.972557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.SER.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -368,7 +368,7 @@ - 1.784422 4.436955 2.124895 - 1.764698 4.397850 0.345787 - 3.971494 2.947416 2.411212 -- 4.374397 3.770738 2.696536 -+ 3.724043 3.456087 3.186855 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.THR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -500,15 +500,15 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.857033 4.748192 2.579338 -- 5.821217 4.249596 2.480083 -- 4.990360 5.695010 3.102655 -- 4.176711 4.112860 3.146449 -- 5.226485 5.898474 0.401698 -- 5.794506 5.938748 1.331123 -- 5.883342 6.134649 -0.435476 -- 4.414018 6.624028 0.441300 -+ 5.354265 4.863179 1.185791 -+ 3.853427 5.762894 -0.062862 -+ 2.773446 5.910110 -0.054565 -+ 4.351509 6.732051 -0.090207 -+ 4.134162 5.185701 -0.943848 -+ 3.881095 5.817649 2.426715 -+ 4.181612 5.279606 3.325770 -+ 4.379188 6.786828 2.400358 -+ 2.801124 5.964886 2.435947 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.LEU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -648,12 +648,12 @@ - 3.671552 3.399212 3.380613 - 3.485641 1.869279 2.490736 - 4.230199 4.986696 1.245167 -- 3.258221 5.469711 1.345449 -- 4.638709 4.784431 2.235272 -- 5.178160 5.906245 0.482655 -- 5.735477 5.933935 1.418994 -- 5.840562 6.170139 -0.341774 -- 4.354989 6.619215 0.529171 -+ 5.312304 4.855747 1.245167 -+ 3.931816 5.541027 0.355344 -+ 3.812283 5.761636 2.490333 -+ 4.110763 5.208108 3.380624 -+ 4.296680 6.738088 2.490828 -+ 2.730275 5.893388 2.490801 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.ILE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -781,9 +781,9 @@ - 3.716963 3.477633 3.370556 - 3.499621 1.931327 2.516833 - 4.274181 5.009604 1.194574 -- 4.690774 4.823320 2.184447 -- 4.954792 5.645336 0.628258 -- 3.310286 5.508600 1.294624 -+ 3.973778 5.548459 0.295968 -+ 3.993550 5.587589 2.075074 -+ 5.354265 4.863179 1.185791 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.VAL.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -897,10 +897,10 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.253694 5.017114 1.232141 -- 3.666601 5.213107 2.293908 -- 5.062354 5.920372 0.673198 -- 5.699537 6.377296 0.036552 -- 4.754312 6.389897 1.512695 -+ 5.005295 5.340406 0.315070 -+ 3.984875 5.817912 2.265912 -+ 4.408006 6.733705 2.314738 -+ 3.359598 5.504301 2.994456 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.ASN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1024,13 +1024,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.220277 5.927344 0.433563 -- 4.913588 6.591689 1.420998 -- 6.050965 6.373808 -0.511346 -- 5.971268 7.107959 0.177690 -- 6.636748 6.497679 -1.324743 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.906966 5.848446 2.410297 -+ 3.138947 5.408353 3.262885 -+ 4.458847 7.061526 2.488328 -+ 4.248421 7.659050 3.274958 -+ 5.084275 7.376210 1.760376 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.GLN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1185,20 +1185,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.125319 6.253797 -0.719124 -- 6.688164 6.300372 -1.556463 -- 6.117846 7.301883 0.099632 -- 5.907135 8.163840 1.090353 -- 5.292210 7.913283 1.851398 -- 6.363014 9.065005 1.077109 -- 6.926823 7.627695 -0.904511 -- 7.501836 7.713669 -1.730386 -- 6.873063 8.384728 -0.238094 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.540311 7.142726 2.424478 -+ 5.151800 7.375491 1.655062 -+ 4.364270 8.040994 3.389374 -+ 3.575005 7.807613 4.434120 -+ 3.088928 6.925430 4.508833 -+ 3.465343 8.513638 5.147984 -+ 5.006244 9.201290 3.286985 -+ 5.604850 9.375324 2.492326 -+ 4.892201 9.903050 4.004360 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.ARG.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1333,13 +1333,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.HID.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1467,13 +1467,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.HIE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1605,14 +1605,14 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.HIP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1770,20 +1770,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 4.941957 6.093161 0.993054 -- 4.555798 6.518222 1.919501 -- 5.833674 6.587638 -0.009560 -- 5.727864 7.297382 0.701192 -- 6.577083 6.691104 -1.083216 -- 6.699953 7.881667 -0.356949 -- 7.350710 8.089828 -1.206234 -- 6.471604 8.773711 0.684306 -- 7.153163 9.167983 -0.069436 -- 6.163215 9.539474 1.752484 -- 6.850900 10.076243 1.098979 -- 5.726463 10.185215 2.927374 -- 6.404130 10.841773 2.381664 -- 5.125146 10.546906 4.138818 -+ 4.023443 5.931088 2.293236 -+ 3.368827 5.705470 3.135064 -+ 4.811936 7.073557 1.949805 -+ 4.882911 7.922013 2.493114 -+ 5.427345 6.842058 0.816764 -+ 6.297161 7.689048 0.119607 -+ 6.531228 8.676646 0.517052 -+ 6.814097 7.187003 -1.069017 -+ 7.498083 7.791848 -1.664355 -+ 6.482667 5.953109 -1.505090 -+ 6.897672 5.575635 -2.439640 -+ 5.604046 5.117349 -0.785625 -+ 5.358725 4.126563 -1.168065 -+ 5.083391 5.623006 0.411551 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.TRP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1930,16 +1930,16 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.021223 6.053049 0.839188 -- 4.662984 6.521610 1.755820 -- 5.904492 6.742286 -0.000329 -- 5.724114 7.440373 0.817130 -- 6.758713 7.099630 -1.050381 -- 6.738282 7.947511 -0.365705 -- 7.536653 7.157250 -2.212917 -- 7.655187 8.096815 -1.673224 -- 8.214242 6.953605 -3.420974 -- 8.451251 7.942064 -3.027432 -+ 3.911603 5.857254 2.409885 -+ 3.236109 5.513847 3.193390 -+ 4.490005 7.129516 2.492349 -+ 4.264839 7.776656 3.340058 -+ 5.357612 7.570590 1.486013 -+ 5.807939 8.561136 1.550217 -+ 5.646816 6.739401 0.397212 -+ 6.322310 7.082808 -0.386292 -+ 5.068414 5.467139 0.314748 -+ 5.293580 4.820000 -0.532961 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.PHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2086,17 +2086,17 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 5.102503 5.984523 0.660315 -- 4.777863 6.502414 1.562811 -- 5.985574 6.611197 -0.227077 -- 5.846174 7.352316 0.559949 -- 6.824378 6.891857 -1.312267 -- 6.854321 7.991157 -0.512116 -- 6.305234 7.900783 0.270147 -- 7.573657 6.866032 -2.494602 -- 7.737299 7.827553 -2.007982 -- 8.211756 6.577405 -3.706841 -- 8.492629 7.576371 -3.373257 -+ 4.059917 5.918914 2.227275 -+ 3.400094 5.668222 3.057870 -+ 4.699989 7.163550 2.192787 -+ 4.538509 7.881896 2.996531 -+ 5.547468 7.485540 1.125968 -+ 6.169252 8.694615 1.092466 -+ 5.956320 9.246984 1.848209 -+ 5.754874 6.562895 0.093637 -+ 6.414696 6.813587 -0.736958 -+ 5.114801 5.318259 0.128125 -+ 5.276282 4.599913 -0.675619 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.TYR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2219,11 +2219,11 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 3.302423 5.493308 1.295046 -- 4.682911 4.808028 2.184869 -- 5.220383 5.890117 0.404729 -- 6.306867 5.987364 1.035359 -- 4.568248 6.850423 -0.085305 -+ 5.347407 4.849844 1.186161 -+ 3.966920 5.535124 0.296338 -+ 3.873721 5.805373 2.428701 -+ 4.594575 5.679017 3.454373 -+ 2.855955 6.542075 2.333709 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.GLU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2328,8 +2328,8 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.275095 5.011382 1.194525 -- 5.214909 5.080371 2.030940 -- 3.476290 5.943429 0.910275 -+ 3.669104 5.954940 0.620005 -+ 5.407723 5.091882 1.740669 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.ASP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2471,18 +2471,18 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.145332 6.228186 -0.769897 -- 7.203874 5.974714 -0.827698 -- 5.823386 6.659994 -1.717522 -- 5.933539 7.203239 0.309601 -- 6.482814 7.265694 1.154880 -- 6.528435 7.362078 -0.491005 -- 5.203409 7.900796 0.330212 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.578316 7.173413 2.389148 -+ 5.658401 7.026988 2.380365 -+ 4.277913 7.712268 1.490542 -+ 4.199407 7.952315 3.576852 -+ 4.478064 7.453372 4.409622 -+ 4.661173 8.850231 3.551971 -+ 3.198660 8.088474 3.584954 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.LYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2600,11 +2600,11 @@ - 4.419995 0.019280 -0.902255 - 3.955884 -0.274036 0.790585 - 5.547124 1.172442 0.544698 -- 6.078592 2.122578 0.598404 -- 6.005141 0.543154 -0.218399 -- 5.532142 0.472642 1.882665 -- 6.368845 0.104645 1.288859 -- 5.876555 1.272377 2.538335 -+ 6.413547 0.741633 0.042886 -+ 5.652946 1.047940 1.622381 -+ 5.369090 2.628183 0.185221 -+ 5.690639 3.251042 1.019939 -+ 5.969291 2.861853 -0.694128 - 3.933608 2.871277 -0.104508 - 3.932642 3.351380 0.874062 - 2.872953 3.958248 -0.204456 -@@ -2714,9 +2714,9 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.309567 5.303525 1.366033 -- 5.145787 5.839753 0.481671 -- 4.563172 5.041444 1.938780 -- 3.657120 5.491212 1.354764 -+ 3.725381 5.622023 2.517634 -+ 4.051868 5.551722 0.788945 -+ 4.957920 5.101954 1.372960 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.CYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2819,8 +2819,8 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.309567 5.303525 1.366033 -- 4.563172 5.041444 1.938780 -- 3.657120 5.491212 1.354764 -+ 4.051868 5.551722 0.788945 -+ 4.957920 5.101954 1.372960 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.CYX.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2950,15 +2950,15 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.402881 6.076526 0.265157 -- 5.724538 5.972445 0.854008 -- 4.818486 6.422214 0.269993 -- 6.377314 6.105674 -1.224148 -- 6.034578 6.467191 -2.193651 -- 6.303017 6.908485 -0.490613 -- 7.415066 5.781911 -1.303828 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.817297 5.981271 2.651702 -+ 4.055297 5.545795 3.115122 -+ 3.149245 5.995564 2.531107 -+ 4.753204 7.463130 2.340945 -+ 4.433578 7.904044 1.396734 -+ 4.585895 8.175303 3.148978 -+ 5.814065 7.218764 2.286557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.MET.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_aminoct91.lib.save amber11/AmberTools/test/sleap/oldleap/ff91/all_aminoct91.lib.save ---- amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_aminoct91.lib.save 2010-03-31 07:05:23.000000000 +0400 -+++ amber11/AmberTools/test/sleap/oldleap/ff91/all_aminoct91.lib.save 2011-03-08 16:38:44.000000000 +0300 -@@ -272,7 +272,7 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.230747 4.925147 1.196914 -- 4.828085 5.500165 0.713033 -+ 3.983296 5.433818 1.972557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -390,7 +390,7 @@ - 1.784422 4.436955 2.124895 - 1.764698 4.397850 0.345787 - 3.971494 2.947416 2.411212 -- 4.374397 3.770738 2.696536 -+ 3.724043 3.456087 3.186855 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -528,15 +528,15 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.857033 4.748192 2.579338 -- 5.821217 4.249596 2.480083 -- 4.990360 5.695010 3.102655 -- 4.176711 4.112860 3.146449 -- 5.226485 5.898474 0.401698 -- 5.794506 5.938748 1.331123 -- 5.883342 6.134649 -0.435476 -- 4.414018 6.624028 0.441300 -+ 5.354265 4.863179 1.185791 -+ 3.853427 5.762894 -0.062862 -+ 2.773446 5.910110 -0.054565 -+ 4.351509 6.732051 -0.090207 -+ 4.134162 5.185701 -0.943848 -+ 3.881095 5.817649 2.426715 -+ 4.181612 5.279606 3.325770 -+ 4.379188 6.786828 2.400358 -+ 2.801124 5.964886 2.435947 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -682,12 +682,12 @@ - 3.671552 3.399212 3.380613 - 3.485641 1.869279 2.490736 - 4.230199 4.986696 1.245167 -- 3.258221 5.469711 1.345449 -- 4.638709 4.784431 2.235272 -- 5.178160 5.906245 0.482655 -- 5.735477 5.933935 1.418994 -- 5.840562 6.170139 -0.341774 -- 4.354989 6.619215 0.529171 -+ 5.312304 4.855747 1.245167 -+ 3.931816 5.541027 0.355344 -+ 3.812283 5.761636 2.490333 -+ 4.110763 5.208108 3.380624 -+ 4.296680 6.738088 2.490828 -+ 2.730275 5.893388 2.490801 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -821,9 +821,9 @@ - 3.716963 3.477633 3.370556 - 3.499621 1.931327 2.516833 - 4.274181 5.009604 1.194574 -- 4.690774 4.823320 2.184447 -- 4.954792 5.645336 0.628258 -- 3.310286 5.508600 1.294624 -+ 3.973778 5.548459 0.295968 -+ 3.993550 5.587589 2.075074 -+ 5.354265 4.863179 1.185791 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -943,10 +943,10 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.253694 5.017114 1.232141 -- 3.666601 5.213107 2.293908 -- 5.062354 5.920372 0.673198 -- 5.699537 6.377296 0.036552 -- 4.754312 6.389897 1.512695 -+ 5.005295 5.340406 0.315070 -+ 3.984875 5.817912 2.265912 -+ 4.408006 6.733705 2.314738 -+ 3.359598 5.504301 2.994456 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1076,13 +1076,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.220277 5.927344 0.433563 -- 4.913588 6.591689 1.420998 -- 6.050965 6.373808 -0.511346 -- 5.971268 7.107959 0.177690 -- 6.636748 6.497679 -1.324743 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.906966 5.848446 2.410297 -+ 3.138947 5.408353 3.262885 -+ 4.458847 7.061526 2.488328 -+ 4.248421 7.659050 3.274958 -+ 5.084275 7.376210 1.760376 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1243,20 +1243,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.125319 6.253797 -0.719124 -- 6.688164 6.300372 -1.556463 -- 6.117846 7.301883 0.099632 -- 5.907135 8.163840 1.090353 -- 5.292210 7.913283 1.851398 -- 6.363014 9.065005 1.077109 -- 6.926823 7.627695 -0.904511 -- 7.501836 7.713669 -1.730386 -- 6.873063 8.384728 -0.238094 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.540311 7.142726 2.424478 -+ 5.151800 7.375491 1.655062 -+ 4.364270 8.040994 3.389374 -+ 3.575005 7.807613 4.434120 -+ 3.088928 6.925430 4.508833 -+ 3.465343 8.513638 5.147984 -+ 5.006244 9.201290 3.286985 -+ 5.604850 9.375324 2.492326 -+ 4.892201 9.903050 4.004360 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1397,13 +1397,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1537,13 +1537,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1681,14 +1681,14 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1852,20 +1852,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 4.941957 6.093161 0.993054 -- 4.555798 6.518222 1.919501 -- 5.833674 6.587638 -0.009560 -- 5.727864 7.297382 0.701192 -- 6.577083 6.691104 -1.083216 -- 6.699953 7.881667 -0.356949 -- 7.350710 8.089828 -1.206234 -- 6.471604 8.773711 0.684306 -- 7.153163 9.167983 -0.069436 -- 6.163215 9.539474 1.752484 -- 6.850900 10.076243 1.098979 -- 5.726463 10.185215 2.927374 -- 6.404130 10.841773 2.381664 -- 5.125146 10.546906 4.138818 -+ 4.023443 5.931088 2.293236 -+ 3.368827 5.705470 3.135064 -+ 4.811936 7.073557 1.949805 -+ 4.882911 7.922013 2.493114 -+ 5.427345 6.842058 0.816764 -+ 6.297161 7.689048 0.119607 -+ 6.531228 8.676646 0.517052 -+ 6.814097 7.187003 -1.069017 -+ 7.498083 7.791848 -1.664355 -+ 6.482667 5.953109 -1.505090 -+ 6.897672 5.575635 -2.439640 -+ 5.604046 5.117349 -0.785625 -+ 5.358725 4.126563 -1.168065 -+ 5.083391 5.623006 0.411551 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2018,16 +2018,16 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.021223 6.053049 0.839188 -- 4.662984 6.521610 1.755820 -- 5.904492 6.742286 -0.000329 -- 5.724114 7.440373 0.817130 -- 6.758713 7.099630 -1.050381 -- 6.738282 7.947511 -0.365705 -- 7.536653 7.157250 -2.212917 -- 7.655187 8.096815 -1.673224 -- 8.214242 6.953605 -3.420974 -- 8.451251 7.942064 -3.027432 -+ 3.911603 5.857254 2.409885 -+ 3.236109 5.513847 3.193390 -+ 4.490005 7.129516 2.492349 -+ 4.264839 7.776656 3.340058 -+ 5.357612 7.570590 1.486013 -+ 5.807939 8.561136 1.550217 -+ 5.646816 6.739401 0.397212 -+ 6.322310 7.082808 -0.386292 -+ 5.068414 5.467139 0.314748 -+ 5.293580 4.820000 -0.532961 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2180,17 +2180,17 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 5.102503 5.984523 0.660315 -- 4.777863 6.502414 1.562811 -- 5.985574 6.611197 -0.227077 -- 5.846174 7.352316 0.559949 -- 6.824378 6.891857 -1.312267 -- 6.854321 7.991157 -0.512116 -- 6.305234 7.900783 0.270147 -- 7.573657 6.866032 -2.494602 -- 7.737299 7.827553 -2.007982 -- 8.211756 6.577405 -3.706841 -- 8.492629 7.576371 -3.373257 -+ 4.059917 5.918914 2.227275 -+ 3.400094 5.668222 3.057870 -+ 4.699989 7.163550 2.192787 -+ 4.538509 7.881896 2.996531 -+ 5.547468 7.485540 1.125968 -+ 6.169252 8.694615 1.092466 -+ 5.956320 9.246984 1.848209 -+ 5.754874 6.562895 0.093637 -+ 6.414696 6.813587 -0.736958 -+ 5.114801 5.318259 0.128125 -+ 5.276282 4.599913 -0.675619 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2319,11 +2319,11 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 3.302423 5.493308 1.295046 -- 4.682911 4.808028 2.184869 -- 5.220383 5.890117 0.404729 -- 6.306867 5.987364 1.035359 -- 4.568248 6.850423 -0.085305 -+ 5.347407 4.849844 1.186161 -+ 3.966920 5.535124 0.296338 -+ 3.873721 5.805373 2.428701 -+ 4.594575 5.679017 3.454373 -+ 2.855955 6.542075 2.333709 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2434,8 +2434,8 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.275095 5.011382 1.194525 -- 5.214909 5.080371 2.030940 -- 3.476290 5.943429 0.910275 -+ 3.669104 5.954940 0.620005 -+ 5.407723 5.091882 1.740669 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2583,18 +2583,18 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.145332 6.228186 -0.769897 -- 7.203874 5.974714 -0.827698 -- 5.823386 6.659994 -1.717522 -- 5.933539 7.203239 0.309601 -- 6.482814 7.265694 1.154880 -- 6.528435 7.362078 -0.491005 -- 5.203409 7.900796 0.330212 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.578316 7.173413 2.389148 -+ 5.658401 7.026988 2.380365 -+ 4.277913 7.712268 1.490542 -+ 4.199407 7.952315 3.576852 -+ 4.478064 7.453372 4.409622 -+ 4.661173 8.850231 3.551971 -+ 3.198660 8.088474 3.584954 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2718,11 +2718,11 @@ - 4.419995 0.019280 -0.902255 - 3.955884 -0.274036 0.790585 - 5.547124 1.172442 0.544698 -- 6.078592 2.122578 0.598404 -- 6.005141 0.543154 -0.218399 -- 5.532142 0.472642 1.882665 -- 6.368845 0.104645 1.288859 -- 5.876555 1.272377 2.538335 -+ 6.413547 0.741633 0.042886 -+ 5.652946 1.047940 1.622381 -+ 5.369090 2.628183 0.185221 -+ 5.690639 3.251042 1.019939 -+ 5.969291 2.861853 -0.694128 - 3.933608 2.871277 -0.104508 - 3.932642 3.351380 0.874062 - 2.872953 3.958248 -0.204456 -@@ -2838,9 +2838,9 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.309567 5.303525 1.366033 -- 5.145787 5.839753 0.481671 -- 4.563172 5.041444 1.938780 -- 3.657120 5.491212 1.354764 -+ 3.725381 5.622023 2.517634 -+ 4.051868 5.551722 0.788945 -+ 4.957920 5.101954 1.372960 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2949,8 +2949,8 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.309567 5.303525 1.366033 -- 4.563172 5.041444 1.938780 -- 3.657120 5.491212 1.354764 -+ 4.051868 5.551722 0.788945 -+ 4.957920 5.101954 1.372960 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -3086,15 +3086,15 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.402881 6.076526 0.265157 -- 5.724538 5.972445 0.854008 -- 4.818486 6.422214 0.269993 -- 6.377314 6.105674 -1.224148 -- 6.034578 6.467191 -2.193651 -- 6.303017 6.908485 -0.490613 -- 7.415066 5.781911 -1.303828 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.817297 5.981271 2.651702 -+ 4.055297 5.545795 3.115122 -+ 3.149245 5.995564 2.531107 -+ 4.753204 7.463130 2.340945 -+ 4.433578 7.904044 1.396734 -+ 4.585895 8.175303 3.148978 -+ 5.814065 7.218764 2.286557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_aminont91.lib.save amber11/AmberTools/test/sleap/oldleap/ff91/all_aminont91.lib.save ---- amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_aminont91.lib.save 2010-03-31 07:05:23.000000000 +0400 -+++ amber11/AmberTools/test/sleap/oldleap/ff91/all_aminont91.lib.save 2011-03-08 16:38:44.000000000 +0300 -@@ -290,7 +290,7 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.230747 4.925147 1.196914 -- 4.828085 5.500165 0.713033 -+ 3.983296 5.433818 1.972557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NSER.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -414,7 +414,7 @@ - 1.784422 4.436955 2.124895 - 1.764698 4.397850 0.345787 - 3.971494 2.947416 2.411212 -- 4.374397 3.770738 2.696536 -+ 3.724043 3.456087 3.186855 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NTHR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -558,15 +558,15 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.857033 4.748192 2.579338 -- 5.821217 4.249596 2.480083 -- 4.990360 5.695010 3.102655 -- 4.176711 4.112860 3.146449 -- 5.226485 5.898474 0.401698 -- 5.794506 5.938748 1.331123 -- 5.883342 6.134649 -0.435476 -- 4.414018 6.624028 0.441300 -+ 5.354265 4.863179 1.185791 -+ 3.853427 5.762894 -0.062862 -+ 2.773446 5.910110 -0.054565 -+ 4.351509 6.732051 -0.090207 -+ 4.134162 5.185701 -0.943848 -+ 3.881095 5.817649 2.426715 -+ 4.181612 5.279606 3.325770 -+ 4.379188 6.786828 2.400358 -+ 2.801124 5.964886 2.435947 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NLEU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -718,12 +718,12 @@ - 3.671552 3.399212 3.380613 - 3.485641 1.869279 2.490736 - 4.230199 4.986696 1.245167 -- 4.638709 4.784431 2.235272 -- 3.258221 5.469711 1.345449 -- 5.178160 5.906245 0.482655 -- 5.735477 5.933935 1.418994 -- 5.840562 6.170139 -0.341774 -- 4.354989 6.619215 0.529171 -+ 3.931816 5.541027 0.355344 -+ 5.312304 4.855747 1.245167 -+ 3.812283 5.761636 2.490333 -+ 4.110763 5.208108 3.380624 -+ 4.296680 6.738088 2.490828 -+ 2.730275 5.893388 2.490801 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NILE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -863,9 +863,9 @@ - 3.716963 3.477633 3.370556 - 3.499621 1.931327 2.516833 - 4.274181 5.009604 1.194574 -- 4.690774 4.823320 2.184447 -- 4.954792 5.645336 0.628258 -- 3.310286 5.508600 1.294624 -+ 3.973778 5.548459 0.295968 -+ 3.993550 5.587589 2.075074 -+ 5.354265 4.863179 1.185791 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NVAL.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -991,10 +991,10 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.253694 5.017114 1.232141 -- 3.666601 5.213107 2.293908 -- 5.062354 5.920372 0.673198 -- 5.699537 6.377296 0.036552 -- 4.754312 6.389897 1.512695 -+ 5.005295 5.340406 0.315070 -+ 3.984875 5.817912 2.265912 -+ 4.408006 6.733705 2.314738 -+ 3.359598 5.504301 2.994456 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NASN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1130,13 +1130,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.220277 5.927344 0.433563 -- 4.913588 6.591689 1.420998 -- 6.050965 6.373808 -0.511346 -- 5.971268 7.107959 0.177690 -- 6.636748 6.497679 -1.324743 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.906966 5.848446 2.410297 -+ 3.138947 5.408353 3.262885 -+ 4.458847 7.061526 2.488328 -+ 4.248421 7.659050 3.274958 -+ 5.084275 7.376210 1.760376 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NGLN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1303,20 +1303,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.125319 6.253797 -0.719124 -- 6.688164 6.300372 -1.556463 -- 6.117846 7.301883 0.099632 -- 5.907135 8.163840 1.090353 -- 5.292210 7.913283 1.851398 -- 6.363014 9.065005 1.077109 -- 6.926823 7.627695 -0.904511 -- 7.501836 7.713669 -1.730386 -- 6.873063 8.384728 -0.238094 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.540311 7.142726 2.424478 -+ 5.151800 7.375491 1.655062 -+ 4.364270 8.040994 3.389374 -+ 3.575005 7.807613 4.434120 -+ 3.088928 6.925430 4.508833 -+ 3.465343 8.513638 5.147984 -+ 5.006244 9.201290 3.286985 -+ 5.604850 9.375324 2.492326 -+ 4.892201 9.903050 4.004360 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NARG.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1463,13 +1463,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NHID.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1609,13 +1609,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NHIE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1759,14 +1759,14 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NHIP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1936,20 +1936,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 4.941957 6.093161 0.993054 -- 4.555798 6.518222 1.919501 -- 5.833674 6.587638 -0.009560 -- 5.727864 7.297382 0.701192 -- 6.577083 6.691104 -1.083216 -- 6.699953 7.881667 -0.356949 -- 7.350710 8.089828 -1.206234 -- 6.471604 8.773711 0.684306 -- 7.153163 9.167983 -0.069436 -- 6.163215 9.539474 1.752484 -- 6.850900 10.076243 1.098979 -- 5.726463 10.185215 2.927374 -- 6.404130 10.841773 2.381664 -- 5.125146 10.546906 4.138818 -+ 4.023443 5.931088 2.293236 -+ 3.368827 5.705470 3.135064 -+ 4.811936 7.073557 1.949805 -+ 4.882911 7.922013 2.493114 -+ 5.427345 6.842058 0.816764 -+ 6.297161 7.689048 0.119607 -+ 6.531228 8.676646 0.517052 -+ 6.814097 7.187003 -1.069017 -+ 7.498083 7.791848 -1.664355 -+ 6.482667 5.953109 -1.505090 -+ 6.897672 5.575635 -2.439640 -+ 5.604046 5.117349 -0.785625 -+ 5.358725 4.126563 -1.168065 -+ 5.083391 5.623006 0.411551 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NTRP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2108,16 +2108,16 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.021223 6.053049 0.839188 -- 4.662984 6.521610 1.755820 -- 5.904492 6.742286 -0.000329 -- 5.724114 7.440373 0.817130 -- 6.758713 7.099630 -1.050381 -- 6.738282 7.947511 -0.365705 -- 7.536653 7.157250 -2.212917 -- 7.655187 8.096815 -1.673224 -- 8.214242 6.953605 -3.420974 -- 8.451251 7.942064 -3.027432 -+ 3.911603 5.857254 2.409885 -+ 3.236109 5.513847 3.193390 -+ 4.490005 7.129516 2.492349 -+ 4.264839 7.776656 3.340058 -+ 5.357612 7.570590 1.486013 -+ 5.807939 8.561136 1.550217 -+ 5.646816 6.739401 0.397212 -+ 6.322310 7.082808 -0.386292 -+ 5.068414 5.467139 0.314748 -+ 5.293580 4.820000 -0.532961 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NPHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2276,17 +2276,17 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 5.102503 5.984523 0.660315 -- 4.777863 6.502414 1.562811 -- 5.985574 6.611197 -0.227077 -- 5.846174 7.352316 0.559949 -- 6.824378 6.891857 -1.312267 -- 6.854321 7.991157 -0.512116 -- 6.305234 7.900783 0.270147 -- 7.573657 6.866032 -2.494602 -- 7.737299 7.827553 -2.007982 -- 8.211756 6.577405 -3.706841 -- 8.492629 7.576371 -3.373257 -+ 4.059917 5.918914 2.227275 -+ 3.400094 5.668222 3.057870 -+ 4.699989 7.163550 2.192787 -+ 4.538509 7.881896 2.996531 -+ 5.547468 7.485540 1.125968 -+ 6.169252 8.694615 1.092466 -+ 5.956320 9.246984 1.848209 -+ 5.754874 6.562895 0.093637 -+ 6.414696 6.813587 -0.736958 -+ 5.114801 5.318259 0.128125 -+ 5.276282 4.599913 -0.675619 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NTYR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2421,11 +2421,11 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 3.302423 5.493308 1.295046 -- 4.682911 4.808028 2.184869 -- 5.220383 5.890117 0.404729 -- 6.306867 5.987364 1.035359 -- 4.568248 6.850423 -0.085305 -+ 5.347407 4.849844 1.186161 -+ 3.966920 5.535124 0.296338 -+ 3.873721 5.805373 2.428701 -+ 4.594575 5.679017 3.454373 -+ 2.855955 6.542075 2.333709 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NGLU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2542,8 +2542,8 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.275095 5.011382 1.194525 -- 5.214909 5.080371 2.030940 -- 3.476290 5.943429 0.910275 -+ 3.669104 5.954940 0.620005 -+ 5.407723 5.091882 1.740669 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NASP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2697,18 +2697,18 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.145332 6.228186 -0.769897 -- 7.203874 5.974714 -0.827698 -- 5.823386 6.659994 -1.717522 -- 5.933539 7.203239 0.309601 -- 6.482814 7.265694 1.154880 -- 6.528435 7.362078 -0.491005 -- 5.203409 7.900796 0.330212 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.578316 7.173413 2.389148 -+ 5.658401 7.026988 2.380365 -+ 4.277913 7.712268 1.490542 -+ 4.199407 7.952315 3.576852 -+ 4.478064 7.453372 4.409622 -+ 4.661173 8.850231 3.551971 -+ 3.198660 8.088474 3.584954 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NLYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2838,11 +2838,11 @@ - 4.408167 0.002206 -0.902255 - 3.942020 -0.287863 0.790585 - 5.543318 1.147472 0.544698 -- 6.081407 2.093874 0.598404 -- 5.996931 0.515001 -0.218399 -- 5.523452 0.447794 1.882665 -- 6.357566 0.073964 1.288859 -- 5.873440 1.245104 2.538335 -+ 6.406713 0.710625 0.042886 -+ 5.648269 1.022234 1.622381 -+ 5.375452 2.604420 0.185221 -+ 5.701342 3.225018 1.019939 -+ 5.977270 2.833894 -0.694128 - 3.941702 2.857530 -0.104508 - 3.944087 3.337627 0.874062 - 2.888662 3.951879 -0.204456 -@@ -2964,9 +2964,9 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.309567 5.303525 1.366033 -- 5.145787 5.839753 0.481671 -- 4.563172 5.041444 1.938780 -- 3.657120 5.491212 1.354764 -+ 3.725381 5.622023 2.517634 -+ 4.051868 5.551722 0.788945 -+ 4.957920 5.101954 1.372960 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NCYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -3081,8 +3081,8 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.309567 5.303525 1.366033 -- 4.563172 5.041444 1.938780 -- 3.657120 5.491212 1.354764 -+ 4.051868 5.551722 0.788945 -+ 4.957920 5.101954 1.372960 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NCYX.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -3224,15 +3224,15 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.402881 6.076526 0.265157 -- 5.724538 5.972445 0.854008 -- 4.818486 6.422214 0.269993 -- 6.377314 6.105674 -1.224148 -- 6.034578 6.467191 -2.193651 -- 6.303017 6.908485 -0.490613 -- 7.415066 5.781911 -1.303828 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.817297 5.981271 2.651702 -+ 4.055297 5.545795 3.115122 -+ 3.149245 5.995564 2.531107 -+ 4.753204 7.463130 2.340945 -+ 4.433578 7.904044 1.396734 -+ 4.585895 8.175303 3.148978 -+ 5.814065 7.218764 2.286557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NMET.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_nucleic91.lib.save amber11/AmberTools/test/sleap/oldleap/ff91/all_nucleic91.lib.save ---- amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_nucleic91.lib.save 2010-03-31 07:05:23.000000000 +0400 -+++ amber11/AmberTools/test/sleap/oldleap/ff91/all_nucleic91.lib.save 2011-03-08 16:38:44.000000000 +0300 -@@ -162,27 +162,27 @@ - 3.710733 0.830490 -3.744234 - 1.911850 1.246480 -4.585645 - 1.227112 2.479938 -4.747250 -- 1.435744 3.548600 -4.696894 -- 1.460583 2.154521 -6.213536 -- 0.611235 3.180043 -6.535735 -- -0.465186 3.098120 -6.567442 -- 1.349267 3.870896 -7.353068 -- -0.036082 3.758044 -7.339885 -- 0.351402 4.533174 -8.439444 -- -0.960336 4.612555 -8.701439 -- -1.624968 4.152050 -8.096212 -- -1.284404 5.132893 -9.504140 -- 1.216752 5.151275 -9.254748 -- -0.058580 5.292957 -9.604538 -- 0.617022 5.800159 -10.277374 -- -1.311694 5.457396 -9.985412 -- -2.648827 5.295295 -9.894316 -+ 1.476326 2.910069 -5.717291 -+ -0.266632 2.222549 -4.860734 -+ -1.220065 2.003738 -3.901574 -+ -0.944101 1.997212 -2.857447 -+ -2.424721 1.879538 -4.374202 -+ -2.264060 2.025899 -5.747107 -+ -3.171716 1.996442 -6.812608 -+ -4.488141 1.800018 -6.657550 -+ -4.872966 1.663197 -5.733813 -+ -5.095547 1.788787 -7.464416 -+ -2.681111 2.175962 -8.046577 -+ -1.373728 2.370469 -8.194275 -+ -0.957583 2.517234 -9.180015 -+ -0.428694 2.418225 -7.273933 -+ -0.949520 2.234705 -6.042040 - 2.953825 2.805883 -3.147902 - 2.001837 3.312549 -3.306355 - 1.598529 3.379160 -3.566738 - 1.132115 3.871151 -2.713214 - 1.786595 4.328794 -4.619224 -- 1.990348 5.218376 -4.321352 -+ 0.918045 4.664210 -4.853138 - 3.951586 3.479347 -3.901109 - !entry.RADE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 30 0 0 0 0 -@@ -367,25 +367,25 @@ - 3.710733 0.830490 -3.744234 - 1.911850 1.246480 -4.585645 - 1.227112 2.479938 -4.747250 -- 1.435744 3.548600 -4.696894 -- 1.485202 2.137699 -6.174261 -- 0.655381 3.211408 -6.264512 -- -0.423435 3.161813 -6.254680 -- 1.273874 3.921103 -7.246041 -- 2.001469 4.404856 -7.897723 -- -0.138537 4.008754 -7.451742 -- 0.496986 4.687819 -8.388428 -- 1.506269 4.703628 -8.353806 -- -0.021913 5.169907 -9.108453 -- -1.467764 3.981289 -7.487821 -- -2.803489 3.801409 -7.305937 -- -2.649940 4.509819 -8.312007 -+ 1.476326 2.910069 -5.717291 -+ -0.230375 2.189658 -4.854806 -+ -0.988446 1.979043 -3.745496 -+ -0.535467 2.020843 -2.765974 -+ -2.318623 1.714239 -3.846032 -+ -2.910767 1.548015 -2.946124 -+ -2.871582 1.669472 -5.164035 -+ -4.156011 1.417550 -5.334852 -+ -4.717568 1.261374 -4.510012 -+ -4.549259 1.385324 -6.264593 -+ -2.122766 1.876681 -6.243498 -+ -0.794090 2.140091 -6.121697 -+ -0.063349 2.338641 -7.103631 - 2.953825 2.805883 -3.147902 - 3.277337 2.955353 -2.117806 - 1.598529 3.379160 -3.566738 - 1.132115 3.871151 -2.713214 - 1.786595 4.328794 -4.619224 -- 1.990348 5.218376 -4.321352 -+ 0.918045 4.664210 -4.853138 - 3.951586 3.479347 -3.901109 - !entry.RCYT.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 28 0 0 0 0 -@@ -581,28 +581,28 @@ - 3.710733 0.830490 -3.744234 - 1.911850 1.246480 -4.585645 - 1.227112 2.479938 -4.747250 -- 1.435744 3.548600 -4.696894 -- 1.485985 2.137078 -6.173971 -- 0.630205 3.182508 -6.455250 -- -0.447083 3.109089 -6.476705 -- 1.375610 3.824568 -7.320253 -- -0.009195 3.704817 -7.311681 -- 0.430021 4.484569 -8.414167 -- -0.743299 4.619666 -8.757634 -- 1.449094 5.077582 -9.169036 -- 2.230864 5.470422 -9.653301 -- 0.193424 5.321243 -9.687036 -- 1.134074 5.907027 -10.440452 -- 2.131730 5.897532 -10.283319 -- 0.809583 6.430577 -11.240890 -- -1.093830 5.428430 -10.003875 -- -2.446615 5.292973 -9.968886 -+ 1.476326 2.910069 -5.717291 -+ -0.230179 2.188641 -4.854706 -+ -1.148250 1.950412 -3.852312 -+ -0.834533 1.961464 -2.818939 -+ -2.363371 1.722968 -4.285727 -+ -2.247746 1.815662 -5.667805 -+ -3.226774 1.665775 -6.685370 -+ -4.425333 1.414365 -6.570704 -+ -2.671302 1.843175 -7.958154 -+ -3.284184 1.755160 -8.743412 -+ -1.346177 2.129674 -8.215759 -+ -1.013622 2.261923 -9.507083 -+ -1.624549 2.163147 -10.305276 -+ -0.043809 2.463028 -9.704869 -+ -0.430928 2.271846 -7.261291 -+ -0.954757 2.102421 -6.017708 - 2.953825 2.805883 -3.147902 - 3.277337 2.955353 -2.117806 - 1.598529 3.379160 -3.566738 - 1.132115 3.871151 -2.713214 - 1.786595 4.328794 -4.619224 -- 1.990348 5.218376 -4.321352 -+ 0.918045 4.664210 -4.853138 - 3.951586 3.479347 -3.901109 - !entry.RGUA.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 31 0 0 0 0 -@@ -876,24 +876,24 @@ - 3.710733 0.830490 -3.744234 - 1.911850 1.246480 -4.585645 - 1.227112 2.479938 -4.747250 -- 1.435744 3.548600 -4.696894 -- 1.462119 2.152380 -6.223183 -- 0.621409 3.225476 -6.359458 -- -0.457084 3.168437 -6.359671 -- 1.227187 3.969404 -7.294982 -- 1.951054 4.453936 -7.950226 -- -0.178556 4.113730 -7.571852 -- 0.321873 4.770160 -8.483756 -- -1.548942 3.990804 -7.465412 -- -1.150751 4.582332 -8.289814 -- -2.922393 3.884686 -7.383122 -- -2.754887 4.581962 -8.370112 -+ 1.476326 2.910069 -5.717291 -+ -0.276459 2.220856 -4.861481 -+ -1.084733 2.020834 -3.773554 -+ -0.665763 2.042111 -2.778360 -+ -2.406530 1.849990 -3.912354 -+ -3.030993 1.692292 -3.032992 -+ -3.019582 1.871650 -5.215158 -+ -4.219997 1.724488 -5.439315 -+ -2.132048 2.078389 -6.251470 -+ -2.549647 2.102845 -7.258005 -+ -0.768247 2.257235 -6.139841 -+ -0.062611 2.434266 -7.119196 - 2.953825 2.805883 -3.147902 - 3.102654 2.968023 -2.080353 - 1.598529 3.379160 -3.566738 - 1.132115 3.871151 -2.713214 - 1.786595 4.328794 -4.619224 -- 1.990348 5.218376 -4.321352 -+ 0.918045 4.664210 -4.853138 - 3.951586 3.479347 -3.901109 - !entry.RURA.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 27 0 0 0 0 -@@ -1080,21 +1080,21 @@ - 3.710733 0.830490 -3.744234 - 1.911850 1.246480 -4.585645 - 1.227112 2.479938 -4.747250 -- 1.435744 3.548600 -4.696894 -- 1.460583 2.154521 -6.213536 -- 0.611235 3.180043 -6.535735 -- -0.465186 3.098120 -6.567442 -- 1.349267 3.870896 -7.353068 -- -0.036082 3.758044 -7.339885 -- 0.351402 4.533174 -8.439444 -- -0.960336 4.612555 -8.701439 -- -1.624968 4.152050 -8.096212 -- -1.284404 5.132893 -9.504140 -- 1.216752 5.151275 -9.254748 -- -0.058580 5.292957 -9.604538 -- 0.617022 5.800159 -10.277374 -- -1.311694 5.457396 -9.985412 -- -2.648827 5.295295 -9.894316 -+ 1.476326 2.910069 -5.717291 -+ -0.266632 2.222549 -4.860734 -+ -1.220065 2.003738 -3.901574 -+ -0.944101 1.997212 -2.857447 -+ -2.424721 1.879538 -4.374202 -+ -2.264060 2.025899 -5.747107 -+ -3.171716 1.996442 -6.812608 -+ -4.488141 1.800018 -6.657550 -+ -4.872966 1.663197 -5.733813 -+ -5.095547 1.788787 -7.464416 -+ -2.681111 2.175962 -8.046577 -+ -1.373728 2.370469 -8.194275 -+ -0.957583 2.517234 -9.180015 -+ -0.428694 2.418225 -7.273933 -+ -0.949520 2.234705 -6.042040 - 2.953825 2.805883 -3.147902 - 3.102654 2.968023 -2.080353 - 1.598529 3.379160 -3.566738 -@@ -1279,19 +1279,19 @@ - 3.710733 0.830490 -3.744234 - 1.911850 1.246480 -4.585645 - 1.227112 2.479938 -4.747250 -- 1.435744 3.548600 -4.696894 -- 1.485202 2.137699 -6.174261 -- 0.655381 3.211408 -6.264512 -- -0.423435 3.161813 -6.254680 -- 1.273874 3.921103 -7.246041 -- 2.001469 4.404856 -7.897723 -- -0.138537 4.008754 -7.451742 -- 0.496986 4.687819 -8.388428 -- 1.506269 4.703628 -8.353806 -- -0.021913 5.169907 -9.108453 -- -1.467764 3.981289 -7.487821 -- -2.803489 3.801409 -7.305937 -- -2.649940 4.509819 -8.312007 -+ 1.476326 2.910069 -5.717291 -+ -0.230375 2.189658 -4.854806 -+ -0.988446 1.979043 -3.745496 -+ -0.535467 2.020843 -2.765974 -+ -2.318623 1.714239 -3.846032 -+ -2.910767 1.548015 -2.946124 -+ -2.871582 1.669472 -5.164035 -+ -4.156011 1.417550 -5.334852 -+ -4.717568 1.261374 -4.510012 -+ -4.549259 1.385324 -6.264593 -+ -2.122766 1.876681 -6.243498 -+ -0.794090 2.140091 -6.121697 -+ -0.063349 2.338641 -7.103631 - 2.953825 2.805883 -3.147902 - 3.277337 2.955353 -2.117806 - 1.598529 3.379160 -3.566738 -@@ -1487,22 +1487,22 @@ - 3.710733 0.830490 -3.744234 - 1.911850 1.246480 -4.585645 - 1.227112 2.479938 -4.747250 -- 1.435744 3.548600 -4.696894 -- 1.485985 2.137078 -6.173971 -- 0.630205 3.182508 -6.455250 -- -0.447083 3.109089 -6.476705 -- 1.375610 3.824568 -7.320253 -- -0.009195 3.704817 -7.311681 -- 0.430021 4.484569 -8.414167 -- -0.743299 4.619666 -8.757634 -- 1.449094 5.077582 -9.169036 -- 2.230864 5.470422 -9.653301 -- 0.193424 5.321243 -9.687036 -- 1.134074 5.907027 -10.440452 -- 2.131730 5.897532 -10.283319 -- 0.809583 6.430577 -11.240890 -- -1.093830 5.428430 -10.003875 -- -2.446615 5.292973 -9.968886 -+ 1.476326 2.910069 -5.717291 -+ -0.230179 2.188641 -4.854706 -+ -1.148250 1.950412 -3.852312 -+ -0.834533 1.961464 -2.818939 -+ -2.363371 1.722968 -4.285727 -+ -2.247746 1.815662 -5.667805 -+ -3.226774 1.665775 -6.685370 -+ -4.425333 1.414365 -6.570704 -+ -2.671302 1.843175 -7.958154 -+ -3.284184 1.755160 -8.743412 -+ -1.346177 2.129674 -8.215759 -+ -1.013622 2.261923 -9.507083 -+ -1.624549 2.163147 -10.305276 -+ -0.043809 2.463028 -9.704869 -+ -0.430928 2.271846 -7.261291 -+ -0.954757 2.102421 -6.017708 - 2.953825 2.805883 -3.147902 - 3.277337 2.955353 -2.117806 - 1.598529 3.379160 -3.566738 -@@ -1788,21 +1788,21 @@ - 3.710733 0.830490 -3.744234 - 1.911850 1.246480 -4.585645 - 1.227112 2.479938 -4.747250 -- 1.435744 3.548600 -4.696894 -- 1.462119 2.152380 -6.223183 -- 0.621409 3.225476 -6.359458 -- -0.457084 3.168437 -6.359671 -- 1.227187 3.969404 -7.294982 -- 2.191055 4.651430 -8.220076 -- 2.843927 3.908200 -8.677753 -- 1.638142 5.177191 -8.998511 -- 2.792502 5.365208 -7.657153 -- -0.178556 4.113730 -7.571852 -- 0.321873 4.770160 -8.483756 -- -1.548942 3.990804 -7.465412 -- -1.150751 4.582332 -8.289814 -- -2.922393 3.884686 -7.383122 -- -2.754887 4.581962 -8.370112 -+ 1.476326 2.910069 -5.717291 -+ -0.276459 2.220856 -4.861481 -+ -1.084733 2.020834 -3.773554 -+ -0.665763 2.042111 -2.778360 -+ -2.406530 1.849990 -3.912354 -+ -3.300021 1.630344 -2.727690 -+ -3.231144 2.486293 -2.056343 -+ -4.330132 1.515881 -3.065138 -+ -2.988981 0.729023 -2.199511 -+ -3.019582 1.871650 -5.215158 -+ -4.219997 1.724488 -5.439315 -+ -2.132048 2.078389 -6.251470 -+ -2.549647 2.102845 -7.258005 -+ -0.768247 2.257235 -6.139841 -+ -0.062611 2.434266 -7.119196 - 2.953825 2.805883 -3.147902 - 3.102654 2.968023 -2.080353 - 1.598529 3.379160 -3.566738 -diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_amino94.lib.save amber11/AmberTools/test/sleap/oldleap/ff94/all_amino94.lib.save ---- amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_amino94.lib.save 2010-03-31 07:05:23.000000000 +0400 -+++ amber11/AmberTools/test/sleap/oldleap/ff94/all_amino94.lib.save 2011-03-08 16:38:44.000000000 +0300 -@@ -260,7 +260,7 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.230747 4.925147 1.196914 -- 4.828085 5.500165 0.713033 -+ 3.983296 5.433818 1.972557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.SER.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -372,7 +372,7 @@ - 1.784422 4.436955 2.124895 - 1.764698 4.397850 0.345787 - 3.971494 2.947416 2.411212 -- 4.374397 3.770738 2.696536 -+ 3.724043 3.456087 3.186855 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.THR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -504,15 +504,15 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.857033 4.748192 2.579338 -- 5.821217 4.249596 2.480083 -- 4.990360 5.695010 3.102655 -- 4.176711 4.112860 3.146449 -- 5.226485 5.898474 0.401698 -- 5.794506 5.938748 1.331123 -- 5.883342 6.134649 -0.435476 -- 4.414018 6.624028 0.441300 -+ 5.354265 4.863179 1.185791 -+ 3.853427 5.762894 -0.062862 -+ 2.773446 5.910110 -0.054565 -+ 4.351509 6.732051 -0.090207 -+ 4.134162 5.185701 -0.943848 -+ 3.881095 5.817649 2.426715 -+ 4.181612 5.279606 3.325770 -+ 4.379188 6.786828 2.400358 -+ 2.801124 5.964886 2.435947 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.LEU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -652,12 +652,12 @@ - 3.671552 3.399212 3.380613 - 3.485641 1.869279 2.490736 - 4.230199 4.986696 1.245167 -- 3.258221 5.469711 1.345449 -- 4.638709 4.784431 2.235272 -- 5.178160 5.906245 0.482655 -- 5.735477 5.933935 1.418994 -- 5.840562 6.170139 -0.341774 -- 4.354989 6.619215 0.529171 -+ 5.312304 4.855747 1.245167 -+ 3.931816 5.541027 0.355344 -+ 3.812283 5.761636 2.490333 -+ 4.110763 5.208108 3.380624 -+ 4.296680 6.738088 2.490828 -+ 2.730275 5.893388 2.490801 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.ILE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -785,9 +785,9 @@ - 3.716963 3.477633 3.370556 - 3.499621 1.931327 2.516833 - 4.274181 5.009604 1.194574 -- 4.690774 4.823320 2.184447 -- 4.954792 5.645336 0.628258 -- 3.310286 5.508600 1.294624 -+ 3.973778 5.548459 0.295968 -+ 3.993550 5.587589 2.075074 -+ 5.354265 4.863179 1.185791 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.VAL.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -901,10 +901,10 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.253694 5.017114 1.232141 -- 3.666601 5.213107 2.293908 -- 5.062354 5.920372 0.673198 -- 5.699537 6.377296 0.036552 -- 4.754312 6.389897 1.512695 -+ 5.005295 5.340406 0.315070 -+ 3.984875 5.817912 2.265912 -+ 4.408006 6.733705 2.314738 -+ 3.359598 5.504301 2.994456 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.ASN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1028,13 +1028,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.220277 5.927344 0.433563 -- 4.913588 6.591689 1.420998 -- 6.050965 6.373808 -0.511346 -- 5.971268 7.107959 0.177690 -- 6.636748 6.497679 -1.324743 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.906966 5.848446 2.410297 -+ 3.138947 5.408353 3.262885 -+ 4.458847 7.061526 2.488328 -+ 4.248421 7.659050 3.274958 -+ 5.084275 7.376210 1.760376 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.GLN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1189,20 +1189,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.125319 6.253797 -0.719124 -- 6.688164 6.300372 -1.556463 -- 6.117846 7.301883 0.099632 -- 5.907135 8.163840 1.090353 -- 5.292210 7.913283 1.851398 -- 6.363014 9.065005 1.077109 -- 6.926823 7.627695 -0.904511 -- 7.501836 7.713669 -1.730386 -- 6.873063 8.384728 -0.238094 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.540311 7.142726 2.424478 -+ 5.151800 7.375491 1.655062 -+ 4.364270 8.040994 3.389374 -+ 3.575005 7.807613 4.434120 -+ 3.088928 6.925430 4.508833 -+ 3.465343 8.513638 5.147984 -+ 5.006244 9.201290 3.286985 -+ 5.604850 9.375324 2.492326 -+ 4.892201 9.903050 4.004360 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.ARG.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1337,13 +1337,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.HID.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1471,13 +1471,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.HIE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1609,14 +1609,14 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.HIP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1774,20 +1774,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 4.941957 6.093161 0.993054 -- 4.555798 6.518222 1.919501 -- 5.833674 6.587638 -0.009560 -- 5.727864 7.297382 0.701192 -- 6.577083 6.691104 -1.083216 -- 6.699953 7.881667 -0.356949 -- 7.350710 8.089828 -1.206234 -- 6.471604 8.773711 0.684306 -- 7.153163 9.167983 -0.069436 -- 6.163215 9.539474 1.752484 -- 6.850900 10.076243 1.098979 -- 5.726463 10.185215 2.927374 -- 6.404130 10.841773 2.381664 -- 5.125146 10.546906 4.138818 -+ 4.023443 5.931088 2.293236 -+ 3.368827 5.705470 3.135064 -+ 4.811936 7.073557 1.949805 -+ 4.882911 7.922013 2.493114 -+ 5.427345 6.842058 0.816764 -+ 6.297161 7.689048 0.119607 -+ 6.531228 8.676646 0.517052 -+ 6.814097 7.187003 -1.069017 -+ 7.498083 7.791848 -1.664355 -+ 6.482667 5.953109 -1.505090 -+ 6.897672 5.575635 -2.439640 -+ 5.604046 5.117349 -0.785625 -+ 5.358725 4.126563 -1.168065 -+ 5.083391 5.623006 0.411551 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.TRP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1934,16 +1934,16 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.021223 6.053049 0.839188 -- 4.662984 6.521610 1.755820 -- 5.904492 6.742286 -0.000329 -- 5.724114 7.440373 0.817130 -- 6.758713 7.099630 -1.050381 -- 6.738282 7.947511 -0.365705 -- 7.536653 7.157250 -2.212917 -- 7.655187 8.096815 -1.673224 -- 8.214242 6.953605 -3.420974 -- 8.451251 7.942064 -3.027432 -+ 3.911603 5.857254 2.409885 -+ 3.236109 5.513847 3.193390 -+ 4.490005 7.129516 2.492349 -+ 4.264839 7.776656 3.340058 -+ 5.357612 7.570590 1.486013 -+ 5.807939 8.561136 1.550217 -+ 5.646816 6.739401 0.397212 -+ 6.322310 7.082808 -0.386292 -+ 5.068414 5.467139 0.314748 -+ 5.293580 4.820000 -0.532961 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.PHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2090,17 +2090,17 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 5.102503 5.984523 0.660315 -- 4.777863 6.502414 1.562811 -- 5.985574 6.611197 -0.227077 -- 5.846174 7.352316 0.559949 -- 6.824378 6.891857 -1.312267 -- 6.854321 7.991157 -0.512116 -- 6.305234 7.900783 0.270147 -- 7.573657 6.866032 -2.494602 -- 7.737299 7.827553 -2.007982 -- 8.211756 6.577405 -3.706841 -- 8.492629 7.576371 -3.373257 -+ 4.059917 5.918914 2.227275 -+ 3.400094 5.668222 3.057870 -+ 4.699989 7.163550 2.192787 -+ 4.538509 7.881896 2.996531 -+ 5.547468 7.485540 1.125968 -+ 6.169252 8.694615 1.092466 -+ 5.956320 9.246984 1.848209 -+ 5.754874 6.562895 0.093637 -+ 6.414696 6.813587 -0.736958 -+ 5.114801 5.318259 0.128125 -+ 5.276282 4.599913 -0.675619 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.TYR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2223,11 +2223,11 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 3.302423 5.493308 1.295046 -- 4.682911 4.808028 2.184869 -- 5.220383 5.890117 0.404729 -- 6.306867 5.987364 1.035359 -- 4.568248 6.850423 -0.085305 -+ 5.347407 4.849844 1.186161 -+ 3.966920 5.535124 0.296338 -+ 3.873721 5.805373 2.428701 -+ 4.594575 5.679017 3.454373 -+ 2.855955 6.542075 2.333709 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.GLU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2332,8 +2332,8 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.275095 5.011382 1.194525 -- 5.214909 5.080371 2.030940 -- 3.476290 5.943429 0.910275 -+ 3.669104 5.954940 0.620005 -+ 5.407723 5.091882 1.740669 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.ASP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2475,18 +2475,18 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.145332 6.228186 -0.769897 -- 7.203874 5.974714 -0.827698 -- 5.823386 6.659994 -1.717522 -- 5.933539 7.203239 0.309601 -- 6.482814 7.265694 1.154880 -- 6.528435 7.362078 -0.491005 -- 5.203409 7.900796 0.330212 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.578316 7.173413 2.389148 -+ 5.658401 7.026988 2.380365 -+ 4.277913 7.712268 1.490542 -+ 4.199407 7.952315 3.576852 -+ 4.478064 7.453372 4.409622 -+ 4.661173 8.850231 3.551971 -+ 3.198660 8.088474 3.584954 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.LYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2634,17 +2634,17 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.145332 6.228186 -0.769897 -- 7.203874 5.974714 -0.827698 -- 5.823386 6.659994 -1.717522 -- 5.933539 7.203239 0.309601 -- 6.528435 7.362078 -0.491005 -- 5.203409 7.900796 0.330212 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.578316 7.173413 2.389148 -+ 5.658401 7.026988 2.380365 -+ 4.277913 7.712268 1.490542 -+ 4.199407 7.952315 3.576852 -+ 4.661173 8.850231 3.551971 -+ 3.198660 8.088474 3.584954 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.LYN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2761,11 +2761,11 @@ - 4.419995 0.019280 -0.902255 - 3.955884 -0.274036 0.790585 - 5.547124 1.172442 0.544698 -- 6.078592 2.122578 0.598404 -- 6.005141 0.543154 -0.218399 -- 5.532142 0.472642 1.882665 -- 5.876555 1.272377 2.538335 -- 6.368845 0.104645 1.288859 -+ 6.413547 0.741633 0.042886 -+ 5.652946 1.047940 1.622381 -+ 5.369090 2.628183 0.185221 -+ 5.969291 2.861853 -0.694128 -+ 5.690639 3.251042 1.019939 - 3.933608 2.871277 -0.104508 - 3.611466 3.488572 0.734105 - 3.505165 3.526388 -1.409786 -@@ -2867,7 +2867,7 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.309567 5.303525 1.366033 -- 5.145787 5.839753 0.481671 -+ 3.725381 5.622023 2.517634 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.CYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -3079,13 +3079,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.402881 6.076526 0.265157 -- 6.377314 6.105674 -1.224148 -- 6.034578 6.467191 -2.193651 -- 6.303017 6.908485 -0.490613 -- 7.415066 5.781911 -1.303828 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.817297 5.981271 2.651702 -+ 4.753204 7.463130 2.340945 -+ 4.433578 7.904044 1.396734 -+ 4.585895 8.175303 3.148978 -+ 5.814065 7.218764 2.286557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.MET.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -3196,9 +3196,9 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.275095 5.011382 1.194525 -- 5.214909 5.080371 2.030940 -- 3.476290 5.943429 0.910275 -- 4.245574 6.470767 0.682862 -+ 3.669104 5.954940 0.620005 -+ 5.407723 5.091882 1.740669 -+ 5.742895 5.987180 1.652921 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.ASH.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -3317,12 +3317,12 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 3.302423 5.493308 1.295046 -- 4.682911 4.808028 2.184869 -- 5.220383 5.890117 0.404729 -- 6.306867 5.987364 1.035359 -- 4.568248 6.850423 -0.085305 -- 5.508873 7.035106 -0.033194 -+ 5.347407 4.849844 1.186161 -+ 3.966920 5.535124 0.296338 -+ 3.873721 5.805373 2.428701 -+ 4.594575 5.679017 3.454373 -+ 2.855955 6.542075 2.333709 -+ 2.710512 6.996629 3.166671 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.GLH.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_aminoct94.lib.save amber11/AmberTools/test/sleap/oldleap/ff94/all_aminoct94.lib.save ---- amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_aminoct94.lib.save 2010-03-31 07:05:23.000000000 +0400 -+++ amber11/AmberTools/test/sleap/oldleap/ff94/all_aminoct94.lib.save 2011-03-08 16:38:44.000000000 +0300 -@@ -272,7 +272,7 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.230747 4.925147 1.196914 -- 4.828085 5.500165 0.713033 -+ 3.983296 5.433818 1.972557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -390,7 +390,7 @@ - 1.784422 4.436955 2.124895 - 1.764698 4.397850 0.345787 - 3.971494 2.947416 2.411212 -- 4.374397 3.770738 2.696536 -+ 3.724043 3.456087 3.186855 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -528,15 +528,15 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.857033 4.748192 2.579338 -- 5.821217 4.249596 2.480083 -- 4.990360 5.695010 3.102655 -- 4.176711 4.112860 3.146449 -- 5.226485 5.898474 0.401698 -- 5.794506 5.938748 1.331123 -- 5.883342 6.134649 -0.435476 -- 4.414018 6.624028 0.441300 -+ 5.354265 4.863179 1.185791 -+ 3.853427 5.762894 -0.062862 -+ 2.773446 5.910110 -0.054565 -+ 4.351509 6.732051 -0.090207 -+ 4.134162 5.185701 -0.943848 -+ 3.881095 5.817649 2.426715 -+ 4.181612 5.279606 3.325770 -+ 4.379188 6.786828 2.400358 -+ 2.801124 5.964886 2.435947 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -682,12 +682,12 @@ - 3.671552 3.399212 3.380613 - 3.485641 1.869279 2.490736 - 4.230199 4.986696 1.245167 -- 3.258221 5.469711 1.345449 -- 4.638709 4.784431 2.235272 -- 5.178160 5.906245 0.482655 -- 5.735477 5.933935 1.418994 -- 5.840562 6.170139 -0.341774 -- 4.354989 6.619215 0.529171 -+ 5.312304 4.855747 1.245167 -+ 3.931816 5.541027 0.355344 -+ 3.812283 5.761636 2.490333 -+ 4.110763 5.208108 3.380624 -+ 4.296680 6.738088 2.490828 -+ 2.730275 5.893388 2.490801 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -821,9 +821,9 @@ - 3.716963 3.477633 3.370556 - 3.499621 1.931327 2.516833 - 4.274181 5.009604 1.194574 -- 4.690774 4.823320 2.184447 -- 4.954792 5.645336 0.628258 -- 3.310286 5.508600 1.294624 -+ 3.973778 5.548459 0.295968 -+ 3.993550 5.587589 2.075074 -+ 5.354265 4.863179 1.185791 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -943,10 +943,10 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.253694 5.017114 1.232141 -- 3.666601 5.213107 2.293908 -- 5.062354 5.920372 0.673198 -- 5.699537 6.377296 0.036552 -- 4.754312 6.389897 1.512695 -+ 5.005295 5.340406 0.315070 -+ 3.984875 5.817912 2.265912 -+ 4.408006 6.733705 2.314738 -+ 3.359598 5.504301 2.994456 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1076,13 +1076,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.220277 5.927344 0.433563 -- 4.913588 6.591689 1.420998 -- 6.050965 6.373808 -0.511346 -- 5.971268 7.107959 0.177690 -- 6.636748 6.497679 -1.324743 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.906966 5.848446 2.410297 -+ 3.138947 5.408353 3.262885 -+ 4.458847 7.061526 2.488328 -+ 4.248421 7.659050 3.274958 -+ 5.084275 7.376210 1.760376 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1243,20 +1243,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.125319 6.253797 -0.719124 -- 6.688164 6.300372 -1.556463 -- 6.117846 7.301883 0.099632 -- 5.907135 8.163840 1.090353 -- 5.292210 7.913283 1.851398 -- 6.363014 9.065005 1.077109 -- 6.926823 7.627695 -0.904511 -- 7.501836 7.713669 -1.730386 -- 6.873063 8.384728 -0.238094 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.540311 7.142726 2.424478 -+ 5.151800 7.375491 1.655062 -+ 4.364270 8.040994 3.389374 -+ 3.575005 7.807613 4.434120 -+ 3.088928 6.925430 4.508833 -+ 3.465343 8.513638 5.147984 -+ 5.006244 9.201290 3.286985 -+ 5.604850 9.375324 2.492326 -+ 4.892201 9.903050 4.004360 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1397,13 +1397,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1537,13 +1537,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1681,14 +1681,14 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -1852,20 +1852,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 4.941957 6.093161 0.993054 -- 4.555798 6.518222 1.919501 -- 5.833674 6.587638 -0.009560 -- 5.727864 7.297382 0.701192 -- 6.577083 6.691104 -1.083216 -- 6.699953 7.881667 -0.356949 -- 7.350710 8.089828 -1.206234 -- 6.471604 8.773711 0.684306 -- 7.153163 9.167983 -0.069436 -- 6.163215 9.539474 1.752484 -- 6.850900 10.076243 1.098979 -- 5.726463 10.185215 2.927374 -- 6.404130 10.841773 2.381664 -- 5.125146 10.546906 4.138818 -+ 4.023443 5.931088 2.293236 -+ 3.368827 5.705470 3.135064 -+ 4.811936 7.073557 1.949805 -+ 4.882911 7.922013 2.493114 -+ 5.427345 6.842058 0.816764 -+ 6.297161 7.689048 0.119607 -+ 6.531228 8.676646 0.517052 -+ 6.814097 7.187003 -1.069017 -+ 7.498083 7.791848 -1.664355 -+ 6.482667 5.953109 -1.505090 -+ 6.897672 5.575635 -2.439640 -+ 5.604046 5.117349 -0.785625 -+ 5.358725 4.126563 -1.168065 -+ 5.083391 5.623006 0.411551 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2018,16 +2018,16 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.021223 6.053049 0.839188 -- 4.662984 6.521610 1.755820 -- 5.904492 6.742286 -0.000329 -- 5.724114 7.440373 0.817130 -- 6.758713 7.099630 -1.050381 -- 6.738282 7.947511 -0.365705 -- 7.536653 7.157250 -2.212917 -- 7.655187 8.096815 -1.673224 -- 8.214242 6.953605 -3.420974 -- 8.451251 7.942064 -3.027432 -+ 3.911603 5.857254 2.409885 -+ 3.236109 5.513847 3.193390 -+ 4.490005 7.129516 2.492349 -+ 4.264839 7.776656 3.340058 -+ 5.357612 7.570590 1.486013 -+ 5.807939 8.561136 1.550217 -+ 5.646816 6.739401 0.397212 -+ 6.322310 7.082808 -0.386292 -+ 5.068414 5.467139 0.314748 -+ 5.293580 4.820000 -0.532961 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2180,17 +2180,17 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 5.102503 5.984523 0.660315 -- 4.777863 6.502414 1.562811 -- 5.985574 6.611197 -0.227077 -- 5.846174 7.352316 0.559949 -- 6.824378 6.891857 -1.312267 -- 6.854321 7.991157 -0.512116 -- 6.305234 7.900783 0.270147 -- 7.573657 6.866032 -2.494602 -- 7.737299 7.827553 -2.007982 -- 8.211756 6.577405 -3.706841 -- 8.492629 7.576371 -3.373257 -+ 4.059917 5.918914 2.227275 -+ 3.400094 5.668222 3.057870 -+ 4.699989 7.163550 2.192787 -+ 4.538509 7.881896 2.996531 -+ 5.547468 7.485540 1.125968 -+ 6.169252 8.694615 1.092466 -+ 5.956320 9.246984 1.848209 -+ 5.754874 6.562895 0.093637 -+ 6.414696 6.813587 -0.736958 -+ 5.114801 5.318259 0.128125 -+ 5.276282 4.599913 -0.675619 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2319,11 +2319,11 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 3.302423 5.493308 1.295046 -- 4.682911 4.808028 2.184869 -- 5.220383 5.890117 0.404729 -- 6.306867 5.987364 1.035359 -- 4.568248 6.850423 -0.085305 -+ 5.347407 4.849844 1.186161 -+ 3.966920 5.535124 0.296338 -+ 3.873721 5.805373 2.428701 -+ 4.594575 5.679017 3.454373 -+ 2.855955 6.542075 2.333709 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2434,8 +2434,8 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.275095 5.011382 1.194525 -- 5.214909 5.080371 2.030940 -- 3.476290 5.943429 0.910275 -+ 3.669104 5.954940 0.620005 -+ 5.407723 5.091882 1.740669 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2583,18 +2583,18 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.145332 6.228186 -0.769897 -- 7.203874 5.974714 -0.827698 -- 5.823386 6.659994 -1.717522 -- 5.933539 7.203239 0.309601 -- 6.482814 7.265694 1.154880 -- 6.528435 7.362078 -0.491005 -- 5.203409 7.900796 0.330212 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.578316 7.173413 2.389148 -+ 5.658401 7.026988 2.380365 -+ 4.277913 7.712268 1.490542 -+ 4.199407 7.952315 3.576852 -+ 4.478064 7.453372 4.409622 -+ 4.661173 8.850231 3.551971 -+ 3.198660 8.088474 3.584954 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -2718,11 +2718,11 @@ - 4.419995 0.019280 -0.902255 - 3.955884 -0.274036 0.790585 - 5.547124 1.172442 0.544698 -- 6.078592 2.122578 0.598404 -- 6.005141 0.543154 -0.218399 -- 5.532142 0.472642 1.882665 -- 5.876555 1.272377 2.538335 -- 6.368845 0.104645 1.288859 -+ 6.413547 0.741633 0.042886 -+ 5.652946 1.047940 1.622381 -+ 5.369090 2.628183 0.185221 -+ 5.969291 2.861853 -0.694128 -+ 5.690639 3.251042 1.019939 - 3.933608 2.871277 -0.104508 - 3.611466 3.488572 0.734105 - 3.505165 3.526388 -1.409786 -@@ -2830,7 +2830,7 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.309567 5.303525 1.366033 -- 5.145787 5.839753 0.481671 -+ 3.725381 5.622023 2.517634 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -@@ -3054,13 +3054,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.402881 6.076526 0.265157 -- 6.377314 6.105674 -1.224148 -- 6.034578 6.467191 -2.193651 -- 6.303017 6.908485 -0.490613 -- 7.415066 5.781911 -1.303828 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.817297 5.981271 2.651702 -+ 4.753204 7.463130 2.340945 -+ 4.433578 7.904044 1.396734 -+ 4.585895 8.175303 3.148978 -+ 5.814065 7.218764 2.286557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - 6.204451 3.702005 0.000000 -diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_aminont94.lib.save amber11/AmberTools/test/sleap/oldleap/ff94/all_aminont94.lib.save ---- amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_aminont94.lib.save 2010-03-31 07:05:23.000000000 +0400 -+++ amber11/AmberTools/test/sleap/oldleap/ff94/all_aminont94.lib.save 2011-03-08 16:38:44.000000000 +0300 -@@ -290,7 +290,7 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.230747 4.925147 1.196914 -- 4.828085 5.500165 0.713033 -+ 3.983296 5.433818 1.972557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NSER.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -414,7 +414,7 @@ - 1.784422 4.436955 2.124895 - 1.764698 4.397850 0.345787 - 3.971494 2.947416 2.411212 -- 4.374397 3.770738 2.696536 -+ 3.724043 3.456087 3.186855 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NTHR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -558,15 +558,15 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.857033 4.748192 2.579338 -- 5.821217 4.249596 2.480083 -- 4.990360 5.695010 3.102655 -- 4.176711 4.112860 3.146449 -- 5.226485 5.898474 0.401698 -- 5.794506 5.938748 1.331123 -- 5.883342 6.134649 -0.435476 -- 4.414018 6.624028 0.441300 -+ 5.354265 4.863179 1.185791 -+ 3.853427 5.762894 -0.062862 -+ 2.773446 5.910110 -0.054565 -+ 4.351509 6.732051 -0.090207 -+ 4.134162 5.185701 -0.943848 -+ 3.881095 5.817649 2.426715 -+ 4.181612 5.279606 3.325770 -+ 4.379188 6.786828 2.400358 -+ 2.801124 5.964886 2.435947 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NLEU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -718,12 +718,12 @@ - 3.671552 3.399212 3.380613 - 3.485641 1.869279 2.490736 - 4.230199 4.986696 1.245167 -- 4.638709 4.784431 2.235272 -- 3.258221 5.469711 1.345449 -- 5.178160 5.906245 0.482655 -- 5.735477 5.933935 1.418994 -- 5.840562 6.170139 -0.341774 -- 4.354989 6.619215 0.529171 -+ 3.931816 5.541027 0.355344 -+ 5.312304 4.855747 1.245167 -+ 3.812283 5.761636 2.490333 -+ 4.110763 5.208108 3.380624 -+ 4.296680 6.738088 2.490828 -+ 2.730275 5.893388 2.490801 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NILE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -863,9 +863,9 @@ - 3.716963 3.477633 3.370556 - 3.499621 1.931327 2.516833 - 4.274181 5.009604 1.194574 -- 4.690774 4.823320 2.184447 -- 4.954792 5.645336 0.628258 -- 3.310286 5.508600 1.294624 -+ 3.973778 5.548459 0.295968 -+ 3.993550 5.587589 2.075074 -+ 5.354265 4.863179 1.185791 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NVAL.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -991,10 +991,10 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.253694 5.017114 1.232141 -- 3.666601 5.213107 2.293908 -- 5.062354 5.920372 0.673198 -- 5.699537 6.377296 0.036552 -- 4.754312 6.389897 1.512695 -+ 5.005295 5.340406 0.315070 -+ 3.984875 5.817912 2.265912 -+ 4.408006 6.733705 2.314738 -+ 3.359598 5.504301 2.994456 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NASN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1130,13 +1130,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.220277 5.927344 0.433563 -- 4.913588 6.591689 1.420998 -- 6.050965 6.373808 -0.511346 -- 5.971268 7.107959 0.177690 -- 6.636748 6.497679 -1.324743 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.906966 5.848446 2.410297 -+ 3.138947 5.408353 3.262885 -+ 4.458847 7.061526 2.488328 -+ 4.248421 7.659050 3.274958 -+ 5.084275 7.376210 1.760376 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NGLN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1303,20 +1303,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.125319 6.253797 -0.719124 -- 6.688164 6.300372 -1.556463 -- 6.117846 7.301883 0.099632 -- 5.907135 8.163840 1.090353 -- 5.292210 7.913283 1.851398 -- 6.363014 9.065005 1.077109 -- 6.926823 7.627695 -0.904511 -- 7.501836 7.713669 -1.730386 -- 6.873063 8.384728 -0.238094 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.540311 7.142726 2.424478 -+ 5.151800 7.375491 1.655062 -+ 4.364270 8.040994 3.389374 -+ 3.575005 7.807613 4.434120 -+ 3.088928 6.925430 4.508833 -+ 3.465343 8.513638 5.147984 -+ 5.006244 9.201290 3.286985 -+ 5.604850 9.375324 2.492326 -+ 4.892201 9.903050 4.004360 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NARG.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1463,13 +1463,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NHID.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1609,13 +1609,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NHIE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1759,14 +1759,14 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.003504 6.072258 0.881472 -- 4.722990 6.580423 1.708019 -- 5.824163 6.508104 -0.056055 -- 5.654216 7.217462 0.753902 -- 6.562760 6.595751 -1.134430 -- 6.629203 7.441424 -0.586231 -- 7.210678 6.375009 -2.309622 -- 7.387392 7.342143 -1.838959 -+ 3.942772 5.885090 2.382967 -+ 3.339711 5.691917 3.169798 -+ 4.624266 6.997644 2.182496 -+ 4.563036 7.811879 2.904557 -+ 5.294008 6.891449 1.061662 -+ 5.896295 7.605082 0.676854 -+ 5.058971 5.678865 0.492455 -+ 5.537740 5.417840 -0.451339 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NHIP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -1936,20 +1936,20 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 4.941957 6.093161 0.993054 -- 4.555798 6.518222 1.919501 -- 5.833674 6.587638 -0.009560 -- 5.727864 7.297382 0.701192 -- 6.577083 6.691104 -1.083216 -- 6.699953 7.881667 -0.356949 -- 7.350710 8.089828 -1.206234 -- 6.471604 8.773711 0.684306 -- 7.153163 9.167983 -0.069436 -- 6.163215 9.539474 1.752484 -- 6.850900 10.076243 1.098979 -- 5.726463 10.185215 2.927374 -- 6.404130 10.841773 2.381664 -- 5.125146 10.546906 4.138818 -+ 4.023443 5.931088 2.293236 -+ 3.368827 5.705470 3.135064 -+ 4.811936 7.073557 1.949805 -+ 4.882911 7.922013 2.493114 -+ 5.427345 6.842058 0.816764 -+ 6.297161 7.689048 0.119607 -+ 6.531228 8.676646 0.517052 -+ 6.814097 7.187003 -1.069017 -+ 7.498083 7.791848 -1.664355 -+ 6.482667 5.953109 -1.505090 -+ 6.897672 5.575635 -2.439640 -+ 5.604046 5.117349 -0.785625 -+ 5.358725 4.126563 -1.168065 -+ 5.083391 5.623006 0.411551 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NTRP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2108,16 +2108,16 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.200807 5.026066 1.321085 -- 5.021223 6.053049 0.839188 -- 4.662984 6.521610 1.755820 -- 5.904492 6.742286 -0.000329 -- 5.724114 7.440373 0.817130 -- 6.758713 7.099630 -1.050381 -- 6.738282 7.947511 -0.365705 -- 7.536653 7.157250 -2.212917 -- 7.655187 8.096815 -1.673224 -- 8.214242 6.953605 -3.420974 -- 8.451251 7.942064 -3.027432 -+ 3.911603 5.857254 2.409885 -+ 3.236109 5.513847 3.193390 -+ 4.490005 7.129516 2.492349 -+ 4.264839 7.776656 3.340058 -+ 5.357612 7.570590 1.486013 -+ 5.807939 8.561136 1.550217 -+ 5.646816 6.739401 0.397212 -+ 6.322310 7.082808 -0.386292 -+ 5.068414 5.467139 0.314748 -+ 5.293580 4.820000 -0.532961 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NPHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2276,17 +2276,17 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 5.102503 5.984523 0.660315 -- 4.777863 6.502414 1.562811 -- 5.985574 6.611197 -0.227077 -- 5.846174 7.352316 0.559949 -- 6.824378 6.891857 -1.312267 -- 6.854321 7.991157 -0.512116 -- 6.305234 7.900783 0.270147 -- 7.573657 6.866032 -2.494602 -- 7.737299 7.827553 -2.007982 -- 8.211756 6.577405 -3.706841 -- 8.492629 7.576371 -3.373257 -+ 4.059917 5.918914 2.227275 -+ 3.400094 5.668222 3.057870 -+ 4.699989 7.163550 2.192787 -+ 4.538509 7.881896 2.996531 -+ 5.547468 7.485540 1.125968 -+ 6.169252 8.694615 1.092466 -+ 5.956320 9.246984 1.848209 -+ 5.754874 6.562895 0.093637 -+ 6.414696 6.813587 -0.736958 -+ 5.114801 5.318259 0.128125 -+ 5.276282 4.599913 -0.675619 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NTYR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2421,11 +2421,11 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.267323 4.996269 1.194944 -- 3.302423 5.493308 1.295046 -- 4.682911 4.808028 2.184869 -- 5.220383 5.890117 0.404729 -- 6.306867 5.987364 1.035359 -- 4.568248 6.850423 -0.085305 -+ 5.347407 4.849844 1.186161 -+ 3.966920 5.535124 0.296338 -+ 3.873721 5.805373 2.428701 -+ 4.594575 5.679017 3.454373 -+ 2.855955 6.542075 2.333709 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NGLU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2542,8 +2542,8 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.275095 5.011382 1.194525 -- 5.214909 5.080371 2.030940 -- 3.476290 5.943429 0.910275 -+ 3.669104 5.954940 0.620005 -+ 5.407723 5.091882 1.740669 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NASP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2697,18 +2697,18 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.226485 5.898474 0.401698 -- 4.414018 6.624028 0.441300 -- 5.794506 5.938748 1.331123 -- 6.145332 6.228186 -0.769897 -- 7.203874 5.974714 -0.827698 -- 5.823386 6.659994 -1.717522 -- 5.933539 7.203239 0.309601 -- 6.482814 7.265694 1.154880 -- 6.528435 7.362078 -0.491005 -- 5.203409 7.900796 0.330212 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.881095 5.817649 2.426715 -+ 2.801124 5.964886 2.435947 -+ 4.181612 5.279606 3.325770 -+ 4.578316 7.173413 2.389148 -+ 5.658401 7.026988 2.380365 -+ 4.277913 7.712268 1.490542 -+ 4.199407 7.952315 3.576852 -+ 4.478064 7.453372 4.409622 -+ 4.661173 8.850231 3.551971 -+ 3.198660 8.088474 3.584954 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NLYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -2838,11 +2838,11 @@ - 4.408167 0.002206 -0.902255 - 3.942020 -0.287863 0.790585 - 5.543318 1.147472 0.544698 -- 6.081407 2.093874 0.598404 -- 5.996931 0.515001 -0.218399 -- 5.523452 0.447794 1.882665 -- 5.873440 1.245104 2.538335 -- 6.357566 0.073964 1.288859 -+ 6.406713 0.710625 0.042886 -+ 5.648269 1.022234 1.622381 -+ 5.375452 2.604420 0.185221 -+ 5.977270 2.833894 -0.694128 -+ 5.701342 3.225018 1.019939 - 3.941702 2.857530 -0.104508 - 3.623877 3.477058 0.734105 - 3.517843 3.515616 -1.409786 -@@ -2956,7 +2956,7 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.309567 5.303525 1.366033 -- 5.145787 5.839753 0.481671 -+ 3.725381 5.622023 2.517634 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NCYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -3192,13 +3192,13 @@ - 2.496989 3.801078 1.241373 - 3.877477 3.115798 2.131196 - 4.274181 5.009604 1.194574 -- 3.310286 5.508600 1.294624 -- 4.690774 4.823320 2.184447 -- 5.402881 6.076526 0.265157 -- 6.377314 6.105674 -1.224148 -- 6.034578 6.467191 -2.193651 -- 6.303017 6.908485 -0.490613 -- 7.415066 5.781911 -1.303828 -+ 5.354265 4.863179 1.185791 -+ 3.973778 5.548459 0.295968 -+ 3.817297 5.981271 2.651702 -+ 4.753204 7.463130 2.340945 -+ 4.433578 7.904044 1.396734 -+ 4.585895 8.175303 3.148978 -+ 5.814065 7.218764 2.286557 - 5.485538 2.705208 0.000000 - 6.008821 1.593175 0.000000 - !entry.NMET.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_nucleic94.lib.save amber11/AmberTools/test/sleap/oldleap/ff94/all_nucleic94.lib.save ---- amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_nucleic94.lib.save 2010-03-31 07:05:23.000000000 +0400 -+++ amber11/AmberTools/test/sleap/oldleap/ff94/all_nucleic94.lib.save 2011-03-08 16:38:44.000000000 +0300 -@@ -181,21 +181,21 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.825854 0.331961 5.463505 -- 2.973744 -0.351218 5.767666 -- 3.198298 -1.353172 5.432908 -- 3.262456 0.147686 6.932887 -- 3.554407 -1.123002 6.450998 -- 3.970615 -1.030384 7.784487 -- 4.371751 -2.299375 7.628436 -- 4.806122 -2.789852 8.397106 -- 4.239728 -2.765377 6.742145 -- 4.154910 -0.430195 8.968298 -- 4.588103 -1.686764 8.920565 -- 4.748481 -1.226887 9.884511 -- 5.030638 -2.930357 8.914329 -- 5.276823 -4.138026 8.363485 -+ 2.623224 0.684847 5.224690 -+ 2.631874 -0.707517 3.706295 -+ 2.874735 -1.252950 2.473241 -+ 2.981754 -0.611820 1.610746 -+ 3.015083 -2.545282 2.486669 -+ 2.854431 -2.887097 3.824373 -+ 2.890057 -4.114829 4.496241 -+ 3.109804 -5.286605 3.884480 -+ 3.124371 -6.141804 4.421623 -+ 3.260868 -5.314611 2.886234 -+ 2.691903 -4.099290 5.821417 -+ 2.474287 -2.933307 6.423105 -+ 2.312232 -2.898303 7.490303 -+ 2.418509 -1.722706 5.899909 -+ 2.621151 -1.767164 4.565946 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 -@@ -394,21 +394,21 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.821628 0.329290 5.472166 -- 3.045980 -0.266556 5.623252 -- 3.300321 -1.253530 5.266050 -- 3.400654 0.078938 6.868419 -- 3.596750 0.739775 8.200650 -- 2.627095 1.008594 8.619702 -- 4.106045 0.052544 8.876247 -- 4.199810 1.639079 8.075463 -- 3.886987 -1.267611 6.713863 -- 4.193797 -1.026107 7.880244 -- 4.182336 -2.491705 6.149271 -- 4.473391 -2.322796 7.186024 -- 4.489928 -3.724276 5.610241 -- 4.916436 -3.803915 6.750481 -+ 2.623224 0.684847 5.224690 -+ 2.632951 -0.717026 3.703395 -+ 2.875701 -1.078946 2.404555 -+ 2.959028 -0.321296 1.639425 -+ 3.067013 -2.361001 2.064944 -+ 3.333430 -2.767543 0.645879 -+ 4.242250 -2.280529 0.292378 -+ 3.457938 -3.849191 0.594530 -+ 2.493973 -2.468751 0.018077 -+ 3.022943 -3.401289 3.059659 -+ 3.186167 -4.600916 2.842510 -+ 2.773364 -2.946913 4.338586 -+ 2.730574 -3.698393 5.126967 -+ 2.572586 -1.635482 4.718372 -+ 2.357489 -1.330164 5.879800 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 -@@ -612,22 +612,22 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.809468 0.366314 5.430851 -- 2.985443 -0.303283 5.701265 -- 3.220128 -1.300453 5.359250 -- 3.217392 0.174542 6.898755 -- 3.501851 -1.098776 6.419335 -- 3.907092 -0.959542 7.773142 -- 4.306119 -2.122793 7.750193 -- 4.034999 -0.202628 8.943920 -- 4.092163 0.401223 9.738965 -- 4.527564 -1.484195 9.083085 -- 4.671337 -0.799117 10.225713 -- 4.406357 0.160408 10.396586 -- 5.109266 -1.288479 10.993073 -- 4.937775 -2.746085 8.992209 -- 5.203174 -3.983662 8.494648 -+ 2.623224 0.684847 5.224690 -+ 2.590680 -0.679098 3.703090 -+ 2.813126 -1.180187 2.436667 -+ 2.923918 -0.505423 1.600713 -+ 2.866567 -2.487992 2.382906 -+ 2.666616 -2.884782 3.699977 -+ 2.618169 -4.183246 4.272728 -+ 2.745111 -5.274676 3.719947 -+ 2.392358 -4.124071 5.653129 -+ 2.340242 -4.991533 6.147896 -+ 2.235991 -2.964895 6.385427 -+ 2.027971 -3.123388 7.699660 -+ 1.962797 -3.996113 8.203846 -+ 1.903765 -2.280234 8.241661 -+ 2.283795 -1.749407 5.847650 -+ 2.502701 -1.789347 4.505978 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 -@@ -819,19 +819,19 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.810222 0.365622 5.431037 -- 3.040503 -0.202936 5.543946 -- 3.303784 -1.184927 5.179558 -- 3.350889 0.129864 6.825549 -- 3.478253 0.640008 7.780343 -- 3.798907 -1.207335 6.588738 -- 4.083865 -0.848420 7.826630 -- 4.553596 -1.522140 8.414470 -- 3.834435 0.071716 8.160148 -- 4.146081 -2.428628 6.192742 -- 4.391834 -3.604440 5.555033 -- 4.829292 -3.701644 6.711226 -+ 2.623224 0.684847 5.224690 -+ 2.591673 -0.679108 3.703398 -+ 2.814053 -0.989708 2.398148 -+ 2.904088 -0.203069 1.663647 -+ 2.926420 -2.283840 1.995414 -+ 3.104659 -2.514231 0.945056 -+ 2.799915 -3.288854 3.004791 -+ 2.898410 -4.565463 2.683902 -+ 2.803322 -5.244627 3.425383 -+ 3.063325 -4.838262 1.725527 -+ 2.582464 -2.976080 4.279070 -+ 2.473124 -1.675585 4.661638 -+ 2.270623 -1.344205 5.839254 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 -@@ -1043,21 +1043,21 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.398936 0.755791 5.236576 -- 5.570721 0.053476 5.133763 -- 5.651435 -0.952100 4.748143 -- 6.248368 0.547472 6.127122 -- 6.337852 -0.727929 5.581736 -- 7.186443 -0.642297 6.691944 -- 7.489983 -1.917831 6.415398 -- 8.153280 -2.415516 6.991980 -- 7.055473 -2.381556 5.630375 -- 7.773936 -0.045280 7.737899 -- 8.144838 -1.308931 7.552106 -- 8.632452 -0.851805 8.400438 -- 8.538915 -2.559764 7.402037 -- 8.562807 -3.771388 6.807145 -+ 5.071990 1.095268 4.737463 -+ 4.538874 -0.297045 3.315659 -+ 4.336740 -0.846471 2.077041 -+ 4.152394 -0.207224 1.226289 -+ 4.452852 -2.140973 2.049069 -+ 4.754050 -2.480049 3.362997 -+ 4.997986 -3.708205 3.989198 -+ 4.976769 -4.883498 3.345899 -+ 5.160704 -5.738821 3.850568 -+ 4.776841 -4.914031 2.356355 -+ 5.265289 -3.689348 5.302131 -+ 5.284973 -2.519883 5.935270 -+ 5.498266 -2.482169 6.993326 -+ 5.072682 -1.308518 5.455764 -+ 4.806134 -1.356364 4.133205 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 -@@ -1274,21 +1274,21 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.397885 0.753191 5.246175 -- 5.590532 0.136915 4.972869 -- 5.691792 -0.854182 4.555888 -- 6.355081 0.476418 6.019675 -- 7.005380 1.133878 7.200716 -- 6.241886 1.418905 7.924551 -- 7.704141 0.438210 7.665344 -- 7.543334 2.022951 6.871696 -- 6.737960 -0.878090 5.715845 -- 7.428954 -0.641760 6.705579 -- 6.803084 -2.106960 5.091315 -- 7.433797 -1.942952 5.965044 -- 6.888321 -3.344512 4.486667 -- 7.677782 -3.431286 5.412745 -+ 5.071990 1.095268 4.737463 -+ 4.538744 -0.306572 3.312620 -+ 4.316895 -0.672508 2.011169 -+ 4.145425 0.083640 1.259346 -+ 4.360306 -1.957588 1.633963 -+ 4.118872 -2.368537 0.211701 -+ 4.859526 -1.896818 -0.434064 -+ 4.201263 -3.452119 0.127068 -+ 3.120134 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1.095268 4.737463 -+ 4.500559 -0.267967 3.326521 -+ 4.258187 -0.582249 2.025720 -+ 4.103951 0.202771 1.300217 -+ 4.205645 -1.878082 1.616262 -+ 4.010240 -2.111427 0.569617 -+ 4.416190 -2.880836 2.613787 -+ 4.378882 -4.158916 2.285883 -+ 4.532450 -4.836391 3.019057 -+ 4.201751 -4.434440 1.330472 -+ 4.652634 -2.564463 3.883788 -+ 4.701224 -1.262318 4.273223 -+ 4.918947 -0.927591 5.447171 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 -@@ -1953,27 +1953,27 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.825854 0.331961 5.463505 -- 2.973744 -0.351218 5.767666 -- 3.198298 -1.353172 5.432908 -- 3.262456 0.147686 6.932887 -- 3.554407 -1.123002 6.450998 -- 3.970615 -1.030384 7.784487 -- 4.371751 -2.299375 7.628436 -- 4.806122 -2.789852 8.397106 -- 4.239728 -2.765377 6.742145 -- 4.154910 -0.430195 8.968298 -- 4.588103 -1.686764 8.920565 -- 4.748481 -1.226887 9.884511 -- 5.030638 -2.930357 8.914329 -- 5.276823 -4.138026 8.363485 -+ 2.623224 0.684847 5.224690 -+ 2.631874 -0.707517 3.706295 -+ 2.874735 -1.252950 2.473241 -+ 2.981754 -0.611820 1.610746 -+ 3.015083 -2.545282 2.486669 -+ 2.854431 -2.887097 3.824373 -+ 2.890057 -4.114829 4.496241 -+ 3.109804 -5.286605 3.884480 -+ 3.124371 -6.141804 4.421623 -+ 3.260868 -5.314611 2.886234 -+ 2.691903 -4.099290 5.821417 -+ 2.474287 -2.933307 6.423105 -+ 2.312232 -2.898303 7.490303 -+ 2.418509 -1.722706 5.899909 -+ 2.621151 -1.767164 4.565946 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 - 4.177807 1.697081 2.650726 - 4.070872 1.663908 4.714248 -- 4.904136 2.139152 4.751846 -+ 4.591405 0.857803 4.743234 - 2.785622 3.721368 4.515694 - !entry.RA5.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 31 0 0 0 0 -@@ -2160,24 +2160,24 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.821628 0.329290 5.472166 -- 3.045980 -0.266556 5.623252 -- 3.300321 -1.253530 5.266050 -- 3.400654 0.078938 6.868419 -- 3.529160 0.584527 7.825480 -- 3.886987 -1.267611 6.713863 -- 4.193797 -1.026107 7.880244 -- 4.182336 -2.491705 6.149271 -- 4.473391 -2.322796 7.186024 -- 4.489928 -3.724276 5.610241 -- 4.916436 -3.803915 6.750481 -+ 2.623224 0.684847 5.224690 -+ 2.632951 -0.717026 3.703395 -+ 2.875701 -1.078946 2.404555 -+ 2.959028 -0.321296 1.639425 -+ 3.067013 -2.361001 2.064944 -+ 3.258724 -2.626638 1.025337 -+ 3.022943 -3.401289 3.059659 -+ 3.186167 -4.600916 2.842510 -+ 2.773364 -2.946913 4.338586 -+ 2.730574 -3.698393 5.126967 -+ 2.572586 -1.635482 4.718372 -+ 2.357489 -1.330164 5.879800 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 - 4.177807 1.697081 2.650726 - 4.070872 1.663908 4.714248 -- 4.904136 2.139152 4.751846 -+ 4.591405 0.857803 4.743234 - 2.785622 3.721368 4.515694 - !entry.RU5.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 28 0 0 0 0 -@@ -2378,28 +2378,28 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.809468 0.366314 5.430851 -- 2.985443 -0.303283 5.701265 -- 3.220128 -1.300453 5.359250 -- 3.217392 0.174542 6.898755 -- 3.501851 -1.098776 6.419335 -- 3.907092 -0.959542 7.773142 -- 4.306119 -2.122793 7.750193 -- 4.034999 -0.202628 8.943920 -- 4.092163 0.401223 9.738965 -- 4.527564 -1.484195 9.083085 -- 4.671337 -0.799117 10.225713 -- 4.406357 0.160408 10.396586 -- 5.109266 -1.288479 10.993073 -- 4.937775 -2.746085 8.992209 -- 5.203174 -3.983662 8.494648 -+ 2.623224 0.684847 5.224690 -+ 2.590680 -0.679098 3.703090 -+ 2.813126 -1.180187 2.436667 -+ 2.923918 -0.505423 1.600713 -+ 2.866567 -2.487992 2.382906 -+ 2.666616 -2.884782 3.699977 -+ 2.618169 -4.183246 4.272728 -+ 2.745111 -5.274676 3.719947 -+ 2.392358 -4.124071 5.653129 -+ 2.340242 -4.991533 6.147896 -+ 2.235991 -2.964895 6.385427 -+ 2.027971 -3.123388 7.699660 -+ 1.962797 -3.996113 8.203846 -+ 1.903765 -2.280234 8.241661 -+ 2.283795 -1.749407 5.847650 -+ 2.502701 -1.789347 4.505978 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 - 4.177807 1.697081 2.650726 - 4.070872 1.663908 4.714248 -- 4.904136 2.139152 4.751846 -+ 4.591405 0.857803 4.743234 - 2.785622 3.721368 4.515694 - !entry.RG5.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 32 0 0 0 0 -@@ -2591,25 +2591,25 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.810222 0.365622 5.431037 -- 3.040503 -0.202936 5.543946 -- 3.303784 -1.184927 5.179558 -- 3.350889 0.129864 6.825549 -- 3.478253 0.640008 7.780343 -- 3.798907 -1.207335 6.588738 -- 4.083865 -0.848420 7.826630 -- 4.553596 -1.522140 8.414470 -- 3.834435 0.071716 8.160148 -- 4.146081 -2.428628 6.192742 -- 4.391834 -3.604440 5.555033 -- 4.829292 -3.701644 6.711226 -+ 2.623224 0.684847 5.224690 -+ 2.591673 -0.679108 3.703398 -+ 2.814053 -0.989708 2.398148 -+ 2.904088 -0.203069 1.663647 -+ 2.926420 -2.283840 1.995414 -+ 3.104659 -2.514231 0.945056 -+ 2.799915 -3.288854 3.004791 -+ 2.898410 -4.565463 2.683902 -+ 2.803322 -5.244627 3.425383 -+ 3.063325 -4.838262 1.725527 -+ 2.582464 -2.976080 4.279070 -+ 2.473124 -1.675585 4.661638 -+ 2.270623 -1.344205 5.839254 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 - 4.177807 1.697081 2.650726 - 4.070872 1.663908 4.714248 -- 4.904136 2.139152 4.751846 -+ 4.591405 0.857803 4.743234 - 2.785622 3.721368 4.515694 - !entry.RC5.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 29 0 0 0 0 -@@ -2821,27 +2821,27 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.398936 0.755791 5.236576 -- 5.570721 0.053476 5.133763 -- 5.651435 -0.952100 4.748143 -- 6.248368 0.547472 6.127122 -- 6.337852 -0.727929 5.581736 -- 7.186443 -0.642297 6.691944 -- 7.489983 -1.917831 6.415398 -- 8.153280 -2.415516 6.991980 -- 7.055473 -2.381556 5.630375 -- 7.773936 -0.045280 7.737899 -- 8.144838 -1.308931 7.552106 -- 8.632452 -0.851805 8.400438 -- 8.538915 -2.559764 7.402037 -- 8.562807 -3.771388 6.807145 -+ 5.071990 1.095268 4.737463 -+ 4.538874 -0.297045 3.315659 -+ 4.336740 -0.846471 2.077041 -+ 4.152394 -0.207224 1.226289 -+ 4.452852 -2.140973 2.049069 -+ 4.754050 -2.480049 3.362997 -+ 4.997986 -3.708205 3.989198 -+ 4.976769 -4.883498 3.345899 -+ 5.160704 -5.738821 3.850568 -+ 4.776841 -4.914031 2.356355 -+ 5.265289 -3.689348 5.302131 -+ 5.284973 -2.519883 5.935270 -+ 5.498266 -2.482169 6.993326 -+ 5.072682 -1.308518 5.455764 -+ 4.806134 -1.356364 4.133205 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 - 5.668203 2.081314 1.781304 - 6.272975 2.049937 3.757138 -- 7.076220 2.511153 3.504793 -+ 6.759270 1.235224 3.610988 - 5.029888 4.128641 3.998289 - 5.911975 4.450154 3.797910 - !entry.RA3.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -3046,24 +3046,24 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.397885 0.753191 5.246175 -- 5.590532 0.136915 4.972869 -- 5.691792 -0.854182 4.555888 -- 6.355081 0.476418 6.019675 -- 6.811115 0.979784 6.872175 -- 6.737960 -0.878090 5.715845 -- 7.428954 -0.641760 6.705579 -- 6.803084 -2.106960 5.091315 -- 7.433797 -1.942952 5.965044 -- 6.888321 -3.344512 4.486667 -- 7.677782 -3.431286 5.412745 -+ 5.071990 1.095268 4.737463 -+ 4.538744 -0.306572 3.312620 -+ 4.316895 -0.672508 2.011169 -+ 4.145425 0.083640 1.259346 -+ 4.360306 -1.957588 1.633963 -+ 4.180681 -2.226400 0.593014 -+ 4.642734 -2.996992 2.589722 -+ 4.702936 -4.199185 2.336724 -+ 4.852811 -2.538498 3.874265 -+ 5.070419 -3.289156 4.634040 -+ 4.814710 -1.223887 4.292292 -+ 5.014652 -0.915008 5.455485 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 - 5.668203 2.081314 1.781304 - 6.272975 2.049937 3.757138 -- 7.076220 2.511153 3.504793 -+ 6.759270 1.235224 3.610988 - 5.029888 4.128641 3.998289 - 5.911975 4.450154 3.797910 - !entry.RU3.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -3282,28 +3282,28 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.372913 0.790414 5.211298 -- 5.559757 0.101208 5.067090 -- 5.647583 -0.899755 4.671160 -- 6.194776 0.575080 6.110305 -- 6.278024 -0.702826 5.569817 -- 7.123995 -0.570401 6.702600 -- 7.472741 -1.740173 6.551245 -- 7.656517 0.184264 7.754694 -- 7.991655 0.787072 8.478783 -- 8.146732 -1.105376 7.724367 -- 8.683403 -0.422802 8.744993 -- 8.507987 0.541027 8.990678 -- 9.349613 -0.919433 9.319121 -- 8.481202 -2.373962 7.505920 -- 8.540900 -3.615812 6.954699 -+ 5.071990 1.095268 4.737463 -+ 4.499521 -0.267941 3.326572 -+ 4.267491 -0.772686 2.063324 -+ 4.096298 -0.099873 1.236030 -+ 4.278725 -2.081203 2.002024 -+ 4.535077 -2.474587 3.310318 -+ 4.665007 -3.772057 3.872536 -+ 4.578030 -4.865461 3.315935 -+ 4.925900 -3.709107 5.246571 -+ 5.032497 -4.575574 5.734292 -+ 5.047695 -2.547474 5.981536 -+ 5.299246 -2.702459 7.288556 -+ 5.396714 -3.573970 7.789625 -+ 5.381197 -1.857343 7.835514 -+ 4.927816 -1.332957 5.452878 -+ 4.673984 -1.376560 4.117488 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 - 5.668203 2.081314 1.781304 - 6.272975 2.049937 3.757138 -- 7.076220 2.511153 3.504793 -+ 6.759270 1.235224 3.610988 - 5.029888 4.128641 3.998289 - 5.911975 4.450154 3.797910 - !entry.RG3.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -3513,25 +3513,25 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.373674 0.789709 5.211219 -- 5.559264 0.200618 4.899855 -- 5.666544 -0.785646 4.473035 -- 6.294463 0.528171 5.996117 -- 6.748720 1.036110 6.846852 -- 6.613356 -0.816346 5.628040 -- 7.310127 -0.462256 6.691775 -- 7.941913 -1.143751 7.087389 -- 7.204329 0.461930 7.085204 -- 6.784882 -2.043285 5.144201 -- 6.779159 -3.223049 4.467648 -- 7.584089 -3.327568 5.405072 -+ 5.071990 1.095268 4.737463 -+ 4.500559 -0.267967 3.326521 -+ 4.258187 -0.582249 2.025720 -+ 4.103951 0.202771 1.300217 -+ 4.205645 -1.878082 1.616262 -+ 4.010240 -2.111427 0.569617 -+ 4.416190 -2.880836 2.613787 -+ 4.378882 -4.158916 2.285883 -+ 4.532450 -4.836391 3.019057 -+ 4.201751 -4.434440 1.330472 -+ 4.652634 -2.564463 3.883788 -+ 4.701224 -1.262318 4.273223 -+ 4.918947 -0.927591 5.447171 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 - 5.668203 2.081314 1.781304 - 6.272975 2.049937 3.757138 -- 7.076220 2.511153 3.504793 -+ 6.759270 1.235224 3.610988 - 5.029888 4.128641 3.998289 - 5.911975 4.450154 3.797910 - !entry.RC3.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -3739,21 +3739,21 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.398936 0.755791 5.236576 -- 5.570721 0.053476 5.133763 -- 5.651435 -0.952100 4.748143 -- 6.248368 0.547472 6.127122 -- 6.337852 -0.727929 5.581736 -- 7.186443 -0.642297 6.691944 -- 7.489983 -1.917831 6.415398 -- 8.153280 -2.415516 6.991980 -- 7.055473 -2.381556 5.630375 -- 7.773936 -0.045280 7.737899 -- 8.144838 -1.308931 7.552106 -- 8.632452 -0.851805 8.400438 -- 8.538915 -2.559764 7.402037 -- 8.562807 -3.771388 6.807145 -+ 5.071990 1.095268 4.737463 -+ 4.538874 -0.297045 3.315659 -+ 4.336740 -0.846471 2.077041 -+ 4.152394 -0.207224 1.226289 -+ 4.452852 -2.140973 2.049069 -+ 4.754050 -2.480049 3.362997 -+ 4.997986 -3.708205 3.989198 -+ 4.976769 -4.883498 3.345899 -+ 5.160704 -5.738821 3.850568 -+ 4.776841 -4.914031 2.356355 -+ 5.265289 -3.689348 5.302131 -+ 5.284973 -2.519883 5.935270 -+ 5.498266 -2.482169 6.993326 -+ 5.072682 -1.308518 5.455764 -+ 4.806134 -1.356364 4.133205 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 -@@ -3964,21 +3964,21 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.397885 0.753191 5.246175 -- 5.590532 0.136915 4.972869 -- 5.691792 -0.854182 4.555888 -- 6.355081 0.476418 6.019675 -- 7.005380 1.133878 7.200716 -- 6.241886 1.418905 7.924551 -- 7.704141 0.438210 7.665344 -- 7.543334 2.022951 6.871696 -- 6.737960 -0.878090 5.715845 -- 7.428954 -0.641760 6.705579 -- 6.803084 -2.106960 5.091315 -- 7.433797 -1.942952 5.965044 -- 6.888321 -3.344512 4.486667 -- 7.677782 -3.431286 5.412745 -+ 5.071990 1.095268 4.737463 -+ 4.538744 -0.306572 3.312620 -+ 4.316895 -0.672508 2.011169 -+ 4.145425 0.083640 1.259346 -+ 4.360306 -1.957588 1.633963 -+ 4.118872 -2.368537 0.211701 -+ 4.859526 -1.896818 -0.434064 -+ 4.201263 -3.452119 0.127068 -+ 3.120134 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-0.099873 1.236030 -+ 4.278725 -2.081203 2.002024 -+ 4.535077 -2.474587 3.310318 -+ 4.665007 -3.772057 3.872536 -+ 4.578030 -4.865461 3.315935 -+ 4.925900 -3.709107 5.246571 -+ 5.032497 -4.575574 5.734292 -+ 5.047695 -2.547474 5.981536 -+ 5.299246 -2.702459 7.288556 -+ 5.396714 -3.573970 7.789625 -+ 5.381197 -1.857343 7.835514 -+ 4.927816 -1.332957 5.452878 -+ 4.673984 -1.376560 4.117488 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 -@@ -4413,19 +4413,19 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.373674 0.789709 5.211219 -- 5.559264 0.200618 4.899855 -- 5.666544 -0.785646 4.473035 -- 6.294463 0.528171 5.996117 -- 6.748720 1.036110 6.846852 -- 6.613356 -0.816346 5.628040 -- 7.310127 -0.462256 6.691775 -- 7.941913 -1.143751 7.087389 -- 7.204329 0.461930 7.085204 -- 6.784882 -2.043285 5.144201 -- 6.779159 -3.223049 4.467648 -- 7.584089 -3.327568 5.405072 -+ 5.071990 1.095268 4.737463 -+ 4.500559 -0.267967 3.326521 -+ 4.258187 -0.582249 2.025720 -+ 4.103951 0.202771 1.300217 -+ 4.205645 -1.878082 1.616262 -+ 4.010240 -2.111427 0.569617 -+ 4.416190 -2.880836 2.613787 -+ 4.378882 -4.158916 2.285883 -+ 4.532450 -4.836391 3.019057 -+ 4.201751 -4.434440 1.330472 -+ 4.652634 -2.564463 3.883788 -+ 4.701224 -1.262318 4.273223 -+ 4.918947 -0.927591 5.447171 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 -@@ -4639,27 +4639,27 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.398936 0.755791 5.236576 -- 5.570721 0.053476 5.133763 -- 5.651435 -0.952100 4.748143 -- 6.248368 0.547472 6.127122 -- 6.337852 -0.727929 5.581736 -- 7.186443 -0.642297 6.691944 -- 7.489983 -1.917831 6.415398 -- 8.153280 -2.415516 6.991980 -- 7.055473 -2.381556 5.630375 -- 7.773936 -0.045280 7.737899 -- 8.144838 -1.308931 7.552106 -- 8.632452 -0.851805 8.400438 -- 8.538915 -2.559764 7.402037 -- 8.562807 -3.771388 6.807145 -+ 5.071990 1.095268 4.737463 -+ 4.538874 -0.297045 3.315659 -+ 4.336740 -0.846471 2.077041 -+ 4.152394 -0.207224 1.226289 -+ 4.452852 -2.140973 2.049069 -+ 4.754050 -2.480049 3.362997 -+ 4.997986 -3.708205 3.989198 -+ 4.976769 -4.883498 3.345899 -+ 5.160704 -5.738821 3.850568 -+ 4.776841 -4.914031 2.356355 -+ 5.265289 -3.689348 5.302131 -+ 5.284973 -2.519883 5.935270 -+ 5.498266 -2.482169 6.993326 -+ 5.072682 -1.308518 5.455764 -+ 4.806134 -1.356364 4.133205 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 - 5.668203 2.081314 1.781304 - 6.272975 2.049937 3.757138 -- 7.076220 2.511153 3.504793 -+ 6.759270 1.235224 3.610988 - 5.029888 4.128641 3.998289 - !entry.RA.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 33 0 0 0 0 -@@ -4858,24 +4858,24 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.397885 0.753191 5.246175 -- 5.590532 0.136915 4.972869 -- 5.691792 -0.854182 4.555888 -- 6.355081 0.476418 6.019675 -- 6.811115 0.979784 6.872175 -- 6.737960 -0.878090 5.715845 -- 7.428954 -0.641760 6.705579 -- 6.803084 -2.106960 5.091315 -- 7.433797 -1.942952 5.965044 -- 6.888321 -3.344512 4.486667 -- 7.677782 -3.431286 5.412745 -+ 5.071990 1.095268 4.737463 -+ 4.538744 -0.306572 3.312620 -+ 4.316895 -0.672508 2.011169 -+ 4.145425 0.083640 1.259346 -+ 4.360306 -1.957588 1.633963 -+ 4.180681 -2.226400 0.593014 -+ 4.642734 -2.996992 2.589722 -+ 4.702936 -4.199185 2.336724 -+ 4.852811 -2.538498 3.874265 -+ 5.070419 -3.289156 4.634040 -+ 4.814710 -1.223887 4.292292 -+ 5.014652 -0.915008 5.455485 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 - 5.668203 2.081314 1.781304 - 6.272975 2.049937 3.757138 -- 7.076220 2.511153 3.504793 -+ 6.759270 1.235224 3.610988 - 5.029888 4.128641 3.998289 - !entry.RU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 30 0 0 0 0 -@@ -5088,28 +5088,28 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.372913 0.790414 5.211298 -- 5.559757 0.101208 5.067090 -- 5.647583 -0.899755 4.671160 -- 6.194776 0.575080 6.110305 -- 6.278024 -0.702826 5.569817 -- 7.123995 -0.570401 6.702600 -- 7.472741 -1.740173 6.551245 -- 7.656517 0.184264 7.754694 -- 7.991655 0.787072 8.478783 -- 8.146732 -1.105376 7.724367 -- 8.683403 -0.422802 8.744993 -- 8.507987 0.541027 8.990678 -- 9.349613 -0.919433 9.319121 -- 8.481202 -2.373962 7.505920 -- 8.540900 -3.615812 6.954699 -+ 5.071990 1.095268 4.737463 -+ 4.499521 -0.267941 3.326572 -+ 4.267491 -0.772686 2.063324 -+ 4.096298 -0.099873 1.236030 -+ 4.278725 -2.081203 2.002024 -+ 4.535077 -2.474587 3.310318 -+ 4.665007 -3.772057 3.872536 -+ 4.578030 -4.865461 3.315935 -+ 4.925900 -3.709107 5.246571 -+ 5.032497 -4.575574 5.734292 -+ 5.047695 -2.547474 5.981536 -+ 5.299246 -2.702459 7.288556 -+ 5.396714 -3.573970 7.789625 -+ 5.381197 -1.857343 7.835514 -+ 4.927816 -1.332957 5.452878 -+ 4.673984 -1.376560 4.117488 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 - 5.668203 2.081314 1.781304 - 6.272975 2.049937 3.757138 -- 7.076220 2.511153 3.504793 -+ 6.759270 1.235224 3.610988 - 5.029888 4.128641 3.998289 - !entry.RG.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 34 0 0 0 0 -@@ -5313,25 +5313,25 @@ - 2.447108 3.477366 3.933855 - 3.228110 1.605160 3.977232 - 4.558604 1.150942 3.777549 -- 5.569373 1.557427 3.742678 -- 4.373674 0.789709 5.211219 -- 5.559264 0.200618 4.899855 -- 5.666544 -0.785646 4.473035 -- 6.294463 0.528171 5.996117 -- 6.748720 1.036110 6.846852 -- 6.613356 -0.816346 5.628040 -- 7.310127 -0.462256 6.691775 -- 7.941913 -1.143751 7.087389 -- 7.204329 0.461930 7.085204 -- 6.784882 -2.043285 5.144201 -- 6.779159 -3.223049 4.467648 -- 7.584089 -3.327568 5.405072 -+ 5.071990 1.095268 4.737463 -+ 4.500559 -0.267967 3.326521 -+ 4.258187 -0.582249 2.025720 -+ 4.103951 0.202771 1.300217 -+ 4.205645 -1.878082 1.616262 -+ 4.010240 -2.111427 0.569617 -+ 4.416190 -2.880836 2.613787 -+ 4.378882 -4.158916 2.285883 -+ 4.532450 -4.836391 3.019057 -+ 4.201751 -4.434440 1.330472 -+ 4.652634 -2.564463 3.883788 -+ 4.701224 -1.262318 4.273223 -+ 4.918947 -0.927591 5.447171 - 4.415598 3.377823 2.961313 - 4.412064 3.941488 2.028377 - 5.230436 2.095693 2.779428 - 5.668203 2.081314 1.781304 - 6.272975 2.049937 3.757138 -- 7.076220 2.511153 3.504793 -+ 6.759270 1.235224 3.610988 - 5.029888 4.128641 3.998289 - !entry.RC.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x - 1 31 0 0 0 0 -@@ -5531,21 +5531,21 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.825854 0.331961 5.463505 -- 2.973744 -0.351218 5.767666 -- 3.198298 -1.353172 5.432908 -- 3.262456 0.147686 6.932887 -- 3.554407 -1.123002 6.450998 -- 3.970615 -1.030384 7.784487 -- 4.371751 -2.299375 7.628436 -- 4.806122 -2.789852 8.397106 -- 4.239728 -2.765377 6.742145 -- 4.154910 -0.430195 8.968298 -- 4.588103 -1.686764 8.920565 -- 4.748481 -1.226887 9.884511 -- 5.030638 -2.930357 8.914329 -- 5.276823 -4.138026 8.363485 -+ 2.623224 0.684847 5.224690 -+ 2.631874 -0.707517 3.706295 -+ 2.874735 -1.252950 2.473241 -+ 2.981754 -0.611820 1.610746 -+ 3.015083 -2.545282 2.486669 -+ 2.854431 -2.887097 3.824373 -+ 2.890057 -4.114829 4.496241 -+ 3.109804 -5.286605 3.884480 -+ 3.124371 -6.141804 4.421623 -+ 3.260868 -5.314611 2.886234 -+ 2.691903 -4.099290 5.821417 -+ 2.474287 -2.933307 6.423105 -+ 2.312232 -2.898303 7.490303 -+ 2.418509 -1.722706 5.899909 -+ 2.621151 -1.767164 4.565946 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 -@@ -5750,21 +5750,21 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.821628 0.329290 5.472166 -- 3.045980 -0.266556 5.623252 -- 3.300321 -1.253530 5.266050 -- 3.400654 0.078938 6.868419 -- 3.596750 0.739775 8.200650 -- 2.627095 1.008594 8.619702 -- 4.106045 0.052544 8.876247 -- 4.199810 1.639079 8.075463 -- 3.886987 -1.267611 6.713863 -- 4.193797 -1.026107 7.880244 -- 4.182336 -2.491705 6.149271 -- 4.473391 -2.322796 7.186024 -- 4.489928 -3.724276 5.610241 -- 4.916436 -3.803915 6.750481 -+ 2.623224 0.684847 5.224690 -+ 2.632951 -0.717026 3.703395 -+ 2.875701 -1.078946 2.404555 -+ 2.959028 -0.321296 1.639425 -+ 3.067013 -2.361001 2.064944 -+ 3.333430 -2.767543 0.645879 -+ 4.242250 -2.280529 0.292378 -+ 3.457938 -3.849191 0.594530 -+ 2.493973 -2.468751 0.018077 -+ 3.022943 -3.401289 3.059659 -+ 3.186167 -4.600916 2.842510 -+ 2.773364 -2.946913 4.338586 -+ 2.730574 -3.698393 5.126967 -+ 2.572586 -1.635482 4.718372 -+ 2.357489 -1.330164 5.879800 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 -@@ -5974,22 +5974,22 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.809468 0.366314 5.430851 -- 2.985443 -0.303283 5.701265 -- 3.220128 -1.300453 5.359250 -- 3.217392 0.174542 6.898755 -- 3.501851 -1.098776 6.419335 -- 3.907092 -0.959542 7.773142 -- 4.306119 -2.122793 7.750193 -- 4.034999 -0.202628 8.943920 -- 4.092163 0.401223 9.738965 -- 4.527564 -1.484195 9.083085 -- 4.671337 -0.799117 10.225713 -- 4.406357 0.160408 10.396586 -- 5.109266 -1.288479 10.993073 -- 4.937775 -2.746085 8.992209 -- 5.203174 -3.983662 8.494648 -+ 2.623224 0.684847 5.224690 -+ 2.590680 -0.679098 3.703090 -+ 2.813126 -1.180187 2.436667 -+ 2.923918 -0.505423 1.600713 -+ 2.866567 -2.487992 2.382906 -+ 2.666616 -2.884782 3.699977 -+ 2.618169 -4.183246 4.272728 -+ 2.745111 -5.274676 3.719947 -+ 2.392358 -4.124071 5.653129 -+ 2.340242 -4.991533 6.147896 -+ 2.235991 -2.964895 6.385427 -+ 2.027971 -3.123388 7.699660 -+ 1.962797 -3.996113 8.203846 -+ 1.903765 -2.280234 8.241661 -+ 2.283795 -1.749407 5.847650 -+ 2.502701 -1.789347 4.505978 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 -@@ -6187,19 +6187,19 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.810222 0.365622 5.431037 -- 3.040503 -0.202936 5.543946 -- 3.303784 -1.184927 5.179558 -- 3.350889 0.129864 6.825549 -- 3.478253 0.640008 7.780343 -- 3.798907 -1.207335 6.588738 -- 4.083865 -0.848420 7.826630 -- 4.553596 -1.522140 8.414470 -- 3.834435 0.071716 8.160148 -- 4.146081 -2.428628 6.192742 -- 4.391834 -3.604440 5.555033 -- 4.829292 -3.701644 6.711226 -+ 2.623224 0.684847 5.224690 -+ 2.591673 -0.679108 3.703398 -+ 2.814053 -0.989708 2.398148 -+ 2.904088 -0.203069 1.663647 -+ 2.926420 -2.283840 1.995414 -+ 3.104659 -2.514231 0.945056 -+ 2.799915 -3.288854 3.004791 -+ 2.898410 -4.565463 2.683902 -+ 2.803322 -5.244627 3.425383 -+ 3.063325 -4.838262 1.725527 -+ 2.582464 -2.976080 4.279070 -+ 2.473124 -1.675585 4.661638 -+ 2.270623 -1.344205 5.839254 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 -@@ -6407,27 +6407,27 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.825854 0.331961 5.463505 -- 2.973744 -0.351218 5.767666 -- 3.198298 -1.353172 5.432908 -- 3.262456 0.147686 6.932887 -- 3.554407 -1.123002 6.450998 -- 3.970615 -1.030384 7.784487 -- 4.371751 -2.299375 7.628436 -- 4.806122 -2.789852 8.397106 -- 4.239728 -2.765377 6.742145 -- 4.154910 -0.430195 8.968298 -- 4.588103 -1.686764 8.920565 -- 4.748481 -1.226887 9.884511 -- 5.030638 -2.930357 8.914329 -- 5.276823 -4.138026 8.363485 -+ 2.623224 0.684847 5.224690 -+ 2.631874 -0.707517 3.706295 -+ 2.874735 -1.252950 2.473241 -+ 2.981754 -0.611820 1.610746 -+ 3.015083 -2.545282 2.486669 -+ 2.854431 -2.887097 3.824373 -+ 2.890057 -4.114829 4.496241 -+ 3.109804 -5.286605 3.884480 -+ 3.124371 -6.141804 4.421623 -+ 3.260868 -5.314611 2.886234 -+ 2.691903 -4.099290 5.821417 -+ 2.474287 -2.933307 6.423105 -+ 2.312232 -2.898303 7.490303 -+ 2.418509 -1.722706 5.899909 -+ 2.621151 -1.767164 4.565946 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 - 4.177807 1.697081 2.650726 - 4.070872 1.663908 4.714248 -- 4.904136 2.139152 4.751846 -+ 4.591405 0.857803 4.743234 - 2.785622 3.721368 4.515694 - 3.677533 4.057871 4.629091 - !entry.RAN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -6620,24 +6620,24 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.821628 0.329290 5.472166 -- 3.045980 -0.266556 5.623252 -- 3.300321 -1.253530 5.266050 -- 3.400654 0.078938 6.868419 -- 3.529160 0.584527 7.825480 -- 3.886987 -1.267611 6.713863 -- 4.193797 -1.026107 7.880244 -- 4.182336 -2.491705 6.149271 -- 4.473391 -2.322796 7.186024 -- 4.489928 -3.724276 5.610241 -- 4.916436 -3.803915 6.750481 -+ 2.623224 0.684847 5.224690 -+ 2.632951 -0.717026 3.703395 -+ 2.875701 -1.078946 2.404555 -+ 2.959028 -0.321296 1.639425 -+ 3.067013 -2.361001 2.064944 -+ 3.258724 -2.626638 1.025337 -+ 3.022943 -3.401289 3.059659 -+ 3.186167 -4.600916 2.842510 -+ 2.773364 -2.946913 4.338586 -+ 2.730574 -3.698393 5.126967 -+ 2.572586 -1.635482 4.718372 -+ 2.357489 -1.330164 5.879800 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 - 4.177807 1.697081 2.650726 - 4.070872 1.663908 4.714248 -- 4.904136 2.139152 4.751846 -+ 4.591405 0.857803 4.743234 - 2.785622 3.721368 4.515694 - 3.677533 4.057871 4.629091 - !entry.RUN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -6844,28 +6844,28 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.809468 0.366314 5.430851 -- 2.985443 -0.303283 5.701265 -- 3.220128 -1.300453 5.359250 -- 3.217392 0.174542 6.898755 -- 3.501851 -1.098776 6.419335 -- 3.907092 -0.959542 7.773142 -- 4.306119 -2.122793 7.750193 -- 4.034999 -0.202628 8.943920 -- 4.092163 0.401223 9.738965 -- 4.527564 -1.484195 9.083085 -- 4.671337 -0.799117 10.225713 -- 4.406357 0.160408 10.396586 -- 5.109266 -1.288479 10.993073 -- 4.937775 -2.746085 8.992209 -- 5.203174 -3.983662 8.494648 -+ 2.623224 0.684847 5.224690 -+ 2.590680 -0.679098 3.703090 -+ 2.813126 -1.180187 2.436667 -+ 2.923918 -0.505423 1.600713 -+ 2.866567 -2.487992 2.382906 -+ 2.666616 -2.884782 3.699977 -+ 2.618169 -4.183246 4.272728 -+ 2.745111 -5.274676 3.719947 -+ 2.392358 -4.124071 5.653129 -+ 2.340242 -4.991533 6.147896 -+ 2.235991 -2.964895 6.385427 -+ 2.027971 -3.123388 7.699660 -+ 1.962797 -3.996113 8.203846 -+ 1.903765 -2.280234 8.241661 -+ 2.283795 -1.749407 5.847650 -+ 2.502701 -1.789347 4.505978 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 - 4.177807 1.697081 2.650726 - 4.070872 1.663908 4.714248 -- 4.904136 2.139152 4.751846 -+ 4.591405 0.857803 4.743234 - 2.785622 3.721368 4.515694 - 3.677533 4.057871 4.629091 - !entry.RGN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -@@ -7063,25 +7063,25 @@ - 0.391890 3.029890 3.571783 - 1.142222 1.169994 3.879663 - 2.468198 0.737932 4.147078 -- 3.422991 1.160472 4.460013 -- 1.810222 0.365622 5.431037 -- 3.040503 -0.202936 5.543946 -- 3.303784 -1.184927 5.179558 -- 3.350889 0.129864 6.825549 -- 3.478253 0.640008 7.780343 -- 3.798907 -1.207335 6.588738 -- 4.083865 -0.848420 7.826630 -- 4.553596 -1.522140 8.414470 -- 3.834435 0.071716 8.160148 -- 4.146081 -2.428628 6.192742 -- 4.391834 -3.604440 5.555033 -- 4.829292 -3.701644 6.711226 -+ 2.623224 0.684847 5.224690 -+ 2.591673 -0.679108 3.703398 -+ 2.814053 -0.989708 2.398148 -+ 2.904088 -0.203069 1.663647 -+ 2.926420 -2.283840 1.995414 -+ 3.104659 -2.514231 0.945056 -+ 2.799915 -3.288854 3.004791 -+ 2.898410 -4.565463 2.683902 -+ 2.803322 -5.244627 3.425383 -+ 3.063325 -4.838262 1.725527 -+ 2.582464 -2.976080 4.279070 -+ 2.473124 -1.675585 4.661638 -+ 2.270623 -1.344205 5.839254 - 2.575655 2.966926 3.331156 - 2.881929 3.535802 2.453274 - 3.424925 1.698847 3.438931 - 4.177807 1.697081 2.650726 - 4.070872 1.663908 4.714248 -- 4.904136 2.139152 4.751846 -+ 4.591405 0.857803 4.743234 - 2.785622 3.721368 4.515694 - 3.677533 4.057871 4.629091 - !entry.RCN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -diff -urN amber11.orig/AmberTools/test/sqm/nma/nma.dftb.go.in amber11/AmberTools/test/sqm/nma/nma.dftb.go.in ---- amber11.orig/AmberTools/test/sqm/nma/nma.dftb.go.in 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/test/sqm/nma/nma.dftb.go.in 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,30 @@ -+Run DFTB geometry optimization for NMA -+ &qmmm -+ qm_theory = 'DFTB', -+ qmcharge = 0, -+ ! SCF settings -+ scfconv = 1.0d-10, ! kcal/mol -+ errconv = 1.d-06, ! au -+ tight_p_conv = 0, -+ diag_routine = 1, -+ itrmax = 100, -+ ! Geometry optimization settings -+ maxcyc = 100, -+ grms_tol = 0.001, ! kcal/(mol*A) -+ ! Output -+ ntpr = 101, -+ verbosity = 0, -+ / -+ 6 C -0.767000 3.380000 4.245000 -+ 6 C -1.809707 2.570219 4.710852 -+ 7 N -2.661673 2.646098 3.869189 -+ 6 C -3.662846 1.855199 3.619926 -+ 8 O -1.634379 2.116691 5.584678 -+ 1 H 0.218271 3.164467 4.684075 -+ 1 H -0.578839 3.210298 3.174581 -+ 1 H -1.024346 4.421330 4.488732 -+ 1 H -2.569216 3.204198 3.074324 -+ 1 H -3.347225 0.824359 3.812610 -+ 1 H -4.529359 1.998602 4.311686 -+ 1 H -4.036138 1.906340 2.552627 -+ -diff -urN amber11.orig/AmberTools/test/sqm/nma/nma.dftb.go.out.save amber11/AmberTools/test/sqm/nma/nma.dftb.go.out.save ---- amber11.orig/AmberTools/test/sqm/nma/nma.dftb.go.out.save 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/test/sqm/nma/nma.dftb.go.out.save 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,81 @@ -+ -------------------------------------------------------- -+ AMBER SQM VERSION 1.4 -+ -+ By -+ Ross C. Walker, Michael F. Crowley, Scott Brozell, -+ Tim Giese, Andreas W. Goetz and David A. Case -+ -+ -------------------------------------------------------- -+ -+ -+-------------------------------------------------------------------------------- -+ QM CALCULATION INFO -+-------------------------------------------------------------------------------- -+ -+| QMMM: Citation for AMBER QMMM Run: -+| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008 -+ -+| QMMM: DFTB Calculation - Additional citation for AMBER DFTB QMMM Run: -+| QMMM: Seabra, G.M., Walker, R.C. et al., J. PHYS. CHEM. A., 111, 5655, (2007) -+ -+ -+QMMM: SINGLET STATE CALCULATION -+QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 15 -+ -+| QMMM: *** SCF convergence criteria *** -+| QMMM: Energy change : 0.1D-09 kcal/mol -+| QMMM: Error matrix |FP-PF| : 0.1D-05 au -+| QMMM: Density matrix change : 0.5D-06 -+| QMMM: Maximum number of SCF cycles : 100 -+ DFTB: Number of atom types = 4 -+ -+ Parameter files: -+ TYP (AT) TYP (AT) SK integral FILE -+| 1 1 (C ) 1 (C ) /Users/andi/sources/amber/dat/slko/C-C.skf -+| 2 1 (C ) 2 (N ) /Users/andi/sources/amber/dat/slko/C-N.skf -+| 3 1 (C ) 3 (O ) /Users/andi/sources/amber/dat/slko/C-O.skf -+| 4 1 (C ) 4 (H ) /Users/andi/sources/amber/dat/slko/C-H.skf -+| 5 2 (N ) 1 (C ) /Users/andi/sources/amber/dat/slko/N-C.skf -+| 6 2 (N ) 2 (N ) /Users/andi/sources/amber/dat/slko/N-N.skf -+| 7 2 (N ) 3 (O ) /Users/andi/sources/amber/dat/slko/N-O.skf -+| 8 2 (N ) 4 (H ) /Users/andi/sources/amber/dat/slko/N-H.skf -+| 9 3 (O ) 1 (C ) /Users/andi/sources/amber/dat/slko/O-C.skf -+| 10 3 (O ) 2 (N ) /Users/andi/sources/amber/dat/slko/O-N.skf -+| 11 3 (O ) 3 (O ) /Users/andi/sources/amber/dat/slko/O-O.skf -+| 12 3 (O ) 4 (H ) /Users/andi/sources/amber/dat/slko/O-H.skf -+| 13 4 (H ) 1 (C ) /Users/andi/sources/amber/dat/slko/H-C.skf -+| 14 4 (H ) 2 (N ) /Users/andi/sources/amber/dat/slko/H-N.skf -+| 15 4 (H ) 3 (O ) /Users/andi/sources/amber/dat/slko/H-O.skf -+| 16 4 (H ) 4 (H ) /Users/andi/sources/amber/dat/slko/H-H.skf -+ -+-------------------------------------------------------------------------------- -+ RESULTS -+-------------------------------------------------------------------------------- -+ -+ ... geometry converged ! -+ -+ Heat of formation = -1220.84132946 kcal/mol ( -52.93965264 eV) -+ Total SCF energy = -8463.39103876 kcal/mol ( -367.00017513 eV) -+ -+ Atomic Charges for Step 1 : -+ Atom Element Mulliken Charge -+ 1 C -0.279 -+ 2 C 0.493 -+ 3 N -0.250 -+ 4 C -0.073 -+ 5 O -0.507 -+ 6 H 0.096 -+ 7 H 0.073 -+ 8 H 0.073 -+ 9 H 0.186 -+ 10 H 0.097 -+ 11 H 0.045 -+ 12 H 0.045 -+ Total Mulliken Charge = 0.000 -+ -+ -+ Final Structure -+ -+ -+ --------- Calculation Completed ---------- -+ -diff -urN amber11.orig/AmberTools/test/sqm/nma/nma.dftb.sp.in amber11/AmberTools/test/sqm/nma/nma.dftb.sp.in ---- amber11.orig/AmberTools/test/sqm/nma/nma.dftb.sp.in 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/test/sqm/nma/nma.dftb.sp.in 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,30 @@ -+Run PM3 single point calculation for NMA -+ &qmmm -+ qm_theory = 'DFTB', -+ qmcharge = 0, -+ ! SCF settings -+ scfconv = 1.0d-10, ! kcal/mol -+ errconv = 1.d-06, ! au -+ tight_p_conv = 0, -+ diag_routine = 1, -+ itrmax = 100, -+ ! Geometry optimization settings -+ maxcyc = 0, -+ grms_tol = 0.02, ! kcal/(mol*A) -+ ! Output -+ ntpr = 10, -+ verbosity = 0, -+ / -+ 6 C -0.767000 3.380000 4.245000 -+ 6 C -1.809707 2.570219 4.710852 -+ 7 N -2.661673 2.646098 3.869189 -+ 6 C -3.662846 1.855199 3.619926 -+ 8 O -1.634379 2.116691 5.584678 -+ 1 H 0.218271 3.164467 4.684075 -+ 1 H -0.578839 3.210298 3.174581 -+ 1 H -1.024346 4.421330 4.488732 -+ 1 H -2.569216 3.204198 3.074324 -+ 1 H -3.347225 0.824359 3.812610 -+ 1 H -4.529359 1.998602 4.311686 -+ 1 H -4.036138 1.906340 2.552627 -+ -diff -urN amber11.orig/AmberTools/test/sqm/nma/nma.dftb.sp.out.save amber11/AmberTools/test/sqm/nma/nma.dftb.sp.out.save ---- amber11.orig/AmberTools/test/sqm/nma/nma.dftb.sp.out.save 1970-01-01 03:00:00.000000000 +0300 -+++ amber11/AmberTools/test/sqm/nma/nma.dftb.sp.out.save 2011-03-08 16:38:44.000000000 +0300 -@@ -0,0 +1,111 @@ -+ -------------------------------------------------------- -+ AMBER SQM VERSION 1.4 -+ -+ By -+ Ross C. Walker, Michael F. Crowley, Scott Brozell, -+ Tim Giese, Andreas W. Goetz and David A. Case -+ -+ -------------------------------------------------------- -+ -+ -+-------------------------------------------------------------------------------- -+ QM CALCULATION INFO -+-------------------------------------------------------------------------------- -+ -+| QMMM: Citation for AMBER QMMM Run: -+| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008 -+ -+| QMMM: DFTB Calculation - Additional citation for AMBER DFTB QMMM Run: -+| QMMM: Seabra, G.M., Walker, R.C. et al., J. PHYS. CHEM. A., 111, 5655, (2007) -+ -+ -+QMMM: SINGLET STATE CALCULATION -+QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 15 -+ -+| QMMM: *** SCF convergence criteria *** -+| QMMM: Energy change : 0.1D-09 kcal/mol -+| QMMM: Error matrix |FP-PF| : 0.1D-05 au -+| QMMM: Density matrix change : 0.5D-06 -+| QMMM: Maximum number of SCF cycles : 100 -+ DFTB: Number of atom types = 4 -+ -+ Parameter files: -+ TYP (AT) TYP (AT) SK integral FILE -+| 1 1 (C ) 1 (C ) /Users/andi/sources/amber/dat/slko/C-C.skf -+| 2 1 (C ) 2 (N ) /Users/andi/sources/amber/dat/slko/C-N.skf -+| 3 1 (C ) 3 (O ) /Users/andi/sources/amber/dat/slko/C-O.skf -+| 4 1 (C ) 4 (H ) /Users/andi/sources/amber/dat/slko/C-H.skf -+| 5 2 (N ) 1 (C ) /Users/andi/sources/amber/dat/slko/N-C.skf -+| 6 2 (N ) 2 (N ) /Users/andi/sources/amber/dat/slko/N-N.skf -+| 7 2 (N ) 3 (O ) /Users/andi/sources/amber/dat/slko/N-O.skf -+| 8 2 (N ) 4 (H ) /Users/andi/sources/amber/dat/slko/N-H.skf -+| 9 3 (O ) 1 (C ) /Users/andi/sources/amber/dat/slko/O-C.skf -+| 10 3 (O ) 2 (N ) /Users/andi/sources/amber/dat/slko/O-N.skf -+| 11 3 (O ) 3 (O ) /Users/andi/sources/amber/dat/slko/O-O.skf -+| 12 3 (O ) 4 (H ) /Users/andi/sources/amber/dat/slko/O-H.skf -+| 13 4 (H ) 1 (C ) /Users/andi/sources/amber/dat/slko/H-C.skf -+| 14 4 (H ) 2 (N ) /Users/andi/sources/amber/dat/slko/H-N.skf -+| 15 4 (H ) 3 (O ) /Users/andi/sources/amber/dat/slko/H-O.skf -+| 16 4 (H ) 4 (H ) /Users/andi/sources/amber/dat/slko/H-H.skf -+ -+ QMMM: QM Region Cartesian Coordinates (*=link atom) -+ QMMM: QM_NO. MM_NO. ATOM X Y Z -+ QMMM: 1 1 C -0.7670 3.3800 4.2450 -+ QMMM: 2 2 C -1.8097 2.5702 4.7109 -+ QMMM: 3 3 N -2.6617 2.6461 3.8692 -+ QMMM: 4 4 C -3.6628 1.8552 3.6199 -+ QMMM: 5 5 O -1.6344 2.1167 5.5847 -+ QMMM: 6 6 H 0.2183 3.1645 4.6841 -+ QMMM: 7 7 H -0.5788 3.2103 3.1746 -+ QMMM: 8 8 H -1.0243 4.4213 4.4887 -+ QMMM: 9 9 H -2.5692 3.2042 3.0743 -+ QMMM: 10 10 H -3.3472 0.8244 3.8126 -+ QMMM: 11 11 H -4.5294 1.9986 4.3117 -+ QMMM: 12 12 H -4.0361 1.9063 2.5526 -+ -+-------------------------------------------------------------------------------- -+ RESULTS -+-------------------------------------------------------------------------------- -+ -+ -+ Heat of formation = -1039.27301701 kcal/mol ( -45.06625979 eV) -+ Total SCF energy = -8281.82272631 kcal/mol ( -359.12678229 eV) -+ Electronic energy = -8895.69306749 kcal/mol ( -385.74619780 eV) -+ Core-core repulsion = 613.87034117 kcal/mol ( 26.61941551 eV) -+ -+ Atomic Charges for Step 1 : -+ Atom Element Mulliken Charge -+ 1 C -0.347 -+ 2 C 0.560 -+ 3 N -0.202 -+ 4 C -0.066 -+ 5 O -0.439 -+ 6 H 0.077 -+ 7 H 0.048 -+ 8 H 0.072 -+ 9 H 0.187 -+ 10 H 0.044 -+ 11 H 0.029 -+ 12 H 0.037 -+ Total Mulliken Charge = 0.000 -+ -+ -+ Final Structure -+ -+ QMMM: QM Region Cartesian Coordinates (*=link atom) -+ QMMM: QM_NO. MM_NO. ATOM X Y Z -+ QMMM: 1 1 C -0.7670 3.3800 4.2450 -+ QMMM: 2 2 C -1.8097 2.5702 4.7109 -+ QMMM: 3 3 N -2.6617 2.6461 3.8692 -+ QMMM: 4 4 C -3.6628 1.8552 3.6199 -+ QMMM: 5 5 O -1.6344 2.1167 5.5847 -+ QMMM: 6 6 H 0.2183 3.1645 4.6841 -+ QMMM: 7 7 H -0.5788 3.2103 3.1746 -+ QMMM: 8 8 H -1.0243 4.4213 4.4887 -+ QMMM: 9 9 H -2.5692 3.2042 3.0743 -+ QMMM: 10 10 H -3.3472 0.8244 3.8126 -+ QMMM: 11 11 H -4.5294 1.9986 4.3117 -+ QMMM: 12 12 H -4.0361 1.9063 2.5526 -+ -+ --------- Calculation Completed ---------- -+ -diff -urN amber11.orig/AmberTools/test/sqm/nma/Run amber11/AmberTools/test/sqm/nma/Run ---- amber11.orig/AmberTools/test/sqm/nma/Run 2010-04-14 17:26:17.000000000 +0400 -+++ amber11/AmberTools/test/sqm/nma/Run 2011-03-08 16:38:44.000000000 +0300 -@@ -3,8 +3,19 @@ - set SQM = ../../../exe/sqm - set SPDIFF = ../../dacdif - set GODIFF = "../../dacdif -a 0.01" --set SPTESTS = (nma.pm3.sp nma.pm6.sp) --set GOTESTS = (nma.pm3.go nma.pm6.go) -+ -+# check if slko files for DFTB are installed -+../../check_slko_files.x -+if( $status > 0) then -+ # no slko files - do not run DFTB tests -+ set SPTESTS = (nma.pm3.sp nma.pm6.sp) -+ set GOTESTS = (nma.pm3.go nma.pm6.go) -+else -+ # slko files present - run DFTB tests -+ set SPTESTS = (nma.pm3.sp nma.pm6.sp nma.dftb.sp) -+ set GOTESTS = (nma.pm3.go nma.pm6.go nma.dftb.go) -+endif -+ - - # single point tests - foreach i ($SPTESTS) -diff -urN amber11.orig/dat/leap/lib/amoeba_aminoct.off amber11/dat/leap/lib/amoeba_aminoct.off ---- amber11.orig/dat/leap/lib/amoeba_aminoct.off 2010-03-31 07:05:27.000000000 +0400 -+++ amber11/dat/leap/lib/amoeba_aminoct.off 2011-03-08 16:38:44.000000000 +0300 -@@ -638,24 +638,24 @@ - !entry.CCYX.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg str - "N" "7" 0 1 131072 1 7 -0.382100 - "H" "10" 0 1 131072 2 1 0.268100 -- "CA" "8" 0 1 131072 3 6 -0.131800 -+ "CA" "44" 0 1 131072 3 6 -0.131800 - "HA" "12" 0 1 131072 4 1 0.093800 -- "CB" "" 0 1 131072 5 6 -0.194300 -- "HB2" "" 0 1 131072 6 1 0.122800 -- "HB3" "" 0 1 131072 7 1 0.122800 -- "SG" "" 0 1 131072 8 16 -0.052900 -+ "CB" "45" 0 1 131072 5 6 -0.194300 -+ "HB2" "46" 0 1 131072 6 1 0.122800 -+ "HB3" "46" 0 1 131072 7 1 0.122800 -+ "SG" "49" 0 1 131072 8 16 -0.052900 - "C" "192" 0 1 131072 9 6 0.761800 - "O" "193" 0 1 131072 10 8 -0.804100 - "OXT" "193" 0 1 131072 11 8 -0.804100 - !entry.CCYX.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg - "N" "7" 0 -1 0.0 - "H" "10" 0 -1 0.0 -- "CA" "8" 0 -1 0.0 -+ "CA" "44" 0 -1 0.0 - "HA" "12" 0 -1 0.0 -- "CB" "" 0 -1 0.0 -- "HB2" "" 0 -1 0.0 -- "HB3" "" 0 -1 0.0 -- "SG" "" 0 -1 0.0 -+ "CB" "45" 0 -1 0.0 -+ "HB2" "46" 0 -1 0.0 -+ "HB3" "46" 0 -1 0.0 -+ "SG" "49" 0 -1 0.0 - "C" "192" 0 -1 0.0 - "O" "193" 0 -1 0.0 - "OXT" "193" 0 -1 0.0 -diff -urN amber11.orig/dat/leap/lib/amoeba_aminont.off amber11/dat/leap/lib/amoeba_aminont.off ---- amber11.orig/dat/leap/lib/amoeba_aminont.off 2010-03-31 07:05:27.000000000 +0400 -+++ amber11/dat/leap/lib/amoeba_aminont.off 2011-03-08 16:38:44.000000000 +0300 -@@ -736,12 +736,12 @@ - "H1" "191" 0 1 131072 2 1 0.181500 - "H2" "191" 0 1 131072 3 1 0.181500 - "H3" "191" 0 1 131072 4 1 0.181500 -- "CA" "8" 0 1 131072 5 6 0.105500 -+ "CA" "44" 0 1 131072 5 6 0.105500 - "HA" "12" 0 1 131072 6 1 0.092200 -- "CB" "" 0 1 131072 7 6 -0.027700 -- "HB2" "" 0 1 131072 8 1 0.068000 -- "HB3" "" 0 1 131072 9 1 0.068000 -- "SG" "" 0 1 131072 10 16 -0.098400 -+ "CB" "45" 0 1 131072 7 6 -0.027700 -+ "HB2" "46" 0 1 131072 8 1 0.068000 -+ "HB3" "46" 0 1 131072 9 1 0.068000 -+ "SG" "49" 0 1 131072 10 16 -0.098400 - "C" "9" 0 1 131072 11 6 0.612300 - "O" "11" 0 1 131072 12 8 -0.571300 - !entry.NCYX.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg -diff -urN amber11.orig/dat/leap/lib/amoeba_amino.off amber11/dat/leap/lib/amoeba_amino.off ---- amber11.orig/dat/leap/lib/amoeba_amino.off 2010-03-31 07:05:27.000000000 +0400 -+++ amber11/dat/leap/lib/amoeba_amino.off 2011-03-08 16:38:44.000000000 +0300 -@@ -880,23 +880,23 @@ - !entry.CYX.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg str - "N" "7" 0 1 131072 1 7 -0.435921 - "H" "10" 0 1 131072 2 1 0.290077 -- "CA" "8" 0 1 131072 3 6 -0.030547 -+ "CA" "44" 0 1 131072 3 6 -0.030547 - "HA" "12" 0 1 131072 4 1 0.132146 -- "CB" "" 0 1 131072 5 6 -0.033006 -- "HB2" "" 0 1 131072 6 1 0.078951 -- "HB3" "" 0 1 131072 7 1 0.078951 -- "SG" "" 0 1 131072 8 16 -0.132272 -+ "CB" "45" 0 1 131072 5 6 -0.033006 -+ "HB2" "46" 0 1 131072 6 1 0.078951 -+ "HB3" "46" 0 1 131072 7 1 0.078951 -+ "SG" "49" 0 1 131072 8 16 -0.132272 - "C" "9" 0 1 131072 9 6 0.624788 - "O" "11" 0 1 131072 10 8 -0.573167 - !entry.CYX.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg - "N" "7" 0 -1 0.0 - "H" "10" 0 -1 0.0 -- "CA" "8" 0 -1 0.0 -+ "CA" "44" 0 -1 0.0 - "HA" "12" 0 -1 0.0 -- "CB" "" 0 -1 0.0 -- "HB2" "" 0 -1 0.0 -- "HB3" "" 0 -1 0.0 -- "SG" "" 0 -1 0.0 -+ "CB" "45" 0 -1 0.0 -+ "HB2" "46" 0 -1 0.0 -+ "HB3" "46" 0 -1 0.0 -+ "SG" "49" 0 -1 0.0 - "C" "9" 0 -1 0.0 - "O" "11" 0 -1 0.0 - !entry.CYX.unit.boundbox array dbl -@@ -990,16 +990,16 @@ - "H" "10" 0 -1 0.0 - "CA" "8" 0 -1 0.0 - "HA" "12" 0 -1 0.0 -- "CB" "" 0 -1 0.0 -- "HB2" "" 0 -1 0.0 -- "HB3" "" 0 -1 0.0 -- "CG" "" 0 -1 0.0 -- "HG2" "" 0 -1 0.0 -- "HG3" "" 0 -1 0.0 -- "CD" "" 0 -1 0.0 -- "OE1" "" 0 -1 0.0 -- "OE2" "" 0 -1 0.0 -- "HE2" "" 0 -1 0.0 -+ "CB" "144" 0 -1 0.0 -+ "HB2" "145" 0 -1 0.0 -+ "HB3" "145" 0 -1 0.0 -+ "CG" "146" 0 -1 0.0 -+ "HG2" "147" 0 -1 0.0 -+ "HG3" "147" 0 -1 0.0 -+ "CD" "148" 0 -1 0.0 -+ "OE1" "149" 0 -1 0.0 -+ "OE2" "149" 0 -1 0.0 -+ "HE2" "10" 0 -1 0.0 - "C" "9" 0 -1 0.0 - "O" "11" 0 -1 0.0 - !entry.GLH.unit.boundbox array dbl -@@ -2147,21 +2147,21 @@ - "H" "10" 0 -1 0.0 - "CA" "8" 0 -1 0.0 - "HA" "12" 0 -1 0.0 -- "CB" "" 0 -1 0.0 -- "HB2" "" 0 -1 0.0 -- "HB3" "" 0 -1 0.0 -- "CG" "" 0 -1 0.0 -- "HG2" "" 0 -1 0.0 -- "HG3" "" 0 -1 0.0 -- "CD" "" 0 -1 0.0 -- "HD2" "" 0 -1 0.0 -- "HD3" "" 0 -1 0.0 -- "CE" "" 0 -1 0.0 -- "HE2" "" 0 -1 0.0 -- "HE3" "" 0 -1 0.0 -- "NZ" "" 0 -1 0.0 -- "HZ2" "" 0 -1 0.0 -- "HZ3" "" 0 -1 0.0 -+ "CB" "159" 0 -1 0.0 -+ "HB2" "160" 0 -1 0.0 -+ "HB3" "160" 0 -1 0.0 -+ "CG" "161" 0 -1 0.0 -+ "HG2" "162" 0 -1 0.0 -+ "HG3" "162" 0 -1 0.0 -+ "CD" "163" 0 -1 0.0 -+ "HD2" "164" 0 -1 0.0 -+ "HD3" "164" 0 -1 0.0 -+ "CE" "165" 0 -1 0.0 -+ "HE2" "166" 0 -1 0.0 -+ "HE3" "166" 0 -1 0.0 -+ "NZ" "167" 0 -1 0.0 -+ "HZ2" "168" 0 -1 0.0 -+ "HZ3" "168" 0 -1 0.0 - "C" "9" 0 -1 0.0 - "O" "11" 0 -1 0.0 - !entry.LYN.unit.boundbox array dbl -diff -urN amber11.orig/dat/leap/parm/gaff.dat amber11/dat/leap/parm/gaff.dat ---- amber11.orig/dat/leap/parm/gaff.dat 2010-03-31 07:05:27.000000000 +0400 -+++ amber11/dat/leap/parm/gaff.dat 2011-03-08 16:38:44.000000000 +0300 -@@ -16,6 +16,7 @@ - cy 12.01 0.360 Sp3 carbons in square systems - cu 12.01 0.360 Sp2 carbons in triangle systems - cv 12.01 0.360 Sp2 carbons in square systems -+cz 12.01 0.360 Sp2 carbon in guanidine group - h1 1.008 0.135 H bonded to aliphatic carbon with 1 electrwd. group - h2 1.008 0.135 H bonded to aliphatic carbon with 2 electrwd. group - h3 1.008 0.135 H bonded to aliphatic carbon with 3 electrwd. group -@@ -852,11 +853,6 @@ - s6-ss 139.6 2.1180 SOURCE3 5 0.0209 - sh-sh 158.9 2.0580 SOURCE2 1 0.0000 - sh-ss 155.8 2.0670 SOURCE3 3 0.0029 --Si-c3 189.8 1.8928 SOURCE4 77 0.0061 --Si-ca 191.1 1.8898 SOURCE4 11 0.0028 --Si-ha 186.3 1.4887 SOURCE4 6 0.0040 --Si-oh 267.6 1.6792 SOURCE4 6 0.0035 --Si-os 287.7 1.6524 SOURCE4 22 0.0057 - s -s 169.0 2.0300 SOURCE3 1 0.0000 - s -s2 229.2 1.8970 SOURCE1 5 0.0000 - s -s4 152.8 2.0760 SOURCE3 4 0.0345 -@@ -1091,7 +1087,6 @@ - hc-c2-s6 54.150 115.450 SOURCE3 1 - hc-c2-sh 53.550 115.630 SOURCE3 1 - hc-c2-ss 54.900 115.620 SOURCE3 1 --hn-c2-n4 0.000 112.740 SOURCE3 1 - hx-c2-n4 48.420 113.030 SOURCE3 3 0.3873 - i -c2-i 60.960 117.940 SOURCE3 1 0.0000 - n1-c2-n1 73.610 124.150 HF/6-31G* 1 -@@ -1464,9 +1459,6 @@ - s6-c3-s6 102.050 111.750 SOURCE3 1 0.0000 - sh-c3-sh 97.420 116.260 SOURCE3 1 0.0000 - sh-c3-ss 99.850 110.730 SOURCE3 1 --Si-c3-c3 74.610 114.340 SOURCE4 26 1.1613 --Si-c3-h1 51.040 110.900 SOURCE4 17 1.0270 --Si-c3-hc 50.960 111.210 SOURCE4 222 0.4865 - s -c3-s 93.400 123.350 SOURCE3 1 0.0000 - ss-c3-ss 99.950 110.570 SOURCE4 15 1.4311 - br-ca-br 67.310 117.600 SOURCE3 1 -@@ -1500,7 +1492,6 @@ - ca-ca-i 58.590 118.470 SOURCE3 10 0.6181 - ca-ca-n1 68.920 118.500 HF/6-31G* 1 - ca-ca-n2 70.950 119.570 SOURCE3 1 --ca-ca-n3 0.000 121.190 SOURCE3 1 - ca-ca-n4 67.280 118.410 SOURCE3 6 0.1691 - ca-ca-n 67.970 119.890 SOURCE3 18 0.2095 - ca-ca-na 70.210 118.340 SOURCE3 54 3.6168 -@@ -1540,7 +1531,6 @@ - cf-ca-nb 68.080 118.140 SOURCE4 12 1.1775 - cg-ca-cp 65.330 121.530 SOURCE4 12 0.1831 - c -ca-ha 46.510 115.900 SOURCE3 1 --c -ca-hc 0.000 120.000 SOURCE3 1 - cl-ca-cl 62.630 118.720 SOURCE3 1 - cl-ca-cp 62.600 120.310 SOURCE4 18 0.5607 - cl-ca-nb 65.810 116.150 SOURCE4 50 0.6047 -@@ -1606,7 +1596,6 @@ - s4-ca-s4 104.060 105.810 SOURCE3 1 - s6-ca-s6 105.770 105.810 SOURCE3 1 - sh-ca-sh 98.150 120.240 SOURCE3 1 --Si-ca-ca 73.850 121.430 SOURCE4 19 0.4235 - s -ca-s 98.380 125.140 SOURCE3 1 - ss-ca-ss 100.760 115.150 SOURCE3 1 - br-c -br 66.910 113.100 SOURCE3 1 -@@ -1636,7 +1625,6 @@ - c3-c -n 67.860 115.150 SOURCE3 153 2.7443 - c3-c -ne 68.090 111.390 SOURCE4 11 2.1430 - c3-c -nf 67.430 113.380 SOURCE3 1 same_as_c3-c-ne --c3-c -nh 0.000 113.580 SOURCE3 1 - c3-c -o 68.030 123.110 SOURCE3 267 3.0977 - c3-c -oh 69.840 112.200 SOURCE3 14 1.8324 - c3-c -os 69.260 111.960 SOURCE3 15 2.3072 -@@ -1832,7 +1820,6 @@ - ha-cc-os 52.490 110.860 SOURCE3 7 1.3846 - ha-cc-pd 42.350 121.760 SOURCE3 84 same_as_ha-cd-pc - ha-cc-ss 53.490 121.640 SOURCE2 5 1.3276 --c -c -hc 0.000 117.080 SOURCE3 1 - ch-c -ch 65.440 115.380 SOURCE3 1 same_as_cg-c-cg - ch-c -ha 47.800 113.900 SOURCE2 1 same_as_cg-c-ha - ch-c -o 70.210 122.310 SOURCE3 2 same_as_cg-c-o -@@ -2183,7 +2170,6 @@ - c -cf-n 66.600 116.790 SOURCE4 8 0.8255 - c -cf-nh 65.940 122.760 SOURCE3 1 same_as_c-ce-nh - f -c -f 72.220 107.350 SOURCE2 2 0.2500 --f -c -h 0.000 109.900 SOURCE2 1 0.0000 - h4-cf-n2 52.210 122.140 SOURCE4 11 0.9297 - h4-cf-ne 52.280 120.210 SOURCE4 6 0.8104 - ha-cf-n1 52.480 115.960 SOURCE3 2 3.5425 -@@ -2239,34 +2225,20 @@ - cf-ch-cg 57.400 177.900 SOURCE4 8 0.4883 - cf-ch-n1 59.370 178.120 SOURCE4 22 1.5200 - cg-ch-ch 58.680 179.670 SOURCE4 7 0.1439 --hc-c -hc 0.000 115.680 SOURCE3 1 --hc-c -n 0.000 120.000 SOURCE3 1 --hc-c -nh 0.000 112.700 SOURCE3 1 --hc-c -o 0.000 120.000 SOURCE3 1 --hc-c -oh 0.000 113.700 SOURCE3 1 --hc-c -os 0.000 113.580 SOURCE3 1 - n1-ch-nf 64.660 176.170 SOURCE2 3 same_as_n1-cg-ne --h -c -o 0.000 127.300 SOURCE2 1 0.0000 - i -c -i 59.790 116.450 SOURCE3 1 0.0000 - i -c -o 55.510 122.020 SOURCE3 4 1.2961 - f -cl-f 50.000 87.500 SOURCE2 1 estimated_force_constant - n2-c -n2 71.830 110.310 SOURCE3 1 --n2-c -na 0.000 118.600 SOURCE3 1 - n2-c -o 73.020 122.500 SOURCE3 1 --n3-c -n3 0.000 112.980 SOURCE3 1 --n3-c -o 0.000 122.260 SOURCE3 1 - n4-c -n4 64.710 114.640 SOURCE3 1 0.0000 - n4-c -o 69.580 118.830 SOURCE3 4 3.8516 --na-c -na 0.000 115.400 SOURCE3 1 --na-c -o 0.000 122.850 SOURCE3 1 - nc-c -o 74.050 123.980 SOURCE4 66 0.9502 - nd-c -o 73.720 121.760 SOURCE4 55 1.1138 - ne-c -ne 73.220 110.310 SOURCE3 1 0.0000 - ne-c -o 72.940 126.030 SOURCE4 39 0.9885 - nf-c -nf 73.070 110.310 SOURCE3 1 same_as_ne-c-ne - nf-c -o 73.320 124.390 SOURCE3 3 same_as_ne-c-o --nh-c -nh 0.000 110.980 SOURCE3 1 --nh-c -o 0.000 124.620 SOURCE3 1 - n -c -n 74.800 113.380 SOURCE4 635 1.4358 - n -c -nc 72.690 117.050 SOURCE4 54 0.7020 - n -c -nd 71.900 117.060 SOURCE4 23 0.9856 -@@ -2318,10 +2290,10 @@ - py-c -py 57.520 123.800 SOURCE3 1 0.0000 - ca-cq-ca 67.000 118.240 SOURCE4 5 0.2181 - ca-cq-cq 64.220 120.410 SOURCE4 12 1.4029 --ca-cq-nb 0.000 122.970 SOURCE3 2 0.0000 -+ca-cq-nb 69.270 121.650 SOURCE4 63 same as ca-cp-nb - cp-cq-cq 62.640 124.470 SOURCE4 5 1.0864 - cq-cq-cq 72.200 90.000 SOURCE3 4 0.0000 --cq-cq-nb 0.000 116.430 SOURCE3 2 0.0000 -+cq-cq-nb 68.050 116.600 SOURCE4 88 same as cp-cp-nb - s4-c -s4 98.110 108.810 SOURCE3 1 - s6-c -s6 95.130 115.750 SOURCE3 1 - sh-c -sh 100.060 115.330 SOURCE3 1 0.0000 -@@ -2454,9 +2426,6 @@ - n -cy-s6 82.570 103.450 SOURCE4 6 0.7197 - n -cy-ss 82.030 105.120 SOURCE4 69 0.3987 - nh-cz-nh 72.970 120.170 SOURCE4 26 0.3964 --ca-i -cl 0.000 90.210 SOURCE3 2 estimated_force_constant --ca-i -o 0.000 97.080 SOURCE3 5 0.2233,estimated_force_constant --cl-i -cl 0.000 179.580 SOURCE3 1 estimated_force_constant - br-n1-c1 51.100 180.000 HF/6-31G* 1 - c1-n1-c1 64.910 179.920 HF/6-31G* 1 - c1-n1-c2 60.250 177.730 HF/6-31G* 1 -@@ -2729,7 +2698,6 @@ - c2-n3-c2 66.220 124.680 SOURCE3 1 - c2-n3-hn 49.110 119.380 SOURCE3 1 - c3-n3-c3 64.010 110.900 SOURCE3 40 2.3048 --c3-n3-ca 0.000 116.390 SOURCE3 1 - c3-n3-cl 62.170 107.230 SOURCE3 3 0.3673 - c3-n3-cx 62.450 116.320 SOURCE4 24 0.5119 - c3-n3-cy 61.690 118.260 SOURCE4 14 0.8788 -@@ -2753,7 +2721,6 @@ - c3-n3-sh 78.550 112.700 SOURCE3 1 0.0000 - c3-n3-ss 77.950 116.010 SOURCE3 3 1.1944 - c3-n3-sy 79.010 115.270 SOURCE4 108 1.7647 --c -n3-c 0.000 127.170 SOURCE3 1 - cl-n3-cl 61.850 108.280 SOURCE3 1 0.0000 - cl-n3-hn 42.590 104.390 SOURCE3 2 0.0000 - cl-n3-n3 63.750 107.650 SOURCE3 1 0.0000 -@@ -2824,7 +2791,6 @@ - c1-n4-hn 48.620 110.190 SOURCE3 7 1.0847 - c2-n4-c2 63.010 112.580 SOURCE3 1 0.0000 - c2-n4-c3 63.100 110.960 SOURCE4 13 2.4632 --c2-n4-h4 0.000 112.460 SOURCE3 1 - c2-n4-hn 46.430 111.360 SOURCE3 13 1.2672 - c3-n4-c3 62.840 110.640 SOURCE3 13 1.3060 - c3-n4-ca 63.610 110.400 SOURCE4 46 1.4643 -@@ -3002,10 +2968,6 @@ - ca-na-s 75.010 125.640 SOURCE3 1 - ca-na-sh 76.630 125.440 SOURCE3 1 - ca-na-ss 74.880 129.910 SOURCE4 8 0.1449 --c -na-c 0.000 126.400 SOURCE3 1 --c -na-c2 0.000 125.090 SOURCE3 1 --c -na-c3 0.000 117.600 SOURCE3 1 --c -na-ca 0.000 125.200 SOURCE3 1 - cc-na-cc 68.940 109.900 SOURCE3 109 1.5547 - cc-na-cd 63.880 128.010 SOURCE3 1 0.0000 - cc-na-ce 63.050 126.610 SOURCE4 8 0.5158 -@@ -3058,7 +3020,6 @@ - cd-na-s 74.800 125.660 SOURCE3 8 0.1880 - cd-na-sh 76.830 123.960 SOURCE3 10 0.3424 - cd-na-ss 77.930 119.180 SOURCE3 36 5.0538 --c -na-hn 0.000 118.000 SOURCE3 1 - cl-na-cl 56.330 122.800 SOURCE3 1 - cl-na-nc 59.890 119.360 SOURCE3 4 1.7128 - cl-na-nd 59.890 119.360 SOURCE3 4 same_as_cl-na-nc -@@ -3067,7 +3028,6 @@ - cl-na-pc 58.780 120.510 SOURCE3 3 2.1985 - cl-na-pd 58.780 120.510 SOURCE3 3 same_as_cl-na-pc - cl-na-ss 77.180 111.910 SOURCE3 1 0.0000 --c -na-n 0.000 124.660 SOURCE3 1 - f -na-f 62.220 120.200 SOURCE3 1 - f -na-nc 66.640 118.050 SOURCE3 4 1.7931 - f -na-nd 66.640 118.050 SOURCE3 4 same_as_f-na-nc -@@ -3231,7 +3191,7 @@ - sy-na-sy 96.930 123.200 SOURCE3 1 - ca-nb-ca 68.590 115.860 SOURCE3 46 1.1645 - ca-nb-cp 68.010 118.040 SOURCE4 58 0.7819 --ca-nb-cq 0.000 117.040 SOURCE3 2 0.0000 -+ca-nb-cq 68.010 118.040 SOURCE4 58 same as ca-nb-cp - ca-nb-nb 69.370 118.890 SOURCE3 10 0.6031 - cp-nb-nb 68.790 121.110 SOURCE4 12 0.4315 - nb-nb-nb 70.440 121.040 SOURCE3 1 0.0000 -@@ -3597,8 +3557,6 @@ - ca-nh-sh 78.190 121.410 SOURCE3 1 0.0000 - ca-nh-ss 78.160 121.500 SOURCE3 3 2.6255 - ca-nh-sy 76.750 125.260 SOURCE4 41 1.7517 --c -nh-c 0.000 119.570 SOURCE3 1 --c -nh-ca 0.000 123.570 SOURCE3 1 - cc-nh-cx 63.320 122.820 SOURCE4 42 1.1841 - cc-nh-hn 48.860 117.160 SOURCE3 11 2.6137 - cc-nh-n2 68.230 119.660 SOURCE4 5 1.3903 -@@ -3610,10 +3568,8 @@ - ce-nh-sy 80.450 112.970 SOURCE4 7 1.0636 - cf-nh-hn 48.620 115.620 SOURCE4 16 1.3549 - cf-nh-o 67.070 129.430 SOURCE3 1 same_as_ce-nh-o --c -nh-hn 0.000 115.730 SOURCE3 1 - cl-nh-cl 62.930 106.600 SOURCE3 1 - cl-nh-hn 43.080 104.140 SOURCE3 1 0.0000 --c -nh-n4 0.000 111.350 SOURCE3 1 - cx-nh-cx 86.530 62.020 SOURCE4 45 0.6189 - cx-nh-hn 45.790 118.890 SOURCE4 8 0.1391 - cz-nh-hn 48.790 121.240 SOURCE4 40 0.5682 -@@ -3783,7 +3739,6 @@ - ho-oh-sh 54.390 106.240 SOURCE3 2 0.0661 - ho-oh-ss 54.540 107.060 SOURCE3 4 0.9967 - ho-oh-sy 55.940 106.410 SOURCE4 33 0.3729 --Si-oh-ho 52.570 115.710 SOURCE4 5 0.1738 - br-os-br 65.080 110.630 SOURCE3 1 0.0000 - c1-os-c1 66.990 115.020 SOURCE3 1 0.0000 - c1-os-c3 64.470 113.390 SOURCE3 1 0.0000 -@@ -3892,7 +3847,6 @@ - s4-os-s4 99.450 111.630 SOURCE3 1 0.0000 - s6-os-s6 103.740 119.070 SOURCE3 2 0.4318 - sh-os-sh 97.950 118.950 SOURCE3 1 0.0000 --Si-os-c3 74.830 124.640 SOURCE4 9 0.2879 - s -os-s 91.270 118.080 SOURCE3 1 0.0000 - ss-os-ss 97.420 115.640 SOURCE3 1 0.0000 - br-p2-br 65.020 108.600 SOURCE3 1 -@@ -4615,7 +4569,6 @@ - f -s4-f 43.790 92.710 SOURCE2 3 0.1490 - f -s4-o 43.870 106.810 SOURCE2 2 0.0100 - f -s4-s 47.340 107.500 SOURCE2 1 0.0000 --hn-s4-hs 0.000 86.990 SOURCE3 1 - hs-s4-hs 23.650 87.000 SOURCE3 2 0.0202 - hs-s4-n1 32.050 90.510 HF/6-31G* 1 - hs-s4-o 31.160 110.270 SOURCE3 5 0.1908 -@@ -4789,12 +4742,6 @@ - hs-sh-s6 33.980 93.830 SOURCE3 3 1.2561 - hs-sh-sh 33.890 99.070 SOURCE3 2 0.0000 - hs-sh-ss 33.730 99.170 SOURCE3 3 0.2457 --c3-Si-c3 34.810 109.820 SOURCE4 88 0.5569 --c3-Si-ca 34.800 110.090 SOURCE4 26 0.7331 --c3-Si-oh 38.160 107.440 SOURCE4 8 1.5150 --c3-Si-os 38.140 108.750 SOURCE4 38 0.7301 --ha-Si-ha 19.530 108.770 SOURCE4 5 0.5372 --os-Si-os 42.630 108.350 SOURCE4 15 1.7995 - br-ss-br 41.920 102.920 SOURCE3 1 0.0000 - br-ss-c3 39.460 99.030 SOURCE3 1 0.0000 - c1-ss-c1 41.480 98.300 SOURCE2 1 0.0000 -@@ -4813,7 +4760,6 @@ - c3-ss-cl 37.940 99.400 SOURCE2 1 0.0000 - c3-ss-cy 38.750 94.320 SOURCE4 62 0.3646 - c3-ss-f 39.670 97.490 SOURCE3 1 0.0000 --c3-ss-ha 0.000 96.500 SOURCE2 1 0.0000 - c3-ss-i 35.060 100.000 SOURCE3 1 0.0000 - c3-ss-n1 41.250 98.440 HF/6-31G* 1 - c3-ss-n2 41.260 96.420 SOURCE3 5 1.3604 -@@ -5883,7 +5829,7 @@ - were replaced with those newly generated. Here are the numbers: - - Bond length: 59 low quality parameters were replaced and 56 new parameters --were introduced. $j -+were introduced. - - Bond angle: 437 low quality parameters were replaced and 618 new - parameters were introduced. diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_1-3.patch b/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_1-3.patch deleted file mode 100644 index 1aebcabce..000000000 --- a/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_1-3.patch +++ /dev/null @@ -1,3831 +0,0 @@ -diff -urN amber11//AmberTools/src/cpptraj/src/Action_Center.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Center.cpp ---- amber11//AmberTools/src/cpptraj/src/Action_Center.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Action_Center.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -72,7 +72,7 @@ - // else - // mass = NULL; - -- if (!origin && P->ifbox==0) { -+ if (!origin && P->BoxType==0) { - mprintf(" Error: Center::setup: Box center specified but no box information.\n"); - //fprintf(stdout," Centering on origin.\n"); - return 1; -diff -urN amber11//AmberTools/src/cpptraj/src/Action_Closest.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Closest.cpp ---- amber11//AmberTools/src/cpptraj/src/Action_Closest.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Action_Closest.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -181,8 +181,8 @@ - // NOTE: Should box be figured out from read-in coords? - imageType = 0; - if (!noimage) { -- imageType = P->ifbox; -- if (P->ifbox==0) { -+ imageType = P->BoxType; -+ if (P->BoxType==0) { - mprintf(" Warning: Closest::setup: "); - mprintf(" Imaging specified but no box information in prmtop %s\n",P->parmName); - mprintf(" No imaging can occur..\n"); -diff -urN amber11//AmberTools/src/cpptraj/src/Action_Distance.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Distance.cpp ---- amber11//AmberTools/src/cpptraj/src/Action_Distance.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Action_Distance.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -68,6 +68,11 @@ - return 0; - } - -+/* -+ * Distance::setup() -+ * Determine what atoms each mask pertains to for the current parm file. -+ * Also determine whether imaging should be performed. -+ */ - int Distance::setup() { - - if ( Mask1.SetupMask(P,debug) ) return 1; -@@ -89,8 +94,8 @@ - // Check imaging - check box based on prmtop box - imageType = 0; - if (!noimage) { -- imageType = P->ifbox; -- if (P->ifbox==0 && debug>0) { -+ imageType = P->BoxType; -+ if (P->BoxType==0 && debug>0) { - mprintf(" Warning: No box info in %s, disabling imaging.\n",P->parmName); - } - } -diff -urN amber11//AmberTools/src/cpptraj/src/Action_Image.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Image.cpp ---- amber11//AmberTools/src/cpptraj/src/Action_Image.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Action_Image.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -98,14 +98,14 @@ - useMass = false; - } - -- if (P->ifbox==0) { -+ if (P->BoxType==0) { - mprintf(" Error: Image::setup: Parm %s does not contain box information.\n", - P->parmName); - return 1; - } - - ortho = false; -- if (P->ifbox==1 && triclinic==OFF) ortho=true; -+ if (P->BoxType==1 && triclinic==OFF) ortho=true; - - if (triclinic == FAMILIAR) { - if (ComMask!=NULL) { -diff -urN amber11//AmberTools/src/cpptraj/src/Action_Outtraj.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Outtraj.cpp ---- amber11//AmberTools/src/cpptraj/src/Action_Outtraj.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Action_Outtraj.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -6,6 +6,9 @@ - // CONSTRUCTOR - Outtraj::Outtraj() { - //fprintf(stderr,"Outtraj Con\n"); -+ min=0.0; -+ max=0.0; -+ Dset=NULL; - } - - // DESTRUCTOR -@@ -13,11 +16,40 @@ - - /* - * Outtraj::init() -- * Action wrapper for trajout -+ * Action wrapper for trajout. -+ * Expected call: outtraj <filename> [ trajout args ] -+ * [maxmin <dataset> min <min> max <max> - */ - int Outtraj::init() { -+ char *datasetName; -+ -+#ifdef MPI -+ mprintf("ERROR: OUTTRAJ currently not functional with MPI.\n"); -+ return 1; -+#endif -+ -+ mprintf(" OUTTRAJ: Will write to [%s]\n",A->Arg(1)); -+ outtraj.SetDebug(debug); -+ // If maxmin, get the name of the dataset as well as the max and min values. -+ datasetName = A->getKeyString("maxmin",NULL); -+ if (datasetName!=NULL) { -+ Dset = DSL->Get(datasetName); -+ if (Dset==NULL) { -+ mprintf("Error: Outtraj maxmin: Could not get dataset %s\n",datasetName); -+ return 1; -+ } else { -+ // Currently dont allow for string datasets -+ if (Dset->Type()==STRING) { -+ mprintf("Error: Outtraj maxmin: String dataset (%s) not supported.\n",datasetName); -+ return 1; -+ } -+ max = A->getKeyDouble("max",0.0); -+ min = A->getKeyDouble("min",0.0); -+ mprintf(" maxmin: Printing trajectory frames based on %lf <= %s <= %lf\n", -+ min, datasetName, max); -+ } -+ } - -- mprintf(" OUTTRAJ: [%s]\n",A->ArgLine()); - return ( outtraj.Add(A,PFL,worldsize) ); - } - -@@ -33,8 +65,32 @@ - * Outtraj::action() - */ - int Outtraj::action() { -+ double dVal; -+ int iVal; - -- return ( outtraj.Write(currentFrame, F, P) ); -+ // If dataset defined, check if frame is within max/min -+ if (Dset!=NULL) { -+ if (Dset->Type() == DOUBLE) { -+ if (Dset->Get(&dVal, currentFrame)) return 1; -+ } else if (Dset->Type() == INT) { -+ if (Dset->Get(&iVal, currentFrame)) return 1; -+ dVal = (double) iVal; -+ } else -+ return 1; -+ //mprintf("DBG: maxmin: dVal = %lf\n",dVal); -+ // If value from dataset not within min/max, exit now. -+ if (dVal < min || dVal > max) return 0; -+ } -+ if ( outtraj.Write(currentFrame, F, P) != 0 ) return 1; -+ return 0; - } - -+/* -+ * Outtraj::print() -+ * Close trajectory. -+ */ -+void Outtraj::print() { -+ mprintf(" OUTTRAJ: [%s] Wrote %i frames.\n",A->Arg(1),outtraj.front()->CurrentFrame()); -+ outtraj.Close(); -+} - -diff -urN amber11//AmberTools/src/cpptraj/src/Action_Outtraj.h amber11.new//AmberTools/src/cpptraj/src/Action_Outtraj.h ---- amber11//AmberTools/src/cpptraj/src/Action_Outtraj.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Action_Outtraj.h 2011-05-19 18:35:57.000000000 +0300 -@@ -6,6 +6,9 @@ - - class Outtraj: public Action { - TrajoutList outtraj; -+ double max; -+ double min; -+ DataSet *Dset; - public: - Outtraj(); - ~Outtraj(); -@@ -13,5 +16,6 @@ - int init(); - //int setup(); - int action(); -+ void print(); - }; - #endif -diff -urN amber11//AmberTools/src/cpptraj/src/Action_Rms2d.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Rms2d.cpp ---- amber11//AmberTools/src/cpptraj/src/Action_Rms2d.cpp 1970-01-01 03:00:00.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Action_Rms2d.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -0,0 +1,71 @@ -+// Rms2d -+#include "Action_Rms2d.h" -+#include "CpptrajStdio.h" -+ -+// CONSTRUCTOR -+Rms2d::Rms2d() { -+ //fprintf(stderr,"Rms2d Con\n"); -+ nofit=false; -+ useMass=false; -+} -+ -+// DESTRUCTOR -+Rms2d::~Rms2d() { } -+ -+/* -+ * Rms2d::init() -+ * Expected call: rms2d <mask> <refmask> [rmsout filename] [mass] [nofit] -+ * Dataset name will be the last arg checked for. Check order is: -+ * 1) Keywords -+ * 2) Masks -+ * 3) Dataset name -+ */ -+int Rms2d::init() { -+ char *mask0, *maskRef; -+ -+ // Get keywords -+ nofit = A->hasKey("nofit"); -+ useMass = A->hasKey("mass"); -+ rmsdFile = A->getKeyString("rmsout",NULL); -+ -+ // Get the RMS mask string for frames -+ mask0 = A->getNextMask(); -+ FrameMask.SetMaskString(mask0); -+ // Get RMS mask string for reference -+ maskRef = A->getNextMask(); -+ // If no reference mask specified, make same as RMS mask -+ if (maskRef==NULL) maskRef=mask0; -+ RefMask.SetMaskString(maskRef); -+ -+ mprintf(" RMS2D: (%s) to (%s)",FrameMask.maskString,RefMask.maskString); -+ if (nofit) -+ mprintf(" (no fitting)"); -+ if (useMass) -+ mprintf(" (mass-weighted)"); -+ if (rmsdFile!=NULL) -+ mprintf(" output to %s",rmsdFile); -+ mprintf("\n"); -+ -+ return 0; -+} -+ -+/* -+ * Rms2d::setup() -+ * Not important for Rms2d, initial pass is only for storing frames. -+ */ -+int Rms2d::setup() { -+ return 0; -+} -+ -+/* -+ * Rms2d::action() -+ * Store current frame as a reference frame. -+ */ -+int Rms2d::action() { -+ -+ ReferenceFrames.Add(F,P); -+ -+ return 0; -+} -+ -+ -diff -urN amber11//AmberTools/src/cpptraj/src/Action_Rms2d.h amber11.new//AmberTools/src/cpptraj/src/Action_Rms2d.h ---- amber11//AmberTools/src/cpptraj/src/Action_Rms2d.h 1970-01-01 03:00:00.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Action_Rms2d.h 2011-05-19 18:35:57.000000000 +0300 -@@ -0,0 +1,21 @@ -+#ifndef INC_ACTION_RMS2D_H -+#define INC_ACTION_RMS2D_H -+// Rms2d -+#include "Action.h" -+ -+class Rms2d: public Action { -+ FrameList ReferenceFrames; -+ bool nofit; -+ bool useMass; -+ AtomMask RefMask; -+ AtomMask FrameMask; -+ char *rmsdFile; -+ public: -+ Rms2d(); -+ ~Rms2d(); -+ -+ int init(); -+ int setup(); -+ int action(); -+}; -+#endif -diff -urN amber11//AmberTools/src/cpptraj/src/AmberNetcdf.cpp amber11.new//AmberTools/src/cpptraj/src/AmberNetcdf.cpp ---- amber11//AmberTools/src/cpptraj/src/AmberNetcdf.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/AmberNetcdf.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -49,6 +49,7 @@ - * and close calls. - */ - void AmberNetcdf::close() { -+ if (ncid<0) return; - checkNCerr(nc_close(ncid),"Closing netcdf file."); - if (debug>0) rprintf("Successfully closed ncid %i\n",ncid); - ncid=-1; -@@ -92,8 +93,10 @@ - * Open the netcdf file, read all dimension and variable IDs, close. - */ - int AmberNetcdf::SetupRead() { -- char *attrText; // For checking conventions and version -- int spatial; // For checking spatial dimensions -+ char *attrText; // For checking conventions and version -+ int spatial; // For checking spatial dimensions -+ double box[6]; // For checking box type -+ size_t start[3], count[3]; // For checking box type - - if (open()) return 1; - -@@ -147,15 +150,15 @@ - if ( nc_inq_varid(ncid,"cell_lengths",&cellLengthVID)==NC_NOERR ) { - if (checkNCerr(nc_inq_varid(ncid,"cell_angles",&cellAngleVID), - "Getting cell angles.")!=0) return 1; -- if (debug>0) mprintf(" Netcdf Box information found.\n"); -- if (P->ifbox==0) { -- mprintf("Warning: Netcdf file contains box info but no box info found\n"); -- mprintf(" in associated parmfile %s; defaulting to orthogonal.\n", -- P->parmName); -- isBox=1; -- } else { -- isBox=P->ifbox; -- } -+ if (debug>0) mprintf(" Netcdf Box information found.\n"); -+ // Determine box type from angles -+ start[0]=0; start[1]=0; start[2]=0; -+ count[0]=1; count[1]=3; count[2]=0; -+ if ( checkNCerr(nc_get_vara_double(ncid, cellLengthVID, start, count, box), -+ "Getting cell lengths.")!=0 ) return 1; -+ if ( checkNCerr(nc_get_vara_double(ncid, cellAngleVID, start, count, box+3), -+ "Getting cell angles.")!=0 ) return 1; -+ CheckBoxType(box); - } - - // Replica Temperatures -@@ -258,7 +261,7 @@ - "Defining cell angular variable.")) return 1; - - // Box Info -- if (isBox>0) { -+ if (BoxType!=0) { - dimensionID[0]=frameDID; - dimensionID[1]=cell_spatialDID; - if (checkNCerr(nc_def_var(ncid,"cell_lengths",NC_DOUBLE,2,dimensionID,&cellLengthVID), -@@ -362,7 +365,7 @@ - "Getting frame %i",set)!=0 ) return 1; - - // Read box info -- if (isBox!=0) { -+ if (BoxType!=0) { - count [1]=3; - count [2]=0; - if ( checkNCerr(nc_get_vara_double(ncid, cellLengthVID, start, count, F->box), -@@ -399,7 +402,7 @@ - F->frameToFloat(Coord); - - // write coords -- start[0]=set; -+ start[0]=currentFrame; - start[1]=0; - start[2]=0; - count[0]=1; -@@ -409,7 +412,7 @@ - "Netcdf Writing frame %i",set)) return 1; - - // write box -- if (isBox>0 && cellLengthVID!=-1) { -+ if (BoxType!=0 && cellLengthVID!=-1) { - count[1]=3; - count[2]=0; - if (checkNCerr(nc_put_vara_double(ncid,cellLengthVID,start,count,F->box), -@@ -427,6 +430,8 @@ - - nc_sync(ncid); // Necessary after every write?? - -+ currentFrame++; -+ - return 0; - } - -diff -urN amber11//AmberTools/src/cpptraj/src/AmberParm.cpp amber11.new//AmberTools/src/cpptraj/src/AmberParm.cpp ---- amber11//AmberTools/src/cpptraj/src/AmberParm.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/AmberParm.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -1,6 +1,12 @@ - /* AmberParm.cpp -- * Class that holds parameter information. Can be read in from Amber Topology -- * or PDB files. -+ * Class that holds parameter information. Can be read in from Amber Topology, -+ * PDB, or Mol2 files (implemented in the ReadParmXXX functions). The following -+ * parameters of AmberParm must always be set: -+ * The NATOM, NRES, and IFBOX entries of the values array. -+ * The names, resnames, resnums arrays. -+ * The natom and nres variables. -+ * NOTES: -+ * Eventually make the mol2 read parm function use the AddBond function. - */ - #include <cstdlib> - #include <cstring> -@@ -11,7 +17,7 @@ - #include "CpptrajStdio.h" - - #define AMBERPOINTERS 31 -- -+#define TRUNCOCTBETA 109.4712206344906917365733534097672 - #define ELECTOAMBER 18.2223 - #define AMBERTOELEC 1/ELECTOAMBER - // ============================================================= -@@ -203,7 +209,9 @@ - bondsh=NULL; - types=NULL; - atomsPerMol=NULL; -- Box=NULL; -+ Box[0]=0.0; Box[1]=0.0; Box[2]=0.0; -+ Box[3]=0.0; Box[4]=0.0; Box[5]=0.0; -+ BoxType=0; - pindex=0; - parmFrames=0; - outFrame=0; -@@ -217,7 +225,6 @@ - solventMoleculeStop=NULL; - natom=0; - nres=0; -- ifbox=0; - parmName=NULL; - SurfaceInfo=NULL; - } -@@ -234,7 +241,6 @@ - if (bonds!=NULL) free(bonds); - if (bondsh!=NULL) free(bondsh); - if (atomsPerMol!=NULL) free(atomsPerMol); -- if (Box!=NULL) free(Box); - if (solventMoleculeStart!=NULL) free(solventMoleculeStart); - if (solventMoleculeStop!=NULL) free(solventMoleculeStop); - if (solventMask!=NULL) free(solventMask); -@@ -271,54 +277,7 @@ - return NULL; - } - --/* -- * AmberParm::OpenParm() -- * Attempt to open file and read in parameters. -- */ --int AmberParm::OpenParm(char *filename) { -- if ( File.SetupFile(filename,READ,UNKNOWN_FORMAT, UNKNOWN_TYPE,debug) ) return 1; -- -- // Copy parm filename to parmName. Separate from File.filename in case of stripped parm -- parmName=(char*) malloc( (strlen(File.basefilename)+1) * sizeof(char)); -- strcpy(parmName,File.basefilename); -- -- if ( File.OpenFile() ) return 1; -- -- switch (File.fileFormat) { -- case AMBERPARM : if (ReadParmAmber()) return 1; break; -- case PDBFILE : if (ReadParmPDB() ) return 1; break; -- case MOL2FILE : if (ReadParmMol2() ) return 1; break; -- default: -- rprintf("Unknown parameter file type: %s\n",File.filename); -- return 1; -- } -- -- File.CloseFile(); -- -- // Create a last dummy residue in resnums that holds natom, which would be -- // the atom number of the next residue if it existed. Atom #s in resnums -- // should correspond with cpptraj atom #s (start from 0) instead of Amber -- // atom #s (start from 1). -- // Do this to be consistent with ptrajmask selection behavior - saves an -- // if-then statement. -- resnums=(int*) realloc(resnums,(nres+1)*sizeof(int)); -- resnums[nres]=natom; -- // DEBUG -- //fprintf(stdout,"==== DEBUG ==== Resnums for %s:\n",File.filename); -- //for (err=0; err<nres; err++) -- // fprintf(stdout," %i: %i\n",err,resnums[err]); -- -- // Set up solvent information -- SetSolventInfo(); -- -- if (debug>0) { -- mprintf(" Number of atoms= %i\n",natom); -- mprintf(" Number of residues= %i\n",nres); -- } -- -- return 0; --} -- -+// ---------========= ROUTINES PERTAINING TO SURFACE AREA =========--------- - /* - * AmberParm::AssignLCPO() - * Assign parameters for LCPO method. All radii are incremented by 1.4 Ang. -@@ -478,6 +437,7 @@ - return 0; - } - -+// ---------========= ROUTINES PERTAINING TO SOLVENT INFO =========--------- - /* - * AmberParm::SetSolventInfo() - * Assuming atomsPerMol has been read in, set solvent information. -@@ -536,7 +496,56 @@ - - return 0; - } -- -+ -+// --------========= ROUTINES PERTAINING TO READING PARAMETERS =========-------- -+/* -+ * AmberParm::OpenParm() -+ * Attempt to open file and read in parameters. -+ */ -+int AmberParm::OpenParm(char *filename) { -+ if ( File.SetupFile(filename,READ,UNKNOWN_FORMAT, UNKNOWN_TYPE,debug) ) return 1; -+ -+ // Copy parm filename to parmName. Separate from File.filename in case of stripped parm -+ parmName=(char*) malloc( (strlen(File.basefilename)+1) * sizeof(char)); -+ strcpy(parmName,File.basefilename); -+ -+ if ( File.OpenFile() ) return 1; -+ -+ switch (File.fileFormat) { -+ case AMBERPARM : if (ReadParmAmber()) return 1; break; -+ case PDBFILE : if (ReadParmPDB() ) return 1; break; -+ case MOL2FILE : if (ReadParmMol2() ) return 1; break; -+ default: -+ rprintf("Unknown parameter file type: %s\n",File.filename); -+ return 1; -+ } -+ -+ File.CloseFile(); -+ -+ // Create a last dummy residue in resnums that holds natom, which would be -+ // the atom number of the next residue if it existed. Atom #s in resnums -+ // should correspond with cpptraj atom #s (start from 0) instead of Amber -+ // atom #s (start from 1). -+ // Do this to be consistent with ptrajmask selection behavior - saves an -+ // if-then statement. -+ resnums=(int*) realloc(resnums,(nres+1)*sizeof(int)); -+ resnums[nres]=natom; -+ // DEBUG -+ //fprintf(stdout,"==== DEBUG ==== Resnums for %s:\n",File.filename); -+ //for (err=0; err<nres; err++) -+ // fprintf(stdout," %i: %i\n",err,resnums[err]); -+ -+ // Set up solvent information -+ SetSolventInfo(); -+ -+ if (debug>0) { -+ mprintf(" Number of atoms= %i\n",natom); -+ mprintf(" Number of residues= %i\n",nres); -+ } -+ -+ return 0; -+} -+ - /* - * AmberParm::ReadParmAmber() - * Read parameters from Amber Topology file -@@ -544,6 +553,7 @@ - int AmberParm::ReadParmAmber() { - int err, atom; - int *solvent_pointer; -+ double *boxFromParm; - - if (debug>0) mprintf("Reading Amber Topology file %s\n",parmName); - -@@ -555,7 +565,6 @@ - - natom=values[NATOM]; - nres=values[NRES]; -- ifbox=values[IFBOX]; - if (debug>0) - mprintf(" Amber top contains %i atoms, %i residues.\n",natom,nres); - -@@ -583,7 +592,8 @@ - if (bonds==NULL) {mprintf("Error in bonds w/o H.\n"); err++;} - bondsh=(int*) getFlagFileValues("BONDS_INC_HYDROGEN",values[NBONH]*3); - if (bondsh==NULL) {mprintf("Error in bonds inc H.\n"); err++;} -- if (ifbox>0) { -+ // Get solvent info if IFBOX>0 -+ if (values[IFBOX]>0) { - solvent_pointer=(int*) getFlagFileValues("SOLVENT_POINTERS",3); - if (solvent_pointer==NULL) { - mprintf("Error in solvent pointers.\n"); -@@ -596,12 +606,20 @@ - } - atomsPerMol=(int*) getFlagFileValues("ATOMS_PER_MOLECULE",molecules); - if (atomsPerMol==NULL) {mprintf("Error in atoms per molecule.\n"); err++;} -- Box=(double*) getFlagFileValues("BOX_DIMENSIONS",4); -- if (Box==NULL) {mprintf("Error in Box information.\n"); err++;} -+ // boxFromParm = {OLDBETA, BOX(1), BOX(2), BOX(3)} -+ boxFromParm=(double*) getFlagFileValues("BOX_DIMENSIONS",4); -+ if (boxFromParm==NULL) {mprintf("Error in Box information.\n"); err++;} -+ // Determine box type: 1-Ortho, 2-Nonortho -+ SetBoxInfo(boxFromParm[0],boxFromParm[1],boxFromParm[2],boxFromParm[3]); -+ free(boxFromParm); - if (debug>0) { - mprintf(" %s contains box info: %i mols, first solvent mol is %i\n", - parmName, molecules, firstSolvMol); -- mprintf(" BOX: %lf %lf %lf %lf\n",Box[0],Box[1],Box[2],Box[3]); -+ mprintf(" BOX: %lf %lf %lf | %lf %lf %lf\n",Box[0],Box[1],Box[2],Box[3],Box[4],Box[5]); -+ if (BoxType==1) -+ mprintf(" Box is orthogonal.\n"); -+ else -+ mprintf(" Box is non-orthogonal.\n"); - } - } - -@@ -686,6 +704,7 @@ - values = (int*) calloc(AMBERPOINTERS, sizeof(int)); - values[NATOM] = natom; - values[NRES] = nres; -+ values[IFBOX] = 0; - - if (debug>0) - mprintf(" PDB contains %i atoms, %i residues, %i molecules.\n", -@@ -799,6 +818,7 @@ - values[NRES] = nres; - values[NBONH] = numbondsh; - values[MBONA] = numbonds; -+ values[IFBOX] = 0; - - mprintf(" Mol2 contains %i atoms, %i residues,\n", natom,nres); - mprintf(" %i bonds to H, %i other bonds.\n", numbondsh,numbonds); -@@ -806,6 +826,61 @@ - return 0; - } - -+// ---------===========================================================--------- -+/* -+ * AmberParm::SetBoxInfo() -+ * Given 3 box lengths and an angle determine the box type and set -+ * the box information. If called with negative beta, set no box. -+ * Currently recognized betas: -+ * 90.00 - Orthogonal -+ * 109.47 - Truncated octahedral -+ * 60.00 - Rhombic dodecahedron -+ * Any other beta just sets all angles to beta and a warning is printed. -+ */ -+int AmberParm::SetBoxInfo(double beta, double bx, double by, double bz) { -+ int ifbox=0; -+ -+ // Determine box type from beta (none, ortho, non-ortho (truncated oct/triclinic) -+ if (beta<=0.0) { -+ if (BoxType>0) -+ mprintf(" %s: Removing box information.\n",parmName); -+ BoxType=0; -+ ifbox=0; -+ Box[0]=0.0; Box[1]=0.0; Box[2]=0.0; -+ Box[3]=0.0; Box[4]=0.0; Box[5]=0.0; -+ } else if (beta == 90.0) { -+ BoxType=1; -+ ifbox=1; -+ Box[0]=bx; Box[1]=by; Box[2]=bz; -+ Box[3]=90.0; Box[4]=90.0; Box[5]=90.0; -+ if (debug>0) mprintf(" %s: Setting box to be orthogonal.\n",parmName); -+ } else if (beta > 109.47 && beta < 109.48) { -+ BoxType=2; -+ ifbox=2; -+ Box[0]=bx; Box[1]=by; Box[2]=bz; -+ //Box[3] = TRUNCOCTBETA; -+ Box[3] = beta; -+ Box[4]=Box[3]; Box[5]=Box[3]; -+ if (debug>0) mprintf(" %s: Setting box to be a truncated octahedron, angle is %lf\n", -+ parmName,Box[3]); -+ } else if (beta == 60.0) { -+ BoxType=2; -+ ifbox=1; -+ Box[0]=bx; Box[1]=by; Box[2]=bz; -+ Box[3]=60.0; Box[4]=90.0; Box[5]=60.0; -+ if (debug>0) -+ mprintf(" %s: Setting box to be a rhombic dodecahedron, alpha=gamma=60.0, beta=90.0\n", -+ parmName); -+ } else { -+ BoxType=2; -+ ifbox=1; -+ Box[0]=bx; Box[1]=by; Box[2]=bz; -+ Box[3]=beta; Box[4]=beta; Box[5]=beta; -+ mprintf(" Warning: %s: Unrecognized box type, beta is %lf\n",beta); -+ } -+ return 0; -+} -+ - /* - * AmberParm::AtomInfo() - * Print parm information for atom. -@@ -829,8 +904,8 @@ - */ - void AmberParm::Info(char *buffer) { - -- sprintf(buffer,"%i atoms, %i res, box %i, %i mol, %i solvent mol, %i frames", -- natom,nres,ifbox,molecules,solventMolecules,parmFrames); -+ sprintf(buffer,"%i atoms, %i res, boxtype %i, %i mol, %i solvent mol, %i frames", -+ natom,nres,BoxType,molecules,solventMolecules,parmFrames); - } - - // NOTE: The following atomToX functions do not do any memory checks! -@@ -963,6 +1038,7 @@ - return bonds; - } - -+// ---------===========================================================--------- - /* - * AmberParm::modifyStateByMap() - * Currently only intended for use with AtomMap. -@@ -1028,24 +1104,21 @@ - // Set up new parm information - newParm->natom = this->natom; - newParm->nres = this->nres; -- newParm->ifbox = this->ifbox; - newParm->parmFrames = this->parmFrames; - - // Give mapped parm the same pindex as original parm - newParm->pindex = this->pindex; - - // Copy box information -- if (this->Box!=NULL) { -- newParm->Box=(double*) malloc(4*sizeof(double)); -- for (int i=0; i<4; i++) -- newParm->Box[i] = this->Box[i]; -- } -+ for (int i=0; i<6; i++) -+ newParm->Box[i] = this->Box[i]; -+ newParm->BoxType=this->BoxType; - - // Set values up - // NOTE: Eventually set all pointers up? - newParm->values[NATOM] = newParm->natom; - newParm->values[NRES] = newParm->nres; -- newParm->values[IFBOX] = newParm->ifbox; -+ newParm->values[IFBOX] = this->values[IFBOX]; - - return newParm; - } -@@ -1152,7 +1225,6 @@ - // Set up new parm information - newParm->natom = j; - newParm->nres = jres+1; -- newParm->ifbox = this->ifbox; - newParm->parmFrames = this->parmFrames; - if (this->molecules>0) - newParm->molecules = jmol+1; -@@ -1184,26 +1256,25 @@ - } - - // Copy box information -- if (this->Box!=NULL) { -- newParm->Box=(double*) malloc(4*sizeof(double)); -- for (i=0; i<4; i++) -- newParm->Box[i] = this->Box[i]; -- } -+ for (i=0; i<6; i++) -+ newParm->Box[i] = this->Box[i]; -+ newParm->BoxType=this->BoxType; - - // Set values up - // NOTE: Eventually set all pointers up? - newParm->values[NATOM] = newParm->natom; - newParm->values[NRES] = newParm->nres; -- newParm->values[IFBOX] = newParm->ifbox; -+ newParm->values[IFBOX] = this->values[IFBOX]; - - mprintf(" New parmtop contains %i atoms.\n",newParm->natom); - mprintf(" %i residues.\n",newParm->nres); - mprintf(" %i molecules.\n",newParm->molecules); -- mprintf(" %i solvent molcules.\n",newParm->solventMolecules); -+ mprintf(" %i solvent molecules.\n",newParm->solventMolecules); - - return newParm; - } - -+// ---------===========================================================--------- - /* - * AmberParm::DataToBuffer() - * Return char buffer containing N data elements stored in I, D, or C with -@@ -1267,6 +1338,7 @@ - char *buffer; - int solvent_pointer[3]; - int atom; -+ double parmBox[4]; - - if (parmName==NULL) return 1; - -@@ -1346,7 +1418,7 @@ - } - - // SOLVENT POINTERS -- if (ifbox>0) { -+ if (values[IFBOX]>0) { - PrintFlagFormat(&outfile, "%FLAG SOLVENT_POINTERS", "%FORMAT(3I8)"); - solvent_pointer[0]=finalSoluteRes; - solvent_pointer[1]=molecules; -@@ -1360,8 +1432,12 @@ - outfile.IO->Write(buffer, sizeof(char), BufferSize); - - // BOX DIMENSIONS -+ parmBox[0] = Box[4]; // beta -+ parmBox[1] = Box[0]; // boxX -+ parmBox[2] = Box[1]; // boxY -+ parmBox[3] = Box[2]; // boxZ - PrintFlagFormat(&outfile, "%FLAG BOX_DIMENSIONS", "%FORMAT(5E16.8)"); -- buffer = DataToBuffer(buffer,"%FORMAT(5E16.8)", NULL, Box, NULL, 4); -+ buffer = DataToBuffer(buffer,"%FORMAT(5E16.8)", NULL, parmBox, NULL, 4); - outfile.IO->Write(buffer, sizeof(char), BufferSize); - } - -diff -urN amber11//AmberTools/src/cpptraj/src/AmberParm.h amber11.new//AmberTools/src/cpptraj/src/AmberParm.h ---- amber11//AmberTools/src/cpptraj/src/AmberParm.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/AmberParm.h 2011-05-19 18:35:57.000000000 +0300 -@@ -75,14 +75,14 @@ - int *resnums; // IPRES(NRES) - int natom; // NATOM - int nres; // NRES -- int ifbox; // IFBOX - int finalSoluteRes; // IPTRES - int molecules; // NSPM - int firstSolvMol; // NSPSOL - int *atomsPerMol; // NSP(NSPM) - double *mass; // AMASS(NATOM) - double *charge; // CHARGE(NATOM) -- double *Box; // OLDBETA, BOX(1), BOX(2), BOX(3) -+ double Box[6]; // X, Y, Z, alpha, beta, gamma -+ int BoxType; // 0: None, 1: Orthogonal, 2: Non-orthogonal - // From Ptraj - char *solventMask; // T for atoms in the solvent - int solventMolecules; // number of solvent molecules -@@ -96,6 +96,7 @@ - ~AmberParm(); - void ResName(char *, int); - int OpenParm(char *); -+ int SetBoxInfo(double,double,double,double); - int SetSurfaceInfo(); - int SetSolventInfo(); - void AtomInfo(int); -diff -urN amber11//AmberTools/src/cpptraj/src/AmberRestart.cpp amber11.new//AmberTools/src/cpptraj/src/AmberRestart.cpp ---- amber11//AmberTools/src/cpptraj/src/AmberRestart.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/AmberRestart.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -109,7 +109,7 @@ - frameSize+=frameSize; - - // If box coords are present, allocate extra space for them -- if (isBox>0) { -+ if (BoxType!=0) { - numBoxCoords=6; - frameSize+=((numBoxCoords*12)+1); - } -@@ -167,13 +167,12 @@ - - // If 0 probably at EOF. No box or velo. - // } else if (lineSize==0) { -- isBox=0; -+ BoxType=0; - hasVelocity=0; - - // If 36 or 72 (+1 newline) box info. - } else if (lineSize==37 || lineSize==73) { -- isBox=1; -- numBoxCoords = (lineSize-1) / 12; -+ getBoxType(frameBuffer,lineSize); - hasVelocity=0; - - // If filled framebuffer again, has velocity info. Check for box after velocity. -@@ -182,15 +181,14 @@ - if (File->IO->Gets(buffer,82)==0) { - lineSize=strlen(buffer); - if (lineSize==37 || lineSize==73) { -- isBox=1; -- numBoxCoords = (lineSize-1) / 12; -+ getBoxType(buffer,lineSize); - } else { - mprintf("Error: AmberRestart::SetupRead():\n"); - mprintf(" Expect only 3 or 6 box coords in box coord line.\n"); - return 1; - } - } else -- isBox=0; -+ BoxType=0; - - // Otherwise, who knows what was read? - } else { -@@ -202,12 +200,12 @@ - - // Recalculate the frame size - if (hasVelocity) frameSize+=frameSize; -- if (isBox) frameSize+=( (numBoxCoords*12) + 1 ); -+ if (BoxType!=0) frameSize+=( (numBoxCoords*12) + 1 ); - frameBuffer=(char*) realloc(frameBuffer, frameSize*sizeof(char)); - - if (debug > 0) { -- mprintf(" Amber Restart isBox=%i hasVelocity=%i numBoxCoords=%i\n", -- isBox,hasVelocity,numBoxCoords); -+ mprintf(" Amber Restart BoxType=%i hasVelocity=%i numBoxCoords=%i\n", -+ BoxType,hasVelocity,numBoxCoords); - mprintf(" Amber Restart frameSize= %i\n",frameSize); - } - -@@ -221,6 +219,20 @@ - } - - /* -+ * AmberRestart::getBoxType() -+ * Based on input buffer, determine box type and num box coords. -+ */ -+void AmberRestart::getBoxType(char *boxline, int boxlineSize) { -+ double box[6]; -+ numBoxCoords = (boxlineSize-1) / 12; -+ if (numBoxCoords>3) { -+ sscanf(boxline, "%8lf%8lf%8lf%8lf%8lf%8lf",box,box+1,box+2,box+3,box+4,box+5); -+ CheckBoxType(box); -+ } else -+ BoxType = P->BoxType; -+} -+ -+/* - * AmberRestart::getFrame() - * Get the restart file frame. If velocities are present, read those too. - */ -@@ -251,7 +263,7 @@ - //F->V->printAtomCoord(0); - } - // Convert box to Frame if present -- if (isBox) { -+ if (BoxType!=0) { - if ( (bufferPosition = F->BufferToBox(bufferPosition, numBoxCoords, 12))==NULL ) { - mprintf("Error: AmberRestart::getFrame: * detected in box coordinates of %s\n", - trajfilename); -@@ -287,7 +299,7 @@ - if (F->V!=NULL) // NOTE: Use hasVelocity in addition/instead? - bufferPosition = F->V->FrameToBuffer(bufferPosition,"%12.7lf",12,6); - // Write box to buffer -- if (isBox) -+ if (BoxType!=0) - bufferPosition = F->BoxToBuffer(bufferPosition, numBoxCoords, "%12.7lf",12); - - //if (seekable) fseek(fp, titleSize+(set*frameSize),SEEK_SET); -@@ -297,6 +309,8 @@ - - File->IO->Close(); - -+ currentFrame++; -+ - return 0; - } - -diff -urN amber11//AmberTools/src/cpptraj/src/AmberRestart.h amber11.new//AmberTools/src/cpptraj/src/AmberRestart.h ---- amber11//AmberTools/src/cpptraj/src/AmberRestart.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/AmberRestart.h 2011-05-19 18:35:57.000000000 +0300 -@@ -14,6 +14,7 @@ - - int SetupRead(); - int SetupWrite(); -+ void getBoxType(char *, int); - - public: - -diff -urN amber11//AmberTools/src/cpptraj/src/AmberRestartNC.cpp amber11.new//AmberTools/src/cpptraj/src/AmberRestartNC.cpp ---- amber11//AmberTools/src/cpptraj/src/AmberRestartNC.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/AmberRestartNC.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -60,15 +60,8 @@ - /* - * AmberRestartNC::open() - * Open up Netcdf restart file and set all dimension and variable IDs. -- * This is done every time the file is opened up since Im not sure -- * the variable IDs stay the same throughout each opening. -- * Could eventually be separated. -- * NOTE: Replace attrText allocs with static buffer? - */ - int AmberRestartNC::open() { -- char *attrText; // For checking conventions and version -- int spatial; // For checking spatial dimensions -- - mprintf("DEBUG: AmberRestartNC::open() called for %s, ncid=%i\n",File->filename,ncid); - // If already open, return - if (ncid!=-1) return 0; -@@ -94,6 +87,23 @@ - // Netcdf files are always seekable - seekable=1; - -+ return 0; -+} -+ -+/* -+ * AmberRestartNC::SetupRead() -+ * Set up netcdf restart file for reading, get all variable and dimension IDs. -+ * Also check number of atoms against associated parmtop. -+ * NOTE: Replace attrText allocs with static buffer? -+ */ -+int AmberRestartNC::SetupRead() { -+ char *attrText; // For checking conventions and version -+ int spatial; // For checking spatial dimensions -+ double box[6]; -+ size_t start[2], count[2]; -+ -+ if (open()) return 1; -+ - // Get global attributes - if (title==NULL) title = GetAttrText(ncid,NC_GLOBAL, "title"); - attrText = GetAttrText(ncid,NC_GLOBAL, "Conventions"); -@@ -147,20 +157,18 @@ - mprintf(" Netcdf restart time= %lf\n",restartTime); - - // Box info -- // NOTE: If no box info found in parm should really try to determine correct -- // box type from angles. - if ( nc_inq_varid(ncid,"cell_lengths",&cellLengthVID)==NC_NOERR ) { - if (checkNCerr(nc_inq_varid(ncid,"cell_angles",&cellAngleVID), - "Getting cell angles.")!=0) return 1; -- if (debug>0) mprintf(" Netcdf restart Box information found.\n"); -- if (P->ifbox==0) { -- mprintf("Warning: Netcdf restart file contains box info but no box info found\n"); -- mprintf(" in associated parmfile %s; defaulting to orthogonal.\n", -- P->parmName); -- isBox=1; -- } else { -- isBox=P->ifbox; -- } -+ if (debug>0) mprintf(" Netcdf restart Box information found.\n"); -+ // Determine box type from angles -+ start[0]=0; start[1]=0; -+ count[0]=3; count[1]=0; -+ if ( checkNCerr(nc_get_vara_double(ncid, cellLengthVID, start, count, box), -+ "Getting cell lengths.")!=0 ) return 1; -+ if ( checkNCerr(nc_get_vara_double(ncid, cellAngleVID, start, count, box+3), -+ "Getting cell angles.")!=0 ) return 1; -+ CheckBoxType(box); - } - - // Replica Temperatures -@@ -175,15 +183,6 @@ - //int cell_spatialDID, cell_angularDID; - //int spatialVID, cell_spatialVID, cell_angularVID; - -- return 0; --} -- --/* -- * AmberRestartNC::SetupRead() -- * Just a frontend to open for now. Also check number of atoms. -- */ --int AmberRestartNC::SetupRead() { -- if (open()) return 1; - if (ncatom!=P->natom) { - mprintf("Warning: Number of atoms in NetCDF restart file %s (%i) does not\n", - File->filename,ncatom); -@@ -210,7 +209,7 @@ - */ - int AmberRestartNC::setupWriteForSet(int set) { - int dimensionID[NC_MAX_VAR_DIMS]; -- size_t start[3], count[3]; -+ size_t start[2], count[2]; - char buffer[1024]; - char xyz[3]; - char abc[15] = { 'a', 'l', 'p', 'h', 'a', -@@ -280,7 +279,7 @@ - "Defining cell angular variable.")) return 1; - - // Box Info -- if (isBox>0) { -+ if (BoxType!=0) { - dimensionID[0]=cell_spatialDID; - if (checkNCerr(nc_def_var(ncid,"cell_lengths",NC_DOUBLE,1,dimensionID,&cellLengthVID), - "Defining cell length variable.")) return 1; -@@ -388,9 +387,9 @@ - } - - // Read box info -- if (isBox!=0) { -- count [0]=3; -- count [1]=0; -+ if (BoxType!=0) { -+ count[0]=3; -+ count[1]=0; - if ( checkNCerr(nc_get_vara_double(ncid, cellLengthVID, start, count, F->box), - "Getting cell lengths.")!=0 ) return 1; - if ( checkNCerr(nc_get_vara_double(ncid, cellAngleVID, start, count, &(F->box[3])), -@@ -425,7 +424,7 @@ - } - - // write box -- if (isBox>0 && cellLengthVID!=-1) { -+ if (BoxType!=0 && cellLengthVID!=-1) { - count[0]=3; - count[1]=0; - if (checkNCerr(nc_put_vara_double(ncid,cellLengthVID,start,count,F->box), -@@ -439,6 +438,8 @@ - // Close file for this set - close(); - -+ currentFrame++; -+ - return 0; - } - -diff -urN amber11//AmberTools/src/cpptraj/src/AmberTraj.cpp amber11.new//AmberTools/src/cpptraj/src/AmberTraj.cpp ---- amber11//AmberTools/src/cpptraj/src/AmberTraj.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/AmberTraj.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -104,16 +104,18 @@ - rprintf("Error: AmberTraj::getFrame: * detected in coordinates of %s\n",trajfilename); - return 1; - } -- if (isBox) { -+ if (BoxType!=0) { - if ( (bufferPosition = F->BufferToBox(bufferPosition,numBoxCoords,8))==NULL ) { - rprintf("Error: AmberTraj::getFrame: * detected in box coordinates of %s\n", - trajfilename); - return 1; - } -- // Set box angles to parmtop default -- F->box[3] = P->Box[0]; -- F->box[4] = P->Box[0]; -- F->box[5] = P->Box[0]; -+ // Set box angles to parmtop default if not read in -+ if (numBoxCoords==3) { -+ F->box[3] = P->Box[3]; -+ F->box[4] = P->Box[4]; -+ F->box[5] = P->Box[5]; -+ } - } - return 0; - } -@@ -138,20 +140,22 @@ - } - - bufferPosition = F->FrameToBuffer(bufferPosition,"%8.3lf",8,10); -- if (isBox) -+ if (BoxType!=0) - bufferPosition = F->BoxToBuffer(bufferPosition,numBoxCoords,"%8.3lf",8); - - outFrameSize = (int) (bufferPosition - frameBuffer); - - //if (seekable) - // NOTE: Seek only needs to happen when traj file changes -- offset = (off_t) set; -- offset *= (off_t) outFrameSize; -- offset += (off_t) titleSize; -- File->IO->Seek( offset); -+ //offset = (off_t) currentFrame; -+ //offset *= (off_t) outFrameSize; -+ //offset += (off_t) titleSize; -+ //File->IO->Seek( offset); - - if (File->IO->Write(frameBuffer,sizeof(char),outFrameSize)) return 1; - -+ currentFrame++; -+ - return 0; - } - -@@ -165,6 +169,7 @@ - int frame_lines; - int lineSize; - long long int file_size, frame_size; -+ double box[6]; // For checking box coordinates - - // Attempt to open the file. open() sets the title and titleSize - if (open()) return 1; -@@ -219,7 +224,7 @@ - - if (strncmp(buffer,"REMD",4)==0 || strncmp(buffer,"HREMD",5)==0) { - // REMD header - no box coords -- isBox=0; -+ BoxType=0; - } else if (lineSize<80) { - /* Line is shorter than 80 chars, indicates box coords. - * Length of the line HAS to be a multiple of 8, and probably could be -@@ -228,21 +233,22 @@ - */ - if (debug>0) mprintf(" Box line is %i chars.\n",lineSize); - if ( ((lineSize-1)%24)!=0 ) { -- rprintf("Error in box coord line.\nExpect only 3 or 6 box coords.\n"); -+ mprintf("Error in box coord line. Expect only 3 or 6 box coords.\n"); - return 1; - } - numBoxCoords=(lineSize-1) / 8; - if (debug>0) mprintf(" Detected %i box coords.\n",numBoxCoords); -- frameSize+=lineSize; -+ // Determine box type based on angles. Angles are usually not printed -+ // for orthogonal and truncated octahedral boxes, but check here just -+ // to be safe. If no angles present use parmtop Box Type. -+ if (numBoxCoords>3) { -+ sscanf(buffer, "%8lf%8lf%8lf%8lf%8lf%8lf",box,box+1,box+2,box+3,box+4,box+5); -+ CheckBoxType(box); -+ } else -+ BoxType = P->BoxType; - // Reallocate frame buffer accordingly -+ frameSize+=lineSize; - frameBuffer=(char*) realloc(frameBuffer,frameSize * sizeof(char)); -- if (P->ifbox==0) { -- rprintf( "Warning: Box coords detected in trajectory but not defined in topology!\n"); -- rprintf(" Setting box type to rectangular.\n"); -- isBox=1; -- } else { -- isBox = P->ifbox; -- } - } - } - -@@ -315,7 +321,9 @@ - frameSize += hasREMD; - - // If box coords are present, allocate extra space for them -- if (isBox>0) { -+ // NOTE: Currently only writing box lengths for all box types. This means -+ // writing triclinic box type is currently not supported. -+ if (BoxType!=0) { - numBoxCoords=3; // Only write out box lengths for trajectories - frameSize+=((numBoxCoords*8)+1); - } -diff -urN amber11//AmberTools/src/cpptraj/src/ArgList.cpp amber11.new//AmberTools/src/cpptraj/src/ArgList.cpp ---- amber11//AmberTools/src/cpptraj/src/ArgList.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/ArgList.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -147,6 +147,16 @@ - } - - /* -+ * ArgList::Arg() -+ * Return arg at specified position. -+ */ -+char *ArgList::Arg(int pos) { -+ if (pos>-1 && pos<nargs) -+ return arglist[pos]; -+ return NULL; -+} -+ -+/* - * ArgList::Command() - * Check the first arg for command - * Mark and return. Return even if marked. -diff -urN amber11//AmberTools/src/cpptraj/src/ArgList.h amber11.new//AmberTools/src/cpptraj/src/ArgList.h ---- amber11//AmberTools/src/cpptraj/src/ArgList.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/ArgList.h 2011-05-19 18:35:57.000000000 +0300 -@@ -15,6 +15,7 @@ - void Add(char *); - void print(); - char *ArgLine(); -+ char *Arg(int); - - char *Command(); - int CommandIs(const char *); -diff -urN amber11//AmberTools/src/cpptraj/src/AtomMap.cpp amber11.new//AmberTools/src/cpptraj/src/AtomMap.cpp ---- amber11//AmberTools/src/cpptraj/src/AtomMap.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/AtomMap.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -6,6 +6,7 @@ - #include "TorsionRoutines.h" - // DEBUG - #include "Mol2File.h" -+#include <cstdio> - - //--------- PRIVATE ROUTINES --------------------------------------- - /* -@@ -463,21 +464,27 @@ - // Write atommap out as a mol2 file, useful for checking bond info - void atommap::WriteMol2(char *m2filename) { - Mol2File outfile; -- int *Selected; -+ AtomMask M1; - // Temporary parm to play with - AmberParm *tmpParm; -+ Frame *tmpFrame; - - // Create mask containing all atoms -- Selected = (int*) malloc(natom*sizeof(int)); -- for (int atom=0; atom<natom; atom++) Selected[atom]=atom; -+ //for (int atom=0; atom<natom; atom++) Selected[atom]=atom; - // Fake strip, just use as crap way to copy -- tmpParm = P->modifyStateByMask(Selected,natom); -- free(Selected); -+ //tmpParm = P->modifyStateByMask(Selected,natom); -+ //free(Selected); - // Modify the bonds array to include this info -- tmpParm->ResetBondInfo(); -- for (int atom=0; atom<natom; atom++) -- for (int bond=0; bond < M[atom].nbond; bond++) -- tmpParm->AddBond(atom, M[atom].bond[bond], 0); -+ //tmpParm->ResetBondInfo(); -+ //for (int atom=0; atom<natom; atom++) -+ // for (int bond=0; bond < M[atom].nbond; bond++) -+ // tmpParm->AddBond(atom, M[atom].bond[bond], 0); -+ // Create mask with all mapped atoms -+ for (int atom=0; atom<natom; atom++) {if (M[atom].isMapped) M1.AddAtom(atom);} -+ // Strip so only mapped atoms remain -+ tmpParm = P->modifyStateByMask(M1.Selected,M1.Nselected); -+ tmpFrame = new Frame(M1.Nselected,NULL); -+ tmpFrame->SetFrameFromMask(F, &M1); - - // Trajectory Setup - outfile.File=new PtrajFile(); -@@ -485,13 +492,14 @@ - outfile.trajfilename = outfile.File->basefilename; - outfile.debug=debug; - outfile.SetTitle(m2filename); -- outfile.P=P; -+ outfile.P=tmpParm; - outfile.SetupWrite(); - outfile.open(); -- outfile.F=F; -+ outfile.F=tmpFrame; - outfile.writeFrame(0); - outfile.close(); - delete tmpParm; -+ delete tmpFrame; - } - // ============================================================================ - -@@ -1032,6 +1040,13 @@ - int iterations=0; - - numAtomsMapped=MapUniqueAtoms(Ref, Tgt); -+ // DEBUG -+ //char name[1024]; -+ //sprintf(name,"Ref.%i.mol2",iterations); -+ //Ref->WriteMol2(name); -+ //sprintf(name,"Tgt.%i.mol2",iterations); -+ //Tgt->WriteMol2(name); -+ // END DEBUG - if (debug>0) - mprintf("* MapUniqueAtoms: %i atoms mapped.\n",numAtomsMapped); - if (numAtomsMapped==0) return 1; -@@ -1045,17 +1060,35 @@ - iterations++; - // First assign based on bonds to unique (already mapped) atoms. - numAtomsMapped=mapBondsToUnique(Ref,Tgt); -+ // DEBUG -+ //sprintf(name,"Ref.%i.u.mol2",iterations); -+ //Ref->WriteMol2(name); -+ //sprintf(name,"Tgt.%i.u.mol2",iterations); -+ //Tgt->WriteMol2(name); -+ // END DEBUG - if (debug>0) - mprintf("* [%3i] mapBondsToUnique: %i atoms mapped.\n",iterations,numAtomsMapped); - if (numAtomsMapped<0) return 1; - // Next assign based on chirality - numAtomsMapped=mapChiral(Ref,Tgt); -+ // DEBUG -+ //sprintf(name,"Ref.%i.c.mol2",iterations); -+ //Ref->WriteMol2(name); -+ //sprintf(name,"Tgt.%i.c.mol2",iterations); -+ //Tgt->WriteMol2(name); -+ // END DEBUG - if (debug>0) - mprintf("* [%3i] mapChiral: %i atoms mapped.\n",iterations,numAtomsMapped); - if (numAtomsMapped<0) return 1; - if (numAtomsMapped>0) continue; - // Last assign based on index/element - numAtomsMapped=mapByIndex(Ref,Tgt); -+ // DEBUG -+ //sprintf(name,"Ref.%i.i.mol2",iterations); -+ //Ref->WriteMol2(name); -+ //sprintf(name,"Tgt.%i.i.mol2",iterations); -+ //Tgt->WriteMol2(name); -+ // END DEBUG - if (debug>0) - mprintf("* [%3i] mapByIndex: %i atoms mapped.\n",iterations,numAtomsMapped); - if (numAtomsMapped<0) return 1; -diff -urN amber11//AmberTools/src/cpptraj/src/cpptrajdepend amber11.new//AmberTools/src/cpptraj/src/cpptrajdepend ---- amber11//AmberTools/src/cpptraj/src/cpptrajdepend 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/cpptrajdepend 2011-05-19 18:35:57.000000000 +0300 -@@ -2,7 +2,7 @@ - AmberNetcdf.o : AmberNetcdf.cpp AmberNetcdf.h AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h Frame.h NetcdfRoutines.h PtrajFile.h Range.h TrajFile.h - AmberParm.o : AmberParm.cpp AmberParm.h BaseFileIO.h CpptrajStdio.h Mol2FileRoutines.h PDBfileRoutines.h PtrajFile.h - AmberTraj.o : AmberTraj.cpp AmberParm.h AmberTraj.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h Frame.h PtrajFile.h Range.h TrajFile.h --TrajFile.o : TrajFile.cpp AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h Frame.h PtrajFile.h PtrajMpi.h Range.h TrajFile.h -+TrajFile.o : TrajFile.cpp AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h Frame.h PtrajFile.h Range.h TrajFile.h - Frame.o : Frame.cpp AmberParm.h AtomMask.h BaseFileIO.h CpptrajStdio.h DistRoutines.h Frame.h PtrajFile.h TorsionRoutines.h vectormath.h - PtrajState.o : PtrajState.cpp Action.h AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CoordFileList.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajActionList.h PtrajFile.h PtrajMpi.h PtrajState.h Range.h ReferenceList.h TrajFile.h TrajinList.h TrajoutList.h - ArgList.o : ArgList.cpp ArgList.h CpptrajStdio.h -@@ -13,7 +13,7 @@ - TrajoutList.o : TrajoutList.cpp AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CoordFileList.h CpptrajStdio.h Frame.h ParmFileList.h PtrajFile.h Range.h TrajFile.h TrajoutList.h - ReferenceList.o : ReferenceList.cpp AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CoordFileList.h CpptrajStdio.h Frame.h FrameList.h ParmFileList.h PtrajFile.h Range.h ReferenceList.h TrajFile.h - CoordFileList.o : CoordFileList.cpp AmberNetcdf.h AmberParm.h AmberRestart.h AmberRestartNC.h AmberTraj.h ArgList.h AtomMask.h BaseFileIO.h Conflib.h CoordFileList.h CpptrajStdio.h Frame.h Mol2File.h PDBfile.h ParmFileList.h PtrajFile.h Range.h RemdTraj.h TrajFile.h TrajinList.h --PtrajActionList.o : PtrajActionList.cpp Action.h Action_Angle.h Action_Center.h Action_Closest.h Action_DSSP.h Action_Dihedral.h Action_Distance.h Action_Hbond.h Action_Image.h Action_Mask.h Action_NAstruct.h Action_Outtraj.h Action_Pucker.h Action_Radgyr.h Action_Rmsd.h Action_Strip.h Action_Surf.h AmberParm.h ArgList.h AtomMap.h AtomMask.h AxisType.h BaseFileIO.h CoordFileList.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajActionList.h PtrajFile.h Range.h TrajFile.h TrajoutList.h -+PtrajActionList.o : PtrajActionList.cpp Action.h Action_Angle.h Action_Center.h Action_Closest.h Action_DSSP.h Action_Dihedral.h Action_Distance.h Action_Hbond.h Action_Image.h Action_Mask.h Action_NAstruct.h Action_Outtraj.h Action_Pucker.h Action_Radgyr.h Action_Rms2d.h Action_Rmsd.h Action_Strip.h Action_Surf.h AmberParm.h ArgList.h AtomMap.h AtomMask.h AxisType.h BaseFileIO.h CoordFileList.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajActionList.h PtrajFile.h Range.h TrajFile.h TrajoutList.h - DataSet.o : DataSet.cpp CpptrajStdio.h DataSet.h - DataSetList.o : DataSetList.cpp CpptrajStdio.h DataSet.h DataSetList.h intDataSet.h mapDataSet.h stringDataSet.h - vectormath.o : vectormath.cpp CpptrajStdio.h vectormath.h -@@ -23,9 +23,9 @@ - DataFile.o : DataFile.cpp BaseFileIO.h CpptrajStdio.h DataFile.h DataSet.h PtrajFile.h - DataFileList.o : DataFileList.cpp BaseFileIO.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h PtrajFile.h - PDBfile.o : PDBfile.cpp AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h Frame.h PDBfile.h PDBfileRoutines.h PtrajFile.h Range.h TrajFile.h --PtrajFile.o : PtrajFile.cpp BaseFileIO.h Bzip2File.h CpptrajStdio.h GzipFile.h MpiFile.h NetcdfRoutines.h PDBfileRoutines.h PtrajFile.h PtrajMpi.h StdFile.h -+PtrajFile.o : PtrajFile.cpp BaseFileIO.h Bzip2File.h CpptrajStdio.h GzipFile.h Mol2FileRoutines.h MpiFile.h NetcdfRoutines.h PDBfileRoutines.h PtrajFile.h PtrajMpi.h StdFile.h - PDBfileRoutines.o : PDBfileRoutines.cpp PDBfileRoutines.h --AtomMap.o : AtomMap.cpp Action.h AmberParm.h ArgList.h AtomMap.h AtomMask.h BaseFileIO.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h PDBfileRoutines.h ParmFileList.h PtrajFile.h TorsionRoutines.h -+AtomMap.o : AtomMap.cpp Action.h AmberParm.h ArgList.h AtomMap.h AtomMask.h BaseFileIO.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h Mol2File.h ParmFileList.h PtrajFile.h Range.h TorsionRoutines.h TrajFile.h - BaseFileIO.o : BaseFileIO.cpp BaseFileIO.h PtrajMpi.h - StdFile.o : StdFile.cpp BaseFileIO.h StdFile.h - GzipFile.o : GzipFile.cpp BaseFileIO.h CpptrajStdio.h GzipFile.h -@@ -62,3 +62,4 @@ - Action_Pucker.o : Action_Pucker.cpp Action.h Action_Pucker.h AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajFile.h - Range.o : Range.cpp ArgList.h CpptrajStdio.h Range.h - Action_Outtraj.o : Action_Outtraj.cpp Action.h Action_Outtraj.h AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CoordFileList.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajFile.h PtrajMpi.h Range.h TrajFile.h TrajoutList.h -+Action_Rms2d.o : Action_Rms2d.cpp Action.h Action_Rms2d.h AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajFile.h -diff -urN amber11//AmberTools/src/cpptraj/src/DataFile.cpp amber11.new//AmberTools/src/cpptraj/src/DataFile.cpp ---- amber11//AmberTools/src/cpptraj/src/DataFile.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/DataFile.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -66,6 +66,49 @@ - } - - /* -+ * DataFile::SetPrecision() -+ * Set precision of the specified dataset to width.precision. If '*' specified -+ * set for all datasets in file. -+ */ -+void DataFile::SetPrecision(char *dsetName, int widthIn, int precisionIn) { -+ int precision, dset; -+ DataSet *Dset = NULL; -+ -+ if (dsetName==NULL) { -+ mprintf("Error: SetPrecision must be called with dataset name or '*'.\n"); -+ return; -+ } -+ if (widthIn<1) { -+ mprintf("Error: SetPrecision (%s): Cannot set width < 1.\n",filename); -+ return; -+ } -+ precision=precisionIn; -+ if (precisionIn<0) precision=0; -+ // If <dsetName>=='*' specified set precision for all data sets -+ if (dsetName[0]=='*') { -+ mprintf(" Setting width.precision for all sets in %s to %i.%i\n", -+ filename,widthIn,precision); -+ for (dset=0; dset<Nsets; dset++) -+ SetList[dset]->SetPrecision(widthIn,precision); -+ -+ // Otherwise find dataset <dsetName> and set precision -+ } else { -+ mprintf(" Setting width.precision for dataset %s to %i.%i\n", -+ dsetName,widthIn,precision); -+ for (dset=0; dset<Nsets; dset++) { -+ if ( strcmp(SetList[dset]->Name(), dsetName)==0 ) { -+ Dset=SetList[dset]; -+ break; -+ } -+ } -+ if (Dset!=NULL) -+ Dset->SetPrecision(widthIn,precision); -+ else -+ mprintf("Error: Dataset %s not found in datafile %s\n",dsetName,filename); -+ } -+} -+ -+/* - * DataFile::AddSet() - * Add given set to this datafile - */ -diff -urN amber11//AmberTools/src/cpptraj/src/DataFile.h amber11.new//AmberTools/src/cpptraj/src/DataFile.h ---- amber11//AmberTools/src/cpptraj/src/DataFile.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/DataFile.h 2011-05-19 18:35:57.000000000 +0300 -@@ -30,6 +30,7 @@ - void SetXlabel(char*); - void SetInverted(); - void SetNoXcol(); -+ void SetPrecision(char *, int, int); - int AddSet(DataSet *); - int NameIs(char *); - void DataSetNames(); -diff -urN amber11//AmberTools/src/cpptraj/src/DataSet.cpp amber11.new//AmberTools/src/cpptraj/src/DataSet.cpp ---- amber11//AmberTools/src/cpptraj/src/DataSet.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/DataSet.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -1,6 +1,7 @@ - // DataSet - #include <cstdlib> - #include <cstring> -+#include <cstdio> // sprintf - #include "DataSet.h" - #include "CpptrajStdio.h" - -@@ -11,12 +12,73 @@ - N=0; - isDynamic=false; - current=0; -+ width = 0; -+ precision = 0; -+ format = NULL; -+ dType = UNKNOWN_DATA; - } - - // DESTRUCTOR - DataSet::~DataSet() { - //fprintf(stderr,"DataSet Destructor\n"); - if (name!=NULL) free(name); -+ if (format!=NULL) free(format); -+} -+ -+/* -+ * DataSet::setFormatString() -+ * Set up the output format string for each data element based on the given -+ * dataType and the current width, and precision. -+ */ -+void DataSet::setFormatString() { -+ size_t stringWidth = 0; -+ int wWidth = 0; -+ int pWidth = 0; -+ -+ if (format!=NULL) {free(format); format=NULL;} -+ -+ // Calc num of chars necessary to hold width -+ wWidth = (width / 10) + 1; -+ -+ switch (dType) { -+ case DOUBLE : -+ // Calc num of chars necessary to hold precision -+ pWidth = (precision / 10) + 1; -+ // String fmt: " %w.plf\0" -+ stringWidth = pWidth + wWidth + 6; -+ format = (char*) malloc( stringWidth * sizeof(char) ); -+ sprintf(format, " %%%i.%ilf", width, precision); -+ break; -+ case STRING : -+ // String fmt: " %s" -+ format = (char*) malloc( 4 * sizeof(char) ); -+ strcpy(format, " %s"); -+ break; -+ case INT : -+ // String fmt: " %wi" -+ stringWidth = wWidth + 4; -+ format = (char*) malloc( stringWidth * sizeof(char) ); -+ sprintf(format, " %%%ii", width); -+ break; -+ case UNKNOWN_DATA : -+ mprintf("Internal Error: setFormatString called with unknown data type.\n"); -+ } -+ -+ if (format==NULL) -+ mprintf("Error: setFormatString: Could not allocate memory for string.\n"); -+ // DEBUG -+ //else -+ // mprintf("DEBUG: Format string: [%s]\n",format); -+} -+ -+/* -+ * DataSet::SetPrecision() -+ * Set dataset width and precision and recalc output format string. -+ */ -+void DataSet::SetPrecision(int widthIn, int precisionIn) { -+ width=widthIn; -+ precision=precisionIn; -+ setFormatString(); - } - - /* -diff -urN amber11//AmberTools/src/cpptraj/src/DataSet.h amber11.new//AmberTools/src/cpptraj/src/DataSet.h ---- amber11//AmberTools/src/cpptraj/src/DataSet.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/DataSet.h 2011-05-19 18:35:57.000000000 +0300 -@@ -36,12 +36,18 @@ - class DataSet { - protected: - char *name; // Name of the dataset -+ dataType dType; // The dataset type - int N; // Number of data elements - int current; // The current data element -+ int width; // The output width of a data element -+ int precision; // The output precision of a data element (if applicable) -+ char *format; // Format of output -+ - bool isDynamic; // True : N is not known, reallocate as N increases - // False: N is known, allocate for N - // If not isDynamic, Allocate will reserve space for N data elements - virtual int Allocate( ) { return 0; } -+ void setFormatString(); - - public: - -@@ -51,13 +57,16 @@ - virtual int Xmax() { return 0; } - virtual int isEmpty(int) { return 0; } - virtual void Add( int, void * ) { return; } -+ virtual int Get( void *, int ) { return 1; } - virtual char *Write(char*, int) { return 0; } - virtual int Width() { return 0; } - virtual int Sync() { return 0; } - -+ void SetPrecision(int,int); - int Setup(char*,int); - void Info(); - char *Name() { return name; } - int CheckSet(); -+ dataType Type() {return dType;} - }; - #endif -diff -urN amber11//AmberTools/src/cpptraj/src/Frame.cpp amber11.new//AmberTools/src/cpptraj/src/Frame.cpp ---- amber11//AmberTools/src/cpptraj/src/Frame.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Frame.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -61,6 +61,40 @@ - } - - /* -+ * Frame::ZeroCoords() -+ * Set all coords to 0.0 -+ */ -+void Frame::ZeroCoords() { -+ for (int coord=0; coord < N; coord++) -+ X[coord]=0.0; -+} -+ -+/* -+ * Frame::AddCoord() -+ * Add the coord values from the input frame to the coord values of -+ * this frame. -+ */ -+void Frame::AddCoord(Frame *FrameIn) { -+ if (FrameIn->N != this->N) { -+ mprintf("Error: Frame::AddCoord: Attempting to add %i coords to %i coords.\n", -+ FrameIn->N,this->N); -+ } else { -+ for (int coord=0; coord < N; coord++) -+ this->X[coord] += FrameIn->X[coord]; -+ } -+} -+ -+/* -+ * Frame::Divide() -+ * Divide all coord values by input. Dont do it if the number is too small. -+ */ -+void Frame::Divide(double divisor) { -+ if (divisor < SMALL) return; -+ for (int coord=0; coord < N; coord++) -+ X[coord] /= divisor; -+} -+ -+/* - * Frame::Copy() - * Return a copy of the frame - */ -@@ -423,21 +457,21 @@ - * Based on useMassIn, calculate geometric center (false) or center of mass - * (true) of the atoms in each mask. - */ --double Frame::DIST2(AtomMask *Mask1, AtomMask *Mask2, bool useMassIn, int ifbox, -+double Frame::DIST2(AtomMask *Mask1, AtomMask *Mask2, bool useMassIn, int boxType, - double *ucell, double *recip) { - double a1[3], a2[3]; - - COM(Mask1, a1, useMassIn); - COM(Mask2, a2, useMassIn); - -- if (ifbox == 0) -+ if (boxType == 0) - return DIST2_NoImage(a1, a2); -- else if (ifbox == 1) -+ else if (boxType == 1) - return DIST2_ImageOrtho(a1, a2, this->box); -- else if (ifbox == 2) -+ else if (boxType == 2) - return DIST2_ImageNonOrtho(a1, a2, ucell, recip); - -- mprintf(" Error: Frame::DIST: Unrecognized box type (%i)\n.", ifbox); -+ mprintf(" Error: Frame::DIST: Unrecognized box type (%i)\n.", boxType); - - return (-1.0); - } -@@ -445,8 +479,11 @@ - /* - * Frame::DIST2() - * Return the distance between atoms A1 and A2 with optional imaging. -+ * 0 = None -+ * 1 = Orthorhombic -+ * 2 = Non-orthorhombic - */ --double Frame::DIST2(int A1, int A2, int ifbox, double *ucell, double *recip) { -+double Frame::DIST2(int A1, int A2, int boxType, double *ucell, double *recip) { - int atom3; - double a1[3], a2[3]; - -@@ -459,14 +496,14 @@ - a2[1] = X[atom3+1]; - a2[2] = X[atom3+2]; - -- if (ifbox == 0) -+ if (boxType == 0) - return DIST2_NoImage(a1, a2); -- else if (ifbox == 1) -+ else if (boxType == 1) - return DIST2_ImageOrtho(a1, a2, this->box); -- else if (ifbox == 2) -+ else if (boxType == 2) - return DIST2_ImageNonOrtho(a1, a2, ucell, recip); - -- mprintf(" Error: Frame::DIST: Unrecognized box type (%i)\n.", ifbox); -+ mprintf(" Error: Frame::DIST: Unrecognized box type (%i)\n.", boxType); - - return (-1.0); - } -diff -urN amber11//AmberTools/src/cpptraj/src/Frame.h amber11.new//AmberTools/src/cpptraj/src/Frame.h ---- amber11//AmberTools/src/cpptraj/src/Frame.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Frame.h 2011-05-19 18:35:57.000000000 +0300 -@@ -22,6 +22,9 @@ - Frame(AtomMask *, double *); - virtual ~Frame(); // Destructor is virtual since this class can be inherited - -+ void ZeroCoords(); -+ void AddCoord(Frame*); -+ void Divide(double); - void printAtomCoord(int); - void GetCoord(double *, int); - void SetCoord(int, double *); -diff -urN amber11//AmberTools/src/cpptraj/src/FrameList.cpp amber11.new//AmberTools/src/cpptraj/src/FrameList.cpp ---- amber11//AmberTools/src/cpptraj/src/FrameList.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/FrameList.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -13,7 +13,8 @@ - delete frameList[i]; - } - --/* FrameList::Add() -+/* -+ * FrameList::Add() - * Add given Frame to the FrameList. Store trajectory name that this frame - * came from in frameNames. Store the associated parm in FrameParm. - */ -@@ -29,6 +30,18 @@ - FrameParm.Add(P); - Nframe++; - return 0; -+} -+ -+/* -+ * FrameList::Add() -+ * Add given Frame to the FrameList. Store the associated parm in FrameParm. -+ */ -+int FrameList::Add(Frame *F, AmberParm *P) { -+ if (F==NULL || P==NULL) return 1; -+ frameList.push_back(F); -+ FrameParm.Add(P); -+ Nframe++; -+ return 0; - } - - /* -diff -urN amber11//AmberTools/src/cpptraj/src/FrameList.h amber11.new//AmberTools/src/cpptraj/src/FrameList.h ---- amber11//AmberTools/src/cpptraj/src/FrameList.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/FrameList.h 2011-05-19 18:35:57.000000000 +0300 -@@ -18,6 +18,7 @@ - ~FrameList(); - - int Add(Frame *, char *, AmberParm *,int); -+ int Add(Frame *, AmberParm *); - AmberParm *GetFrameParm(int); - int GetFrameIndex(char *); - Frame *GetFrame(int idx); -diff -urN amber11//AmberTools/src/cpptraj/src/intDataSet.cpp amber11.new//AmberTools/src/cpptraj/src/intDataSet.cpp ---- amber11//AmberTools/src/cpptraj/src/intDataSet.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/intDataSet.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -5,6 +5,14 @@ - #include "PtrajMpi.h" - #include "CpptrajStdio.h" - using namespace std; -+ -+// CONSTRUCTOR -+intDataSet::intDataSet() { -+ width=12; -+ dType=INT; -+ setFormatString(); -+} -+ - /* - * intDataSet::Xmax(() - * Return the maximum X value added to this set. By convention this is -@@ -34,6 +42,21 @@ - } - - /* -+ * intDataSet::Get() -+ * Get data at frame, put into vOut. Return 1 if no data at frame. -+ */ -+int intDataSet::Get(void *vOut, int frame) { -+ int *value; -+ -+ if (vOut==NULL) return 1; -+ value = (int*) vOut; -+ it=Data.find( frame ); -+ if (it == Data.end()) return 1; -+ *value = (*it).second; -+ return 0; -+} -+ -+/* - * intDataSet::isEmpty() - */ - int intDataSet::isEmpty(int frame) { -@@ -52,17 +75,17 @@ - it = Data.find( frame ); - if (it == Data.end()) - //sprintf(buffer," %12s","NoData"); -- sprintf(buffer," %12i", 0); -+ sprintf(buffer, format, 0); - else -- sprintf(buffer," %12i",(*it).second); -- return (buffer + 13); -+ sprintf(buffer, format, (*it).second); -+ return (buffer + width + 1); - } - - /* - * intDataSet::Width() - */ - int intDataSet::Width() { -- return 13; -+ return (width + 1); - } - - /* -diff -urN amber11//AmberTools/src/cpptraj/src/intDataSet.h amber11.new//AmberTools/src/cpptraj/src/intDataSet.h ---- amber11//AmberTools/src/cpptraj/src/intDataSet.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/intDataSet.h 2011-05-19 18:35:57.000000000 +0300 -@@ -11,9 +11,12 @@ - std::map<int,int> Data; - std::map<int,int>::iterator it; - public: -+ intDataSet(); -+ - int Xmax(); - int isEmpty(int); - void Add( int, void * ); -+ int Get(void *, int); - char *Write(char *, int); - int Width(); - int Sync(); -diff -urN amber11//AmberTools/src/cpptraj/src/main.cpp amber11.new//AmberTools/src/cpptraj/src/main.cpp ---- amber11//AmberTools/src/cpptraj/src/main.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/main.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -6,7 +6,7 @@ - #include "PtrajMpi.h" - #include "CpptrajStdio.h" - #ifndef CPPTRAJ_VERSION_STRING --#define CPPTRAJ_VERSION_STRING "V1.0.5" -+#define CPPTRAJ_VERSION_STRING "V1.0.8" - #endif - - void Usage(char *programName) { -diff -urN amber11//AmberTools/src/cpptraj/src/Makefile amber11.new//AmberTools/src/cpptraj/src/Makefile ---- amber11//AmberTools/src/cpptraj/src/Makefile 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Makefile 2011-05-19 18:35:57.000000000 +0300 -@@ -16,7 +16,8 @@ - Action_Radgyr.cpp Conflib.cpp Action_Mask.cpp Action_Closest.cpp \ - NetcdfRoutines.cpp AmberRestartNC.cpp CpptrajStdio.cpp Mol2File.cpp \ - Mol2FileRoutines.cpp Action_NAstruct.cpp DistRoutines.cpp AxisType.cpp \ -- TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp -+ TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp \ -+ Action_Rms2d.cpp - - OBJECTS=main.o AmberNetcdf.o AmberParm.o AmberTraj.o TrajFile.o \ - Frame.o PtrajState.o ArgList.o ptrajmask.o Action_Distance.o \ -@@ -32,7 +33,8 @@ - Action_Radgyr.o Conflib.o Action_Mask.o Action_Closest.o \ - NetcdfRoutines.o AmberRestartNC.o CpptrajStdio.o Mol2File.o \ - Mol2FileRoutines.o Action_NAstruct.o DistRoutines.o AxisType.o \ -- TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o -+ TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o \ -+ Action_Rms2d.o - - HEADERS=AmberNetcdf.h AmberParm.h AmberTraj.h TrajFile.h \ - Frame.h PtrajState.h ArgList.h ptrajmask.h Action.h Action_Distance.h \ -@@ -48,7 +50,8 @@ - Action_Radgyr.h Conflib.h Action_Mask.h Action_Closest.h \ - NetcdfRoutines.h AmberRestartNC.h CpptrajStdio.h Mol2File.h \ - Mol2FileRoutines.h Action_NAstruct.h DistRoutines.h AxisType.h \ -- TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h -+ TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h \ -+ Action_Rms2d.h - - all: cpptraj$(SFX) - -diff -urN amber11//AmberTools/src/cpptraj/src/Makefile_at amber11.new//AmberTools/src/cpptraj/src/Makefile_at ---- amber11//AmberTools/src/cpptraj/src/Makefile_at 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Makefile_at 2011-05-19 18:35:57.000000000 +0300 -@@ -16,7 +16,8 @@ - Action_Radgyr.cpp Conflib.cpp Action_Mask.cpp Action_Closest.cpp \ - NetcdfRoutines.cpp AmberRestartNC.cpp CpptrajStdio.cpp Mol2File.cpp \ - Mol2FileRoutines.cpp Action_NAstruct.cpp DistRoutines.cpp AxisType.cpp \ -- TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp -+ TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp \ -+ Action_Rms2d.cpp - - OBJECTS=main.o AmberNetcdf.o AmberParm.o AmberTraj.o TrajFile.o \ - Frame.o PtrajState.o ArgList.o ptrajmask.o Action_Distance.o \ -@@ -32,7 +33,8 @@ - Action_Radgyr.o Conflib.o Action_Mask.o Action_Closest.o \ - NetcdfRoutines.o AmberRestartNC.o CpptrajStdio.o Mol2File.o \ - Mol2FileRoutines.o Action_NAstruct.o DistRoutines.o AxisType.o \ -- TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o -+ TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o \ -+ Action_Rms2d.o - - HEADERS=AmberNetcdf.h AmberParm.h AmberTraj.h TrajFile.h \ - Frame.h PtrajState.h ArgList.h ptrajmask.h Action.h Action_Distance.h \ -@@ -48,7 +50,8 @@ - Action_Radgyr.h Conflib.h Action_Mask.h Action_Closest.h \ - NetcdfRoutines.h AmberRestartNC.h CpptrajStdio.h Mol2File.h \ - Mol2FileRoutines.h Action_NAstruct.h DistRoutines.h AxisType.h \ -- TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h -+ TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h \ -+ Action_Rms2d.h - - all: cpptraj$(SFX) - -diff -urN amber11//AmberTools/src/cpptraj/src/mapDataSet.cpp amber11.new//AmberTools/src/cpptraj/src/mapDataSet.cpp ---- amber11//AmberTools/src/cpptraj/src/mapDataSet.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/mapDataSet.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -6,6 +6,14 @@ - #include "CpptrajStdio.h" - using namespace std; - -+// CONSTRUCTOR -+mapDataSet::mapDataSet() { -+ width = 12; -+ precision = 4; -+ dType=DOUBLE; -+ setFormatString(); -+} -+ - /* - * mapDataSet::Xmax(() - * Return the maximum X value added to this set. By convention this is -@@ -35,6 +43,23 @@ - } - - /* -+ * mapDataSet::Get() -+ * Get data at frame, put into vOut. Return 1 if no data at frame. -+ */ -+int mapDataSet::Get(void *vOut, int frame) { -+ double *value; -+ -+ if (vOut==NULL) return 1; -+ //mprintf("DEBUG: Attempting to get double frame %i\n",frame); -+ value = (double*) vOut; -+ it=Data.find( frame ); -+ if (it == Data.end()) return 1; -+ //mprintf("DEBUG: Double frame %i is %lf\n",frame,(*it).second); -+ *value = (*it).second; -+ return 0; -+} -+ -+/* - * mapDataSet::isEmpty() - */ - int mapDataSet::isEmpty(int frame) { -@@ -53,17 +78,17 @@ - it = Data.find( frame ); - if (it == Data.end()) - //sprintf(buffer," %12s","NoData"); -- sprintf(buffer," %12.4lf", 0.0); -+ sprintf(buffer, format, 0.0); - else -- sprintf(buffer," %12.4lf",(*it).second); -- return (buffer + 13); -+ sprintf(buffer, format,(*it).second); -+ return (buffer + width + 1); - } - - /* - * mapDataSet::Width() - */ - int mapDataSet::Width() { -- return 13; -+ return (width + 1); - } - - /* -diff -urN amber11//AmberTools/src/cpptraj/src/mapDataSet.h amber11.new//AmberTools/src/cpptraj/src/mapDataSet.h ---- amber11//AmberTools/src/cpptraj/src/mapDataSet.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/mapDataSet.h 2011-05-19 18:35:57.000000000 +0300 -@@ -7,14 +7,16 @@ - */ - #include <map> - #include "DataSet.h" --//using namespace std; - class mapDataSet : public DataSet { - std::map<int,double> Data; - std::map<int,double>::iterator it; - public: -+ mapDataSet(); -+ - int Xmax(); - int isEmpty(int); - void Add( int, void * ); -+ int Get(void *, int); - char *Write(char *, int); - int Width(); - int Sync(); -diff -urN amber11//AmberTools/src/cpptraj/src/Mol2File.cpp amber11.new//AmberTools/src/cpptraj/src/Mol2File.cpp ---- amber11//AmberTools/src/cpptraj/src/Mol2File.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/Mol2File.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -239,6 +239,8 @@ - if (writeMode==2) - File->IO->Close(); - -+ currentFrame++; -+ - return 0; - } - -diff -urN amber11//AmberTools/src/cpptraj/src/PDBfile.cpp amber11.new//AmberTools/src/cpptraj/src/PDBfile.cpp ---- amber11//AmberTools/src/cpptraj/src/PDBfile.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/PDBfile.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -207,6 +207,9 @@ - } else if (writeMode==1) { - File->IO->Printf("ENDMDL\n"); - } -+ -+ currentFrame++; -+ - return 0; - } - -diff -urN amber11//AmberTools/src/cpptraj/src/PtrajActionList.cpp amber11.new//AmberTools/src/cpptraj/src/PtrajActionList.cpp ---- amber11//AmberTools/src/cpptraj/src/PtrajActionList.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/PtrajActionList.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -20,6 +20,7 @@ - #include "Action_NAstruct.h" - #include "Action_Pucker.h" - #include "Action_Outtraj.h" -+#include "Action_Rms2d.h" - - // Constructor - PtrajActionList::PtrajActionList() { -@@ -56,6 +57,7 @@ - - // Decide what action this is based on the command. - if (A->CommandIs("distance")) {Act=new Distance;} -+ else if (A->CommandIs("rms2d")) {Act=new Rms2d; } - else if (A->CommandIs("rmsd",3)) {Act=new Rmsd; } - else if (A->CommandIs("dihedral")) {Act=new Dihedral;} - else if (A->CommandIs("atommap")) {Act=new AtomMap; } -@@ -166,6 +168,8 @@ - err = ActionList[act]->DoAction(FrameAddress, frameIn); - if (err==1) { - // Treat actions that fail as if they could not be set up -+ mprintf("Warning: Action [%s] failed, frame %i.\n",ActionList[act]->CmdLine(), -+ frameIn); - ActionList[act]->noSetup=1; - } else if (err==2) { - // Return value of 2 requests return to original frame -diff -urN amber11//AmberTools/src/cpptraj/src/PtrajFile.cpp amber11.new//AmberTools/src/cpptraj/src/PtrajFile.cpp ---- amber11//AmberTools/src/cpptraj/src/PtrajFile.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/PtrajFile.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -113,6 +113,7 @@ - void PtrajFile::CloseFile() { - if (isOpen) { - IO->Close(); -+ if (debug>0) rprintf("Closed %s.\n",filename); - isOpen=0; - } - } -diff -urN amber11//AmberTools/src/cpptraj/src/PtrajMpi.c amber11.new//AmberTools/src/cpptraj/src/PtrajMpi.c ---- amber11//AmberTools/src/cpptraj/src/PtrajMpi.c 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/PtrajMpi.c 2011-05-19 18:35:57.000000000 +0300 -@@ -460,7 +460,10 @@ - } - - err = MPI_Allreduce(input, Return, count, currentType, currentOp, MPI_COMM_WORLD); -- if (err!=MPI_SUCCESS) printMPIerr(err, "Performing allreduce for %i elements\n",count); -+ if (err!=MPI_SUCCESS) { -+ printMPIerr(err, "Performing allreduce.\n"); -+ rprintf("Error: allreduce failed for %i elements.\n",count); -+ } - - if (parallel_check_error(err)!=0) return 1; - return 0; -diff -urN amber11//AmberTools/src/cpptraj/src/PtrajState.cpp amber11.new//AmberTools/src/cpptraj/src/PtrajState.cpp ---- amber11//AmberTools/src/cpptraj/src/PtrajState.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/PtrajState.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -7,7 +7,8 @@ - #include "CpptrajStdio.h" - - // Constructor --PtrajState::PtrajState() { -+PtrajState::PtrajState() { -+ TotalErrors=0; - debug=0; - showProgress=1; - } -@@ -291,6 +292,7 @@ - char *df_cmd = NULL; - char *name1 = NULL; - char *name2 = NULL; -+ int width,precision; - DataFile *df; - - if (DF_Args.empty()) return; -@@ -349,6 +351,19 @@ - } - mprintf(" Not printing x column for datafile %s\n",name1); - df->SetNoXcol(); -+ -+ // datafile precision -+ // Usage: datafile precision <filename> <dataset> [<width>] [<precision>] -+ // If width/precision not specified default to 12.4 -+ } else if ( strcmp(df_cmd,"precision")==0 ) { -+ if (df==NULL) { -+ mprintf("Error: datafile precision: DataFile %s does not exist.\n",name1); -+ continue; -+ } -+ name2 = A->getNextString(); -+ width = A->getNextInteger(12); -+ precision = A->getNextInteger(4); -+ df->SetPrecision(name2,width,precision); - } - - } // END loop over datafile args -@@ -374,7 +389,7 @@ - - // ========== S E T U P P H A S E ========== - // Calculate frame division among trajectories -- maxFrames=trajFileList.SetupFrames(); -+ maxFrames=trajFileList.SetupFrames(worldrank,worldsize); - - // Parameter file information - parmFileList.Print(); -diff -urN amber11//AmberTools/src/cpptraj/src/PtrajState.h amber11.new//AmberTools/src/cpptraj/src/PtrajState.h ---- amber11//AmberTools/src/cpptraj/src/PtrajState.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/PtrajState.h 2011-05-19 18:35:57.000000000 +0300 -@@ -20,6 +20,7 @@ - DataFileList DFL; // List of datafiles that data sets will be written to - ArgList *A; // Current argument list - std::list<ArgList*> DF_Args; // List of commands pertaining to datafile creation etc -+ int TotalErrors; // Sum of all returned error statuses - int debug; - - void SetGlobalDebug(int); // Set debug level for all components -diff -urN amber11//AmberTools/src/cpptraj/src/ReferenceList.cpp amber11.new//AmberTools/src/cpptraj/src/ReferenceList.cpp ---- amber11//AmberTools/src/cpptraj/src/ReferenceList.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/ReferenceList.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -20,11 +20,15 @@ - */ - int ReferenceList::Add(ArgList *A, ParmFileList *parmFileList, int worldsize) { - TrajFile *T; -- int startArg; -+ int startArg,stopArg,offsetArg; -+ bool average = false; - - // Set up common arguments from arglist - if (this->ProcessArgList(A,parmFileList)) return 1; - -+ // Check if we want to obtain the average structure -+ average = A->hasKey("average"); -+ - // Set up basic file to determine type and format - T = this->SetupTrajectory(trajfilename, fileAccess, UNKNOWN_FORMAT, UNKNOWN_TYPE); - -@@ -45,10 +49,18 @@ - // Get user-specified start arg - // NOTE: For compatibility with ptraj start from 1 - startArg=A->getNextInteger(1); -- T->SetArgs(startArg,startArg,1); -+ stopArg=startArg; -+ offsetArg=1; -+ // Get user-specified stop and offset only if getting avg structure -+ if (average) { -+ stopArg=A->getNextInteger(-1); -+ offsetArg=A->getNextInteger(1); -+ } -+ T->SetArgs(startArg,stopArg,offsetArg); - - // Add to trajectory file list -- this->push_back(T); -+ this->push_back(T); -+ Average.push_back(average); - - return 0; - } -@@ -60,9 +72,11 @@ - * place that frame in refFrames. - */ - int ReferenceList::SetupRefFrames(FrameList *refFrames) { -- int trajFrames; -- Frame *F; -+ int trajFrames, global_set; -+ double Nframes; -+ Frame *F, *AvgFrame; - int skipValue; -+ int refTrajNum = 0; - - mprintf("\nREFERENCE COORDS:\n"); - if (this->empty()) { -@@ -72,7 +86,13 @@ - - for (it = this->begin(); it != this->end(); it++) { - // Setup the reference traj for reading. Should only be 1 frame. -- trajFrames=(*it)->setupFrameInfo(-1); -+ // NOTE: For MPI, calling setupFrameInfo with worldrank 0, worldsize 1 for -+ // all ranks. This is to ensure each thread has a copy of the ref -+ // struct. -+ // Calling setupFrameInfo with -1 to ensure the Parm frame count is -+ // not updated. -+ -+ trajFrames=(*it)->setupFrameInfo(-1,0,1); - if ((*it)->total_read_frames<1) { - rprintf("Error: No frames could be read for reference %s, skipping\n", - (*it)->trajfilename); -@@ -89,12 +109,34 @@ - skipValue=(*it)->skip; - (*it)->skip=0; - } -- (*it)->Begin(&trajFrames, 0); -- // Get and copy the 1 frame from Traj, then close -- // NOTE: What happens when not seekable? -+ // Start trajectory read -+ global_set=0; -+ (*it)->Begin(&global_set, 0); - (*it)->PrintInfo(1); -- (*it)->NextFrame(&trajFrames); -- F=(*it)->F->Copy(); -+ // If averaging requested, loop over specified frames and avg coords. -+ if (Average[refTrajNum++]) { -+ mprintf(" Averaging over %i frames.\n",trajFrames); -+ AvgFrame = new Frame((*it)->P->natom, (*it)->P->mass); -+ AvgFrame->ZeroCoords(); -+ global_set = 0; -+ Nframes = 0.0; -+ while ( (*it)->NextFrame(&global_set) ) { -+ AvgFrame->AddCoord( (*it)->F ); -+ Nframes++; -+ } -+ if (Nframes < 1.0) { -+ mprintf("Error: reference average: # frames read is less than 1.\n"); -+ F=NULL; -+ } else { -+ AvgFrame->Divide( Nframes ); -+ F=AvgFrame->Copy(); -+ } -+ delete AvgFrame; -+ // If no averaging, get and copy the 1 frame from Traj, then close -+ } else { -+ (*it)->NextFrame(&trajFrames); -+ F=(*it)->F->Copy(); -+ } - // DEBUG - //fprintf(stdout,"DEBUG: Ref Coord Atom 0\n"); - //F->printAtomCoord(0); -diff -urN amber11//AmberTools/src/cpptraj/src/ReferenceList.h amber11.new//AmberTools/src/cpptraj/src/ReferenceList.h ---- amber11//AmberTools/src/cpptraj/src/ReferenceList.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/ReferenceList.h 2011-05-19 18:35:57.000000000 +0300 -@@ -5,7 +5,7 @@ - #include "FrameList.h" - - class ReferenceList : public CoordFileList { -- -+ std::vector<bool> Average; - public: - - ReferenceList(); -diff -urN amber11//AmberTools/src/cpptraj/src/RemdTraj.cpp amber11.new//AmberTools/src/cpptraj/src/RemdTraj.cpp ---- amber11//AmberTools/src/cpptraj/src/RemdTraj.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/RemdTraj.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -88,7 +88,7 @@ - // NOTE: Should check that this is the case for ALL frames. - stop = T->Frames; - Frames = T->Frames; -- isBox = T->isBox; -+ BoxType = T->BoxType; - trajfilename = T->File->basefilename; - // Add it to the list - REMDtraj.push_back(T); -@@ -190,12 +190,12 @@ - return 1; - } - // Check that #Frames and box info matches -- if ( Frames!=T->Frames || isBox!=T->isBox ) { -+ if ( Frames!=T->Frames || BoxType!=T->BoxType ) { - mprintf( -- " ERROR: REMDTRAJ: #Frames (%i) or box info (%i) in replica does not match\n", -- T->Frames, T->isBox); -- mprintf(" values in lowest replica (Frames=%i, box=%i)\n", -- Frames,isBox); -+ " ERROR: REMDTRAJ: #Frames (%i) or box type (%i) in replica does not match\n", -+ T->Frames, T->BoxType); -+ mprintf(" values in lowest replica (Frames=%i, boxtype=%i)\n", -+ Frames,BoxType); - delete T; - free(repFilename); - free(Prefix); -diff -urN amber11//AmberTools/src/cpptraj/src/stringDataSet.cpp amber11.new//AmberTools/src/cpptraj/src/stringDataSet.cpp ---- amber11//AmberTools/src/cpptraj/src/stringDataSet.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/stringDataSet.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -6,6 +6,13 @@ - #include "PtrajMpi.h" - #include "CpptrajStdio.h" - using namespace std; -+ -+// CONSTRUCTOR -+stringDataSet::stringDataSet() { -+ dType=STRING; -+ setFormatString(); -+} -+ - /* - * stringDataSet::Xmax(() - * Return the maximum X value added to this set. By convention this is -@@ -54,10 +61,10 @@ - - it = Data.find( frame ); - if (it == Data.end()) { -- sprintf(buffer," %s", "NoData"); -+ sprintf(buffer, format, "NoData"); - return (buffer + 7); - } else -- sprintf(buffer," %s",(*it).second.c_str()); -+ sprintf(buffer, format, (*it).second.c_str()); - - return (buffer + (*it).second.size() + 1); - } -diff -urN amber11//AmberTools/src/cpptraj/src/stringDataSet.h amber11.new//AmberTools/src/cpptraj/src/stringDataSet.h ---- amber11//AmberTools/src/cpptraj/src/stringDataSet.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/stringDataSet.h 2011-05-19 18:35:57.000000000 +0300 -@@ -12,6 +12,8 @@ - std::map<int,std::string> Data; - std::map<int,std::string>::iterator it; - public: -+ stringDataSet(); -+ - int Xmax(); - int isEmpty(int); - void Add( int, void * ); -diff -urN amber11//AmberTools/src/cpptraj/src/TrajFile.cpp amber11.new//AmberTools/src/cpptraj/src/TrajFile.cpp ---- amber11//AmberTools/src/cpptraj/src/TrajFile.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/TrajFile.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -2,7 +2,6 @@ - #include <cstdlib> - #include <cstring> - #include "TrajFile.h" --#include "PtrajMpi.h" // worldrank and worldsize needed to calc frame division - #include "CpptrajStdio.h" - - // CONSTRUCTOR -@@ -18,7 +17,7 @@ - start=0; - stop=-1; - offset=1; -- isBox=0; -+ BoxType=0; - title=NULL; - P=NULL; - frameskip=0; -@@ -45,12 +44,17 @@ - void TrajFile::SetTitle(char *titleIn) { - size_t titleSize; - -+ //mprintf("DEBUG: Attempting to set title for %s: [%s]\n",trajfilename,titleIn); - if (titleIn==NULL) return; - titleSize = strlen(titleIn); -- if (titleSize==0) return; -+ //mprintf(" Title size is %i\n",titleSize); -+ if (titleSize==0) { -+ mprintf("Warning: TrajFile::SetTitle(): Title for %s is 0 length.\n",trajfilename); -+ return; -+ } - this->title = (char*) malloc( (titleSize+1) * sizeof(char)); - if (this->title==NULL) { -- mprintf("Error: TrajFile::SetTitle(): Could not allocate memory for title.\n"); -+ mprintf("Error: SetTitle: Could not allocate memory for title of %s.\n",trajfilename); - return; - } - strcpy(this->title, titleIn); -@@ -59,6 +63,30 @@ - } - - /* -+ * TrajFile::CheckBoxType() -+ * Set the trajectory box type (ortho/nonortho) based on box angles. -+ * Check the current box type against the associated parmfile box type. -+ * Print a warning if they are different. -+ */ -+void TrajFile::CheckBoxType(double *box) { -+ // Determine orthogonal / non-orthogonal from angles -+ if (box[3]==0.0 || box[4]==0.0 || box[5]==0.0) -+ BoxType=0; -+ else if (box[3]==90.0 && box[4]==90.0 && box[5]==90.0) -+ BoxType=1; -+ else -+ BoxType=2; -+ if (P->BoxType != BoxType) { -+ mprintf("Warning: %s contains box info of type %i (beta %lf)\n",trajfilename, -+ BoxType,box[4]); -+ mprintf(" but associated parmfile %s has box type %i (beta %lf)\n",P->parmName, -+ P->BoxType,P->Box[4]); -+ //mprintf(" Box information from trajectory will be used.\n"); -+ } -+ if (debug>0) mprintf(" %s: Box type is %i (beta=%lf)\n",trajfilename,BoxType,box[4]); -+} -+ -+/* - * TrajFile::PrintInfo() - * Print general trajectory information. Call TrajFile->Info for specific information. - */ -@@ -68,7 +96,7 @@ - - mprintf(", Parm %i",P->pindex); - -- if (isBox) mprintf(" (with box info)"); -+ if (BoxType>0) mprintf(" (with box info)"); - - if (showExtended==0) { - mprintf("\n"); -@@ -85,7 +113,7 @@ - mprintf(": Writing %i frames", P->parmFrames); - if (File->access==APPEND) mprintf(", appended"); // NOTE: Dangerous if REMD - } -- if (debug>0) mprintf(", %i atoms, Box %i, seekable %i",P->natom,isBox,seekable); -+ if (debug>0) mprintf(", %i atoms, Box %i, seekable %i",P->natom,BoxType,seekable); - mprintf("\n"); - } - -@@ -164,7 +192,7 @@ - * Note that the input frames start counting from 1, output starts counting from 0! - * If called with maxFrames=-1 dont update the frame in parm file. - */ --int TrajFile::setupFrameInfo(int maxFrames) { -+int TrajFile::setupFrameInfo(int maxFrames, int worldrank, int worldsize) { - int Nframes; - int ptraj_start_frame, ptraj_end_frame; - int traj_start_frame, traj_end_frame; -diff -urN amber11//AmberTools/src/cpptraj/src/TrajFile.h amber11.new//AmberTools/src/cpptraj/src/TrajFile.h ---- amber11//AmberTools/src/cpptraj/src/TrajFile.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/TrajFile.h 2011-05-19 18:35:57.000000000 +0300 -@@ -25,44 +25,44 @@ - int offset; // Number of frames to skip while processing - - // --== Inherited by child classes ==-- -- virtual int open() { return 0; } // Open the file, prepare for coord read/write -- virtual void close() {} // Close the file -+ virtual int open() { return 0; } // Open the file, prepare for coord read/write -+ virtual void close() {} // Close the file -+ -+ void CheckBoxType(double *); // Check that traj boxtype matches parm - - public: - int debug; // Level of debug information to print - char *trajfilename; // The base trajectory filename -- // NOTE: I hate that the following are public. Only necessary for REMD processing!! -+ // NOTE: I hate that the 2 following are public. Only necessary for REMD processing!! - int Frames; // Total number of frames in trajectory - int total_read_frames; // Total number of frames that will be read -- int isBox; // >0 means trajectory has box information -- -+ int BoxType; // 0: None, 1: Ortho, 2: NonOrtho - Range *FrameRange; // list of frames to be written out - int hasTemperature; // 1 means trajectory has temperature information - PtrajFile *File; // Class that handles basic file IO - AmberParm *P; // Memory address of the associated parmfile - Frame *F; // Hold coordinates of the current frame -- int skip; /* READ: If =1 do not process this input trajectory -- WRITE: If =1 this traj has been set up for write */ -+ int skip; // READ: If =1 do not process this input trajectory -+ // WRITE: If =1 this traj has been set up for write - - TrajFile(); // Constructor - virtual ~TrajFile(); // Destructor - virtual since this class is inherited. - -- int Start() { return start; } -+ int Start() { return start; } -+ int CurrentFrame() { return currentFrame; } - void SetTitle(char *); // Set trajectory title. - void PrintInfo(int); // Print trajectory Information -- int setupFrameInfo(int); // Set actual start/stop based on total #frames and #threads -- int Begin(int *, int); /* Prepare traj for processing. Set output start value, calcd in -- * setupFrameInfo. Allocate memory for F. -- */ -- int Begin(); // Prepare trajectory for output -- int NextFrame(int*); // Put the next target frame into F. -- void End(); // Close trajectory and free F memory -- void progressBar(); // Display trajectory progress to screen --// void progressBar2(); // Display trajectory progress to screen -- -- void SetArgs(int,int,int); // Set the stop, start, and offset args from user input -+ int Begin(int *, int); // Prepare traj for processing. Set output start value, calcd in -+ // setupFrameInfo. Allocate memory for F. -+ int Begin(); // Prepare trajectory for output -+ int NextFrame(int*); // Put the next target frame into F. -+ void End(); // Close trajectory and free F memory -+ void progressBar(); // Display trajectory progress to screen -+// void progressBar2(); // Display trajectory progress to screen -+ int setupFrameInfo(int,int,int); // Set actual start/stop based on total #frames and #threads -+ void SetArgs(int,int,int); // Set the stop, start, and offset args from user input - // --== Inherited by child classes ==-- -- virtual int getFrame(int) { return 1; } // Read the next coord frame into F -+ virtual int getFrame(int) { return 1; } // Read specified frame into F - virtual int SetupRead() { return 1; } // Set file up for reading - virtual int WriteArgs(ArgList*){ return 0; } // (Opt.) Process any args related to writing - virtual int SetupWrite() { return 1; } // Set file up for writing -diff -urN amber11//AmberTools/src/cpptraj/src/TrajinList.cpp amber11.new//AmberTools/src/cpptraj/src/TrajinList.cpp ---- amber11//AmberTools/src/cpptraj/src/TrajinList.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/TrajinList.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -70,7 +70,7 @@ - * actual start and stop and how many frames total will be processed. - * Return the number of frames to be processed. - */ --int TrajinList::SetupFrames() { -+int TrajinList::SetupFrames(int worldrank, int worldsize) { - int maxFrames, trajFrames; - - mprintf("\nTRAJECTORIES:\n"); -@@ -78,7 +78,7 @@ - maxFrames=0; - - for (it = this->begin(); it != this->end(); it++) { -- trajFrames = (*it)->setupFrameInfo(maxFrames); -+ trajFrames = (*it)->setupFrameInfo(maxFrames,worldrank,worldsize); - if (trajFrames==-1) { - maxFrames=-1; - } -diff -urN amber11//AmberTools/src/cpptraj/src/TrajinList.h amber11.new//AmberTools/src/cpptraj/src/TrajinList.h ---- amber11//AmberTools/src/cpptraj/src/TrajinList.h 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/TrajinList.h 2011-05-19 18:35:57.000000000 +0300 -@@ -13,7 +13,7 @@ - // NOTE: worldsize is passed in as last arg to avoid include of PtrajMpi - int Add(ArgList *A, ParmFileList *, int); - // TRAJIN: Set up frames to be processed -- int SetupFrames(); -+ int SetupFrames(int,int); - }; - #endif - -diff -urN amber11//AmberTools/src/cpptraj/src/TrajoutList.cpp amber11.new//AmberTools/src/cpptraj/src/TrajoutList.cpp ---- amber11//AmberTools/src/cpptraj/src/TrajoutList.cpp 2011-04-14 15:30:16.000000000 +0300 -+++ amber11.new//AmberTools/src/cpptraj/src/TrajoutList.cpp 2011-05-19 18:35:57.000000000 +0300 -@@ -20,7 +20,6 @@ - */ - int TrajoutList::Add(ArgList *A, ParmFileList *parmFileList, int worldsize) { - TrajFile *T; -- int boxInfo; - FileFormat writeFormat; - FileType writeType; - char *onlyframes; -@@ -29,7 +28,6 @@ - if (this->ProcessArgList(A,parmFileList)) return 1; - - // Init variables -- boxInfo=0; - writeFormat=AMBERTRAJ; - writeType=UNKNOWN_TYPE; - -@@ -56,10 +54,6 @@ - if (worldsize>1 && writeFormat!=AMBERRESTART) - writeType=MPIFILE; - -- // Set box info from parm file unless nobox is set. -- boxInfo=P->ifbox; -- if (A->hasKey("nobox")) boxInfo=0; -- - // Set up basic file for given type and format - // If type is unknown it will be determined from extension or will be standard (default) - T = this->SetupTrajectory(trajfilename, fileAccess, writeFormat, writeType); -@@ -90,10 +84,11 @@ - // Set parameter file - T->P=P; - -- // Set box information (only needed for write) -- T->isBox=boxInfo; -+ // Set box type from parm file unless "nobox" specified -+ T->BoxType=P->BoxType; -+ if (A->hasKey("nobox")) T->BoxType=0; - -- // No setup here; Write is set up after first frame read in PtrajState::Run -+ // No more setup here; Write is set up when first frame written. - // Add to trajectory file list - this->push_back(T); - -diff -urN amber11//AmberTools/src/leap/src/leap/amber.c amber11.new//AmberTools/src/leap/src/leap/amber.c ---- amber11//AmberTools/src/leap/src/leap/amber.c 2011-03-10 20:12:06.000000000 +0200 -+++ amber11.new//AmberTools/src/leap/src/leap/amber.c 2011-05-19 18:35:57.000000000 +0300 -@@ -36,6 +36,10 @@ - * UNITs and PARMSETs. - */ - -+ /* Arunima Singh (UGA) */ -+ /* 20110420 */ -+ /* Added SCEE/SCNB */ -+ - #include "basics.h" - #include "vector.h" - #include "classes.h" -@@ -240,23 +244,47 @@ - * - * Read the proper torsion parameter terms. - */ -+ -+/* Arunima Singh added reading in of scee and scnb fields for proper torsions 20110420 */ - static void - zAmberReadParmSetPropers( PARMSET psParms, FILE *fIn ) - { - STRING sLine; --int iRead, iN; -+int iRead, iN, iRead2, iRead3; - STRING saStr[10]; --double dDivisions, dKp, dP0, dN; -+double dDivisions, dKp, dP0, dN, dScee, dScnb; -+char *cScee, *cScnb; - - memset(saStr, 0, sizeof(saStr)); /* for Purify */ - while (1) { - FGETS( sLine, fIn ); - NODASHES(sLine); -- iRead = sscanf( sLine, "%s %s %s %s %lf %lf %lf %lf", -+ -+ iRead = sscanf( sLine, "%s %s %s %s %lf %lf %lf %lf ", - saStr[0], saStr[1], saStr[2], saStr[3], - &dDivisions, &dKp, &dP0, &dN ); -- if ( iRead <= 0 ) -+ -+ cScee = strstr(sLine, "SCEE"); -+ if(cScee!=NULL) { -+ iRead2 = sscanf( cScee, "SCEE=%lf", &dScee); -+ iRead++; -+ } -+ -+ cScnb = strstr(sLine, "SCNB"); -+ if(cScnb!=NULL) { -+ iRead3 = sscanf( cScnb, "SCNB=%lf", &dScnb); -+ iRead++; -+ } -+ -+ if ( iRead <= 0 ) - break; -+ -+ if ( iRead == 8 ) /*Arunima Singh*/ -+ { -+ dScee = 1.2; -+ dScnb = 2.0; -+ } -+ - MESSAGE(( "Read: %s\n", sLine )); - - if ( sLine[0] == ' ' && sLine[1] == ' ') { -@@ -277,14 +305,37 @@ - zAmberConvertWildCard( saStr[3] ); - iParmSetAddProperTerm( psParms, - saStr[0], saStr[1], saStr[2], saStr[3], -- abs(iN), dKp, dP0*DEGTORAD, "" ); -+ abs(iN), dKp, dP0*DEGTORAD, dScee, dScnb, "" ); -+ -+ - while( iN < 0 ) { - FGETS( sLine, fIn ); - NODASHES(sLine); - MESSAGE(( "Read extra term: %s\n", sLine )); -- iRead = sscanf( &sLine[11], "%lf %lf %lf %lf", -+ iRead = sscanf( &sLine[11], "%lf %lf %lf %lf ", - &dDivisions, &dKp, &dP0, &dN ); -- if ( iRead<=0 ) break; -+ -+ cScee = strstr(sLine, "SCEE"); -+ if(cScee!=NULL) { -+ iRead2 = sscanf( cScee, "SCEE=%lf", &dScee); -+ iRead++; -+ } -+ -+ cScnb = strstr(sLine, "SCNB"); -+ if(cScnb!=NULL) { -+ iRead3 = sscanf( cScnb, "SCNB=%lf", &dScnb); -+ iRead++; -+ } -+ -+ -+ if ( iRead == 4 ) /*Arunima Singh*/ -+ { -+ dScee = 1.2; -+ dScnb = 2.0; -+ } -+ -+ -+ if ( iRead<=0 ) break; - - if ( dDivisions == 0.0 ) - dDivisions = 1.0; -@@ -292,7 +343,7 @@ - iN = (int)floor(dN+0.5); - iParmSetAddProperTerm( psParms, - saStr[0], saStr[1], saStr[2], saStr[3], -- abs(iN), dKp, dP0*DEGTORAD, "" ); -+ abs(iN), dKp, dP0*DEGTORAD, dScee, dScnb, "" ); - } - if ( iRead <= 0 ) - break; -@@ -311,7 +362,7 @@ - STRING sLine; - int iRead, iN; - STRING saStr[10]; --double dKp, dP0, dN; -+double dKp, dP0, dN, dScee, dScnb; - BOOL bPrintLine; - - memset(saStr, 0, sizeof(saStr)); /* for Purify */ -@@ -335,6 +386,8 @@ - zAmberConvertWildCard( saStr[2] ); - zAmberConvertWildCard( saStr[3] ); - iN = (int)dN; -+ dScee = 0.0; -+ dScnb = 0.0; - - /* - * check everything in case a format or other user error -@@ -362,7 +415,7 @@ - - iParmSetAddImproperTerm( psParms, - saStr[0], saStr[1], saStr[2], saStr[3], -- iN, dKp, dP0*DEGTORAD, "" ); -+ iN, dKp, dP0*DEGTORAD, dScee, dScnb, "" ); - } - if ( iRead > 0 ) - VP0(( "WARNING: incomplete Improper Torsion line:\n%s", sLine )); -diff -urN amber11//AmberTools/src/leap/src/leap/build.c amber11.new//AmberTools/src/leap/src/leap/build.c ---- amber11//AmberTools/src/leap/src/leap/build.c 2011-03-10 20:12:06.000000000 +0200 -+++ amber11.new//AmberTools/src/leap/src/leap/build.c 2011-05-19 18:35:57.000000000 +0300 -@@ -42,8 +42,9 @@ - * - */ - -- -- -+ /* Arunima Singh (UGA) */ -+ /* 20110420 */ -+ /* Added SCEE/SCNB */ - - #include "basics.h" - -@@ -1567,7 +1568,7 @@ - LOOP lAtoms, lTemp; - ATOM aAtom, aAtom1, aAtom2, aAtom3, aAtom4; - BOOL bM1, bM2, bM3, bM4, bOneMinimizedAtom; --double dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0; -+double dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0, dScee, dScnb; - STRING sAtom1, sAtom2, sAtom3, sAtom4, sDesc; - PARMSET psTemp; - TORSION tTorsion; -@@ -1757,7 +1758,7 @@ - ParmSetTORSIONTerm( tTorsion, i, - &iIndex, - sAtom1, sAtom2, sAtom3, sAtom4, -- &iN, &dKp, &dP0, sDesc ); -+ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc ); - if ( !bMinimizerAddTorsion( mStrain, - aAtom1, aAtom2, aAtom3, aAtom4, - (double)iN, dKp, dP0 )) { -diff -urN amber11//AmberTools/src/leap/src/leap/model.c amber11.new//AmberTools/src/leap/src/leap/model.c ---- amber11//AmberTools/src/leap/src/leap/model.c 2011-04-14 15:30:17.000000000 +0300 -+++ amber11.new//AmberTools/src/leap/src/leap/model.c 2011-05-19 18:35:57.000000000 +0300 -@@ -39,7 +39,9 @@ - * are determined from atom types. - */ - -- -+ /* Arunima Singh (UGA) */ -+ /* 20110420 */ -+ /* Added SCEE/SCNB */ - - - #include "basics.h" -@@ -781,16 +783,6 @@ - maPAtom++; - } - } -- if ( iAtomCoordination(aX) != -- 1 + maPAtom - &(mtTorsions.maaXBonds[0]) ) { -- VP0(( "Error: Atom %s has force field coordination %i\n" -- " but only %i bonded neighbors.\n" -- " The cause may be an incorrect atom type, and\n" -- " the effect may be a crash very soon.\n", -- sContainerFullDescriptor((CONTAINER)aX,s1), -- iAtomCoordination(aX), -- 1 + maPAtom - &(mtTorsions.maaXBonds[0]) )); -- } - for ( i=iAtomCoordination(aX); i<MAXBONDS; i++ ) { - maPAtom->aAtom = NULL; - maPAtom++; -@@ -824,16 +816,6 @@ - maPAtom++; - } - } -- if ( iAtomCoordination(aY) != -- 1 + maPAtom - &(mtTorsions.maaYBonds[0]) ) { -- VP0(( "Error: Atom %s has force field coordination %i\n" -- " but only %i bonded neighbors.\n" -- " The cause may be an incorrect atom type, and\n" -- " the effect may be a crash very soon.\n", -- sContainerFullDescriptor((CONTAINER)aY,s1), -- iAtomCoordination(aY), -- 1 + maPAtom - &(mtTorsions.maaYBonds[0]) )); -- } - for ( i=iAtomCoordination(aY); i<MAXBONDS; i++ ) { - maPAtom->aAtom = NULL; - maPAtom++; -@@ -1205,6 +1187,8 @@ - int iN; - double dK; - double dE; -+ double dSce; /*Arunima Singh*/ -+ double dScn; /*Arunima Singh*/ - } H_PROPERPARMt; - - typedef struct { -@@ -1222,12 +1206,13 @@ - - /* Keep iHybrid2 <= iHybrid3 */ - -+/* Arunima Singh 20110413. Added Scee and Scnb AMBER defaults of 1.2 and 2.0 */ - #define TFORCE 20.0 - static H_PROPERPARMt SppaPropers[] = { --{ HSP3, HSP3, 3, 1.0, 0.0 }, /* Non bond */ --{ HSP2, HSP3, 6, -2.0, 0.0 }, /* Non bond */ --{ HSP2, HSP2, 2, -4.0, 0.0 }, /* Pi bond overlap */ --{ HSP1, HSP1, 1, 0.0, 0.0 } /* Not interesting */ -+{ HSP3, HSP3, 3, 1.0, 0.0, 1.2, 2.0 }, /* Non bond */ -+{ HSP2, HSP3, 6, -2.0, 0.0, 1.2, 2.0 }, /* Non bond */ -+{ HSP2, HSP2, 2, -4.0, 0.0, 1.2, 2.0 }, /* Pi bond overlap */ -+{ HSP1, HSP1, 1, 0.0, 0.0, 1.2, 2.0 } /* Not interesting */ - }; - - #define AFORCE 100.0 -@@ -1290,6 +1275,8 @@ - SppaPropers[i].iN, - SppaPropers[i].dK, - SppaPropers[i].dE, -+ SppaPropers[i].dSce, -+ SppaPropers[i].dScn, - sDesc ); - } - } -diff -urN amber11//AmberTools/src/leap/src/leap/parmSet.c amber11.new//AmberTools/src/leap/src/leap/parmSet.c ---- amber11//AmberTools/src/leap/src/leap/parmSet.c 2011-03-10 20:12:06.000000000 +0200 -+++ amber11.new//AmberTools/src/leap/src/leap/parmSet.c 2011-05-19 18:35:57.000000000 +0300 -@@ -54,7 +54,9 @@ - * search routines REQUIRE pre-ordering. - */ - -- -+ /* Arunima Singh (UGA) */ -+ /* 20110420 */ -+ /* Added SCEE/SCNB */ - - #include "basics.h" - -@@ -965,6 +967,8 @@ - /* - * copy into 1 vararray & set iType - */ -+ -+ /*Arunima Singh added scee and scnb into the database */ - vaTorsTypes = vaVarArrayCopy2( psLib->vaTorsions, psLib->vaImpropers ); - tP = PVAI(vaTorsTypes,TORSIONPARMt,0); - for (i=0; i<iVarArrayElementCount(psLib->vaTorsions); i++, tP++) -@@ -980,8 +984,12 @@ - 7, "n", - (char *)&(PVAI(vaTorsTypes,TORSIONPARMt,0)->iN), - iVarArrayElementSize(vaTorsTypes), -- 0, NULL, NULL, 0, -- 0, NULL, NULL, 0, -+ 9, "scee", -+ (char *)&(PVAI(vaTorsTypes,TORSIONPARMt,0)->dScee), -+ iVarArrayElementSize(vaTorsTypes), -+ 10, "scnb", -+ (char *)&(PVAI(vaTorsTypes,TORSIONPARMt,0)->dScnb), -+ iVarArrayElementSize(vaTorsTypes), - 0, NULL, NULL, 0, - 0, NULL, NULL, 0, - 0, NULL, NULL, 0, -@@ -1008,7 +1016,7 @@ - 4, "type4", - (char *)&(PVAI(vaTorsTypes,TORSIONPARMt,0)->sType4), - iVarArrayElementSize(vaTorsTypes), -- 9, "desc", -+ 11, "desc", - (char *)&(PVAI(vaTorsTypes,TORSIONPARMt,0)->sDesc), - iVarArrayElementSize(vaTorsTypes) - ); -@@ -1586,10 +1594,15 @@ - * Add a torsion parameter to the PARMSET. - * Return the index. - */ -+ -+ /* Arunima Singh (UGA) */ -+ /* 20110420 */ -+ /* Added SCEE/SCNB */ -+ - int - iParmSetAddProperTerm( PARMSET psLib, - char *sType1, char *sType2, char *sType3, char *sType4, -- int iN, double dKp, double dP0, char *sDesc ) -+ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc ) - { - TORSIONPARMt tpTorsion; - -@@ -1605,6 +1618,8 @@ - tpTorsion.dKp = dKp; - tpTorsion.iN = iN; - tpTorsion.dP0 = dP0; -+ tpTorsion.dScee = dScee; -+ tpTorsion.dScnb = dScnb; - strcpy( tpTorsion.sOrder, "0123" ); - if ( sDesc != NULL ) - strcpy( tpTorsion.sDesc, sDesc ); -@@ -1633,7 +1648,7 @@ - int - iParmSetAddImproperTerm( PARMSET psLib, - char *sType1, char *sType2, char *sType3, char *sType4, -- int iN, double dKp, double dP0, char *sDesc ) -+ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc ) - { - TORSIONPARMt tpImproper; - orderStr sOrder; -@@ -2022,7 +2037,7 @@ - void - ParmSetTORSIONTerm( TORSION tTorsion, int iTorsionIndex, int *iPParmSetIndex, - char *cPType1, char *cPType2, char *cPType3, char *cPType4, -- int *iPN, double *dPKp, double *dPP0, char *sDesc ) -+ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc ) - { - TORSION_MATCHt *tmPCur; - -@@ -2035,6 +2050,8 @@ - *iPN = tmPCur->tpTorsion.iN; - *dPKp = tmPCur->tpTorsion.dKp; - *dPP0 = tmPCur->tpTorsion.dP0; -+ *dPScee = tmPCur->tpTorsion.dScee; -+ *dPScnb = tmPCur->tpTorsion.dScnb; - strcpy(sDesc, tmPCur->tpTorsion.sDesc); - } - -@@ -2050,7 +2067,7 @@ - BOOL - bParmSetTORSIONAddProperTerm( TORSION tTorsion, - char *cPType1, char *cPType2, char *cPType3, char *cPType4, -- int iN, double dKp, double dP0, char *sDesc ) -+ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc ) - { - TORSIONPARMt tpTorsion; - -@@ -2066,6 +2083,8 @@ - tpTorsion.iN = iN; - tpTorsion.dKp = dKp; - tpTorsion.dP0 = dP0; -+ tpTorsion.dScee = dScee; -+ tpTorsion.dScnb = dScnb; - strcpy(tpTorsion.sDesc, sDesc); - strcpy( tpTorsion.sOrder, "0123" ); - -@@ -2087,7 +2106,7 @@ - BOOL - bParmSetTORSIONAddImproperTerm( TORSION tTorsion, - char *cPType1, char *cPType2, char *cPType3, char *cPType4, -- int iN, double dKp, double dP0, char *sDesc ) -+ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc ) - { - TORSIONPARMt tpTorsion; - orderStr sOrder; -@@ -2104,6 +2123,8 @@ - tpTorsion.iN = iN; - tpTorsion.dKp = dKp; - tpTorsion.dP0 = dP0; -+ tpTorsion.dScee = dScee; -+ tpTorsion.dScnb = dScnb; - strcpy(tpTorsion.sDesc, sDesc); - strcpy( tpTorsion.sOrder, sOrder ); - -@@ -2516,7 +2537,7 @@ - void - ParmSetTorsion( PARMSET psLib, int i, - char *sType1, char *sType2, char *sType3, char *sType4, -- int *iPN, double *dPKp, double *dPP0, char *sDesc) -+ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc) - { - TORSIONPARMt *tpPTorsion; - -@@ -2531,6 +2552,8 @@ - strcpy( sType4, WILD_CARD_TYPE ); - *iPN = 0; - *dPKp = 0; -+ *dPScee = 0; -+ *dPScnb = 0; - *dPP0 = 0; - strcpy( sDesc, "??" ); - return; -@@ -2543,7 +2566,10 @@ - *iPN = tpPTorsion->iN; - *dPKp = tpPTorsion->dKp; - *dPP0 = tpPTorsion->dP0; -+ *dPScee = tpPTorsion->dScee; -+ *dPScnb = tpPTorsion->dScnb; - strcpy( sDesc, tpPTorsion->sDesc ); -+ - } - - -@@ -2557,7 +2583,7 @@ - void - ParmSetImproper( PARMSET psLib, int i, - char *sType1, char *sType2, char *sType3, char *sType4, -- int *iPN, double *dPKp, double *dPP0, char *sDesc) -+ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc) - { - TORSIONPARMt *tpPImproper; - -@@ -2573,6 +2599,8 @@ - *iPN = 0; - *dPKp = 0; - *dPP0 = 0; -+ *dPScee = 0; -+ *dPScnb = 0; - strcpy( sDesc, "??" ); - return; - } -@@ -2584,6 +2612,8 @@ - *iPN = tpPImproper->iN; - *dPKp = tpPImproper->dKp; - *dPP0 = tpPImproper->dP0; -+ *dPScee = tpPImproper->dScee; -+ *dPScnb = tpPImproper->dScnb; - strcpy( sDesc, tpPImproper->sDesc ); - } - -@@ -2740,7 +2770,7 @@ - void - ParmSetUpdateTorsion( PARMSET psLib, int i, - char *sType1, char *sType2, char *sType3, char *sType4, -- int *iPN, double *dPKp, double *dPP0, char *sDescription) -+ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDescription) - { - TORSIONPARMt *tpPTorsion; - orderStr sOrder; -@@ -2754,6 +2784,8 @@ - if ( iPN != (int*)NULL ) tpPTorsion->iN = *iPN; - if ( dPKp != (double*)NULL) tpPTorsion->dKp = *dPKp; - if ( dPP0 != (double*)NULL) tpPTorsion->dP0 = *dPP0; -+ if ( dPScee != (double*)NULL) tpPTorsion->dScee = *dPScee; -+ if ( dPScnb != (double*)NULL) tpPTorsion->dScnb = *dPScnb; - if (sDescription != (char*)NULL ) strcpy(tpPTorsion->sDesc, sDescription); - - strcpy( sOrder, "0123" ); -@@ -2777,7 +2809,7 @@ - void - ParmSetUpdateImproper( PARMSET psLib, int i, - char *sType1, char *sType2, char *sType3, char *sType4, -- int *iPN, double *dPKp, double *dPP0, char *sDescription) -+ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDescription) - { - TORSIONPARMt *tpPTorsion; - orderStr sOrder; -@@ -2790,6 +2822,8 @@ - if ( iPN != (int*)NULL ) tpPTorsion->iN = *iPN; - if ( dPKp != (double*)NULL) tpPTorsion->dKp = *dPKp; - if ( dPP0 != (double*)NULL) tpPTorsion->dP0 = *dPP0; -+ if ( dPScee != (double*)NULL) tpPTorsion->dScee = *dPScee; -+ if ( dPScnb != (double*)NULL) tpPTorsion->dScnb = *dPScnb; - if (sDescription != (char*)NULL ) strcpy(tpPTorsion->sDesc, sDescription); - - strcpy( sOrder, "0123" ); -@@ -2979,6 +3013,7 @@ - tpPCur->sType1, tpPCur->sType2, - tpPCur->sType3, tpPCur->sType4, - tpPCur->iN, tpPCur->dKp, tpPCur->dP0/DEGTORAD, -+ tpPCur->dScee, tpPCur->dScnb, - tpPCur->sOrder, tpPCur->sDesc ); - } - } -@@ -2996,6 +3031,7 @@ - tpPCur->sType1, tpPCur->sType2, - tpPCur->sType3, tpPCur->sType4, - tpPCur->iN, tpPCur->dKp, tpPCur->dP0/DEGTORAD, -+ tpPCur->dScee, tpPCur->dScnb, - tpPCur->sDesc ); - } - } -diff -urN amber11//AmberTools/src/leap/src/leap/parmSet.h amber11.new//AmberTools/src/leap/src/leap/parmSet.h ---- amber11//AmberTools/src/leap/src/leap/parmSet.h 2011-03-10 20:12:06.000000000 +0200 -+++ amber11.new//AmberTools/src/leap/src/leap/parmSet.h 2011-05-19 18:35:57.000000000 +0300 -@@ -42,6 +42,9 @@ - * - * - */ -+ /* Arunima Singh (UGA) */ -+ /* 20110420 */ -+ /* Added SCEE/SCNB */ - - #ifndef PARMSET_H - #define PARMSET_H -@@ -96,6 +99,8 @@ - int iN; - double dKp; - double dP0; -+ double dScee; /* for propers */ /* Arunima Singh */ -+ double dScnb; /* for propers */ /* Arunima Singh */ - orderStr sOrder; /* for impropers */ - DESCRIPTION sDesc; - } TORSIONPARMt; -@@ -158,10 +163,10 @@ - double dKt, double dT0, double dTkub, double dRkub, char *sDesc); - extern int iParmSetAddProperTerm(PARMSET psLib, - char *sType1, char *sType2, char *sType3, char *sType4, -- int iN, double dKp, double dP0, char *sDesc); -+ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc); /* for proper dihedrals */ /* Arunima Singh */ - extern int iParmSetAddImproperTerm(PARMSET psLib, - char *sType1, char *sType2, char *sType3, char *sType4, -- int iN, double dKp, double dP0, char *sDesc); -+ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc); /* Arunima Singh : added for proper dihedrals, but has to be included in impropers to maintain common data structure usage */ - extern int iParmSetAddHBond(PARMSET psLib, char *sType1, char *sType2, - double dA, double dB, char *sDesc); - -@@ -216,15 +221,15 @@ - extern void ParmSetTORSIONTerm(TORSION tTorsion, int iTorsionIndex, - int *iPParmSetIndex, - char *cPTyp1, char *cPTyp2, char *cPTyp3, char *cPTyp4, -- int *iPN, double *dPKp, double *dPP0, char *sDesc ); -+ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc ); - extern BOOL bParmSetTORSIONAddProperTerm(TORSION tTorsion, - char *cPType1, char *cPType2, - char *cPType3, char *cPType4, -- int iN, double dKp, double dP0, char *sDesc); -+ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc); - extern BOOL bParmSetTORSIONAddImproperTerm(TORSION tTorsion, - char *cPType1, char *cPType2, - char *cPType3, char *cPType4, -- int iN, double dKp, double dP0, char *sDesc); -+ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc); - extern void ParmSetTORSIONOrderAtoms(); - extern void ParmSetImproperOrderAtoms( TORSION tTorsion, int iTorsionIndex, - char *cPaTypes[4], int iaIndexes[4] ); -@@ -268,10 +273,10 @@ - char *sDesc); - extern void ParmSetTorsion(PARMSET psLib, int i, - char *sType1, char *sType2, char *sType3, char *sType4, -- int *iPN, double *dPKp, double *dPP0, char *sDesc); -+ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc); - extern void ParmSetImproper(PARMSET psLib, int i, - char *sType1, char *sType2, char *sType3, char *sType4, -- int *iPN, double *dPKp, double *dPP0, char *sDesc); -+ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc); - extern void ParmSetHBond(PARMSET psLib, int i, char *sType1, char *sType2, - double *dPA, double *dPB, char *sDesc); - -@@ -296,11 +301,11 @@ - double *dPKt, double *dPT0, char *sDescription); - extern void ParmSetUpdateTorsion(PARMSET psLib, int i, - char *sType1, char *sType2, char *sType3, char *sType4, -- int *iPN, double *dPKp, double *dPP0, -+ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, - char *sDescription); - extern void ParmSetUpdateImproper(PARMSET psLib, int i, - char *sType1, char *sType2, char *sType3, char *sType4, -- int *iPN, double *dPKp, double *dPP0, -+ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, - char *sDescription); - extern void ParmSetUpdateHBond(PARMSET psLib, int i, - char *sType1, char *sType2, -diff -urN amber11//AmberTools/src/leap/src/leap/unitio.c amber11.new//AmberTools/src/leap/src/leap/unitio.c ---- amber11//AmberTools/src/leap/src/leap/unitio.c 2011-03-10 20:12:06.000000000 +0200 -+++ amber11.new//AmberTools/src/leap/src/leap/unitio.c 2011-05-19 18:35:57.000000000 +0300 -@@ -70,6 +70,10 @@ - * zbUnitIOIndexBondParameters and zUnitDoAtoms are now "extern functions" - */ - -+ /* Arunima Singh (UGA) */ -+ /* 20110420 */ -+ /* Added SCEE/SCNB */ -+ - #include <time.h> - - #include "basics.h" -@@ -1585,7 +1589,9 @@ - tC.dKp = tpA->dKp; - tC.iN = tpA->iN; - tC.dP0 = tpA->dP0; -- VarArrayAdd(vaB, (GENP) & tC); -+ tC.dScee = tpA->dScee; -+ tC.dScnb = tpA->dScnb; -+ VarArrayAdd(vaB, (GENP) & tC); - iIndex++; - iOldIndex = iParmOffset + iA + 1; - -@@ -1615,6 +1621,10 @@ - continue; - if (tpB->dP0 != tpA->dP0) - continue; -+ if (tpB->dScee != tpA->dScee) -+ continue; -+ if (tpB->dScnb != tpA->dScnb) -+ continue; - - /* - * B is a duplicate of A -@@ -1698,12 +1708,12 @@ - int iTerm, iPertTerm; - BOOL bDone, bUse, bUsePert, bCopy, bCopyPert, bEnd, bPertEnd; - int iN, iPertIndex, iPertN, iLastN, iLastPertN; -- double dKp, dP0, dPertKp, dPertP0; -+ double dKp, dP0, dScee, dScnb, dPertKp, dPertP0, dPertScee, dPertScnb; - BOOL bCalc14, bCalcPert14; - #ifdef DEBUG2 - STRING s1, s2, s3, s4; - int iTParm, iTmp; -- double dTK, dTP; -+ double dTK, dTP, dTScee, dTScnb; - STRING sT1, sT2, sT3, sT4, sTemp; - #endif - STRING sDesc; -@@ -2016,9 +2026,9 @@ - ParmSetTORSIONTerm(tTorsion, i, - &iTParm, - sT1, sT2, sT3, sT4, -- &iTmp, &dTK, &dTP, sTemp); -- MESSAGE(("Term %3d %d %s-%s-%s-%s %d %lf %lf\n", -- i, iTParm, sT1, sT2, sT3, sT4, iTmp, dTK, dTP)); -+ &iTmp, &dTK, &dTP, &dTScee, &dTScnb, sTemp); -+ MESSAGE(("Term %3d %d %s-%s-%s-%s %d %lf %lf %lf %lf\n", -+ i, iTParm, sT1, sT2, sT3, sT4, iTmp, dTK, dTP, dTScee, dTScnb)); - } - if (bPerturbTorsion) { - MESSAGE(("Pert%s %s-%s-%s-%s found %d terms\n", -@@ -2029,9 +2039,9 @@ - ParmSetTORSIONTerm(tPertTorsion, i, - &iTParm, - sT1, sT2, sT3, sT4, -- &iTmp, &dTK, &dTP, sTemp); -- MESSAGE(("Term %3d %d %s-%s-%s-%s %d %lf %lf\n", -- i, iTParm, sT1, sT2, sT3, sT4, iTmp, dTK, dTP)); -+ &iTmp, &dTK, &dTP, &dTScee, &dTScnb, sTemp); -+ MESSAGE(("Term %3d %d %s-%s-%s-%s %d %lf %lf %lf %lf\n", -+ i, iTParm, sT1, sT2, sT3, sT4, iTmp, dTK, dTP dTScee, dTScnb)); - } - } - #endif -@@ -2061,7 +2071,7 @@ - ParmSetTORSIONTerm(tTorsion, iTerm, - &iIndex, - sAtom1, sAtom2, sAtom3, sAtom4, -- &iN, &dKp, &dP0, sDesc); -+ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); - MESSAGE(("First non-perturbed multiplicity: %d\n", iN)); - } else { - if (bProper) { -@@ -2082,7 +2092,7 @@ - ParmSetTORSIONTerm(tPertTorsion, iPertTerm, - &iPertIndex, - sPert1, sPert2, sPert3, sPert4, -- &iPertN, &dPertKp, &dPertP0, sDesc); -+ &iPertN, &dPertKp, &dPertP0, &dPertScee, &dPertScnb, sDesc); - MESSAGE(("First perturbed multiplicity: %d\n", iPertN)); - } else - bPertEnd = TRUE; -@@ -2175,14 +2185,14 @@ - if (bProper) - iIndex = iParmSetAddProperTerm(uUnit->psParameters, - sAtom1, sAtom2, sAtom3, -- sAtom4, iN, dKp, dP0, -- sDesc); -+ sAtom4, iN, dKp, dP0, -+ dScee, dScnb, sDesc); - /* else if ( !GDefaults.iCharmm ) ???---should I do this???? */ - else - iIndex = iParmSetAddImproperTerm(uUnit->psParameters, - sAtom1, sAtom2, - sAtom3, sAtom4, iN, -- dKp, dP0, sDesc); -+ dKp, dP0, dScee, dScnb, sDesc); - } - if (bCopyPert) { - if (bProper) { -@@ -2190,13 +2200,13 @@ - sPert1, sPert2, - sPert3, sPert4, - iPertN, dPertKp, -- dPertP0, sDesc); -+ dPertP0, dScee, dScnb, sDesc); - } else { - iPertIndex = - iParmSetAddImproperTerm(uUnit->psParameters, - sPert1, sPert2, sPert3, - sPert4, iPertN, dPertKp, -- dPertP0, sDesc); -+ dPertP0, dScee, dScnb, sDesc); - } - MESSAGE(("iPertIndex = %d\n", iPertIndex)); - } -@@ -2215,7 +2225,7 @@ - ParmSetTORSIONTerm(tTorsion, iTerm, - &iIndex, - sAtom1, sAtom2, sAtom3, sAtom4, -- &iN, &dKp, &dP0, sDesc); -+ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); - } - MESSAGE( - ("Advancing non-perturbed multiplicity to %d\n", -@@ -2231,7 +2241,7 @@ - ParmSetTORSIONTerm(tPertTorsion, iPertTerm, - &iPertIndex, - sPert1, sPert2, sPert3, sPert4, -- &iPertN, &dPertKp, &dPertP0, sDesc); -+ &iPertN, &dPertKp, &dPertP0, &dPertScee, &dPertScnb, sDesc); - } - MESSAGE( - ("Advancing perturbed multiplicity to %d\n", -@@ -3988,7 +3998,7 @@ - SAVEATOMt *saPAtom; - SAVETORSIONt *stPTorsion; - SAVERESTRAINTt *srPRestraint; -- double dMass, dPolar, dR, dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0, -+ double dMass, dPolar, dR, dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0, dScee, dScnb, - dC, dD, dTemp; - STRING sAtom1, sAtom2, sAtom3, sAtom4, sType1, sType2; - int iN, iAtoms, iMaxAtoms, iTemp, iAtom, iCalc14, iProper; -@@ -4585,16 +4595,16 @@ - iParmSetTotalImproperParms(uUnit->psParameters))); - for (i = 0; i < iParmSetTotalTorsionParms(uUnit->psParameters); i++) { - ParmSetTorsion(uUnit->psParameters, i, sAtom1, sAtom2, -- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc); -- MESSAGE(("Torsion %d %s-%s-%s-%s %d %lf %lf\n", -- i, sAtom1, sAtom2, sAtom3, sAtom4, iN, dKp, dP0)); -+ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); -+ MESSAGE(("Torsion %d %s-%s-%s-%s %d %lf %lf %lf %lf\n", -+ i, sAtom1, sAtom2, sAtom3, sAtom4, iN, dKp, dP0, dScee, dScnb)); - FortranWriteDouble(dKp); - } - for (i = 0; i < iParmSetTotalImproperParms(uUnit->psParameters); i++) { - ParmSetImproper(uUnit->psParameters, i, sAtom1, sAtom2, -- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc); -- MESSAGE(("Improper %d %s-%s-%s-%s %d %lf %lf\n", -- i, sAtom1, sAtom2, sAtom3, sAtom4, iN, dKp, dP0)); -+ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); -+ MESSAGE(("Improper %d %s-%s-%s-%s %d %lf %lf %lf %lf\n", -+ i, sAtom1, sAtom2, sAtom3, sAtom4, iN, dKp, dP0, dScee, dScnb)); - FortranWriteDouble(dKp); - } - /* Write the torsion RESTRAINT constants AND set the index */ -@@ -4612,13 +4622,13 @@ - FortranFormat(5, DBLFORMAT); - for (i = 0; i < iParmSetTotalTorsionParms(uUnit->psParameters); i++) { - ParmSetTorsion(uUnit->psParameters, i, sAtom1, sAtom2, -- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc); -+ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); - dTemp = iN; - FortranWriteDouble(dTemp); - } - for (i = 0; i < iParmSetTotalImproperParms(uUnit->psParameters); i++) { - ParmSetImproper(uUnit->psParameters, i, sAtom1, sAtom2, -- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc); -+ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); - dTemp = iN; - FortranWriteDouble(dTemp); - } -@@ -4637,12 +4647,12 @@ - FortranFormat(5, DBLFORMAT); - for (i = 0; i < iParmSetTotalTorsionParms(uUnit->psParameters); i++) { - ParmSetTorsion(uUnit->psParameters, i, sAtom1, sAtom2, -- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc); -+ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); - FortranWriteDouble(dP0); - } - for (i = 0; i < iParmSetTotalImproperParms(uUnit->psParameters); i++) { - ParmSetImproper(uUnit->psParameters, i, sAtom1, sAtom2, -- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc); -+ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); - FortranWriteDouble(dP0); - } - /* Write the torsion RESTRAINT constants AND set the index */ -@@ -4650,6 +4660,60 @@ - RESTRAINTLOOP(RESTRAINTTORSION, dN, i + 1); - FortranEndLine(); - -+ /* Arunima Singh (UGA) */ -+ /* 20110420 */ -+ /* Added Printing SCEE/SCNB */ -+ -+ -+ /* -17.5A- SCEE for torsions */ -+ FortranDebug("-17.5A-"); -+ -+ MESSAGE(("Writing SCEE scale factor for torsion interaction\n")); -+ FortranFormat(1, "%-80s"); -+ FortranWriteString("%FLAG SCEE_SCALE_FACTOR"); -+ FortranWriteString("%FORMAT(5E16.8)"); -+ FortranFormat(5, DBLFORMAT); -+ for (i = 0; i < iParmSetTotalTorsionParms(uUnit->psParameters); i++) { -+ ParmSetTorsion(uUnit->psParameters, i, sAtom1, sAtom2, -+ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); -+ FortranWriteDouble(dScee); -+ } -+ for (i = 0; i < iParmSetTotalImproperParms(uUnit->psParameters); i++) { -+ ParmSetImproper(uUnit->psParameters, i, sAtom1, sAtom2, -+ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); -+ FortranWriteDouble(dScee); -+ } -+ /* Write the torsion RESTRAINT constants AND set the index */ -+ /* for where the interaction can find its constants */ -+ RESTRAINTLOOP(RESTRAINTTORSION, dX0, i + 1); -+ FortranEndLine(); -+ -+ /* -17.5B- SCNB for torsions */ -+ FortranDebug("-17.5B-"); -+ -+ MESSAGE(("Writing SCNB scale factor for torsion interaction\n")); -+ FortranFormat(1, "%-80s"); -+ FortranWriteString("%FLAG SCNB_SCALE_FACTOR"); -+ FortranWriteString("%FORMAT(5E16.8)"); -+ FortranFormat(5, DBLFORMAT); -+ for (i = 0; i < iParmSetTotalTorsionParms(uUnit->psParameters); i++) { -+ ParmSetTorsion(uUnit->psParameters, i, sAtom1, sAtom2, -+ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); -+ FortranWriteDouble(dScnb); -+ } -+ for (i = 0; i < iParmSetTotalImproperParms(uUnit->psParameters); i++) { -+ ParmSetImproper(uUnit->psParameters, i, sAtom1, sAtom2, -+ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc); -+ FortranWriteDouble(dScnb); -+ } -+ /* Write the torsion RESTRAINT constants AND set the index */ -+ /* for where the interaction can find its constants */ -+ RESTRAINTLOOP(RESTRAINTTORSION, dX0, i + 1); -+ FortranEndLine(); -+ -+ /* Arunima Singh */ -+ /* End of adding SCEE/SCNB */ -+ - /* -18- Not used, reserved for future use, uses NATYP */ - /* Corresponds to the AMBER SOLTY array */ - FortranDebug("-18-"); -@@ -6009,7 +6073,7 @@ - SAVEATOMt *saPAtom; - SAVETORSIONt *stPTorsion; - SAVERESTRAINTt *srPRestraint; --double dMass, dPolar, dR, dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0, dC, dD, dTemp; -+double dMass, dPolar, dR, dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0, dScee, dScnb, dC, dD, dTemp; - STRING sAtom1, sAtom2, sAtom3, sAtom4, sType1, sType2; - int iN, iAtoms, iMaxAtoms, iTemp, iAtom, iCalc14, iProper; - int iElement, iHybridization, iStart, iFirstSolvent; -@@ -6547,19 +6611,19 @@ - for ( i=0; i<iParmSetTotalTorsionParms(uUnit->psParameters); i++ ) { - ParmSetTorsion( uUnit->psParameters, i, sAtom1, sAtom2, - sAtom3, sAtom4, -- &iN, &dKp, &dP0, sDesc ); -- MESSAGE(( "Torsion %d %s-%s-%s-%s %d %lf %lf\n", -+ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc ); -+ MESSAGE(( "Torsion %d %s-%s-%s-%s %d %lf %lf %lf %lf\n", - i, sAtom1, sAtom2, sAtom3, sAtom4, -- iN, dKp, dP0 )); -+ iN, dKp, dP0, dScee, dScnb )); - FortranWriteDouble( dKp ); - } - for ( i=0; i<iParmSetTotalImproperParms(uUnit->psParameters); i++ ) { - ParmSetImproper( uUnit->psParameters, i, sAtom1, sAtom2, - sAtom3, sAtom4, -- &iN, &dKp, &dP0, sDesc ); -- MESSAGE(( "Improper %d %s-%s-%s-%s %d %lf %lf\n", -+ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc ); -+ MESSAGE(( "Improper %d %s-%s-%s-%s %d %lf %lf %lf %lf\n", - i, sAtom1, sAtom2, sAtom3, sAtom4, -- iN, dKp, dP0 )); -+ iN, dKp, dP0, dScee, dScnb )); - FortranWriteDouble( dKp ); - } - /* Write the torsion RESTRAINT constants AND set the index */ -@@ -6575,14 +6639,14 @@ - for ( i=0; i<iParmSetTotalTorsionParms(uUnit->psParameters); i++ ) { - ParmSetTorsion( uUnit->psParameters, i, sAtom1, sAtom2, - sAtom3, sAtom4, -- &iN, &dKp, &dP0, sDesc ); -+ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc ); - dTemp = iN; - FortranWriteDouble( dTemp ); - } - for ( i=0; i<iParmSetTotalImproperParms(uUnit->psParameters); i++ ) { - ParmSetImproper( uUnit->psParameters, i, sAtom1, sAtom2, - sAtom3, sAtom4, -- &iN, &dKp, &dP0, sDesc ); -+ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc ); - dTemp = iN; - FortranWriteDouble( dTemp ); - } -@@ -6599,13 +6663,13 @@ - for ( i=0; i<iParmSetTotalTorsionParms(uUnit->psParameters); i++ ) { - ParmSetTorsion( uUnit->psParameters, i, sAtom1, sAtom2, - sAtom3, sAtom4, -- &iN, &dKp, &dP0, sDesc ); -+ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc ); - FortranWriteDouble( dP0 ); - } - for ( i=0; i<iParmSetTotalImproperParms(uUnit->psParameters); i++ ) { - ParmSetImproper( uUnit->psParameters, i, sAtom1, sAtom2, - sAtom3, sAtom4, -- &iN, &dKp, &dP0, sDesc ); -+ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc ); - FortranWriteDouble( dP0 ); - } - /* Write the torsion RESTRAINT constants AND set the index */ -diff -urN amber11//AmberTools/src/leap/src/leap/xaImproperParmTable.c amber11.new//AmberTools/src/leap/src/leap/xaImproperParmTable.c ---- amber11//AmberTools/src/leap/src/leap/xaImproperParmTable.c 2011-03-10 20:12:06.000000000 +0200 -+++ amber11.new//AmberTools/src/leap/src/leap/xaImproperParmTable.c 2011-05-19 18:35:57.000000000 +0300 -@@ -37,7 +37,9 @@ - * Handle editing of parameters in a table format. - */ - -- -+ /* Arunima Singh (UGA) */ -+ /* 20110420 */ -+ /* Added SCEE/SCNB */ - - #include <X11/IntrinsicP.h> - #include <X11/StringDefs.h> -@@ -59,7 +61,10 @@ - #define NC 4 - #define KPC 5 - #define P0C 6 --#define DESCC 7 -+#define SCEE 7 /*Arunima Singh*/ -+#define SCNB 8 /*Arunima Singh*/ -+#define DESCC 9 /*Arunima Singh: Changed value from 7 to 9 to include scee and scnb*/ -+ - - #define MAXTYPELEN 5 - #define DESCLEN 32 -@@ -129,13 +134,15 @@ - int iN; - double dKp; - double dP0; -+double dScee; -+double dScnb; - char sDesc[DESCLEN]; - - - iptPCur = (IMPROPERPARMTABLEt*)PXATClientPointer(tTable); - - ParmSetImproper( iptPCur->psParmSet, iRow, -- sType1, sType2, sType3, sType4, &iN, &dKp, &dP0, sDesc ); -+ sType1, sType2, sType3, sType4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc ); - - switch ( iCol ) { - case TYPE1C: -@@ -171,6 +178,14 @@ - } - return(SsBuffer); - break; -+ case SCEE: -+ sprintf( SsBuffer, DBLFMT, dScee ); -+ return(SsBuffer); -+ break; -+ case SCNB: -+ sprintf( SsBuffer, DBLFMT, dScnb ); -+ return(SsBuffer); -+ break; - case DESCC: - strcpy( SsBuffer, sDesc ); - return( SsBuffer ); -@@ -259,6 +274,16 @@ - if ( !strcmp( cPData, "0" )) break; - return("P0 field must be '0' or 'Pi'."); - break; -+ case SCEE: -+ if ( !bStringToDouble( cPData, &dValue ) ) { -+ return("Invalid character in Scee field."); -+ } -+ break; -+ case SCNB: -+ if ( !bStringToDouble( cPData, &dValue ) ) { -+ return("Invalid character in Scnb field."); -+ } -+ break; - case DESCC: - if ( strlen(cPData)>DESCLEN-1 ) { - sprintf( SsError, "%s %d characters.", -@@ -384,11 +409,33 @@ - return("P0 field must be '0' or 'Pi'."); - } - -+ /* -+ * Scee -+ */ -+ *iPErrCol = 7; -+ cPData = col[7]; -+ if ( !bStringToDouble( cPData, &dValue ) ) { -+ return("Invalid character in Scee field."); -+ } else if ( dValue < 0.0 ) { -+ return("Scee cannot be negative."); -+ } -+ -+ /* -+ * Scnb -+ */ -+ *iPErrCol = 8; -+ cPData = col[8]; -+ if ( !bStringToInt( cPData, &iValue ) ) { -+ return("Invalid character in Scnb field."); -+ } else if ( dValue < 0.0 ) { -+ return("Scnb cannot be negative."); -+ } -+ - /* - * Desc - */ -- *iPErrCol = 7; -- cPData = col[7]; -+ *iPErrCol = 9; -+ cPData = col[9]; - if ( strlen(cPData) > DESCLEN-1 ) { - sprintf( SsError, "%s %d characters.", - "Parameter Description cannot be longer than", -@@ -413,7 +460,8 @@ - int iN; - double dKp; - double dP0; -- -+double dScee; -+double dScnb; - - iptPCur = (IMPROPERPARMTABLEt*) PXATClientPointer(tTable); - psParmSet = iptPCur->psParmSet; -@@ -444,7 +492,7 @@ - col[0], col[1], col[2], col[3] )); - if ( iRow != iParmSetAddImproperTerm( psParmSet, - col[0], col[1], col[2], col[3], -- iN, dKp, dP0, col[7] ) ) -+ iN, dKp, dP0, dScee, dScnb, col[9] ) ) - DFATAL(( "programming err 2 in zXAIPTAcceptRow\n" )); - } else { - /* -@@ -452,7 +500,7 @@ - */ - ParmSetUpdateImproper( psParmSet, iRow, - col[0], col[1], col[2], col[3], -- &iN, &dKp, &dP0, col[7] ); -+ &iN, &dKp, &dP0, &dScee, &dScnb, col[9] ); - } - } - -diff -urN amber11//AmberTools/src/leap/src/leap/xaTorsionParmTable.c amber11.new//AmberTools/src/leap/src/leap/xaTorsionParmTable.c ---- amber11//AmberTools/src/leap/src/leap/xaTorsionParmTable.c 2011-03-10 20:12:06.000000000 +0200 -+++ amber11.new//AmberTools/src/leap/src/leap/xaTorsionParmTable.c 2011-05-19 18:35:57.000000000 +0300 -@@ -37,6 +37,9 @@ - * Handle editing of parameters in a table format. - */ - -+ /* Arunima Singh (UGA) */ -+ /* 20110420 */ -+ /* Added SCEE/SCNB */ - - #include <X11/IntrinsicP.h> - #include <X11/StringDefs.h> -@@ -58,7 +61,9 @@ - #define NC 4 - #define KPC 5 - #define P0C 6 --#define DESCC 7 -+#define SCEE 7 /*Arunima Singh*/ -+#define SCNB 8 /*Arunima Singh*/ -+#define DESCC 9 /*Arunima Singh: Changed value from 7 to 9 to include scee and scnb*/ - - #define MAXTYPELEN 5 - #define DESCLEN 32 -@@ -112,7 +117,7 @@ - * zcPXATPTGetElement - * - * Get the values for the elements of the TABLE from the -- * particular Torsion Parmeter Entry. -+ * particular Torsion Parameter Entry. - */ - static char * - zcPXATPTGetElement( TABLE tTable, int iCol, int iRow ) -@@ -126,13 +131,15 @@ - int iN; - double dKp; - double dP0; -+double dScee; -+double dScnb; - char sDesc[DESCLEN]; - - - tptPCur = (TORSIONPARMTABLEt*)PXATClientPointer(tTable); - - ParmSetTorsion( tptPCur->psParmSet, iRow, -- sType1, sType2, sType3, sType4, &iN, &dKp, &dP0, sDesc ); -+ sType1, sType2, sType3, sType4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc ); - - switch ( iCol ) { - case TYPE1C: -@@ -168,6 +175,14 @@ - } - return(SsBuffer); - break; -+ case SCEE: -+ sprintf( SsBuffer, DBLFMT, dScee ); -+ return(SsBuffer); -+ break; -+ case SCNB: -+ sprintf( SsBuffer, DBLFMT, dScnb ); -+ return(SsBuffer); -+ break; - case DESCC: - strcpy( SsBuffer, sDesc ); - return( SsBuffer ); -@@ -256,6 +271,16 @@ - if ( !strcmp( cPData, "0" )) break; - return("P0 field must be '0' or 'Pi'."); - break; -+ case SCEE: -+ if ( !bStringToDouble( cPData, &dValue ) ) { -+ return("Invalid character in Scee field."); -+ } -+ break; -+ case SCNB: -+ if ( !bStringToDouble( cPData, &dValue ) ) { -+ return("Invalid character in Scnb field."); -+ } -+ break; - case DESCC: - if ( strlen(cPData)>DESCLEN-1 ) { - sprintf( SsError, "%s %d characters.", -@@ -379,11 +404,33 @@ - return("P0 field must be '0' or 'Pi'."); - } - -+ /* -+ * Scee -+ */ -+ *iPErrCol = 7; -+ cPData = col[7]; -+ if ( !bStringToDouble( cPData, &dValue ) ) { -+ return("Invalid character in Scee field."); -+ } else if ( dValue < 0.0 ) { -+ return("Scee cannot be negative."); -+ } -+ -+ /* -+ * Scnb -+ */ -+ *iPErrCol = 8; -+ cPData = col[8]; -+ if ( !bStringToInt( cPData, &iValue ) ) { -+ return("Invalid character in Scnb field."); -+ } else if ( dValue < 0.0 ) { -+ return("Scnb cannot be negative."); -+ } -+ - /* - * Desc - */ -- *iPErrCol = 7; -- cPData = col[7]; -+ *iPErrCol = 9; -+ cPData = col[9]; - if ( strlen(cPData) > DESCLEN-1 ) { - sprintf( SsError, "%s %d characters.", - "Parameter Description cannot be longer than", -@@ -408,6 +455,8 @@ - int iN; - double dKp; - double dP0; -+double dScee; -+double dScnb; - - tptPCur = (TORSIONPARMTABLEt*) PXATClientPointer(tTable); - psParmSet = tptPCur->psParmSet; -@@ -438,15 +487,15 @@ - col[0], col[1], col[2], col[3] )); - if ( iRow != iParmSetAddProperTerm( psParmSet, - col[0], col[1], col[2], col[3], -- iN, dKp, dP0, col[7] ) ) -- DFATAL(( "programming err 2 in zXATPTAcceptRow\n" )); -+ iN, dKp, dP0, dScee, dScnb, col[9] ) ) /*Arunima singh*/ -+ DFATAL(( "programming err 2 in zXATPTAcceptRow\n" )); - } else { - /* - * update row in place - */ - ParmSetUpdateTorsion( psParmSet, iRow, - col[0], col[1], col[2], col[3], -- &iN, &dKp, &dP0, col[7] ); -+ &iN, &dKp, &dP0, &dScee, &dScnb, col[9] ); /*Arunima singh*/ - } - } - -diff -urN amber11//AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py amber11.new//AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py ---- amber11//AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py 2011-04-14 15:30:17.000000000 +0300 -+++ amber11.new//AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py 2011-05-19 18:35:57.000000000 +0300 -@@ -371,7 +371,7 @@ - coords_received = _scaledistance(coords_tosend, chdist) - - for i in range(3): -- new_coords.append(coords_received[x+3]) -+ new_coords.append(coords_received[i+3]) - - coords_tosend = [] - coords_received = [] -diff -urN amber11//AmberTools/src/mmpbsa_py/setup.sh amber11.new//AmberTools/src/mmpbsa_py/setup.sh ---- amber11//AmberTools/src/mmpbsa_py/setup.sh 2011-04-14 15:30:18.000000000 +0300 -+++ amber11.new//AmberTools/src/mmpbsa_py/setup.sh 2011-05-19 18:35:57.000000000 +0300 -@@ -10,7 +10,8 @@ - - # require AMBERHOME - if [ -z $AMBERHOME ]; then -- export AMBERHOME=`dirname \`dirname $PWD\`` -+ AMBERHOME=`dirname \`dirname $PWD\`` -+ export AMBERHOME=`dirname $AMBERHOME` - echo "AMBERHOME is not set. Assuming it is $AMBERHOME" - fi - -diff -urN amber11//AmberTools/test/nab/Run.prm amber11.new//AmberTools/test/nab/Run.prm ---- amber11//AmberTools/test/nab/Run.prm 2011-04-14 15:30:23.000000000 +0300 -+++ amber11.new//AmberTools/test/nab/Run.prm 2011-05-19 18:35:57.000000000 +0300 -@@ -17,7 +17,7 @@ - - echo "checking the prmtop file:" - echo "" --tail -3209 tprmtop > tprmtop1 -+tail -3228 tprmtop > tprmtop1 - ../dacdif tprmtop.check tprmtop1 - - rm -f prm prm.c tleap.out leap.log tprmcrd prm.out1 tprmtop -diff -urN amber11//AmberTools/test/nab/tprmtop.check amber11.new//AmberTools/test/nab/tprmtop.check ---- amber11//AmberTools/test/nab/tprmtop.check 2011-03-10 20:12:18.000000000 +0200 -+++ amber11.new//AmberTools/test/nab/tprmtop.check 2011-05-19 18:35:57.000000000 +0300 -@@ -1,3 +1,4 @@ -+%VERSION VERSION_STAMP = V0001.000 DATE = 05/09/11 12:59:19 - %FLAG TITLE - %FORMAT(20a4) - -@@ -541,6 +542,24 @@ - 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 - 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 - 3.14159400E+00 3.14159400E+00 3.14159400E+00 -+%FLAG SCEE_SCALE_FACTOR -+%FORMAT(5E16.8) -+ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 -+ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 -+ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 -+ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 -+ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 -+ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 -+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 -+%FLAG SCNB_SCALE_FACTOR -+%FORMAT(5E16.8) -+ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 -+ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 -+ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 -+ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 -+ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 -+ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 -+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 - %FLAG SOLTY - %FORMAT(5E16.8) - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 diff --git a/sci-chemistry/avogadro/ChangeLog b/sci-chemistry/avogadro/ChangeLog new file mode 100644 index 000000000..c532aa2c4 --- /dev/null +++ b/sci-chemistry/avogadro/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for sci-chemistry/avogadro +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> avogadro-9999.ebuild, + metadata.xml: + migrate from 'git' to 'git-2' + diff --git a/sci-chemistry/avogadro/Manifest b/sci-chemistry/avogadro/Manifest index 872d0931b..5f3ca2260 100644 --- a/sci-chemistry/avogadro/Manifest +++ b/sci-chemistry/avogadro/Manifest @@ -1,22 +1,13 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 -EBUILD avogadro-9999.ebuild 1154 RMD160 72ab78f9f875fc54aded8d3453328f4c8f0f9619 SHA1 26434ea38782a15b42ff6d4eb6685f04795e1b63 SHA256 7cecb5f75ae42d570d7ba84a07f82e459e9e4ede4ba09bf233280caf7cc2b466 -MISC metadata.xml 600 RMD160 d3559123f9438a9d0a49783ebb38027f91492e8d SHA1 f0dc9728b4196c6b09e8a0c4fdb02cd9f692cda4 SHA256 298cc4b9c2fc652f167bf9ae6e9faec1cfd1aa41a276295f4d1a6814912b58af +EBUILD avogadro-9999.ebuild 1095 RMD160 beae741e5f3e652d101d28050bdec6ac3283b433 SHA1 9f5794ca3fdd0b9065b46f461042bea7dbb77359 SHA256 c87a29116cad6b390ed88cf7a1a56548a95e677d8756770fed5f18950d6c561a +MISC ChangeLog 241 RMD160 3493e175f603b030be4761c9fa4d7737deb1aa7b SHA1 c54261a63880c8df51637c77d9785756e2b2c7f4 SHA256 51981200a5a120210cbc5e3b3601350ab221bd39780cd2ccef84d6162341f7c5 +MISC metadata.xml 590 RMD160 53e6b7b5af0f261d6e30f778ef4fe5bddb8e849d SHA1 3727db63252401bce02028a2307ab69a0e67e780 SHA256 8cb23fc2731fe1d8a56abf4a33f3f80f89853fdb9c378c816715eec0ec0c507d -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBCAAGBQJMZFVlAAoJEOf+E+/4L5Lm6rYP+wUOHui2111YdWps3HF3Mdz+ -RGxA2I0wqbJNcsIoRocZNkp+TMMFYmgHrAR0p5gnr8r+/OpJ38blUYNCThczFF8O -Ww7qdHXsClWaj2vpxa3H2VVBq+n6ATng/1nprYF20Wz1ZFEz92MFc442Re1Kahzp -V4SANjdBjnxHdVZDa2qJ794kLuFyVl5EDAkx+dwhgmMX2i5tk9VOkj90HzbrRU2r -GK3rbD8S5Vp9FeAhEUXiXkf+RRcAariT1qNJbWX2r0d2x2RecJlzLYIRNcYhLdYf -wXncmu5eGnSSW6kcNZG1yVxPd2CccrNN0M8JWC3QEz7bkjk4qmAdUU5UNOCBLKRh -b9b1jrjF2wygetICqCvKnbwfc49fIVCAWRD+nQJTapUG12ih3umoja2+i/PwOnUC -faEWkAhwlUcaYSjONKup4lTGstwGFp9PbdjgHp+1wCwZIeTI+Bzr4yVTi05IDGNC -gAnKtqE+V9CduKF5AsfGUAIm/XY6G0uYUz/H2L/vVQr482GUgEkSQfcAwe2jIMhw -Zx5QixSFbH6aQVsUZV1+1kjNlDwDk0oyD/WUFutiZ43JuQxwLa/CjPV+eKRmydAN -JHrxUkL8edv44hhAp+432ww64jxz6ApOKFaSBH58qkKB3HPdHO1SUSnw04LhVXV0 -U9n5Dy9vbd/imgrKczbR -=q3nR +iEYEAREIAAYFAk4GAvIACgkQgAnW8HDreRbkGQCfXEQ1q6FcuD07+KRIabFhTZFd +JoQAn1jfwgFjAe63JW7LaSdOaeW1b9zt +=auQH -----END PGP SIGNATURE----- diff --git a/sci-chemistry/avogadro/avogadro-9999.ebuild b/sci-chemistry/avogadro/avogadro-9999.ebuild index a69d3b534..9bdd436d1 100644 --- a/sci-chemistry/avogadro/avogadro-9999.ebuild +++ b/sci-chemistry/avogadro/avogadro-9999.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/avogadro/avogadro-1.0.1.ebuild,v 1.1 2010/05/21 15:33:28 jlec Exp $ -EAPI="3" +EAPI=3 PYTHON_DEPEND="python? 2:2.5" -inherit cmake-utils eutils python git +inherit cmake-utils eutils git-2 python DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL" HOMEPAGE="http://avogadro.sourceforge.net/" @@ -17,20 +17,20 @@ SLOT="0" KEYWORDS="" IUSE="+glsl python" -RDEPEND=">=sci-chemistry/openbabel-2.2.3 - >=x11-libs/qt-gui-4.5.3:4 - >=x11-libs/qt-opengl-4.5.3:4 +RDEPEND=" + sci-chemistry/openbabel + x11-libs/qt-gui:4 + x11-libs/qt-opengl:4 x11-libs/gl2ps glsl? ( >=media-libs/glew-1.5.0 ) python? ( - >=dev-libs/boost-1.35 >=dev-libs/boost-1.35.0-r5[python] dev-python/numpy dev-python/sip - )" + )" DEPEND="${RDEPEND} - >=dev-cpp/eigen-2.0.9 - >=dev-util/cmake-2.6.2" + dev-cpp/eigen:2 + dev-util/cmake" pkg_setup() { python_set_active_version 2 diff --git a/sci-chemistry/avogadro/metadata.xml b/sci-chemistry/avogadro/metadata.xml index 4f8df4c8f..a34dd561f 100644 --- a/sci-chemistry/avogadro/metadata.xml +++ b/sci-chemistry/avogadro/metadata.xml @@ -1,17 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>cryos@gentoo.org</email> - </maintainer> - <longdescription> + <herd>sci-chemistry</herd> + <maintainer> + <email>cryos@gentoo.org</email> + </maintainer> + <longdescription> Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture. </longdescription> - <use> - <flag name="glsl">Enable glsl features via GLEW.</flag> - </use> + <use> + <flag name="glsl">Enable glsl features via GLEW.</flag> + </use> </pkgmetadata> diff --git a/sci-chemistry/bist/Manifest b/sci-chemistry/bist/Manifest index a5ff6b6ec..dea29892e 100644 --- a/sci-chemistry/bist/Manifest +++ b/sci-chemistry/bist/Manifest @@ -4,23 +4,13 @@ Hash: SHA1 AUX bist-0.5.1-bracket.patch 379 RMD160 4d9d835a8c189862ec53f069862069a005b4c4ff SHA1 7c6ec5afb2bf2f1d6bc4ed931c5dbf03fe2abb98 SHA256 3fd94f204a237d3b00c2fd86b45259f65ac31606ebfe7ab076c3e24f8f855671 AUX bist-0.5.1-install.patch 4074 RMD160 35136ca7aa40e34c543efae3def45ced6d9d2886 SHA1 fc69c1a111ca724409674a35b40d7bc342b99388 SHA256 b94add3bed813222d29f4156668668c3296f6d817eb8f097709fcabd37d5ae67 DIST bist-0.5.1.tar.gz 766731 RMD160 a848cf778c9096239ca964dce352eeeab1ee4dc2 SHA1 22fd8186ef3a4fcc2776a3cf5b57ca78bfb4ab69 SHA256 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2a31a618c..bba456ce8 100644 --- a/sci-chemistry/bist/bist-0.5.1-r1.ebuild +++ b/sci-chemistry/bist/bist-0.5.1-r1.ebuild @@ -2,12 +2,12 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 -inherit eutils base +inherit base eutils -DESCRIPTION="Bist, the chemical drawing tool" -HOMEPAGE="http://www.autistici.org/interzona/index.php?mod=03_Bist" +DESCRIPTION="Chemical drawing tool" +HOMEPAGE="http://www.autistici.org/interzona/index.php?mod=03_Bist/" SRC_URI="http://www.autistici.org/interzona/ftrack.php?url=sections/06_Download/${P}.tar.gz" LICENSE="GPL-3" @@ -15,13 +15,13 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND="net-misc/curl +RDEPEND=" + media-libs/plotutils + net-misc/curl dev-libs/expat - >=x11-libs/fltk-1.1.7:1.1 + sci-chemistry/openbabel sci-libs/gsl - >=sci-chemistry/openbabel-2.2.0 - >=media-libs/plotutils-2.5" - + x11-libs/fltk:1" DEPEND="${RDEPEND}" src_prepare() { diff --git a/sci-chemistry/camshift/Manifest b/sci-chemistry/camshift/Manifest index 6261fe294..757908ec2 100644 --- a/sci-chemistry/camshift/Manifest +++ b/sci-chemistry/camshift/Manifest @@ -3,13 +3,13 @@ Hash: SHA1 AUX 1.35.0-gentoo.patch 974 RMD160 5428853e3e2c0b9c307a9bfc73d3b4397bdd220f SHA1 eb7d5412b97a532bd01662b52c4609eb224e0069 SHA256 4c849000c133d3890a6e945449cede8de961e33d6b6ecd5aa66502f9df0fe10d DIST camshift-1.35.0.tar.gz 6297498 RMD160 79d389b7c2533b87b8333be89b76a1901556c2de SHA1 0c6dbaabcddfb9de65bc0500bd0a9f18a1eefa8a SHA256 21d64fa08b51f01fb8526592fb4b382060e20fd677ec1c31aff14e5d7eef3316 -EBUILD camshift-1.35.0.ebuild 938 RMD160 9f53d9d3ecf2ba88d8e7e57829e5f6a5741551d0 SHA1 6ecd242865f88286bd421fe801a564d20769d04e SHA256 6ea7c4ff06ef6d6695f515fc67c61032f07c3d60d99e33092c320c4f88acdf45 +EBUILD camshift-1.35.0.ebuild 938 RMD160 f2e5ebd8e7d1675bc18f27c9a4aba284e2377b54 SHA1 0027304a8cf11029a2f070fdc1ca43099a4118ee SHA256 67292a81c9243500e72cc3138bcae82f4abbf34c575edda27256d0b72e47732a MISC ChangeLog 303 RMD160 ee4ca6178f06f5151def68aa278b888e9cf37604 SHA1 ac2f7378fb64132e0a8c30c208eeef8621db9d59 SHA256 eeece68d1fa9b485599e6cddd336659225b9096888bd5ba8e89db2951f2f5180 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk1BsdUACgkQgAnW8HDreRao7wCfVYGnNjMsM04/yP6PwYvrWlWc -mh4An1piC+nWlazaK73ebjPdYOriVZnB -=A15F +iEYEARECAAYFAk4EidkACgkQgAnW8HDreRZyHgCgzL581rc66U+qWgEDn9isH1rY +0mcAnirMc0+fGGOuNcrr8M1SQK1o7yIO +=u/17 -----END PGP SIGNATURE----- diff --git a/sci-chemistry/camshift/camshift-1.35.0.ebuild b/sci-chemistry/camshift/camshift-1.35.0.ebuild index 268593d53..c4adb6026 100644 --- a/sci-chemistry/camshift/camshift-1.35.0.ebuild +++ b/sci-chemistry/camshift/camshift-1.35.0.ebuild @@ -4,7 +4,7 @@ EAPI="3" -inherit eutils flag-o-matic autotools +inherit autotools eutils flag-o-matic sDESCRIPTION="Structure based prediction of protein chemical shifts" HOMEPAGE="http://www-vendruscolo.ch.cam.ac.uk/camshift/camshift.php" diff --git a/sci-chemistry/chooch/Manifest b/sci-chemistry/chooch/Manifest index 16e30c5b6..e10af02b5 100644 --- a/sci-chemistry/chooch/Manifest +++ b/sci-chemistry/chooch/Manifest @@ -1,7 +1,27 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +- -----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX 5.0.2-Makefile.am.patch 1203 RMD160 e1f4748e7450dfecfcee73656182e8c2aad1358f SHA1 e80b0815ce2ae8c3502087c401a792f24c033a23 SHA256 d57b06248fd0d555a93f3d82e8aa5d3020eb348fc0931ddfddc4d5458d0dd3a2 AUX 5.0.2-Makefile.patch 1222 RMD160 42dc4f8807a369023d802036fabea14e33239a05 SHA1 0a4e0a3558b3a1cc28d94f82b4cf09e3a1d00b45 SHA256 ba11ed4ecaafacae6442b05faffb06d4ee86a2c5f6df194f79014c7fa1c02b6c AUX 5.0.2-aclocal.patch 351 RMD160 307eb3e53f0ab9c760471c2d6eb848c496577470 SHA1 e33c832a0ef278ed7b0ea87d0b96cab32c20d2d7 SHA256 388554ec0ae899aa7dffc7bf0a0045e8adf78a2fdb83de044754916d63e43e57 DIST chooch-5.0.2.tar.gz 3057641 RMD160 5eb6d2b33f58e3a0b6379713184cd0c11d3a5956 SHA1 ec6cefd5044487c79e8099329c9f6eb3061e047d SHA256 ad80d5d296bfbd2bb8f9fac930df5a4e9ba583e23b2de298209b7a6925240643 -EBUILD chooch-5.0.2-r1.ebuild 1124 RMD160 9169096a7957e84613e1331cf1113b59c13529cc SHA1 edd8d41ce89551dd68354b8180044cc8d611b162 SHA256 3405475a638459b0c1c0309edbb21e8c3f90805b060988bb6c5763bea41b5719 +EBUILD chooch-5.0.2-r1.ebuild 1124 RMD160 8d297e7085f68499df7db17c13da30cc6d3f29fe SHA1 4ebafc44349580288e5e715826b6118a5157688a SHA256 fc47450627514de2cf4f97a9ab488150defe41570bc0d383414ac33dbb4c3b99 MISC ChangeLog 758 RMD160 46ce012a076f34ea28ad10d66f4654fa8ff6cb58 SHA1 c8ec744f10d972f90350b83283a95db127bbb9ac SHA256 3d0707564f68910a68cd71a1d6f7b68967a00a18fb260069b6752874d38db3d2 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c +- -----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Eij8ACgkQgAnW8HDreRaS4gCfaJc8nF7MDKcblBUmxaImArN6 +nTQAnRgp2wR+d21nKbmfyI2Z441/rgyi +=uibF +- -----END PGP SIGNATURE----- +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EikQACgkQgAnW8HDreRYhUwCg0dEjjDNqK2PWiUjTqyGpRX4c +ThAAni9pfnGsYm4VaMvghmhWmj6O1+7J +=PiID +-----END PGP SIGNATURE----- diff --git a/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild b/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild index 985550f04..2ddd7a2e6 100644 --- a/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild +++ b/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild @@ -4,7 +4,7 @@ EAPI="2" -inherit eutils multilib toolchain-funcs autotools +inherit autotools eutils multilib toolchain-funcs DESCRIPTION="a program that will automatically determine values of the anomalous scattering factors" HOMEPAGE="http://www.gwyndafevans.co.uk/id2.html" diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog index 2d688c292..c4d79818c 100644 --- a/sci-chemistry/coot/ChangeLog +++ b/sci-chemistry/coot/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 29 Jun 2011; Justin Lecher <jlec@gentoo.org> + +files/9999-clipper-config.patch, +files/9999-mmdb-config.patch, + coot-9999.ebuild, +files/9999-test.patch, metadata.xml: + Imported changes from tree + 15 Jun 2011; Justin Lecher <jlec@gentoo.org> -files/9999-align.patch, coot-9999.ebuild: Updated to current HEAD diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest index 9418aabe1..4a77b0424 100644 --- a/sci-chemistry/coot/Manifest +++ b/sci-chemistry/coot/Manifest @@ -1,18 +1,21 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA512 +AUX 9999-clipper-config.patch 431 RMD160 7a00939760bc4c062bbde1a65f53b9556b93c3bc SHA1 0d72c4c898fd29802c74d237b54f715444922956 SHA256 9ae9129e733d845ad2e4dd505bc5e0987147fc3a5e5dd2457b5857643809db2f AUX 9999-gl.patch 383 RMD160 6460e87e4da57ff845f96f072dec1354ed117bee SHA1 00bc0bbfc7d4fb00ebc8477941469bef2ed6b670 SHA256 9d47a6cf2d0c7644b945f88acdc7af146df4f9a5a8f883a0e72e1bc8ccf8b380 AUX 9999-goocanvas.patch 702 RMD160 9b26975eb658f15dfd806e47be9c11bcb7f850db SHA1 37bb70847ced34b754fe7cf5fea878b93bb6ed12 SHA256 162b21a3afb2d523df315ec021faf7a6497eb3b4fe00f90f601527fe1c22621a AUX 9999-include.patch 345 RMD160 6e42ce2afa7141f9cdcda0ca3ea5a11ef4f0f15f SHA1 3df3955307115ed8527f55fb49452905991c36cc SHA256 07b61fb298da857c5c37abb492cf192c65f9b538a3fc2d316aca7f4269e25a75 AUX 9999-lidia.patch 518 RMD160 bc1ac82f5d0e1c51f5cebaceb758ca306ea638d9 SHA1 7eb4f7e08ab0aea2f94d2ef27f26fc2aa796f21e SHA256 4b0cc3ed5a0a21cc9af5c2148779a6b82d2ad555720843af237efe0a3cc15be8 +AUX 9999-mmdb-config.patch 432 RMD160 8418198b08d15af9ee5d80b15ea46bb9efd2b973 SHA1 3e6f5c888b476d8d37da4effa67a8053784a7a3c SHA256 41484424f2f7f61b0555c893a51884d02f7bd471e70c4c0903c8740dcc273f77 +AUX 9999-test.patch 457 RMD160 1a3e0956d8b7f051fdd964524c0ba9eabf8c2aca SHA1 a8f9584be09cc58e7cb55801115e9649b05aa910 SHA256 494ef09e407c3047145c250c70b90c7679a1c5b9f84c57a680e40580bd980397 DIST greg-data.tar.gz 8041684 RMD160 355c54c63e83cbe28932278b4d19ae1cb353d530 SHA1 79da6d49a80c4744d406b8ecdbf6c04fc3bbdf3f SHA256 81828d3e257bfe98a5e04e74256a9217c7ad7dc7194948e8b0fac194ae2fbab8 -EBUILD coot-9999.ebuild 4066 RMD160 dbd1a1b9f00c90d010c74b8e91d9bb20489b254b SHA1 65473fb1dac322b09f02222b45c81cb5d5f16735 SHA256 7c19748e60b92792521391999685438b73b07bf3cd90733c6f031e6c2a352ea7 -MISC ChangeLog 10043 RMD160 987e35bde80350195e1cc25e18ebe0dd801f1812 SHA1 657c7ab4132c9a500f27c99e824cfdba32705c69 SHA256 18ebb91258fcfc188df91da2c6e997a591b4813083c7dd1236d683e4c394dd3c -MISC metadata.xml 306 RMD160 303613d4bb58ea149f418efc0d41f550ecbb94ca SHA1 1caeb2549f7f6a1dd44f2200784be8f2a7f294ab SHA256 f0ead885a2ede3186db2797473c72249fb525de661c279ca2ce7b8b152399bf6 +EBUILD coot-9999.ebuild 4187 RMD160 6c0cfa176f55078f2dcede25d570e9294eb60173 SHA1 64293e37406b4c075a2498f3ce004fa604ec26ff SHA256 706dae8547408c9613d3546252e6ccf81d0f71f84c834efccf0bbcda16b4a648 +MISC ChangeLog 10245 RMD160 acd43e0cdb75e1bc1a96b8eff0817990cdd48c78 SHA1 a4dc46b2dfdaaef968cd46ab14070da8fb5a32ac SHA256 997b222cc39bc31697b22b91a3704f80df7c0a297b276f7afc043d0007d2f30e +MISC metadata.xml 309 RMD160 62b0b67572300bd5b40f1ac76c9e198b1b241391 SHA1 cf618b7b327adc672fa00a392e96a3c60ce4b8db SHA256 1adfc298fdb6b02eac868761ad3ce2b93074cb83a61b730dc39fe6bfa7f51142 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk34zsMACgkQgAnW8HDreRZBqwCfdANcRZ8sS4oOIQ0BR22mRRxN -/g4AnAl4oDLBpP1leqVZd5udqONkS9a7 -=AEDp +iEYEAREKAAYFAk4LKWMACgkQgAnW8HDreRbhTgCgs/bo052gPyPuCN7FQ7Y9RBe9 +ReIAoKqlz68QsoECQHafJ7arFJzz0bYe +=/H46 -----END PGP SIGNATURE----- diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild index bfeee1e85..ecb5ff027 100644 --- a/sci-chemistry/coot/coot-9999.ebuild +++ b/sci-chemistry/coot/coot-9999.ebuild @@ -2,11 +2,11 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=3 PYTHON_DEPEND="2" -inherit autotools base versionator python subversion toolchain-funcs +inherit autotools base python subversion toolchain-funcs versionator MY_S2_PV=$(replace_version_separator 2 - ${PV}) MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} @@ -23,16 +23,17 @@ SRC_URI="test? ( http://www.biop.ox.ac.uk/coot/devel/greg-data.tar.gz )" SLOT="0" LICENSE="GPL-3" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" +IUSE="+openmp test" SCIDEPS=" >=sci-libs/ccp4-libs-6.1 >=sci-libs/clipper-20090520 >=sci-libs/coot-data-2 >=sci-libs/gsl-1.3 - sci-libs/mmdb + >=sci-libs/mmdb-1.23 + <sci-libs/monomer-db-1 sci-chemistry/reduce - sci-chemistry/refmac + <sci-chemistry/refmac-5.6 sci-chemistry/probe" XDEPS=" @@ -67,14 +68,20 @@ DEPEND="${RDEPEND} S="${WORKDIR}" pkg_setup() { + if use openmp; then + tc-has-openmp || die "Please use an OPENMP capable compiler" + fi python_set_active_version 2 } PATCHES=( + "${FILESDIR}"/${PV}-clipper-config.patch "${FILESDIR}"/${PV}-lidia.patch "${FILESDIR}"/${PV}-goocanvas.patch "${FILESDIR}"/${PV}-include.patch "${FILESDIR}"/${PV}-gl.patch + "${FILESDIR}"/${PV}-mmdb-config.patch + "${FILESDIR}"/${PV}-test.patch ) src_unpack() { @@ -85,12 +92,6 @@ src_unpack() { src_prepare() { base_src_prepare - # Link against single-precision fftw - sed -i \ - -e "s:\}fftw:}sfftw:g" \ - -e "s:\}rfftw:}srfftw:g" \ - "${S}"/macros/clipper.m4 - cat >> src/svn-revision.cc <<- EOF extern "C" { int svn_revision() { @@ -107,17 +108,15 @@ src_configure() { # Yes, this is broken behavior. econf \ --includedir='${prefix}/include/coot' \ - --with-gtkcanvas-prefix="${EPREFIX}"/usr \ - --with-clipper-prefix="${EPREFIX}"/usr \ - --with-mmdb-prefix="${EPREFIX}"/usr \ - --with-ssmlib-prefix="${EPREFIX}"/usr \ - --with-gtkgl-prefix="${EPREFIX}"/usr \ + --with-gtkcanvas-prefix="${EPREFIX}/usr" \ + --with-ssmlib-prefix="${EPREFIX}/usr" \ + --with-gtkgl-prefix="${EPREFIX}/usr" \ --with-guile \ - --with-python="${EPREFIX}"/usr \ + --with-python="${EPREFIX}/usr" \ --with-guile-gtk \ --with-gtk2 \ --with-pygtk \ - --enable-openmp + $(use_enable openmp) } src_compile() { @@ -133,16 +132,16 @@ src_test() { export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" export COOT_SCHEME_DIR="${S}/scheme/" export COOT_RESOURCES_FILE="${S}/cootrc" - export COOT_PIXMAPS_DIR="${S}/pixmaps" - export COOT_DATA_DIR="${S}" - export COOT_PYTHON_DIR="${S}/python" + export COOT_PIXMAPS_DIR="${S}/pixmaps/" + export COOT_DATA_DIR="${S}/" + export COOT_PYTHON_DIR="${S}/python/" export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" - export PYTHONHOME="${EPREFIX}"/usr - export CCP4_SCR="${T}"/coot_test + export PYTHONHOME="${EPREFIX}"/usr/ + export CCP4_SCR="${T}"/coot_test/ export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" export SYMINFO="${S}/syminfo.lib" - export COOT_TEST_DATA_DIR="${S}"/data/greg-data + export COOT_TEST_DATA_DIR="${S}"/data/greg-data/ cat > command-line-greg.scm <<- EOF (use-modules (ice-9 greg)) @@ -169,4 +168,5 @@ src_test() { einfo "SYMINFO ${SYMINFO}" "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die + "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die } diff --git a/sci-chemistry/coot/files/9999-clipper-config.patch b/sci-chemistry/coot/files/9999-clipper-config.patch new file mode 100644 index 000000000..311b5e88d --- /dev/null +++ b/sci-chemistry/coot/files/9999-clipper-config.patch @@ -0,0 +1,17 @@ + macros/clipper.m4 | 3 +++ + 1 files changed, 3 insertions(+), 0 deletions(-) + +diff --git a/macros/clipper.m4 b/macros/clipper.m4 +index 0bf087a..d0e8b6b 100644 +--- a/macros/clipper.m4 ++++ b/macros/clipper.m4 +@@ -98,6 +98,9 @@ case $ac_cv_build_alias in + ;; + esac + ++CLIPPER_CXXFLAGS=`clipper-config --cflags` ++CLIPPER_LDOPTS=`clipper-config --libs` ++ + AC_MSG_CHECKING([for Clipper]) + + LIBS="$save_LIBS $CLIPPER_LDOPTS" diff --git a/sci-chemistry/coot/files/9999-mmdb-config.patch b/sci-chemistry/coot/files/9999-mmdb-config.patch new file mode 100644 index 000000000..1d7cbd452 --- /dev/null +++ b/sci-chemistry/coot/files/9999-mmdb-config.patch @@ -0,0 +1,18 @@ + macros/mmdb.m4 | 4 ++++ + 1 files changed, 4 insertions(+), 0 deletions(-) + +diff --git a/macros/mmdb.m4 b/macros/mmdb.m4 +index b477597..d05cf66 100644 +--- a/macros/mmdb.m4 ++++ b/macros/mmdb.m4 +@@ -86,6 +86,10 @@ else + ac_MMDB_LDOPTS="-lmmdb -lm" + fi + ++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2]) ++ac_MMDB_LDOPTS="${MMDB_LIBS}" ++ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}" ++ + AC_MSG_CHECKING([for MMDB]) + + LIBS="$save_LIBS $ac_MMDB_LDOPTS" diff --git a/sci-chemistry/coot/files/9999-test.patch b/sci-chemistry/coot/files/9999-test.patch new file mode 100644 index 000000000..8cb79e65d --- /dev/null +++ b/sci-chemistry/coot/files/9999-test.patch @@ -0,0 +1,16 @@ + src/testing.cc | 4 +++- + 1 files changed, 3 insertions(+), 1 deletions(-) + +diff --git a/src/testing.cc b/src/testing.cc +index f767bf6..097b9b9 100644 +--- a/src/testing.cc ++++ b/src/testing.cc +@@ -86,6 +86,8 @@ std::string greg_test(const std::string &file_name) { + const char *c = getenv("COOT_TEST_DATA_DIR"); + if (c) { + dd = c; ++ dd += "/"; ++ dd += file_name; + } else { + const char *d = getenv("HOME"); + if (d) { diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml index d7156cfd6..702e0737e 100644 --- a/sci-chemistry/coot/metadata.xml +++ b/sci-chemistry/coot/metadata.xml @@ -1,10 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> + <herd>sci</herd> + <maintainer> + <email>sci@gentoo.org</email> + </maintainer> <maintainer> <email>jlec@gentoo.org</email> <name>Justin Lecher</name> diff --git a/sci-chemistry/drawxtl/Manifest b/sci-chemistry/drawxtl/Manifest index 884ce754f..769f54197 100644 --- a/sci-chemistry/drawxtl/Manifest +++ b/sci-chemistry/drawxtl/Manifest @@ -7,14 +7,14 @@ AUX 54-gentoo.patch 2152 RMD160 44c0765007f49fa6f55aaec7e3c384432f63a905 SHA1 3a AUX 54-ldflags.patch 371 RMD160 554457b44f872d95e0d1378b46d3473ccae76ba2 SHA1 2c53ee48e6bcebad97cc00ef284d752af2f521ca SHA256 53cadce7b423b77e348123d1229a693402b8b84d10f0120e4c0b73e620514cab DIST DRAWxtl44.tar.gz 4214313 RMD160 c4a4dbc14eb67b9f28768715eadd62b96d7e494d SHA1 f9e235ff044f01fed8146321f562eb833b78c824 SHA256 6fc92098290bcf319f8b3002d017d83d052e276693d012d84c75e3c0ff319c92 DIST DRAWxtl54.tar.gz 4284006 RMD160 78b8b0241a492964355c808959eb6e4a8b03339c SHA1 476c7950ca901d13b20058c71bb86fa5d7be8fa2 SHA256 6bf11e7a0aff0a32daef54b9d90f6ffe88ba3b1a61ff2f9f8aa1dfc85b2660d6 -EBUILD drawxtl-44.ebuild 1806 RMD160 7b58ceca6857bbcf90f2c5387ea489e1412f730b SHA1 a4c232569adeb44b7770e8d2a8bfb8dca158fa64 SHA256 80706279e6eb3dfd57d86ff47dfe4cee0d84def9c49dfcc617185b62533ad57e -EBUILD drawxtl-54.ebuild 1332 RMD160 8c679bc6f511917c69ab805c736488b70e9ccb58 SHA1 1bdecc92385d4ded3d0d7dfff8aaa571f4231a4a SHA256 f09da4774d16d1d5b6f95eb5654279edd557cd5a8dd288201a998b62c5d394f4 +EBUILD drawxtl-44.ebuild 1806 RMD160 3cceb890501975284d0c57691f1327ba4e2ba881 SHA1 646ffea2a3d513b4eaf5d79bbb02cb09628cd332 SHA256 64dee278886714a6781b2acb729fb9ecb17c6911cbe76e2e5c5acdc17128955b +EBUILD drawxtl-54.ebuild 1332 RMD160 e48ee134cfa1ff1ea478db1bd73b8ecad2c8e6db SHA1 1ff9e6cc8bc96dd3d04d9097956611a3bbc1991a SHA256 35e73297ad4932864e02d84ea7942aba14271fd5f4613af64158eff19e7c5252 MISC ChangeLog 1443 RMD160 cf28f3d5d2583d54432dda6d9e53d8a1ca63b2bc SHA1 a816f27003efb301789e84c1c2ec2a2abdee64af SHA256 07b5aeadd4b9938f9799f1975d6d004bec4d2440c9579bac69b9841abda93845 MISC metadata.xml 291 RMD160 eb898254774c5f27ec3b0f0df56cb7508a31b7ab SHA1 e6420a9b34a51c05fb1de16eb1bd6a9a1ae0b11d SHA256 1d90c251ab305064c4e065c2e1d38f4e5e565a6a33dc3dcaa9540704f862a764 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2bJHMACgkQgAnW8HDreRazyQCgplUX5eQEUxR3E1f/TdS88t4l -ekAAoMY6NEf2Su0O4sW7JAYQC3D5Z1Vi -=7wa7 +iEYEARECAAYFAk4EilQACgkQgAnW8HDreRZF/ACgoGU4bAZp3iwmA9okhuT1ppsX +eFsAoKtvfRwz8ULrG0EDhAZ/FzxAgDKn +=/EcX -----END PGP SIGNATURE----- diff --git a/sci-chemistry/drawxtl/drawxtl-44.ebuild b/sci-chemistry/drawxtl/drawxtl-44.ebuild index ada036a6f..17f0ad0dd 100644 --- a/sci-chemistry/drawxtl/drawxtl-44.ebuild +++ b/sci-chemistry/drawxtl/drawxtl-44.ebuild @@ -4,7 +4,7 @@ EAPI="2" -inherit toolchain-funcs base +inherit base toolchain-funcs MY_PN="DRAWxtl" MY_P=${MY_PN}${PV} diff --git a/sci-chemistry/drawxtl/drawxtl-54.ebuild b/sci-chemistry/drawxtl/drawxtl-54.ebuild index 8b5c8649f..20f591d1e 100644 --- a/sci-chemistry/drawxtl/drawxtl-54.ebuild +++ b/sci-chemistry/drawxtl/drawxtl-54.ebuild @@ -4,7 +4,7 @@ EAPI="2" -inherit toolchain-funcs base +inherit base toolchain-funcs MY_PN="DRAWxtl" MY_P=${MY_PN}${PV} diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index 0aeec1bab..dfa2b2863 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -2,6 +2,26 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild: + migrate to git-2 + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild, metadata.xml: + migrate from 'git' to 'git-2' + + 21 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild: + only USE=fkernels needs fortran + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild: + Added fortran-2.eclass support + + 19 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild, + metadata.xml: + autotools is broken + 10 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.0.9999.ebuild: remove 4.0.* (EOM) diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 5cfe6fb63..83682c593 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,20 +1,6 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361 DIST gromacs-manual-4.5.4.pdf 2463242 RMD160 309a1d9bc5f4821076d53f668c36f1c6bfc1714f SHA1 58c0261308212af29fa0c4f4a6d1b81da6d84766 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252 -EBUILD gromacs-4.5.9999.ebuild 7545 RMD160 69969f6ad0593b4fadfe45aa1df24a82d75536f3 SHA1 55f40f07cd3affa411c7169ac2ca83b8421295f3 SHA256 435eb79316f5d61a5c116e0ba122efa7ef6950684b9c37ea6506c517cdbeef7f -EBUILD gromacs-9999.ebuild 6949 RMD160 9faa82a67668cfb24d18a1f5cb219367f145ec5e SHA1 546217bdd0a13e0f2f3ad61fb24cb7834241a7e3 SHA256 124feeb94b1d44e6c80f8b15b2d8ffe8f2ffe04ddeedbf540b9fe44b46a997c9 -MISC ChangeLog 8191 RMD160 8ed43c9efd0bf0c3696b525530b9b1064b97520d SHA1 37f9aab566e89cbcebf071570a519f4bc045192f SHA256 cd8f5e6acbaf4c251e4b605a0893455ce4d2cc0182af1dd0e7d3280849f14f3c -MISC metadata.xml 621 RMD160 7875bd7f4880d1f08123d4457e98df4421c259ea SHA1 fee39a7fd465f3c4944be645ce622353c1ab5480 SHA256 ce14ff9ec55fd9c34c2ca75d796cff3fb443a1c5e94204089d58a7fff0598ef1 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iQEcBAEBAgAGBQJNvXifAAoJEOeBhlrCAAWGmlYH/jpIhCKz2jOfzx1IsM2a8dqp -H/14ASVNLYggbn4majWXozaxre+meWw7qIPcpByGsTUMyrQSNSowVX5HgUl/Yb+C -f0zRNSOoHdQJAbd96mOC2/9bZr7fr+nJJa6/5Bv/JCSBIyXPTpdtbzn633oA8Hl0 -hcyAkwfkEmMn/OadubsQcoNOZSlmt0dIN7Ov97Y08tEabDuiASWF1nFfcQZlvZ7d -gTd8A3tKmAKTVXaHsUhve6T5ITr7jgdjQGRjpfNoS6ZI1oRbXm03ljwBEE0B8m+R -vrozeC2w1HmVKl5s9oRosCVenZkGmlScisMX6t6kHs3B9rzIT+HoImjQkrAy5+0= -=aHGC ------END PGP SIGNATURE----- +EBUILD gromacs-4.5.9999.ebuild 7189 RMD160 12486dafb102a6488660cde00a8594059a85e341 SHA1 f1acf9501be52ff4c62da91978640c013ddbbca0 SHA256 48eea5a8bf86d247adc2f0b1c12da67c145ad9421d820499c377489b6f1e6898 +EBUILD gromacs-9999.ebuild 7046 RMD160 e537569b65336b7848fab8143170a7eb45b2b15f SHA1 ef74076816e1a5b4f39cb03cd16646f6c78a3962 SHA256 a40fd3825a300ffe45f96ca829d8d6ae20a6ccda07ad2e9ac6fa0922b630b534 +MISC ChangeLog 8839 RMD160 b223aec401bb274dffa17d85f77b47abd4535390 SHA1 90f681867697cd6426baff74b36dee34d12cc1ea SHA256 d9426f0f18987f97c2532853bde16070adb8fbacf6b3a7f656a922c6e9ace49b +MISC metadata.xml 564 RMD160 b7357b87a8c27d8540e14470312880b6597a71e9 SHA1 c99cb915680170596d0c45255fd8b0670e263c9a SHA256 772f8da05c1bb636017fb6a8f9beb217d998b30060a8da0fa3067d97a3ef6f7e diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild index 469f60402..349e82878 100644 --- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild @@ -4,11 +4,10 @@ EAPI="4" -LIBTOOLIZE="true" TEST_PV="4.0.4" MANUAL_PV="4.5.4" -inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs +inherit bash-completion cmake-utils eutils fortran-2 multilib toolchain-funcs SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz ) doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )" @@ -16,7 +15,7 @@ SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz ) if [ "${PV%9999}" != "${PV}" ]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs" EGIT_BRANCH="release-4-5-patches" - inherit git + inherit git-2 else SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz" fi @@ -27,17 +26,17 @@ HOMEPAGE="http://www.gromacs.org/" LICENSE="GPL-2" SLOT="0" KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux" -IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack -mpi +single-precision sse2 static-libs test +threads +xml zsh-completion" +IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack +mpi +single-precision sse2 test +threads xml zsh-completion" REQUIRED_USE="fkernels? ( !threads )" CDEPEND=" + fkernels? ( virtual/fortran ) X? ( x11-libs/libX11 x11-libs/libSM x11-libs/libICE ) - dmalloc? ( dev-libs/dmalloc ) blas? ( virtual/blas ) fftw? ( sci-libs/fftw:3.0 ) gsl? ( sci-libs/gsl ) @@ -51,7 +50,14 @@ RDEPEND="${CDEPEND} RESTRICT="test" +pkg_setup() { + use fkernels && fortran-2_pkg_setup +} + src_prepare() { + #add user patches from /etc/portage/patches/sci-chemistry/gromacs + epatch_user + if use mpi && use threads; then elog "mdrun uses only threads OR mpi, and gromacs favours the" elog "use of mpi over threads, so a mpi-version of mdrun will" @@ -59,10 +65,6 @@ src_prepare() { elog "machines only, you can safely disable mpi" fi - autotools-utils_src_prepare || die - - eautoreconf || die - GMX_DIRS="" use single-precision && GMX_DIRS+=" float" use double-precision && GMX_DIRS+=" double" @@ -77,8 +79,12 @@ src_prepare() { } src_configure() { + local mycmakeargs_pre=( ) #from gromacs configure - if ! use fftw; then + if use fftw; then + mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3") + else + mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack") ewarn "WARNING: The built-in FFTPACK routines are slow." ewarn "Are you sure you don\'t want to use FFTW?" ewarn "It is free and much faster..." @@ -119,65 +125,52 @@ src_configure() { elog "libmd with and without mpi support." fi - # if we need external blas or lapack - use blas && export LIBS+=" $(pkg-config blas --libs)" - use lapack && export LIBS+=" $(pkg-config lapack --libs)" - local sseflag="x86-64-sse" - use x86 && sseflag="ia32-sse" - - #missing flag in autotools (bug #339837) - use sse2 && append-flags -msse2 + #go from slowest to fasterest acceleration + local acce="none" + use fkernels && acce="fortran" + use altivec && acce="altivec" + use ia64 && acce="ia64" + use sse2 && acce="sse" + + mycmakeargs_pre+=( + $(cmake-utils_use X GMX_X11) + $(cmake-utils_use blas GMX_EXTERNAL_BLAS) + $(cmake-utils_use gsl GMX_GSL) + $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) + $(cmake-utils_use threads GMX_THREADS) + $(cmake-utils_use xml GMX_XML) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_ACCELERATION="$acce" + ) for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" local suffix="" #if we build single and double - double is suffixed use double-precision && use single-precision && \ [ "${x}" = "double" ] && suffix="_d" - myeconfargs=( - --bindir="${EPREFIX}"/usr/bin - --docdir="${EPREFIX}"/usr/share/doc/"${PF}" - --enable-"${x}" - $(use_with dmalloc) - $(use_with fftw fft fftw3) - $(use_with gsl) - $(use_with X x) - $(use_with xml) - $(use_enable threads) - $(use_enable altivec ppc-altivec) - $(use_enable ia64 ia64-asm) - $(use_with lapack external-lapack) - $(use_with blas external-blas) - $(use_enable fkernels fortran) - --disable-bluegene - --disable-la-files - --disable-power6 - --disable-ia32-sse - --disable-x86-64-sse - $(use_enable sse2 $sseflag) - ) - #disable ia32-sse and x86-64-sse and enable what we really need in last line - - einfo "Configuring for ${x} precision" - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\ - autotools-utils_src_configure --disable-mpi --program-suffix="${suffix}" \ - CC="$(tc-getCC)" F77="$(tc-getFC)" + local p + [ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF + -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" ) + CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure use mpi || continue einfo "Configuring for ${x} precision with mpi" - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - autotools-utils_src_configure --enable-mpi --program-suffix="_mpi${suffix}" \ - CC="$(tc-getCC)" F77="$(tc-getFC)" + mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON + -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) + CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure done } src_compile() { for x in ${GMX_DIRS}; do einfo "Compiling for ${x} precision" - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\ - autotools-utils_src_compile + CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile use mpi || continue einfo "Compiling for ${x} precision with mpi" - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - autotools-utils_src_compile mdrun + CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile mdrun done } @@ -193,18 +186,13 @@ src_test() { src_install() { for x in ${GMX_DIRS}; do - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}" \ - autotools-utils_src_install + CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install use mpi || continue - #autotools-utils_src_install does not support args - #using autotools-utils_src_compile instead - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - autotools-utils_src_compile install-mdrun DESTDIR="${D}" - - #stolen from autotools-utils_src_install see comment above - local args - has static-libs ${IUSE//+} && ! use static-libs || args='none' - remove_libtool_files ${args} + #cmake-utils_src_install does not support args + #using cmake-utils_src_compile instead + CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_make install-mdrun DESTDIR="${D}" done sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs" diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 817444e08..4a9888275 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -9,7 +9,7 @@ TEST_PV="4.0.4" EGIT_REPO_URI="git://git.gromacs.org/gromacs" EGIT_BRANCH="master" -inherit bash-completion cmake-utils eutils git multilib toolchain-funcs +inherit bash-completion cmake-utils eutils fortran-2 git-2 multilib toolchain-funcs DESCRIPTION="The ultimate molecular dynamics simulation package" HOMEPAGE="http://www.gromacs.org/" @@ -23,6 +23,7 @@ mpi +single-precision sse2 test +threads xml zsh-completion" REQUIRED_USE="fkernels? ( !threads )" CDEPEND=" + fkernels? ( virtual/fortran ) X? ( x11-libs/libX11 x11-libs/libSM @@ -42,6 +43,10 @@ PDEPEND="doc? ( app-doc/gromacs-manual )" RESTRICT="test" +pkg_setup() { + use fkernels && fortran-2_pkg_setup +} + src_prepare() { #add user patches from /etc/portage/patches/sci-chemistry/gromacs epatch_user diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 4aa2d9900..3735fb73a 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -7,9 +7,8 @@ <name>Christoph Junghans</name> </maintainer> <use> - <flag name='dmalloc'>Enable use of Debug Malloc</flag> - <flag name='double-precision'>More precise calculations at the expense of speed</flag> - <flag name='fkernels'>Enable building of Fortran Kernels for platforms that dont have assembly loops</flag> - <flag name='single-precision'>Single precision version of gromacs (default)</flag> + <flag name="double-precision">More precise calculations at the expense of speed</flag> + <flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag> + <flag name="single-precision">Single precision version of gromacs (default)</flag> </use> </pkgmetadata> diff --git a/sci-chemistry/icm/ChangeLog b/sci-chemistry/icm/ChangeLog index 99e4bda8c..b65ebbd68 100644 --- a/sci-chemistry/icm/ChangeLog +++ b/sci-chemistry/icm/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Added local USE description + 09 May 2011; Justin Lecher <jlec@gentoo.org> icm-3.7.2a.ebuild: Moved from media-libs/tiff to media-libs/tiff-compat diff --git a/sci-chemistry/icm/Manifest b/sci-chemistry/icm/Manifest index 11122aba8..1552eaaea 100644 --- a/sci-chemistry/icm/Manifest +++ b/sci-chemistry/icm/Manifest @@ -1,16 +1,16 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX 90icm 84 RMD160 e994059f717008f62d35dcbe3a4dca5571e38b4c SHA1 019ae240f76734dae6fdcbd7f332e37ecdf89f11 SHA256 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pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-chemistry</herd> -<maintainer> - <email>alexxy@gentoo.org</email> - <name>Alexey Shvetsov</name> -</maintainer> + <herd>sci-chemistry</herd> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> + <use> + <flag name="32bit">Automatically generated description for 32bit</flag> + <flag name="64bit">Automatically generated description for 64bit</flag> + </use> </pkgmetadata> diff --git a/sci-chemistry/jana2000/ChangeLog b/sci-chemistry/jana2000/ChangeLog index 935ee8d7c..9ce5cfa4a 100644 --- a/sci-chemistry/jana2000/ChangeLog +++ b/sci-chemistry/jana2000/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/jana2000 -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> jana2000-20071218.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> jana2000-20071218.ebuild: + Added fortran-2.eclass support + 17 Dec 2010; Justin Lecher <jlec@gentoo.org> jana2000-20071218.ebuild: Fix for fortran.eclass removal diff --git a/sci-chemistry/jana2000/Manifest b/sci-chemistry/jana2000/Manifest index 7c547f927..7e6b6175a 100644 --- a/sci-chemistry/jana2000/Manifest +++ b/sci-chemistry/jana2000/Manifest @@ -4,13 +4,13 @@ Hash: SHA1 AUX 20071218-g77.diff 2497 RMD160 481534a1839611b9b21975afb4d8fa60cc7c182d SHA1 64531e7eda145e08b4251d7a3bf6284b4f6c5226 SHA256 9d115c0a216ebda5b69c45f7df6f7f3c26e953ee0baf59d39aff36aadd6e394f AUX 20071218-gfortran.diff 2560 RMD160 cb22047fa61f67568c481c467145c0c57bf2f755 SHA1 aeeb8aaeff08a5b7c30e698f8b8cc3a1e44a3cf8 SHA256 283bee1581ef8bcfe3c288e7249815a57f920d77ea85589824cf32e1a5c792ec DIST jana2000.tar.gz 3261905 RMD160 dd61f0f65da066b61b91d3ad69d045705a894e93 SHA1 0a0851e8340bb3f37ee881fa94a581a19d04d8ea SHA256 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13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk0LEPQACgkQgAnW8HDreRZv/QCgjkxzgjCejZm0OLV+QSnvgtNo -QFcAn0LadL0DcaVtIJg9qYzkweBx/+r3 -=SZ6x +iEYEARECAAYFAk4DB+EACgkQgAnW8HDreRaf4ACgkyt97d9bb87uz4cNmocaxBjG +f3MAoLLTKKnY3YgXOlLn1KbAR3hkmxW7 +=G/Tv -----END PGP SIGNATURE----- diff --git a/sci-chemistry/jana2000/jana2000-20071218.ebuild b/sci-chemistry/jana2000/jana2000-20071218.ebuild index cd408a62f..cfd10b0f1 100644 --- a/sci-chemistry/jana2000/jana2000-20071218.ebuild +++ b/sci-chemistry/jana2000/jana2000-20071218.ebuild @@ -1,10 +1,12 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit eutils toolchain-funcs +EAPI=4 -DESCRIPTION="the crystallographic computing system" +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="The crystallographic computing system" HOMEPAGE="http://www-xray.fzu.cz/jana/jana.html" SRC_URI="ftp://ftp.fzu.cz/pub/cryst/beta2000/${PN}.tar.gz" @@ -13,17 +15,16 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND="x11-libs/libX11" +RDEPEND=" + x11-libs/libX11 + virtual/fortran" DEPEND="${RDEPEND} x11-proto/xproto sys-apps/gawk" S="${WORKDIR}/${PN}" -src_unpack() { - unpack ${A} - cd "${S}" - +src_prepare() { einfo "setting up the Makefile for $(tc-getFC)" if [[ $(tc-getFC) =~ gfortran ]]; then @@ -34,18 +35,18 @@ src_unpack() { } src_compile() { - emake -j1 CCOM="$(tc-getCC)" || die "emake failed" + emake -j1 CCOM="$(tc-getCC)" } src_install() { - dobin jana2000 || die "dobin failed" - dodoc README.TXT || die "dodoc failed" + dobin jana2000 + dodoc README.TXT insinto /usr/share/${PN}/source - doins -r source/{fg,data} || die "doins failed" + doins -r source/{fg,data} echo "JANADIR=/usr/share/${PN}" >"${T}/jana2000env" - newenvd "${T}/jana2000env" 99jana2000env || die "newenvd failed" + newenvd "${T}/jana2000env" 99jana2000env } pkg_postinst() { diff --git a/sci-chemistry/jligand/ChangeLog b/sci-chemistry/jligand/ChangeLog index 4c553a166..3444d0cee 100644 --- a/sci-chemistry/jligand/ChangeLog +++ b/sci-chemistry/jligand/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*jligand-1.0.19 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -jligand-0.1.ebuild, + -jligand-1.0.7.ebuild, +jligand-1.0.19.ebuild, metadata.xml: + Version Bump, cleaned old + *jligand-1.0.7 (26 Feb 2011) 26 Feb 2011; Justin Lecher <jlec@gentoo.org> +jligand-1.0.7.ebuild: diff --git a/sci-chemistry/jligand/Manifest b/sci-chemistry/jligand/Manifest index 90904979c..9fa8a579b 100644 --- a/sci-chemistry/jligand/Manifest +++ b/sci-chemistry/jligand/Manifest @@ -1,16 +1,14 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 -DIST JLigand.1.0.7.tar.gz 62402 RMD160 5c803d1a06c22e28d5a8896338973d230733712c SHA1 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-iEYEARECAAYFAk1o6CoACgkQgAnW8HDreRaIMgCfQlLUYu9bdRVC46/7C4w+BfJV -B8gAoJG9rwdOLfQwO3YtuK10phqr9jF3 -=2T4E +iEYEAREIAAYFAk4F4BYACgkQgAnW8HDreRb5VACg0aaKqwGuEqrjdM2adJQXgW1/ +29MAoMgDUoT5euIBZfA6/9FmkHXlZ5sn +=SMbX -----END PGP SIGNATURE----- diff --git a/sci-chemistry/jligand/jligand-0.1.ebuild b/sci-chemistry/jligand/jligand-0.1.ebuild deleted file mode 100644 index f2b9752cd..000000000 --- a/sci-chemistry/jligand/jligand-0.1.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -inherit java-pkg-2 java-ant-2 multilib - -MY_PN="JLigand" - -DESCRIPTION="a Java interface which allows links descriptions to be created" -HOMEPAGE="http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html" -SRC_URI="http://www.ysbl.york.ac.uk/~pyoung/${MY_PN}/${MY_PN}_${PV}_Source.tar" - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=">=virtual/jre-1.5 - sci-chemistry/refmac - sci-libs/monomer-db" -DEPEND=">=virtual/jdk-1.5" - -S="${WORKDIR}"/${MY_PN} - -EANT_EXTRA_ARGS="-Dfile.encoding=ISO-8859-1" - -src_install() { - java-pkg_dojar dist/${MY_PN}.jar - java-pkg_dolauncher ${PN} \ - --main uk.ac.york.ysbl.JLigand \ - --jar ${MY_PN}.jar \ - --pkg_args "/usr/$(get_libdir)/${PN} ${CLIBD_MON} /usr/bin/libcheck /usr/bin/refmac" - - insinto /usr/$(get_libdir)/${PN} - doins -r src/{images,resources} || die - fperms 775 /usr/$(get_libdir)/${PN}/resources/runLibcheck.csh || die - fperms 775 /usr/$(get_libdir)/${PN}/resources/runRefmac.csh || die -} diff --git a/sci-chemistry/jligand/jligand-1.0.7.ebuild b/sci-chemistry/jligand/jligand-1.0.19.ebuild index 378f006a6..3a13a64e1 100644 --- a/sci-chemistry/jligand/jligand-1.0.7.ebuild +++ b/sci-chemistry/jligand/jligand-1.0.19.ebuild @@ -2,13 +2,13 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="4" +EAPI=4 inherit java-pkg-2 java-ant-2 multilib MY_PN="JLigand" -DESCRIPTION="a Java interface which allows links descriptions to be created" +DESCRIPTION="Java interface which allows links descriptions to be created" HOMEPAGE="http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html" SRC_URI="http://www.ysbl.york.ac.uk/mxstat/${MY_PN}/${MY_PN}.${PV}.tar.gz" diff --git a/sci-chemistry/jligand/metadata.xml b/sci-chemistry/jligand/metadata.xml index efb490d78..d747d72a2 100644 --- a/sci-chemistry/jligand/metadata.xml +++ b/sci-chemistry/jligand/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> + <herd>sci</herd> + <maintainer> + <email>sci@gentoo.org</email> + </maintainer> </pkgmetadata> diff --git a/sci-chemistry/jmol/Manifest b/sci-chemistry/jmol/Manifest index 412136fb7..055996fc9 100644 --- a/sci-chemistry/jmol/Manifest +++ b/sci-chemistry/jmol/Manifest @@ -1,13 +1,29 @@ -AUX 12.0.34/jmol-manifest.patch 3726 RMD160 03e1e11fdd29fb63de15934fff166348577084b0 SHA1 925a957bc30e1fbab9fd773dc07f83411f667d30 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd -AUX 12.0.34/jmol-nointl.patch 13315 RMD160 9b6ca307d5e40af72bf07e668d3ad58bbde66a48 SHA1 f98f3df84369a2c63e54fd891ed1f63410dc6472 SHA256 6bbf13c59bc3633dc089346c1133ad2b3d0614463abdf364f5ec2e2ccd658df0 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX 12.0.45/jmol-manifest.patch 3726 RMD160 03e1e11fdd29fb63de15934fff166348577084b0 SHA1 925a957bc30e1fbab9fd773dc07f83411f667d30 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd +AUX 12.0.45/jmol-nointl.patch 13315 RMD160 9b6ca307d5e40af72bf07e668d3ad58bbde66a48 SHA1 f98f3df84369a2c63e54fd891ed1f63410dc6472 SHA256 6bbf13c59bc3633dc089346c1133ad2b3d0614463abdf364f5ec2e2ccd658df0 AUX caffeine.xyz 1116 RMD160 92b432c6584cd927fa1bfb155ea41011ab7a82d8 SHA1 d0f35a447b333b8ea51c15ab0ac67d887556e43c SHA256 45a9afac0b247780595944a98f8e1076a7e7e0dbb3e02cb54cecb0764b1cb67f AUX index.html 328 RMD160 60d2a573c228e018a864fd7d9cfc7554264ccd6b SHA1 7ab256d768d3a4da43b5e497dfb1c3a53a8068a9 SHA256 8cba2c5eb7f25c0ecf23bc007eb61549a7d2177ac327db6c1e5f51f333ae2451 -AUX jmol-11.6-manifest.patch 3726 RMD160 03e1e11fdd29fb63de15934fff166348577084b0 SHA1 925a957bc30e1fbab9fd773dc07f83411f667d30 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd -AUX jmol-11.6-nointl.patch 11528 RMD160 3d36d42b4cf07330f7fac6357c84d2a08e220294 SHA1 9d9588b2179871bf07438acb8f7e3a99dcf2f234 SHA256 c16cd2d14434f273ba99ec03209814e1028e8ff2425d9ef8789f196c38aa5d5d AUX selfSignedCertificate.store 1516 RMD160 583b7bab5578e1e32f649388b7009dc654df1199 SHA1 88d9123bdc1a376ba00e00c8abef4751adefe3a5 SHA256 81b69722530d94dc599ce79382a3386cce518baa7ab79fbb530d13483b51bed5 -DIST Jmol-12.0.34-full.tar.gz 26361617 RMD160 f4e0e9a9b89ab84f6e020659120ca00151357dad SHA1 ef19971e27ef056a6159784b4d93ceb60c8d250d SHA256 14865be23d3c480a36dc2dc1386b26391fa29d6d49746ee6896f531846df8177 -DIST jmol-11.6-full.tar.gz 26294021 RMD160 6f7f86b8debcfd1c89f5c40d902713e5ae2da0a3 SHA1 50e9be1b8cdb1f3f29f97a9ad97611348d2308a1 SHA256 ffabdbcb9d656fe365136da1ad5f40830a4882d355a9efde93fa29383d2bb70f -EBUILD jmol-11.6.ebuild 3205 RMD160 4b94f8dc026684d7720c74a2d2868df87ad18123 SHA1 7e120bbc6e353301ca503d5d7767fbbf10e79651 SHA256 4172ab00b35ba277a137411a90dcba949d728221cf4cd70a6602fcc55692f1fa -EBUILD jmol-12.0.34.ebuild 3250 RMD160 eaa762e8e61f00778384ac220b08071f1aeb9406 SHA1 991c79a83a9688db491e5d598f758ea86dea49b2 SHA256 3ffa01835657cf9c896d44df562b7eba0d4a135ff8256cf9b8f28f61abfd5f26 +DIST Jmol-12.0.45-full.tar.gz 26501382 RMD160 0d9a4212abf45852706f92cb16aedae7632763c5 SHA1 c43b0542be8bd845dadbcacdd41e47482e23fe03 SHA256 f9a3fe242841f9b56a718f8da2efe4130e497afe2c12d77f2e68344c62d7f70e +EBUILD jmol-12.0.45-r1.ebuild 3250 RMD160 eaa762e8e61f00778384ac220b08071f1aeb9406 SHA1 991c79a83a9688db491e5d598f758ea86dea49b2 SHA256 3ffa01835657cf9c896d44df562b7eba0d4a135ff8256cf9b8f28f61abfd5f26 MISC ChangeLog 2003 RMD160 960626caf1def31a90d863b1952717cd6218030f SHA1 9df828fc1ea6cfd197368bdde825f54eba47262b SHA256 65a02d8e6fbb0943b4c815ffda116fb78cb3a3718909551d6678bf6674606f16 MISC metadata.xml 355 RMD160 2c279aeab8c72ba2ac5573ccd72a69726166c638 SHA1 3cf53d45ceec1ed494d8c7312f60933657356e48 SHA256 a26dbd57c95fd7f37b7ade989dca90933da7f75fe7c27ac54c030d275edf12b4 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iQIcBAEBCAAGBQJOCgWjAAoJEOf+E+/4L5LmgxMQAIzn3LOsz8/UdViuN3iGDilX +2EIACCXARcNQYyZOvG4dCQSTnf1+mfP50dmKdQLVggl38UijBqZk72iJS7K11r7e +hmYuXq6ZpGTW+l7qXLvtGtJokwb/yo5kbkHGzBOj6Dh+LOjUFltJLpgidNDpWuZI +BrcZqR/vD8B9gveNxJy4Hih0sWOuodIy1o1hcaI7ZHwYZcARkHlAjhrf1dYStof+ +ZGjtWnxIl18uwSDU7plvQASH4yjsqSFBc+yf1NXVZ3nmkWIpTLnV+AM3oj0ogOg+ +G5I5BLyKdrVJH3D4N6O/WNucxnBBdlfg4ZekMTD/ytoLPf2uFB9mmLxUwPVeyOz5 +CU+5RkVvKKLo3Tl8CU+xoTmsB8gCDsbtTyOcEfVuBjs60jXcD/gUyfPrWscNkVnm +Po1lh5TMoBt7i52IhGokkcQe/WevVirKOhv5oqPDivY7PHJLucRIh38rYZLgXClx +kH4mIhMYq8k5WLX9myEz2CelkIw94uEQH+NPC1wh0zfRzT0BZefvaBnKWDgbuzoB +0Rxo3e5TuWbB5bXVRTI6sp/SGiR5w1siA6BYJzcJiQsrh5qNbYfSkRxzo/CSpoE9 +uLzVWazODJVztPA6Wir/DaotxShOfURr6wkUxrHeAjMVaJ6j1eqv4qMmdmwZAI2s +g83ZU2IA4ryr1y1xdFO1 +=O6DZ +-----END PGP SIGNATURE----- diff --git a/sci-chemistry/jmol/files/12.0.34/jmol-manifest.patch b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch index 3b43c219d..3b43c219d 100644 --- a/sci-chemistry/jmol/files/12.0.34/jmol-manifest.patch +++ b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch diff --git a/sci-chemistry/jmol/files/12.0.34/jmol-nointl.patch b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch index c1b22e83c..c1b22e83c 100644 --- a/sci-chemistry/jmol/files/12.0.34/jmol-nointl.patch +++ b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch diff --git a/sci-chemistry/jmol/files/jmol-11.6-manifest.patch b/sci-chemistry/jmol/files/jmol-11.6-manifest.patch deleted file mode 100644 index 3b43c219d..000000000 --- a/sci-chemistry/jmol/files/jmol-11.6-manifest.patch +++ /dev/null @@ -1,96 +0,0 @@ -diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt ---- jmol-11.0.3-orig/manifest/applet0.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/applet0.txt 2007-05-16 01:54:10.000000000 -0500 -@@ -0,0 +1,6 @@ -+Main-Class: JmolApplet
-+Sealed: true
-+
-+Name: org/jmol/api/
-+Sealed: false
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt ---- jmol-11.0.3-orig/manifest/applet1.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/applet1.txt 2007-05-16 01:54:10.000000000 -0500 -@@ -0,0 +1,6 @@ -+Name: org/jmol/api/
-+Sealed: false
-+
-+Name: org/jmol/applet/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt ---- jmol-11.0.3-orig/manifest/applet2.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/applet2.txt 2007-05-16 01:56:19.000000000 -0500 -@@ -0,0 +1,3 @@ -+Name: javax/vecmath/ -+ -+ -diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt ---- jmol-11.0.3-orig/manifest/applet3.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/applet3.txt 2007-05-16 01:56:47.000000000 -0500 -@@ -0,0 +1,4 @@ -+ -+Name: org/jmol/g3d/ -+Sealed: true -+ -diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt ---- jmol-11.0.3-orig/manifest/applet4.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/applet4.txt 2007-05-16 01:57:05.000000000 -0500 -@@ -0,0 +1,4 @@ -+ -+Name: org/jmol/adapter/smarter/ -+Sealed: true -+ -diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt ---- jmol-11.0.3-orig/manifest/applet5.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/applet5.txt 2007-05-16 01:57:23.000000000 -0500 -@@ -0,0 +1,4 @@ -+Name: org/openscience/jmol/ui/ -+Sealed: true -+ -+ -diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt ---- jmol-11.0.3-orig/manifest/applet6.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/applet6.txt 2007-05-16 01:57:46.000000000 -0500 -@@ -0,0 +1,4 @@ -+ -+Name: org/jmol/viewer/ -+Sealed: true -+ -diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt ---- jmol-11.0.3-orig/manifest/appletMain.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/appletMain.txt 2007-05-16 01:54:10.000000000 -0500 -@@ -0,0 +1,5 @@ -+Manifest-Version: 1.0
-+Sealed: true
-+
-+Name: org/jmol/api/
-+Sealed: false
-diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt ---- jmol-11.0.3-orig/manifest/appletMonolithic.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/appletMonolithic.txt 2007-05-16 01:54:10.000000000 -0500 -@@ -0,0 +1,7 @@ -+Main-Class: JmolApplet
-+Sealed: true
-+
-+Name: org/jmol/api/
-+Sealed: false
-+
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt ---- jmol-11.0.3-orig/manifest/applet.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/applet.txt 2007-05-16 01:54:10.000000000 -0500 -@@ -0,0 +1,2 @@ -+Manifest-Version: 1.0
-+Sealed: true
-\ No newline at end of file -diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt ---- jmol-11.0.3-orig/manifest/application.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/application.txt 2007-05-16 01:54:10.000000000 -0500 -@@ -0,0 +1 @@ -+Main-Class: org.openscience.jmol.app.Jmol
-diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt ---- jmol-11.0.3-orig/manifest/jvxl.txt 1969-12-31 18:00:00.000000000 -0600 -+++ jmol-11.0.3/manifest/jvxl.txt 2007-05-16 01:54:10.000000000 -0500 -@@ -0,0 +1 @@ -+Main-Class: org.openscience.jvxl.Jvxl
diff --git a/sci-chemistry/jmol/files/jmol-11.6-nointl.patch b/sci-chemistry/jmol/files/jmol-11.6-nointl.patch deleted file mode 100644 index 351093faf..000000000 --- a/sci-chemistry/jmol/files/jmol-11.6-nointl.patch +++ /dev/null @@ -1,274 +0,0 @@ ---- jmol-11.6/build.xml 2008-10-08 19:03:17.000000000 +0200 -+++ jmol-11.6/build.xml.new 2009-04-23 11:05:58.000000000 +0200 -@@ -100,10 +100,6 @@ - <srcfiles dir="doc/source"
- includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>
- </uptodate>
-- <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">
-- <srcfiles dir="doc/source"
-- includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>
-- </uptodate>
- </and>
- </condition>
-
-@@ -113,14 +109,6 @@ - <srcfiles dir="doc/source"
- includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />
- </uptodate>
-- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">
-- <srcfiles dir="doc/source"
-- includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />
-- </uptodate>
-- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">
-- <srcfiles dir="doc/source"
-- includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />
-- </uptodate>
- </and>
- </condition>
-
-@@ -130,14 +118,6 @@ - <srcfiles dir="doc/source"
- includes="JmolDevelopersGuide.docbook.xml"/>
- </uptodate>
-- <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">
-- <srcfiles dir="doc/source"
-- includes="JmolDevelopersGuide_fr.docbook.xml"/>
-- </uptodate>
-- <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">
-- <srcfiles dir="doc/source"
-- includes="JmolDevelopersGuide_de.docbook.xml"/>
-- </uptodate>
- </and>
- </condition>
-
-@@ -147,14 +127,6 @@ - <srcfiles dir="doc/source"
- includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>
- </uptodate>
-- <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">
-- <srcfiles dir="doc/source"
-- includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>
-- </uptodate>
-- <uptodate targetfile="build/doc/JmolAppletGuide_de.html">
-- <srcfiles dir="doc/source"
-- includes="JmolAppletGuide_de.docbook.xml"/>
-- </uptodate>
- </and>
- </condition>
-
-@@ -348,17 +320,12 @@ - </target>
-
- <target name="jar" id="jar"
-- depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">
-+ depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">
- <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >
- <fileset dir="build/doc/JmolUserGuide">
- <include name="**/*.html" />
- </fileset>
- </copy>
-- <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >
-- <fileset dir="build/doc/JmolUserGuide_fr">
-- <include name="**/*.html" />
-- </fileset>
-- </copy>
- <copy todir="${classes.dir}/org/openscience/jmol/Data" >
- <fileset dir="build/doc/JmolHistory">
- <include name="**/*.html" />
-@@ -505,11 +472,6 @@ - </fileset>
- <fileset dir="${appletjars.dir}" includes="**/*"/>
- </jar>
-- <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n.jar" manifest="manifest/applet_i18n.txt" >
-- <fileset dir="${applet.classes.dir}">
-- <include name="org/jmol/translation/**" />
-- </fileset>
-- </jar>
- <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
- <fileset dir="${applet.classes.dir}">
- <include name="org/jmol/minimize/**" />
-@@ -606,7 +568,6 @@ - <include name="org/jmol/bspt/**" />
- <include name="org/jmol/g3d/**" />
- <include name="org/jmol/geodesic/**" />
-- <include name="org/jmol/i18n/**" />
- <include name="org/jmol/modelset/**" />
- <include name="org/jmol/shape/**" />
- <include name="org/jmol/util/**" />
-@@ -628,7 +589,6 @@ - <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
- <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
- <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
-- <pathelement path="${jmol.applet.build.dir}/JmolApplet0_i18n.jar" />
- </indexjars>
- </jar>
- <!-- changes to this must be replicated below for the signed applet -->
-@@ -713,11 +673,6 @@ - keystore="selfSignedCertificate/selfSignedCertificate.store"
- storepass="selfSignedCertificate" alias="selfSignedCertificate" />
-
-- <signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n.jar"
-- signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n.jar"
-- keystore="selfSignedCertificate/selfSignedCertificate.store"
-- storepass="selfSignedCertificate" alias="selfSignedCertificate" />
--
- <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
- <!-- this one must be treated specially because of jar indexing
- we cannot simply rename the jar file, because the index has
-@@ -743,7 +698,6 @@ - <include name="org/jmol/shape/**" />
- <include name="org/jmol/viewer/**" />
- <include name="org/jmol/util/**" />
-- <include name="org/jmol/i18n/**" />
- </fileset>
- <indexjars>
- <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Popup.jar" />
-@@ -757,7 +711,6 @@ - <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />
- <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />
- <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />
-- <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_i18n.jar" />
- </indexjars>
- </jar>
- <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
-@@ -767,7 +720,7 @@ - </target>
-
- <target name="dist" id="dist"
-- depends="doc,main-i18n,main,signed-applet">
-+ depends="doc,main,signed-applet">
- <!-- first build binary distribution -->
- <delete dir="build/dist/jmol-${version}"/>
- <mkdir dir="build/dist/jmol-${version}"/>
-@@ -824,7 +777,6 @@ - <fileset dir=".">
- <include name="applet.classes" />
- <include name="build.xml" />
-- <include name="build-i18n.xml" />
- </fileset>
- </copy>
-
-@@ -903,7 +855,6 @@ - <fileset dir=".">
- <include name="apisio.classes" />
- <include name="build.xml" />
-- <include name="build-i18n.xml" />
- </fileset>
- </copy>
-
-@@ -995,7 +946,7 @@ - <target name="xclean" id="xclean">
- </target>
-
-- <target name="spotless" id="spotless" depends="clean,spotless-i18n">
-+ <target name="spotless" id="spotless" depends="clean">
- <delete dir="build"/>
- <delete dir="${javadoc.dir}"/>
- <delete dir="packaging/rpm/dist"/>
-@@ -1058,16 +1009,6 @@ - <arg value="../../../doc/source/JmolGuide.docbook.xml" />
- <arg value="../../${docbook-xsl}/html/chunk.xsl" />
- </java>
-- <echo message="Generating user's guide (fr)" />
-- <mkdir dir="build/doc/JmolUserGuide_fr" />
-- <java fork="true" dir="build/doc/JmolUserGuide_fr"
-- classname="com.icl.saxon.StyleSheet"
-- classpath="${lib.dir}/saxon.jar" >
-- <jvmarg value="${proxyHost}" />
-- <jvmarg value="${proxyPort}" />
-- <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />
-- <arg value="../../${docbook-xsl}/html/chunk.xsl" />
-- </java>
- </target>
-
- <target name="jmolHistory" id="jmolHistory"
-@@ -1082,26 +1023,6 @@ - <arg value="../../../doc/source/JmolHistory.xml" />
- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
- </java>
-- <echo message="Generating history of changes (fr)" />
-- <java fork="true" dir="build/doc/JmolHistory"
-- classname="com.icl.saxon.StyleSheet"
-- classpath="${lib.dir}/saxon.jar" >
-- <arg value="-o" />
-- <arg value="ChangeLog_fr.html" />
-- <arg value="../../../doc/source/JmolHistory_fr.xml" />
-- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
-- <arg value="lang=fr" />
-- </java>
-- <echo message="Generating history of changes (nl)" />
-- <java fork="true" dir="build/doc/JmolHistory"
-- classname="com.icl.saxon.StyleSheet"
-- classpath="${lib.dir}/saxon.jar" >
-- <arg value="-o" />
-- <arg value="ChangeLog_nl.html" />
-- <arg value="../../../doc/source/JmolHistory_nl.xml" />
-- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
-- <arg value="lang=nl" />
-- </java>
- </target>
-
- <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"
-@@ -1115,24 +1036,6 @@ - <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />
- <arg value="../${docbook-xsl}/html/docbook.xsl" />
- </java>
-- <echo message="Generating developer's guide (fr)" />
-- <java fork="true" dir="build/doc"
-- classname="com.icl.saxon.StyleSheet"
-- classpath="${lib.dir}/saxon.jar" >
-- <arg value="-o" />
-- <arg value="JmolDevelopersGuide_fr.html" />
-- <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />
-- <arg value="../${docbook-xsl}/html/docbook.xsl" />
-- </java>
-- <echo message="Generating developer's guide (de)" />
-- <java fork="true" dir="build/doc"
-- classname="com.icl.saxon.StyleSheet"
-- classpath="${lib.dir}/saxon.jar" >
-- <arg value="-o" />
-- <arg value="JmolDevelopersGuide_de.html" />
-- <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />
-- <arg value="../${docbook-xsl}/html/docbook.xsl" />
-- </java>
- </target>
-
- <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
-@@ -1146,24 +1049,6 @@ - <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
- <arg value="../${docbook-xsl}/html/docbook.xsl" />
- </java>
-- <echo message="Generating applet guide (fr)" />
-- <java fork="true" dir="build/doc"
-- classname="com.icl.saxon.StyleSheet"
-- classpath="${lib.dir}/saxon.jar" >
-- <arg value="-o" />
-- <arg value="JmolAppletGuide_fr.html" />
-- <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />
-- <arg value="../${docbook-xsl}/html/docbook.xsl" />
-- </java>
-- <echo message="Generating applet guide (de)" />
-- <java fork="true" dir="build/doc"
-- classname="com.icl.saxon.StyleSheet"
-- classpath="${lib.dir}/saxon.jar" >
-- <arg value="-o" />
-- <arg value="JmolAppletGuide_de.html" />
-- <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />
-- <arg value="../${docbook-xsl}/html/docbook.xsl" />
-- </java>
- </target>
-
- <target name="test" id="test" depends="main,compile-tests">
-@@ -1195,12 +1080,4 @@ - <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
- </target>
-
-- <!-- i18n stuff -->
-- <target name="main-i18n" depends="classes">
-- <ant antfile="build-i18n.xml" target="main-i18n"/>
-- </target>
-- <target name="spotless-i18n">
-- <ant antfile="build-i18n.xml" target="spotless-i18n"/>
-- </target>
--
- </project>
diff --git a/sci-chemistry/jmol/jmol-11.6.ebuild b/sci-chemistry/jmol/jmol-11.6.ebuild deleted file mode 100644 index 1409f461e..000000000 --- a/sci-chemistry/jmol/jmol-11.6.ebuild +++ /dev/null @@ -1,119 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=1 -WEBAPP_OPTIONAL="yes" - -inherit eutils webapp java-pkg-2 java-ant-2 - -DESCRIPTION="Jmol is a java molecular viever for 3-D chemical structures." -SRC_URI="mirror://sourceforge/${PN}/${P}-full.tar.gz" -HOMEPAGE="http://jmol.sourceforge.net/" -KEYWORDS="~x86 ~amd64" -LICENSE="LGPL-2.1" - -IUSE="client-only vhosts" - -WEBAPP_MANUAL_SLOT="yes" -SLOT="0" - -COMMON_DEP="dev-java/commons-cli:1 - dev-java/itext:0 - sci-libs/jmol-acme:0 - sci-libs/vecmath-objectclub:0" - -RDEPEND=">=virtual/jre-1.4 - ${COMMON_DEP}" -DEPEND=">=virtual/jdk-1.4 - !client-only? ( ${WEBAPP_DEPEND} ) - ${COMMON_DEP}" - -pkg_setup() { - - if ! use client-only ; then - webapp_pkg_setup || die "Failed to setup webapp" - fi - - java-pkg-2_pkg_setup - -} - -src_unpack() { - - unpack ${A} - epatch "${FILESDIR}"/${P}-nointl.patch - epatch "${FILESDIR}"/${P}-manifest.patch - - mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory." - cp "${FILESDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \ - || die "Failed to install Cert file." - - rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die - cd "${S}/jars" - -# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along. - if use amd64; then - mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar." - rm -v *.jar *.tar.gz || die "Failed to remove jars." - mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar." - fi - - java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar - java-pkg_jar-from itext iText.jar itext-1.4.5.jar - java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar - java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar - - mkdir -p "${S}/build/appjars" || die -} - -src_compile() { - # prevent absorbing dep's classes - eant -Dlibjars.uptodate=true main -} - -src_install() { - - java-pkg_dojar build/Jmol.jar - dohtml -r build/doc/* || die "Failed to install html docs." - dodoc *.txt doc/*license* || die "Failed to install licenses." - - java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \ - --java_args "-Xmx512m" - - if ! use client-only ; then - webapp_src_preinst || die "Failed webapp_src_preinst." - cmd="cp Jmol.js build/Jmol.jar "${D}${MY_HTDOCSDIR}"" ; ${cmd} \ - || die "${cmd} failed." - cmd="cp build/JmolApplet*.jar "${D}${MY_HTDOCSDIR}"" ; ${cmd} \ - || die "${cmd} failed." - cmd="cp applet.classes "${D}${MY_HTDOCSDIR}"" ; ${cmd} \ - || die "${cmd} failed." - cmd="cp -r build/classes/* "${D}${MY_HTDOCSDIR}"" ; ${cmd} \ - || die "${cmd} failed." - cmd="cp -r build/appletjars/* "${D}${MY_HTDOCSDIR}"" ; ${cmd} \ - || die "${cmd} failed." - cmd="cp "${FILESDIR}"/caffeine.xyz "${D}${MY_HTDOCSDIR}"" ; ${cmd} \ - || die "${cmd} failed." - cmd="cp "${FILESDIR}"/index.html "${D}${MY_HTDOCSDIR}"" ; ${cmd} \ - || die "${cmd} failed." - - webapp_src_install || die "Failed running webapp_src_install" - fi -} - -pkg_postinst() { - - if ! use client-only ; then - webapp_pkg_postinst || die "webapp_pkg_postinst failed" - fi - -} - -pkg_prerm() { - - if ! use client-only ; then - webapp_pkg_prerm || die "webapp_pkg_prerm failed" - fi - -} diff --git a/sci-chemistry/jmol/jmol-12.0.34.ebuild b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild index 722c99d8e..722c99d8e 100644 --- a/sci-chemistry/jmol/jmol-12.0.34.ebuild +++ b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild diff --git a/sci-chemistry/nmrpipe/ChangeLog b/sci-chemistry/nmrpipe/ChangeLog index fc4beb36d..6a0a362d0 100644 --- a/sci-chemistry/nmrpipe/ChangeLog +++ b/sci-chemistry/nmrpipe/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*nmrpipe-5.91.2011.167.16.39 (18 Jun 2011) + + 18 Jun 2011; Justin Lecher <jlec@gentoo.org> + +files/5.91.2011.167.16.39-lib.patch, -files/5.91.2011.138.14.57-lib.patch, + -nmrpipe-5.91.2011.138.14.57.ebuild, +nmrpipe-5.91.2011.167.16.39.ebuild: + Version BUmp, added missing die + *nmrpipe-5.91.2011.138.14.57 (20 May 2011) 20 May 2011; Justin Lecher <jlec@gentoo.org> diff --git a/sci-chemistry/nmrpipe/Manifest b/sci-chemistry/nmrpipe/Manifest index 5952fc79a..3f46f3fca 100644 --- a/sci-chemistry/nmrpipe/Manifest +++ b/sci-chemistry/nmrpipe/Manifest @@ -1,22 +1,22 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 -AUX 5.91.2011.138.14.57-lib.patch 997 RMD160 09e9dbed8e1e2e4964bdf381a15b556d0ea9f3bb SHA1 881a3554f21fb23973e0b8a31b59cff495f5edbb SHA256 011aea3e38ef3eb650be7b5d6274913bbb4f5367838f4bb86f97556ad247b57f +AUX 5.91.2011.167.16.39-lib.patch 997 RMD160 09e9dbed8e1e2e4964bdf381a15b556d0ea9f3bb SHA1 881a3554f21fb23973e0b8a31b59cff495f5edbb SHA256 011aea3e38ef3eb650be7b5d6274913bbb4f5367838f4bb86f97556ad247b57f AUX env-nmrpipe-new 915 RMD160 653b278864eb6b9db84d15b00421bad4c148f1f8 SHA1 2f33e5f4acbaa4a04aba8e8ce6d09f9c5706f05e SHA256 0b02b83e39d18e7d3d6c1567c99ae7fdc181746114458988a39fe1dead8719f9 -DIST NMRPipeX.tZ 117015303 RMD160 b0a8b1b0ee0cd1926bd1724306dbbf611bf0b97d SHA1 9efdde1057f4a355bb688e4e00bb1ba535ea7522 SHA256 acfd8e082bdf9e9fc0db362d4bbd389befdf7a0ba1f0063407d566014e315fb9 +DIST NMRPipeX.tZ 117216777 RMD160 1c8c21b7b96d4f0553d269b2a8da5f2a33577a71 SHA1 b95f6c50a02607dfaabb104c627eea82cfa4578b SHA256 8a29eef20a46ea9731dc34c16e9ecce4464f254f2c66925902b44dcaf70dc5c7 DIST acme.tar.Z 11681951 RMD160 fdcf35fab1b63ddda55288b1b2ed0f82c8299bef SHA1 5093f92a4d7e4173bc056b6b1922a6da8e6bbf0c SHA256 5713452a1461e636f0de48e5ce3476fc0ae60b3f78a0288744f45e455f3445d9 DIST binval.com 3807 RMD160 263195035981216833da16afa4dcea568ba06303 SHA1 d90062ee85c77157e421fd684e32d59a3118c6f9 SHA256 349a6b3b3bac0f82d645a44ee6073b95b9ad9573c548367a3528d32cf0c5694e -DIST dyn.tZ 136698401 RMD160 24ddfdb8fa01862ac2384a8c348ed099a44ba78b SHA1 83431d54ac1a8e59edf316e8645fb15e9152c2c5 SHA256 044d8d996ce22b5c69936dfbb248a3ffd9484f205af04b0f676278d884f2febe +DIST dyn.tZ 136738779 RMD160 15151c49fa2f94926ec580e8fe979e9aa9ddee2d SHA1 5520bae9f4bdf659b493d63f1cace6c9ccd5fdc0 SHA256 a6e66810b95830afb637881f5fda15c22b5d5b78a7c8b0630dbca141a4c18058 DIST install.com 40301 RMD160 801887ab36a1934c07a69a9b0a1e5699c8eba02f SHA1 4dd1856c302bf756c0d8ec75f5dcd9994e226e81 SHA256 90364e33bfb55406cd9026067315e8aed4854e9a5f70332e99f558837e4dc577 -DIST talos.tZ 56592679 RMD160 268b8d5e7607dc0275e5ca24a8b5116aaf22b8cd SHA1 cb7b45ecaba7fb4a1fb9b4edc927091dd2765933 SHA256 f256bb6987b26315cc89e33aa22630b67aeea6f84f1eea7ee5279b66c6992872 +DIST talos.tZ 56665163 RMD160 2ac3f07b6499f58e3e9044b09ad94bd590a0b185 SHA1 322562e2405cce0d3b20f40b589eae2011657b84 SHA256 4537e4677bbbcc79402fbde627fa2faf5128b816821fb495dd980765d9973c3f DIST valpha_all.tar 699166720 RMD160 75ebf0a84524212cd25d62ba33f6a5edca05dd20 SHA1 a8be07ac97a826e44ed240946217a50fd3e8ba1e SHA256 3f2ff243e1d0e2508f20ec1ab6108eb986bcc1bc4c9ec79b4ff8ce6584805b0a -EBUILD nmrpipe-5.91.2011.138.14.57.ebuild 5718 RMD160 c5c26110e57839f3697605644bf350b7b0f96954 SHA1 5385aac4c108cc2a3aea4b5a365a6702cf91fa8a SHA256 d81c616d8a4b9368c47a7b8477fe42785937eae4e7d241c89363306d9cec1625 -MISC ChangeLog 11388 RMD160 c5e114a7e51c6ef83b62d4426f8fa2d0a05cebf3 SHA1 7cc1421009caa0264492a1b09ba9de297a938138 SHA256 8efba4ec16dc8b667d0b96c2b079a72caf04c0ee9a89fc3d0e7c1cc5114ab9e5 +EBUILD nmrpipe-5.91.2011.167.16.39.ebuild 5725 RMD160 abbcc16d8c7fd43117c12dd5ac93a39ccfc1743f SHA1 8be76595f7d9e5c34f495d0fd153871c549f22c1 SHA256 bafb897da3f8e8ef9d3f54358e290eb021e409662cc7ed8c75853ea3f5ed2621 +MISC ChangeLog 11668 RMD160 03831e9f4d744fb09cc14c082654bd3e96e2d17a SHA1 211a643298dcba01f30232e69de29a7c4f02823b SHA256 a518b6ff0213348774c8333b61cbfb044d94720e23945670bdd310f06d49bb53 MISC metadata.xml 249 RMD160 789eca813b850a4619f671586826b824098ec47b SHA1 554c0cc8335f6d6410f6f504bf032a7c6de36c89 SHA256 c3f71fe107b700acc3c21923ed360604cfd47ac3181d9ed7605a0472250a8064 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk3WLl4ACgkQgAnW8HDreRaOEACcDj3StTTItS5FygvHkuG8VX97 -2UQAnA3ovyBfUMbY2ChxK118EFID3TT1 -=DleU +iEYEARECAAYFAk38ukUACgkQgAnW8HDreRb4qgCdF0VOz0jdzay91JF9iRv4VLmW +7jQAoJqZNANJiZEdxnhKqLik/Z920Eb8 +=w6uw -----END PGP SIGNATURE----- diff --git a/sci-chemistry/nmrpipe/files/5.91.2011.138.14.57-lib.patch b/sci-chemistry/nmrpipe/files/5.91.2011.167.16.39-lib.patch index 91abd611d..91abd611d 100644 --- a/sci-chemistry/nmrpipe/files/5.91.2011.138.14.57-lib.patch +++ b/sci-chemistry/nmrpipe/files/5.91.2011.167.16.39-lib.patch diff --git a/sci-chemistry/nmrpipe/nmrpipe-5.91.2011.138.14.57.ebuild b/sci-chemistry/nmrpipe/nmrpipe-5.91.2011.167.16.39.ebuild index 705e4e3c4..4c191d969 100644 --- a/sci-chemistry/nmrpipe/nmrpipe-5.91.2011.138.14.57.ebuild +++ b/sci-chemistry/nmrpipe/nmrpipe-5.91.2011.167.16.39.ebuild @@ -141,7 +141,7 @@ src_install() { sed \ -e "s:/opt/nmrpipe:${EPREFIX}/opt/nmrpipe:g" \ "${FILESDIR}"/env-${PN}-new \ - > env-${PN}-new + > env-${PN}-new || die newenvd env-${PN}-new 40${PN} || die "Failed to install env file." # PREFIX stuff diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest index f37ca42dd..24b9d547f 100644 --- a/sci-chemistry/phaser/Manifest +++ b/sci-chemistry/phaser/Manifest @@ -4,24 +4,14 @@ Hash: SHA1 AUX 2.1.4-sadf.patch 2417 RMD160 1450cf3135cbdb97d9c170fa574f361fa58acf7b SHA1 acb3995c065bd5cd0d49f68ca32bb9f38a1dc755 SHA256 f386d2c72e211d340c2d2cdf4c96ad20e62efedcc918ea52a0c5533b27791c33 AUX phaser-2.1.4-chmod.patch 490 RMD160 83a28e6e9fa2f7fecac04d302a7613121eb4d751 SHA1 f09a2d6ae869b7629583a34f7727fabf3e3faaf6 SHA256 c54a6ca87b2ff3347a5a52c010c2c7f8e57f7bb7ad10f47cf218ea7a78b1cce0 DIST phaser-2.1.4-cctbx-src.tar.gz 22388206 RMD160 65d65411ceb98f678488265c10e4159150db80ce SHA1 f388eb39b834f013e5120a82c34000a5fdd5e060 SHA256 594829cc82cb3c57e223ded99faf1fe86b192f2b48a935f93d2a4b89b9018970 -EBUILD phaser-2.1.4-r1.ebuild 3399 RMD160 b3fa317fe4de949e4722adbdb139db41007b069c SHA1 ce5843224ef030ec7e887a48addd08815b91046e SHA256 89154fc5d89905aebbd85a38d76e0094b154e923cb7d9b3e507cd16282990cf1 -EBUILD phaser-2.1.4.ebuild 2647 RMD160 d932a465af9ffb33a5dfdefda64b7eb19540b740 SHA1 1e3c5cd9b5527c8d07b5701d09c63d919444908d SHA256 df9f4fa9a30a67ce679a9d3eeb81010c585b204a1ac71290317850cb084bcb5c +EBUILD phaser-2.1.4-r1.ebuild 3399 RMD160 9e1df8766715c0de5ad81fc26506ed35cb408fc1 SHA1 9885c3b3a53ab451e196d6d3ed8d4aa0abd73286 SHA256 d148d4ac725e9ae84a1e4b0d10d39b770543cb9c940353df52202e62222fdfb7 +EBUILD phaser-2.1.4.ebuild 2647 RMD160 7f7eb64db631c9128d7026db2a68423d50dc0d7a SHA1 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a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild index beb867e4c..73f18f4ee 100644 --- a/sci-chemistry/phaser/phaser-2.1.4.ebuild +++ b/sci-chemistry/phaser/phaser-2.1.4.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit toolchain-funcs python eutils +inherit eutils python toolchain-funcs DESCRIPTION="Phasing macromolecular crystal structures with maximum likelihood methods" SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/${P}-cctbx-src.tar.gz" diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index a6920f00a..24af34ec1 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -10,13 +10,13 @@ AUX pymol-1.2.2-shaders.patch 441 RMD160 c0d9e177f701a015aec192b2bdf6b1df31e8de1 AUX pymol-9999-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8 AUX pymol-9999-prefix.patch 1183 RMD160 25a3e3fb1639e0c5cc93928b4fcba412a3e9b371 SHA1 3c61c3552a579a48883c61b646f05ce1f059744e SHA256 35b14c60163517debfdeae52b3be00bc0fc6ab96c58d2bf3efb65e22728522d4 AUX pymol-9999-shaders.patch 2507 RMD160 2dea0805fcc8a993d7f5fa8668257be860c7d5e8 SHA1 4548f93fbe92a511dc0d2425c86402a776567cb4 SHA256 b0cbb5bc81bb8f85bef8cbb6cd76f91b02b076ef5798075e152626becf3b5ae5 -EBUILD pymol-9999.ebuild 2526 RMD160 112a577b0922b97dfab2c07fd2de30beb3ac3c14 SHA1 c03b594aa988f37028410a3922d327c10ba975ca SHA256 4231c86a847a6866292ac6413124dd01e6e59991d8162b9be19ffcefed11892a +EBUILD pymol-9999.ebuild 2526 RMD160 cdb42c39304cb1e7ca73def85fc2d4d5a1e26ba9 SHA1 55664aeede4145ab9d3aeeb7b75624a811f96e10 SHA256 3124a3a90289923e8d547b01cff91463458bfd6d45cf39fefa5685a52cddbaa9 MISC ChangeLog 8604 RMD160 d085a62a6690f5aa7eabc496aafdd96b5b4083b0 SHA1 b47fdc5ef58d8a5ebba1db7ba2095e612aa2f9d6 SHA256 3c4f6b370b0a42f0a2404fc98ffea677494ba4dec4f2b5846a205a23de418d32 MISC metadata.xml 412 RMD160 dba8c0b7439c44e31e3e05207272c6e46c8fc0c3 SHA1 7eb3a638d6c1d7b05345af61d50e4a6caf0dfe42 SHA256 0b991b292dc1b6c0abd145e78db118e4705d81195b1b48d5d485f5b0709e48a7 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk3nTYMACgkQgAnW8HDreRZR8gCdHNf2OL3eYZlkTnN8/Jp3eguo -QgEAn0AjQyaKrIXx5hWdbuitAMk7Py4R -=WowW +iEYEARECAAYFAk4Ei8IACgkQgAnW8HDreRZ+PQCdGu/AcF7jG2GUrLwQjdOZWBxn +w2kAn0na/71UEt2vB5DqpIuqCeVY9OYE +=ngk/ -----END PGP SIGNATURE----- diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild index 53f9bb236..62a7a60b7 100644 --- a/sci-chemistry/pymol/pymol-9999.ebuild +++ b/sci-chemistry/pymol/pymol-9999.ebuild @@ -10,7 +10,7 @@ RESTRICT_PYTHON_ABIS="2.4 2.5 3.*" PYTHON_USE_WITH="tk" PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx" -inherit eutils distutils prefix subversion versionator +inherit distutils eutils prefix subversion versionator DESCRIPTION="A Python-extensible molecular graphics system." HOMEPAGE="http://pymol.sourceforge.net/" diff --git a/sci-chemistry/rosetta/Manifest b/sci-chemistry/rosetta/Manifest index 017524446..9c9b8547a 100644 --- a/sci-chemistry/rosetta/Manifest +++ b/sci-chemistry/rosetta/Manifest @@ -8,14 +8,13 @@ AUX 3.0-platform.patch 431 RMD160 2359b805d3d87f58eeff88864e1ebd0cba02d2ae SHA1 AUX 3.0-user-settings.patch 989 RMD160 fbdb678459c4663d181eb83b1ed4d58fcc507065 SHA1 e90cfd9b9055d8dc3b0e3029ff20ae05fd5fb601 SHA256 0b751e7a885faa0645de0d3450f6b3229c2959d5b42dc7dd77956199947b77df AUX 3.0-zlib.patch 289 RMD160 dac6ffb48adff95d7ea5a8aa90ebe8be13087a6a SHA1 6336f6d23a924ce42943ea5959937ab397cb9365 SHA256 ee8cae00b2098b4e672fa46b60a35d381cc17d5ccbc6bbf38cdf966777ff1f03 DIST rosetta3_source.tgz 98443598 RMD160 09c7bdaef58ef761bfdc8143c38f81f814be41a4 SHA1 3477856807a6fb4898c8c2aa7852b3b6e4fe90ee SHA256 1870727caea342c3b55af7c353b991758fe1cf4a395a65b48543708e52dc75c5 -EBUILD rosetta-3.0-r1.ebuild 3423 RMD160 6f2d3c21353f943bc3a4cb246bcafd0491c78ee1 SHA1 de3b6153a139c9f3e8fd4d0699af4fbc182bc8e5 SHA256 b8bb9a29208b308de314b244ee43f9e1b6dec190d09849989b9d72a49ad0332f -EBUILD rosetta-3.0.ebuild 2914 RMD160 f535a0716d7d6c50251ed62af0858866da1eccfc SHA1 c036a94ba58ffac71a0ed3ca3223fe7d0a954292 SHA256 fab910170f4c65ae3eb1277be0e0063f2148f638f29f59e2aafb3cb40703e6c6 +EBUILD rosetta-3.0-r1.ebuild 3423 RMD160 48c459b3e149d60a59a1c536da42b548bc3d461f SHA1 53465e695ee22b31c15b1e82ad3f08fce18be526 SHA256 6e12bf887186d3038d824bd48d3926c04cf74b6f91d7ba6d17b369750b6e2292 MISC ChangeLog 1212 RMD160 6017f34695998e08fa47ffe7c8234b80764b9175 SHA1 467bced72b308ef42aff65867dd5f210f0d51471 SHA256 a7f2135a922ef4865a1e2fd1a37c0e060957149c6449c681e713a291dc82a7a1 MISC metadata.xml 450 RMD160 13d6fc607a68ab354ae5e01887aa96152c1838fd SHA1 857337c1113dfe1826ea2ba81694e416440a4e55 SHA256 979b679698fd4b06b80ce01558fba3759219e071787a56fd036ee8dfa51ee8ac -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkyV4vkACgkQgAnW8HDreRZjYgCeKt03LOMTj3rfHeLTSnYd5nRT -KzUAoM6J6ZphPiigh5XHxUpJx2Y17jd4 -=hcJ+ +iEYEARECAAYFAk4EjDIACgkQgAnW8HDreRbGMgCgw1s0CVXNEiWiqMiRPrdjbkn1 +0I8An05W+4AMfBB4RQVRryQMywBSpJMM +=yABE -----END PGP SIGNATURE----- diff --git a/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild b/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild index 1e26712ab..da1d22620 100644 --- a/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild +++ b/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild @@ -6,7 +6,7 @@ EAPI="2" -inherit versionator eutils multilib +inherit eutils multilib versionator MY_P="${PN}$(get_major_version)_source" @@ -17,7 +17,7 @@ SRC_URI="${MY_P}.tgz" LICENSE="|| ( rosetta-academic rosetta-commercial )" SLOT="0" KEYWORDS="" -IUSE="boinc boost X mpi debug doc" +IUSE="boinc boost debug doc mpi X" RESTRICT="fetch" RDEPEND="mpi? ( virtual/mpi ) diff --git a/sci-chemistry/rosetta/rosetta-3.0.ebuild b/sci-chemistry/rosetta/rosetta-3.0.ebuild deleted file mode 100644 index c4056e8ad..000000000 --- a/sci-chemistry/rosetta/rosetta-3.0.ebuild +++ /dev/null @@ -1,128 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -inherit versionator eutils multilib - -MY_P="${PN}$(get_major_version)_source" - -DESCRIPTION="Prediction and design of protein structures, folding mechanisms, and protein-protein interactions" -HOMEPAGE="http://www.rosettacommons.org/" -SRC_URI="${MY_P}.tgz" - -LICENSE="|| ( rosetta-academic rosetta-commercial )" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="boost X mpi debug" -RESTRICT="fetch" - -RDEPEND="mpi? ( virtual/mpi ) - boost? ( dev-libs/boost ) - sci-libs/rosetta-db" -DEPEND="${RDEPEND} - >=dev-util/scons-0.96.1 - doc? ( app-doc/doxygen ) - X? ( media-libs/freeglut )" - -MYCONF="" - -S="${WORKDIR}/${MY_P}" - -pkg_nofetch() { - einfo "Go to ${HOMEPAGE} and get ${A}" - einfo "which must be placed in ${DISTDIR}" -} - -src_prepare() { - local myCXXFLAGS - local myLDFLAGS - - epatch "${FILESDIR}"/${PV}-platform.patch - epatch "${FILESDIR}"/${PV}-fix-scons-warnings.patch - epatch "${FILESDIR}"/${PV}-user-settings.patch - epatch "${FILESDIR}"/${PV}-fix-valgrind.patch - rm bin/* -f - - for i in ${CXXFLAGS}; do - myCXXFLAGS="${myCXXFLAGS} \"${i/-/}\"," - done - - for i in ${LDFLAGS}; do - myLDFLAGS="${myLDFLAGS} \"${i/-/}\"," - done - - sed -e "s:GENTOO_CXXFLAGS:${myCXXFLAGS}:g" \ - -e "s:GENTOO_LDFLAGS:${myCXXFLAGS} ${myLDFLAGS}:g" \ - -e "s:GENTOO_LIBDIR:$(get_libdir):g" \ - -i tools/build/user.settings - - use mpi && \ - sed -e 's:mpiCC:mpicxx:g' \ - -i tools/build/basic.settings -} - -src_configure() { - local myextras="" - local mycxx="" - - use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost") - use X && EXTRAS=$(my_list_append "${EXTRAS}" "graphics") - use mpi && EXTRAS=$(my_list_append "${EXTRAS}" "mpi") - - COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)') - mycxx="cxx=${COMPILER}" - - test -n "${EXTRAS}" && myextras="extras=${EXTRAS}" - - if use debug; then - MODE="debug" - else - MODE="release" - fi - - MAKEOPTS=$(my_filter_option "${MAKEOPTS}" "--load-average[=0-9.]*") - MAKEOPTS=$(my_filter_option "${MAKEOPTS}" "-l[0-9.]*") - - MYCONF="${MAKEOPTS} mode=${MODE} ${myextras} ${mycxx}" -} - -src_compile() { - einfo "running 'scons bin cat=src ${MYCONF}' ..." - scons bin cat=src ${MYCONF} || die "scons bin cat=src ${MYCONF} failed" -} - -src_install() { - local BIT - - use amd64 && BIT="64" - use x86 && BIT="32" - - dolib.so build/src/${MODE}/linux/2.6/${BIT}/x86/${COMPILER}/${EXTRAS//,/-}/*.so || \ - die "failed to install libs" - - cd bin - for BIN in *; do - newbin ${BIN} ${BIN%%.*} || die "could not install rosetta program files" - done - - mv "${D}"/usr/bin/cluster{,-${PN}} - mv "${D}"/usr/bin/benchmark{,-${PN}} -} - -my_filter_option() { - local value="$1" - local exp="$2" - local result=`echo ${value} | sed -e s/${exp}//g` - echo "${result}" - return 0; -} - -my_list_append() { - local old_value="$1" - local new_value="$2" - test -n "${old_value}" && old_value="${old_value}," - echo "${old_value}${new_value}" - return 0; -} diff --git a/sci-chemistry/simpson/ChangeLog b/sci-chemistry/simpson/ChangeLog index 419cb6887..a18970526 100644 --- a/sci-chemistry/simpson/ChangeLog +++ b/sci-chemistry/simpson/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-chemistry/simpson -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> simpson-3.0.1.ebuild, + metadata.xml: + Cleaned ebuild + *simpson-3.0.1 (11 Aug 2010) 11 Aug 2010; Justin Lecher <jlec@gentoo.org> -files/2.0.0-gentoo.patch, diff --git a/sci-chemistry/simpson/Manifest b/sci-chemistry/simpson/Manifest index 54e47234e..761ac3cb5 100644 --- a/sci-chemistry/simpson/Manifest +++ b/sci-chemistry/simpson/Manifest @@ -1,16 +1,16 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX 3.0.1-gentoo.patch 716 RMD160 9c90f3c9deee8a0ff1f583a34fcc1bd3d55fdbbf SHA1 472288c2c041d66aed13212958a765325d5e735f SHA256 cc85cdd872b7f60288037ada586f8373b0b2f6c7dfa9af122d0143c489dbb4df AUX 3.0.1-type.patch 2600 RMD160 97b061cfa1a1fd5b3ebc9c7d597135122b552b2d SHA1 6c79eb9e92d40524e326263e218f5d90580753df SHA256 c079575af39c32cd58223be2356b9bed56ad5eb8a75900d06571ee0d2beddc81 DIST simpson-source-3.0.1.tgz 383619 RMD160 8d596831d5f413cd5c18a984b965e8171a5b5da7 SHA1 7d9f219da1c146642e80350d8ea54570a462118a SHA256 77c5946b4a02b4e743b11dae4514935a2a66f4ed12e700845ccb49ee4c56ed17 -EBUILD simpson-3.0.1.ebuild 925 RMD160 4d98d3513874ea1b978468b6e42102854dbc9a7b SHA1 ff9c6f9174540c466af15a4dd5157f6d5ad9336e SHA256 1bb187ce58c62c396d7a1c85dd5d70d171e5be1422cdfcf22af5a97e1d93712a -MISC ChangeLog 517 RMD160 d2c39cd8046975fcaf4167659d243df463a5be09 SHA1 f53468c963b83ecb04fd6fa86e1854971e86758a SHA256 0e1a8417d6604617b5fd703b01fec2781c52094aebc730d90b7263c3457b2c1a -MISC metadata.xml 1238 RMD160 c82938e77f387291d6a1c3bf9b0d802f2878dd12 SHA1 b5738f14922c69e78cfb867acdc65eeea25977bf SHA256 2c13f98be5fa8bdaf21ac86bcd00bbeb8944df5615de0cfce35ae4c00ef4b4d5 +EBUILD simpson-3.0.1.ebuild 895 RMD160 3f8b035ec44813497202ce33b5fc18cdafafb88c SHA1 735650ddb203399c7b50b59df22940e991f0c31b SHA256 85adff3d3608313752f92fd60f9b55eebb90043cf8145947d180cce408b262bc +MISC ChangeLog 620 RMD160 dc31571a4115c9bce27d9cc65e09ad1de337fde0 SHA1 498341ba9b43463e266992f5594e40490e200b90 SHA256 4cf0d33e2e3c1abb81f7a2191e19b1fa5e5ca1c355a87958bbea24041b492dd8 +MISC metadata.xml 1245 RMD160 72c16503a72d12dd42d40d3801f4f99f35d089a6 SHA1 8837dd404bda91e16227d8ec36d61fd77fb673a6 SHA256 24fc9f665e8d53941bc4f537777f5f9ae2b1e817d1d703d75ae78c62da27981a -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkxjCPoACgkQgAnW8HDreRbejQCcCMTqtWKthtiNMJSFQXF0e2p9 -8GwAoISRI98e2unpNdlapfEkhFPA4sOu -=+Sl7 +iEYEAREIAAYFAk4GAm4ACgkQgAnW8HDreRYaMACfUjXC4pjCUQdn5pivYiRP1mIq +DpAAnRnyZvZSDfWaPtf4Kht9JXW4jHfx +=hipz -----END PGP SIGNATURE----- diff --git a/sci-chemistry/simpson/metadata.xml b/sci-chemistry/simpson/metadata.xml index 46a44e575..11535840f 100644 --- a/sci-chemistry/simpson/metadata.xml +++ b/sci-chemistry/simpson/metadata.xml @@ -16,13 +16,13 @@ Before committing, please remove the comments from this file. They are not relevant for general metadata.xml files. --> <pkgmetadata> -<herd>no-herd</herd> -<maintainer> - <email>@gentoo.org</email> -<!-- <description>Description of the maintainership</description> --> -</maintainer> -<!-- <longdescription>Long description of the package</longdescription> --> -<!-- + <herd>no-herd</herd> + <maintainer> + <email>@gentoo.org</email> + <!-- <description>Description of the maintainership</description> --> + </maintainer> + <!-- <longdescription>Long description of the package</longdescription> --> + <!-- <use> <flag name='flag'>Description of how USE='flag' affects this package</flag> <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this diff --git a/sci-chemistry/simpson/simpson-3.0.1.ebuild b/sci-chemistry/simpson/simpson-3.0.1.ebuild index 16c6ee870..3a7f74543 100644 --- a/sci-chemistry/simpson/simpson-3.0.1.ebuild +++ b/sci-chemistry/simpson/simpson-3.0.1.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=4 -inherit autotools eutils prefix +inherit eutils prefix DESCRIPTION="General-purpose software package for simulation virtually all kinds of solid-state NMR experiments" HOMEPAGE="http://bionmr.chem.au.dk/bionmr/software/index.php" @@ -13,7 +13,7 @@ SRC_URI="http://www.bionmr.chem.au.dk/download/${PN}/3.0/${PN}-source-${PV}.tgz" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux" LICENSE="GPL-2" -IUSE="threads gtk tk" +IUSE="gtk threads tk" RDEPEND=" dev-libs/libf2c @@ -35,10 +35,9 @@ src_prepare() { src_compile() { emake \ CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS}" \ - || die + CFLAGS="${CFLAGS}" } src_install() { - dobin ${PN} || die + dobin ${PN} } diff --git a/sci-chemistry/smmp/ChangeLog b/sci-chemistry/smmp/ChangeLog index 1e848e7a3..cddd7bfbb 100644 --- a/sci-chemistry/smmp/ChangeLog +++ b/sci-chemistry/smmp/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/smmp -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> smmp-3.0.5.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> smmp-3.0.5.ebuild: + Added fortran-2.eclass support + 29 Jun 2010; Justin Lecher <jlec@gentoo.org> smmp-3.0.5.ebuild: Python ABI fixes diff --git a/sci-chemistry/smmp/Manifest b/sci-chemistry/smmp/Manifest index c6c0fcc7d..fb11fc677 100644 --- a/sci-chemistry/smmp/Manifest +++ b/sci-chemistry/smmp/Manifest @@ -3,13 +3,13 @@ Hash: SHA1 AUX 3.0.5-flags.patch 2801 RMD160 ace7706b1f1e47def71176994bdf96ad24d2ddfb SHA1 ec19536f048b7ba3635c14a9f60ddbe4ccc730a4 SHA256 c05d6fa67dcfb3e5cced5efaff07e4a7422903df6ae1ce15576cefafe985c0ef DIST SMMP-3.0.5.tar.bz2 233378 RMD160 a951eb826c3af743aae4156fb21bffe028d68846 SHA1 fda498e9aac93efcf57787da4aa190ec3f70f1c7 SHA256 70d6b719d2c2ef1d34fd9897ad1c89a37c4d7531d80c904eee39dc8855aca31c -EBUILD smmp-3.0.5.ebuild 1170 RMD160 f65c3a70e253c901017fa8bcdf72b262c3026cb0 SHA1 8cba83714eed0981096834ee5fe6556cb67b4642 SHA256 572adbce39a42db40b3af8550cdd27fde721826fc3e2b23f4a232e8272503ec4 -MISC ChangeLog 385 RMD160 88cd4af4ef67adec7b07397aeecad91beaefa2e4 SHA1 418b8862c0f2416219ec6c0019c73ba083385c88 SHA256 058bcdc4e5267b971640deb4e8e3f8aad809a912f76dbac6f0bfca1f74fb5225 +EBUILD smmp-3.0.5.ebuild 1151 RMD160 3968f3f7f93cfc2f4126b62f2b077f6d8e6fd179 SHA1 af5f0168f9e34c56ca2ae6682d18c77002f8ab4f SHA256 70e0b11616f3dd14de1f002b47a4740bb24405bf5ba9fd0fcb0fc603cc3e6dca +MISC ChangeLog 589 RMD160 7ead21d9c7300f38bdf5dc96ed2a1efbb51f346f SHA1 25525e1e25eb4c142601d43de427f5f6b099d85d SHA256 af596d14a5f4f23d1bfa65fb48d92bdcbbb424e4b39c6a39d747ed47e9e9936a MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkwqGK0ACgkQgAnW8HDreRb+OgCePX4aJm8zcyr544atZyR03CY/ -FykAoMPGpx5dzH84fuqJOEMOu2H78jkR -=Qq9Z +iEYEARECAAYFAk4EfvcACgkQgAnW8HDreRbqOwCgyAwU8wGO1Yk7+JKYl1eKoS9p +FBwAniy9iQHfgz7UoTIXGoy/eez5kILw +=bBHf -----END PGP SIGNATURE----- diff --git a/sci-chemistry/smmp/smmp-3.0.5.ebuild b/sci-chemistry/smmp/smmp-3.0.5.ebuild index 9540246f3..8f49f3d29 100644 --- a/sci-chemistry/smmp/smmp-3.0.5.ebuild +++ b/sci-chemistry/smmp/smmp-3.0.5.ebuild @@ -1,13 +1,14 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=2 PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.*" -inherit eutils python toolchain-funcs +inherit eutils fortran-2 python toolchain-funcs MY_PN="SMMP" MY_P="${MY_PN}-${PV}" @@ -21,12 +22,12 @@ KEYWORDS="~amd64 ~x86" LICENSE="GPL-2" IUSE="doc mpi test" -RDEPEND="mpi? ( virtual/mpi )" +RDEPEND=" + virtual/fortran + mpi? ( virtual/mpi )" DEPEND="${RDEPEND} doc? ( app-doc/doxygen )" -RESTRICT_PYTHON_ABIS="3.*" - S="${WORKDIR}/${MY_P}" src_prepare() { @@ -38,18 +39,16 @@ src_compile() { FC="mpif90" target="parallel" else - FC=$(tc-getFC) target="${PN}" fi - emake FC=${FC} ${target} || die + tc-export FC - if use test; then - emake FC=${FC} examples || die - fi + emake ${target} || die } src_test() { + emake examples || die cd EXAMPLES bash smmp.cmd || die } diff --git a/sci-chemistry/sparta+/ChangeLog b/sci-chemistry/sparta+/ChangeLog index 1f9831bcf..234f68a7f 100644 --- a/sci-chemistry/sparta+/ChangeLog +++ b/sci-chemistry/sparta+/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/sparta+ -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*sparta+-2.60.2011.167.16.39 (24 Jun 2011) + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> + -sparta+-1.00.2010.0804.14.ebuild, +sparta+-2.60.2011.167.16.39.ebuild: + Version Bump + *sparta+-1.00.2010.0804.14 (28 Oct 2010) 28 Oct 2010; Justin Lecher <jlec@gentoo.org> diff --git a/sci-chemistry/sparta+/Manifest b/sci-chemistry/sparta+/Manifest index 565e5f020..61b159d6f 100644 --- a/sci-chemistry/sparta+/Manifest +++ b/sci-chemistry/sparta+/Manifest @@ -1,14 +1,14 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 -DIST sparta+.tar.Z 5491497 RMD160 002f62577443341a7c3949fe024e4cab331e19f1 SHA1 14074cbc60292e09eec9b8229d78f7e3285d716b SHA256 4d8fece4dcc875def5e964aae376f2a66eff3381566708627a83e4ab6dd39556 -EBUILD sparta+-1.00.2010.0804.14.ebuild 712 RMD160 7634ac6212a3c0bb359888abc20988aea9422535 SHA1 6dead86a5560be58483083c936af8803db4ac923 SHA256 1946691c98a72ff50e6529cf4d947899e60bc60d53bfa624ad3130618f01bd41 -MISC ChangeLog 279 RMD160 8b5fc36e026e205bc4f05ce0432e93ac0fdbc291 SHA1 f6caa465d8342f0a0d406cb5b4342fe6e5194888 SHA256 f32c91b614015a5b55ed78e52256613d355e3e9bf3836896b4243dae2201cdb5 +DIST sparta+-2.60.2011.167.16.39.tar.Z 3972715 RMD160 708abf92c92ea16a605dd885709eb95946894fa7 SHA1 28226eb87f7e80d3120ea1c4fade77dcadde8574 SHA256 00888e1528c579469474339c09dbc0e55c53f98b301bb3a600a7467fac3f156c +EBUILD sparta+-2.60.2011.167.16.39.ebuild 713 RMD160 02695cc0b4630f5aaf78bc0254782b05263d2c02 SHA1 da556114f1da6a5985896e4649eae00e08f16596 SHA256 7f8e86ef9c41a5f52862a51b253c75aa1af8c00fdc3cf8f63736692e5bc42e5e +MISC ChangeLog 460 RMD160 854e354ebf3f16f96b4d87bd1b29d457f4b2b83a SHA1 f15e3e1a66346a3feaaa4df8062dc48ac96b8510 SHA256 bc0d68edadccc241ed687260bfd31aeabdebd51cc100ffb1dd44061bddb10773 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkzJ26oACgkQgAnW8HDreRbofACdHvU/BGQlJOiv+/rMmXGStzF6 -hbAAoITjupoNX/R6jQ8GUUROUQhJ1Sda -=IoE0 +iEYEARECAAYFAk4EhH8ACgkQgAnW8HDreRZFxwCgk2KKqdaZIirBZCX17/0DLjp/ +S2IAnicM5Tuua0OT4gRa/IVYDsb/E6qr +=/Hd9 -----END PGP SIGNATURE----- diff --git a/sci-chemistry/sparta+/sparta+-1.00.2010.0804.14.ebuild b/sci-chemistry/sparta+/sparta+-2.60.2011.167.16.39.ebuild index 4a134ecf8..cca12aea2 100644 --- a/sci-chemistry/sparta+/sparta+-1.00.2010.0804.14.ebuild +++ b/sci-chemistry/sparta+/sparta+-2.60.2011.167.16.39.ebuild @@ -1,14 +1,12 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" - -# inherit +EAPI=4 DESCRIPTION="Shifts Predicted from Analogy in Residue type and Torsion Angle with neural" HOMEPAGE="http://spin.niddk.nih.gov/bax//software/SPARTA+/" -SRC_URI="http://spin.niddk.nih.gov/bax/software/SPARTA+/sparta+.tar.Z" +SRC_URI="http://spin.niddk.nih.gov/bax/software/SPARTA+/sparta+.tar.Z -> ${P}.tar.Z" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" diff --git a/sci-chemistry/votca-csg/ChangeLog b/sci-chemistry/votca-csg/ChangeLog index b2b06941f..940b1baf3 100644 --- a/sci-chemistry/votca-csg/ChangeLog +++ b/sci-chemistry/votca-csg/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> votca-csg-9999.ebuild: + Sort inherit and/or USE + 03 Jun 2011; Christoph Junghans <ottxor@gentoo.org> votca-csg-9999.ebuild: use default instead of tip commit diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest index 65c0f6813..86a84c385 100644 --- a/sci-chemistry/votca-csg/Manifest +++ b/sci-chemistry/votca-csg/Manifest @@ -1,17 +1,13 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 -EBUILD votca-csg-9999.ebuild 1829 RMD160 d457e05801aaac0dc56aed74215e75d07365f60d SHA1 e0be34d8f12f4b5d35c0081386aef3476d95771b SHA256 d7b84dce193f43b6779c2c247bcf60bedda7a3ef3b64332d72ac92c65db1c647 -MISC ChangeLog 3614 RMD160 fe313f800c32f242f3ed0aff523a776678a5864d SHA1 a4e0a7ccadc8039ff4958013d629c231bceec103 SHA256 e2dadb844c40723cef87b49b4386efe3e9d28e45121ea3661d4369bb92ece0c9 +EBUILD votca-csg-9999.ebuild 1827 RMD160 0d8178ce76bfb3745992b780d1286decab015d63 SHA1 15edbcde2df27726209b5aa175ba0129ad7f8838 SHA256 2ab85d2651a561aa0284106fddda841635feb3ecc1206233c095efc64582152b +MISC ChangeLog 3711 RMD160 ed637ad1ce61b2eefbc46bb26e3008d3c32a9f96 SHA1 be5de3caf567933cfab51cfd5e3ca0bd8d91ae0e SHA256 6f84312515bba604e141b4fb3648a56d21ad7ee1fd76e00aeac5e7256c06c00c MISC metadata.xml 455 RMD160 d99a1f4890743f913a85d3bcc0c560e802dbba16 SHA1 288fd2ae6a3cddcae99cd254de7a53ae656af51c SHA256 ab0ff4b353c05f875c88f8d96d9cfa705ed61a0079c7a07b798d2be6ecf988e7 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iQEcBAEBAgAGBQJN6VgdAAoJEOeBhlrCAAWGyDEIAKsQH3wSQq1u9MsVbqI2q+jf -3ucBcTng0nAyBY4QptGt59qH2l5eoEQje5JrrpItQ2V1px7UwXT+2ajcCP/6YpJX -urNibSxC8awufFh+5Mksskq53mTDop0i5wHc+QpAxk1ZehLAN5sXmh6eYENrvrsA -xGIw7g13zFUbqjQmEH1X/2HEZhggBjar3JE0PmQ2hQpPdXDlJDm1ANBMtVY3ZzhQ -iWgUbPU+rUJLxFiJQ7kpo8Lj/ZlxMYbO7MVvbUdNK1FEi7M7DA25Pdn6k+rhNu5v -qDYl6w6mkW1M28+jw3zNJ7dGYtFC9rAcSPs5CwhN8pdR6bND44Wlh2OwBa53dwM= -=IjQt +iEYEARECAAYFAk4EhLMACgkQgAnW8HDreRZnOQCgsIn1jNeD1M11fae9LRIKVGoA +LDEAnRhj5+GXOorDvMs0RTOklc7HdlE7 +=FWya -----END PGP SIGNATURE----- diff --git a/sci-chemistry/votca-csg/votca-csg-9999.ebuild b/sci-chemistry/votca-csg/votca-csg-9999.ebuild index 8782dc4ca..224fa2afa 100644 --- a/sci-chemistry/votca-csg/votca-csg-9999.ebuild +++ b/sci-chemistry/votca-csg/votca-csg-9999.ebuild @@ -2,9 +2,9 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=3 -inherit cmake-utils bash-completion +inherit bash-completion cmake-utils MANUAL_PV=1.1 if [ "${PV}" != "9999" ]; then diff --git a/sci-electronics/player/Manifest b/sci-electronics/player/Manifest index b4cd62c9c..9ba6d3fcc 100644 --- a/sci-electronics/player/Manifest +++ b/sci-electronics/player/Manifest @@ -2,13 +2,13 @@ Hash: SHA1 DIST player-2.0.4.tar.bz2 1707996 RMD160 8b70fef48595afcf9fafe24cf57f7a3fa9ba8628 SHA1 96ae46abe9a81cab045b2a9ae6479a44fc6f2ac2 SHA256 615225f22e0585df2a5fdf9adaddbe6e2a9ca25f1015607f51a47023fcc2cdf9 -EBUILD player-2.0.4.ebuild 3307 RMD160 768c1e54c9cd4fd55739f72f9b7bf4957aed8c2a SHA1 bb401882e30f00aef10fd1266f30e1412c8e5f14 SHA256 ba6d0ac23c48e005363c3d57f37f3bc6ea890b7150335a33225c12ab49dfd6d2 +EBUILD player-2.0.4.ebuild 3307 RMD160 2aa5c8a6560ad8ea20c931cd8d607d8a21c1e7bf SHA1 8748ad4253b3d87618706b2b3e4b9cdf79859c3c SHA256 8f2dc41a16b5221f40d96d764b1e35da5b41dc83ffd8a88d417d7cff90cac161 MISC ChangeLog 1383 RMD160 47e40a436854c96d06ced4406de894c5025d4f34 SHA1 ce378767f6aa97f768cbeddf19625618ebfa0175 SHA256 1069e5cb8adbe954f2c8f031a4d663f1510c1aeeb17973a4512a3cf591633ea7 -MISC metadata.xml 169 RMD160 c200fa2c4703eb26cf6ba49efb830c4f23678a5b SHA1 f97e1ffdd53446fb93f5b6b1225099c45337b0b4 SHA256 0b291e8666ec5ca169baa47793c8865f2f930efd84136d69b9010770a910930a +MISC metadata.xml 505 RMD160 6c6527830b1063b6f1f254a4662f6fe95ba661b9 SHA1 0f3ab5b69555db7b23f616c1f1b29f69c048edfa SHA256 c5dfbcb037f0b68b2fa8a53dbac9d9c5b8149ed6f3eaacf84f4ecf3486015d19 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk197aQACgkQgAnW8HDreRYT8ACfbp7xr8uzMi83E71uF/FRnreB -rZYAn1KJGY/AxsPIHEEO/MGxd4bPgQpo -=mmN5 +iEYEARECAAYFAk4EpqMACgkQgAnW8HDreRaqigCgkf36yiMn81QNl2XItmv5DJuz +MucAoLIv2lOBWYKZ9qpid8uTcitxKd8c +=GY/w -----END PGP SIGNATURE----- diff --git a/sci-electronics/player/metadata.xml b/sci-electronics/player/metadata.xml index aa78ded2d..50de93857 100644 --- a/sci-electronics/player/metadata.xml +++ b/sci-electronics/player/metadata.xml @@ -1,6 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-electronics</herd> + <herd>sci-electronics</herd> + <use> + <flag name="sphinx2">Automatically generated description for sphinx2</flag> + <flag name="boost">Automatically generated description for boost</flag> + <flag name="openssl">Automatically generated description for openssl</flag> + <flag name="festival">Automatically generated description for festival</flag> + </use> </pkgmetadata> - diff --git a/sci-electronics/player/player-2.0.4.ebuild b/sci-electronics/player/player-2.0.4.ebuild index 1407002a9..c1234826b 100644 --- a/sci-electronics/player/player-2.0.4.ebuild +++ b/sci-electronics/player/player-2.0.4.ebuild @@ -30,7 +30,7 @@ KEYWORDS="~amd64 ~x86" # yarpimage - needs YarpCam (not in portage) # rcore_xbridge - needs libparticle (not in portage) -IUSE="ieee1394 sphinx2 wifi v4l test imagemagick +IUSE="ieee1394 imagemagick sphinx2 test v4l wifi boost gnome gtk openssl festival opengl glut gsl java python doc" diff --git a/sci-electronics/tnt/ChangeLog b/sci-electronics/tnt/ChangeLog index d5fd56c42..e34c3239d 100644 --- a/sci-electronics/tnt/ChangeLog +++ b/sci-electronics/tnt/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> tnt-1.2.2.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> tnt-1.2.2.ebuild: + Added fortran-2.eclass support + 24 Feb 2011; Andreas K. Huettel <dilfridge@gentoo.org> tnt-1.2.2.ebuild, -files/tnt-1.2.2-Makefile-am.patch, -files/tnt-1.2.2-doc-Makefile-am.patch, +files/tnt-1.2.2-docs.patch, diff --git a/sci-electronics/tnt/Manifest b/sci-electronics/tnt/Manifest index 505854cf8..d1b3640bc 100644 --- a/sci-electronics/tnt/Manifest +++ b/sci-electronics/tnt/Manifest @@ -9,23 +9,13 @@ AUX tnt-1.2.2-gui.patch 900 RMD160 acfa4c03aa92c97b257f3d7d5a08e01d94834e77 SHA1 AUX tnt-1.2.2-namespaces.patch 6862 RMD160 2a32bb175e4769f35bd9d91521da7c9ac13c11d9 SHA1 7a181abc878951f631d576188144e44422743eea SHA256 d777646d0e7a43aee5c68e5061a85cd99be45cd539b683afff7752d7581d16c1 AUX tnt-1.2.2-tkcon.patch 447 RMD160 d3b708d681a5a468c9f17b27dba6c273e3b472ad SHA1 55e8f6bb54d4e59ce73620d2909d6d8b23197770 SHA256 1302823cd11ad31dcca115abb93a6f1c07299872bf5d48d51815b5436bbee846 DIST tnt-1.2.2.tar.gz 2020099 RMD160 1a2ba68a93ee21590bb25a3eacf85d3773c3e77d SHA1 bd089863ca2cd939009253e83f4ab75317191047 SHA256 cbb418d0de4f244d8174e8826e4d8272bce753f50431c9d87af08928f5817445 -EBUILD tnt-1.2.2.ebuild 1560 RMD160 cf0dc81a332f776ea0d74861a840b0f65c5c5055 SHA1 d64b470d0edf236e2447e646c4cc31c81d3a6579 SHA256 db439bd394e69329ace1f76cba887df819c1f67a9a4e9f01cc04eca743efe15c -MISC ChangeLog 1471 RMD160 40f5cb7452c76c3c9d9b49662ea2bee7523517eb SHA1 5d2b379e449fe2a19de5b1437db0c48e5ae334db SHA256 11c0975f971df7b61f92f646192e76fc99b5e91bbbd727a04497922a4859dcbd +EBUILD tnt-1.2.2.ebuild 1410 RMD160 ec63c42e24b4b29f8844a783a3a9044c9ecd9ffd SHA1 4d57dabb2a0a33987e2056a30cdf7d3ba6f0020f SHA256 3233496e49ce7a85bcb9886e8ed53ee954c8e45517e37bddeec1741ea2d0fefc +MISC ChangeLog 1673 RMD160 5e60ad10d4186023f496cc36b2f5cef79a386fab SHA1 3d71ec3af4ff26b44b4514d2e74451974e2b616e SHA256 16f516aa4c63e2c8f9a0cd49fef904e0aacc26f0af4fb45839ec83f6a9091bc2 MISC metadata.xml 169 RMD160 64326712291b01dc0338c2d7e25ee531c79070d4 SHA1 af996dd4475f4ed9db91e2661af914b63818b061 SHA256 d4bef2a959b97ce8ccc4593e629e4743b9bb8303843d9edf72d148ffbf076939 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJNZ9ckAAoJENwGBM22xffetAkP/juRzl2U6n3nnm0FjCPLHtQ/ -RFAV2ft3axnDyy1sWGq4Zwbd1eFPi9X2qRC72lTo/4YS2KrDnoYMK1ku4Qr22Y+O -KgZ8VALMBrOq9lwyQJmhlWxEqHZCw00PlaDAOR4Rx2BXDftS9+zQFOmtUXKMqbjX -T2EdtHTIllwtrH/pT4atYlMw/c5LK3OctC9ABMMqsjvIXz1UX58oTFTj51xQl2fo -bt2A2xYwu0lMPoT/ehzhKEwfGye9ZdJ2Sa/C18A7h8GVr1MVjLsa77yuZ0O4DWAy -A74w5OvfDdT33luJUapvCLf3oPzue1qO/sS6IUXMSQiThhseu5D1cSs344C4OVu4 -SOafn6hQPVIPD1thRFYtIgynjJrYCF9BsYRF6v9cxxoyxTajXRITsC/9MzIBmwEp -zgNy6HhSCVzTUYjOFlvMNCyRY+F6HSYz5AbV/3ScozFqma310+kBhNZpbcSIHnqh -LPub6hXYpRJTvKibP9pIDsx7Tm4zIGyRs3iyeBFnVn65TICpJyPj1chlQeUqnUIa -gSLmf2E6dmj5f9YCc+6ATlohzOo2S4AjcZxbeficslCKoSc8Fcnk0/WlFWMJ1fpO -QRzMub6bKaOUztHLbaHqiT7bFd46O9A79zFda8rYI5e7FjPwLfUihFzuXY7w1TyW -VTRyc8fRpa3IIhLA1n8W -=K/xF +iEYEARECAAYFAk4EfyUACgkQgAnW8HDreRaaWwCeJDjh4SP9syEL64p0TwGt4SWc +N3sAoJqF7MLIRz8dkeIl+0kP2GnhFAKD +=pCfz -----END PGP SIGNATURE----- diff --git a/sci-electronics/tnt/tnt-1.2.2.ebuild b/sci-electronics/tnt/tnt-1.2.2.ebuild index 8ce4ae021..e13371811 100644 --- a/sci-electronics/tnt/tnt-1.2.2.ebuild +++ b/sci-electronics/tnt/tnt-1.2.2.ebuild @@ -3,15 +3,16 @@ # $Header: $ EAPI=4 -inherit base autotools eutils toolchain-funcs + +inherit autotools base eutils fortran-2 toolchain-funcs DESCRIPTION="MoM 2.5 D stripline simulator" -SRC_URI="mirror://sourceforge/mmtl/${P}.tar.gz" HOMEPAGE="http://mmtl.sourceforge.net/" -LICENSE="BSD GPL-2" -KEYWORDS="~amd64 ~ppc ~x86" +SRC_URI="mirror://sourceforge/mmtl/${P}.tar.gz" SLOT="0" +LICENSE="BSD GPL-2" +KEYWORDS="~amd64 ~ppc ~x86" IUSE="doc" RDEPEND=" @@ -19,13 +20,11 @@ RDEPEND=" dev-tcltk/tcllib dev-tcltk/itcl dev-tcltk/bwidget - sys-devel/gcc[fortran] -" + virtual/fortran" DEPEND="${RDEPEND} dev-texlive/texlive-latex dev-tex/latex2html - media-gfx/imagemagick -" + media-gfx/imagemagick" PATCHES=( "${FILESDIR}/${P}"-{calc,bem-nmmtl,namespaces,f77,tkcon,docs,gui}.patch ) @@ -40,21 +39,19 @@ src_prepare() { } src_install () { - emake DESTDIR="${D}" install || die "make install failed" - - dodoc AUTHORS ChangeLog NEWS README THANKS || die + default # tcl cannot handle the archives created by dodoc dohtml COPYING || die if use doc; then - dodoc doc/*.pdf doc/*.png || die - dohtml doc/user-guide/* || die + dodoc doc/*.pdf doc/*.png + dohtml doc/user-guide/* fi # Install icon convert gui/logo.gif gui/tnt.png docinto "examples" - dodoc examples/* || die "failed to install exampels" + dodoc examples/* newicon gui/tnt.png tnt.png make_desktop_entry ${PN} "tnt" ${PN} } diff --git a/sci-geosciences/pydap_handlers_sql/ChangeLog b/sci-geosciences/pydap_handlers_sql/ChangeLog index e98c5e7ee..c180cfe2e 100644 --- a/sci-geosciences/pydap_handlers_sql/ChangeLog +++ b/sci-geosciences/pydap_handlers_sql/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-geosciences/pydap_handlers_sql -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> pydap_handlers_sql-0.1.0.ebuild, + metadata.xml: + Cleaned repoman issues, don't know if ebuild is still working + *pydap_handlers_sql-0.1.0 (09 Aug 2010) 09 Aug 2010; Tim Cera <timcera@earthlink.net> diff --git a/sci-geosciences/pydap_handlers_sql/Manifest b/sci-geosciences/pydap_handlers_sql/Manifest index c8809618b..99953d70f 100644 --- a/sci-geosciences/pydap_handlers_sql/Manifest +++ b/sci-geosciences/pydap_handlers_sql/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST pydap.handlers.sql-0.1.0.tar.gz 35477 RMD160 6ca9669063cadbc1394f35cc347d4b767981be82 SHA1 5a6c31fdcd5e01562c3ac78aa89f2ce9f5c68637 SHA256 6edf271b3e90187a7b62686d31a9b9c978056d0209c77005a401e19df1a24aed -EBUILD pydap_handlers_sql-0.1.0.ebuild 973 RMD160 21edf90a904746bac4ed8cf0f47a4e645d255d31 SHA1 06781413f7222fdf92ae7bea4f3f138083012910 SHA256 f3e20618f3aed122e0493d090b08e6bbf12e0e9a6eda5f26c72d84bc2b4c09a0 -MISC ChangeLog 294 RMD160 63e0b1ccad68c0b5d816cbe8c48a4febd577e2ee SHA1 8e4d5f88fd3e0ba5728976fe96a36b35fa01b282 SHA256 bc1aa03e8741cda7b9998b4cde554e5c91f8ee9cbe3f6d48e6212757e42b223c -MISC metadata.xml 434 RMD160 482bc484a5c2c1dcfa87c10b1ce37ce8b7f5b2cf SHA1 1ea823eac57ef42be569d4f8044f3e5fcd276d04 SHA256 959da38fa8bafbd6a283e0f73f6c37bdd5f20cd3647d5202ba610c0edbc1e70e +EBUILD pydap_handlers_sql-0.1.0.ebuild 945 RMD160 3b8d97f872bf5939d8e4220c0ae6e7935e833018 SHA1 c301b5e0dd7116b64be6471aae0f8c1fc318b52c SHA256 f6dafd0eaef853f7b1fdfaca1f1acf29f622abfb31c74fe52faee46bf9074ea5 +MISC ChangeLog 455 RMD160 585f2d3aed22e92bf78b0c9801c36d4122a90771 SHA1 665b3661434a3d5eb88c2d88a5e35f4d3c78b596 SHA256 8b65f09aa6008afd25ae9b88db76e7fd566c0ba3cbd927611650c151d614864f +MISC metadata.xml 442 RMD160 b44b30057687bc6624e788a0b7fe34c885e55237 SHA1 b51eadde0c6e1fd3cbfc5b25377824ffd7fa693d SHA256 e9bf17f4d62c73e3d059af53a0c103dd870ba36f8722dc8bbb44abae63730576 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F3QIACgkQgAnW8HDreRYCQwCePyVX2Dijxi2YdAPWY6Y2JPi9 +8EwAniw4nCAxnqoGuUVsYoLllVabvM6N +=BMFi +-----END PGP SIGNATURE----- diff --git a/sci-geosciences/pydap_handlers_sql/metadata.xml b/sci-geosciences/pydap_handlers_sql/metadata.xml index b946abd5e..c9ce2a99f 100644 --- a/sci-geosciences/pydap_handlers_sql/metadata.xml +++ b/sci-geosciences/pydap_handlers_sql/metadata.xml @@ -1,12 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> -<email>timcera@earthlink.net</email> -<name>Tim Cera</name> -</maintainer> -<longdescription lang="en"> + <herd>sci</herd> + <maintainer> + <email>timcera@earthlink.net</email> + <name>Tim Cera</name> + </maintainer> + <longdescription lang="en"> Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_sql allows Pydap server to serve data from SQL databases. </longdescription> diff --git a/sci-geosciences/pydap_handlers_sql/pydap_handlers_sql-0.1.0.ebuild b/sci-geosciences/pydap_handlers_sql/pydap_handlers_sql-0.1.0.ebuild index 753fda3d5..3f5d90ebd 100644 --- a/sci-geosciences/pydap_handlers_sql/pydap_handlers_sql-0.1.0.ebuild +++ b/sci-geosciences/pydap_handlers_sql/pydap_handlers_sql-0.1.0.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=3 PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" @@ -13,7 +13,7 @@ inherit distutils MY_PN=${PN//_/.} MY_P=${P//_/.} -DESCRIPTION="SQL handler for Pydap server that allows serving data from SQL databases." +DESCRIPTION="SQL handler for Pydap server that allows serving data from SQL databases" HOMEPAGE="http://pydap.org/handlers.html#cdms" SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz" @@ -23,11 +23,12 @@ KEYWORDS="~amd64" IUSE="" DEPEND=">=dev-python/setuptools-0.6_rc3" -RDEPEND=">=sci-geosciences/pydap-3.0_rc8 +RDEPEND=" + >=sci-geosciences/pydap-3.0_rc8 >=sci-geosciences/cdat-lite-5.2 >=dev-python/arrayterator-1.0.1 - postgresql? ( >=dev-python/psycopg-2 ) - mysql? ( >=dev-python/mysql-python-1.2.3_rc1 )" + >=dev-python/psycopg-2 + >=dev-python/mysql-python-1.2.3_rc1" # When cx_oracle is available... # oracle? >=dev-python/cx_oracle diff --git a/sci-geosciences/qgis/Manifest b/sci-geosciences/qgis/Manifest index 71eab3a7a..c3b8ff1f5 100644 --- a/sci-geosciences/qgis/Manifest +++ b/sci-geosciences/qgis/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST qgis_sample_data.tar.gz 13601736 RMD160 048f6f984a8f2a03b0700896acfd6d345d53f1d0 SHA1 024aac8ac32c41ee9fe507599d197644c78f87a1 SHA256 a31c54056776e8476e1f959870830f850423645cfb80d88811f3b365c29f2b4a -EBUILD qgis-9999.ebuild 2318 RMD160 7eed3063fd8b5e12c60f79ba2a592211296af87c SHA1 862cf3b930822254bc4c3aff99aa2538954bdfc9 SHA256 833ee7c24184927869b243a517d813e6089e774d60bb2f34cbbd6554e881911d +EBUILD qgis-9999.ebuild 2318 RMD160 3ff2861e7e1dd0aad1e07f50b631975ac7da5f72 SHA1 ced5d58e8ce90c75e1adb8a0a0b727ada09e6fc5 SHA256 cce960405690a28d6517fbb5303acb4a2a538087add88d292fbe493ffee8d207 MISC ChangeLog 422 RMD160 ee66e01f9ff08026b752b0eb9e79d47cf48636ee SHA1 bbec1b99c475c90f77ba4631b538ac257a4c72c8 SHA256 0f4022f1564ce14fc98c276425c44060c3b764c2d87f969d42866e60a08a27a6 MISC metadata.xml 664 RMD160 586f9cc0e1fcdf0f7610a749dfd766b468487196 SHA1 45e80ed6b803f6e8cec7b25cd32443a17efe519d SHA256 85807d824103a40c5e236cdf9fc287c0bf70b511274818a2242ac6efc203ff21 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EpqQACgkQgAnW8HDreRZM/gCeJReW82Y95EqpfrnwEQTxlHes +mtQAnji4yl9ZjoRKSS+jwAv4fbXhIphH +=aU3b +-----END PGP SIGNATURE----- diff --git a/sci-geosciences/qgis/qgis-9999.ebuild b/sci-geosciences/qgis/qgis-9999.ebuild index c2dad770d..9975c7acb 100644 --- a/sci-geosciences/qgis/qgis-9999.ebuild +++ b/sci-geosciences/qgis/qgis-9999.ebuild @@ -6,7 +6,7 @@ EAPI="2" PYTHON_USE_WITH="sqlite" PYTHON_DEPEND="python? 2" -inherit python cmake-utils subversion +inherit cmake-utils python subversion DESCRIPTION="User friendly Geographic Information System" HOMEPAGE="http://www.qgis.org/" diff --git a/sci-geosciences/tcd-editor/ChangeLog b/sci-geosciences/tcd-editor/ChangeLog deleted file mode 100644 index d065b6bf2..000000000 --- a/sci-geosciences/tcd-editor/ChangeLog +++ /dev/null @@ -1,8 +0,0 @@ -# ChangeLog for sci-geosciences/tcd-editor -# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 16 May 2008; Tim Cera <timcera@earthlink.net> +tcd-editor-1.4.1.ebuild, - +metadata.xml: - Initial import. - diff --git a/sci-geosciences/tcd-editor/Manifest b/sci-geosciences/tcd-editor/Manifest deleted file mode 100644 index d2649d8cb..000000000 --- a/sci-geosciences/tcd-editor/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST tideEditor-1.4.1.tar.bz2 106055 RMD160 3f464e71de8fab075ad9924e978e14e205e64a77 SHA1 4762f43cacc51ccd311340842c4a7c61628454be SHA256 ee4ab66b8e878c6ba54be7ba83e9c2423ad6af6732937aed9ea385c4abb45927 -EBUILD tcd-editor-1.4.1.ebuild 843 RMD160 912e57b7621fd8db2571298274bafa066cc2eb42 SHA1 88a9356b54f08c3112014c16a504edc96c166684 SHA256 8fadbf9bc0019984a627981de7a3a4870fcc0a4379916ed97437b79e5677a952 -MISC ChangeLog 237 RMD160 3ed16ce2dda8b3cd4bbc4264be202061f7da3d4a SHA1 7fc7d76f3f1deccbcb39c5dc227fb034e30fe30e SHA256 116a6b95d4da006517768cec126a9bf3a5912ae090ce2cedf14d18716bc1096f -MISC metadata.xml 356 RMD160 ccc1ea6981de588b8c57784753f9b2257ad6d7f7 SHA1 954467cf9f27f302375993dbd54eb25f9408298a SHA256 d50550ae1098922219465b64a2e7ed9be65a5e9014de30d8e3ed1efef4b30e66 diff --git a/sci-geosciences/tcd-editor/tcd-editor-1.4.1.ebuild b/sci-geosciences/tcd-editor/tcd-editor-1.4.1.ebuild deleted file mode 100644 index 21da13bb8..000000000 --- a/sci-geosciences/tcd-editor/tcd-editor-1.4.1.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit versionator - -MY_PN=${PN/tcd-editor/tideEditor} -MY_PV=${PV/_p/-r} -MY_SPV=$(get_version_component_range 1-3) -S=${WORKDIR}/${MY_PN}-${MY_SPV} - -DESCRIPTION="Tide editor is a graphical editor for Tidal Constituent Databases." -HOMEPAGE="http://www.flaterco.com/xtide/" -SRC_URI="ftp://ftp.flaterco.com/xtide/${MY_PN}-${MY_PV}.tar.bz2" -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" -DEPEND=">=sci-geosciences/libtcd-2.2.3 - =x11-libs/qt-3*" -RDEPEND="${DEPEND}" - -src_compile() { - sed -i \ - "s;\(#include <qlistbox.h>\);&1\n#include <qmetaobject.h>;" map.h - MOC="/usr/qt/3/bin/moc" econf || die "econf failed" - emake || die "emake failed" -} - -src_install() { - emake DESTDIR="${D}" install || die "emake install failed" -} diff --git a/sci-libs/Cgraph/Cgraph-2.04.ebuild b/sci-libs/Cgraph/Cgraph-2.04.ebuild index d8a4bfac9..ff28e22d3 100644 --- a/sci-libs/Cgraph/Cgraph-2.04.ebuild +++ b/sci-libs/Cgraph/Cgraph-2.04.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 -inherit multilib eutils flag-o-matic +inherit eutils flag-o-matic multilib DESCRIPTION="A set of C functions that generate PostScript for publication quality scientific plots" HOMEPAGE="http://neurovision.berkeley.edu/software/A_Cgraph.html" @@ -18,26 +18,21 @@ IUSE="" S="${WORKDIR}"/${PN}/source src_prepare() { - epatch "${FILESDIR}"/Makefile.patch - epatch "${FILESDIR}"/fix-src.patch + epatch \ + "${FILESDIR}"/Makefile.patch \ + "${FILESDIR}"/fix-src.patch } src_compile() { use amd64 && append-flags -fPIC && append-ldflags -fPIC - emake \ - CC=$(tc-getCC) \ - CCFLAGS="${CFLAGS}" || \ - die "compilation failed" + emake CC=$(tc-getCC) CCFLAGS="${CFLAGS}" } src_install() { - emake \ - DESTDIR="${D}" \ - LIB_DIR=/usr/$(get_libdir) \ - install || die "install failed" - dolib.so libcgraph.so.0.0.0 || die - dosym libcgraph.so.0.0.0 /usr/$(get_libdir)/libcgraph.so.0 || die - dosym libcgraph.so.0.0.0 /usr/$(get_libdir)/libcgraph.so || die + emake DESTDIR="${D}" LIB_DIR=/usr/$(get_libdir) install + dolib.so libcgraph.so.0.0.0 + dosym libcgraph.so.0.0.0 /usr/$(get_libdir)/libcgraph.so.0 + dosym libcgraph.so.0.0.0 /usr/$(get_libdir)/libcgraph.so dodoc ../docs/* } diff --git a/sci-libs/Cgraph/ChangeLog b/sci-libs/Cgraph/ChangeLog index f1dc05988..7163bbbd3 100644 --- a/sci-libs/Cgraph/ChangeLog +++ b/sci-libs/Cgraph/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/Cgraph -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> Cgraph-2.04.ebuild: + Sort inherit and/or USE + 26 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> Cgraph-2.04.ebuild: QA diff --git a/sci-libs/Cgraph/Manifest b/sci-libs/Cgraph/Manifest index f59650331..f301fdffe 100644 --- a/sci-libs/Cgraph/Manifest +++ b/sci-libs/Cgraph/Manifest @@ -1,6 +1,26 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +- -----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX Makefile.patch 4720 RMD160 6131006c1c31e74c3617d5dec74265a9b3025d59 SHA1 2d98a61cde85cfed2f34a7ccb64ba86c08db75b8 SHA256 f41f15cad4de648d161c0b9f17b4f24317fc3ffb2d15d5f39786b3ad6b66ea33 AUX fix-src.patch 1565 RMD160 9535567c1ea6e454f28566b953f3e0d70a023c31 SHA1 4e3daa467aceb01bb5b3d3ff0226538f946b3c94 SHA256 26a5be732ac8365d2b8118bc618c25b886afd445ca95a39d858066128f5eb0ef DIST Cgraph2.04.tar.gz 198572 RMD160 dbccd69125c93f10b7776c6520d4e8123ab9dfa8 SHA1 5dc9ccb74a30f2ba05dda708706fcc34c00e0c06 SHA256 694559bd85439e72773c63aad461759751472e6afd7853198296416fcf6fe67e -EBUILD Cgraph-2.04.ebuild 1038 RMD160 e59f6b96f2d1dd213c51105dd2487bc5556fc0ce SHA1 991779131825ec7602f3222b2ad0f00c2f954024 SHA256 7fc386162fbeb855d80dcf6cf304e04fe43005883390ba18cad26cad178e8584 -MISC ChangeLog 344 RMD160 68105136ec94065976dd2911f429e33f03438ecd SHA1 8f4001f1a9636ba42f7f2656563125fbea217564 SHA256 5bd52e347c6eeaaff1620cd492702acd63786848b7b66eb5a696d75c7e252815 +EBUILD Cgraph-2.04.ebuild 940 RMD160 4b78fe331635ea49f2f490b16ba4295af3c9d7e7 SHA1 6aed3b493afd03ba4652233b128803c76bff080d SHA256 c93596463c149cbaee4c95cd86a74f5b0f84fa8e328eaa3c47887786c2df0ba4 +MISC ChangeLog 438 RMD160 31a77df2859411e92cbd6177965b2506a1b52974 SHA1 c5067ad80c4cd6d1b87e69922dcd1ec9e78940fc SHA256 856d261a442ee0bcbdef0416580017f74afdf8826923dcd15a3762347953946a MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c +- -----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EikQACgkQgAnW8HDreRZHiQCglJfdiITyFpQYbrVQCpgtGucB +PN8AnjBakK7SCjOeMCd/imw18y+7Gv1B +=RBGr +- -----END PGP SIGNATURE----- +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EikkACgkQgAnW8HDreRboiACdFzELPY0BzglwD9E4Jr178nsI +w/YAni96xoBBhdcixweSV89CpEW2iFF1 +=NenJ +-----END PGP SIGNATURE----- diff --git a/sci-libs/bigdft/ChangeLog b/sci-libs/bigdft/ChangeLog index 4aa039a4a..3511aab36 100644 --- a/sci-libs/bigdft/ChangeLog +++ b/sci-libs/bigdft/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bigdft-1.2.0.2.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> bigdft-1.2.0.2.ebuild, + +metadata.xml: + Added fortran-2.eclass support + *bigdft-1.2.0.2 (17 Jan 2011) 17 Jan 2011; Honza Macháček <Hloupy.Honza@centrum.cz> diff --git a/sci-libs/bigdft/Manifest b/sci-libs/bigdft/Manifest index 52ba40e10..40aa9e2df 100644 --- a/sci-libs/bigdft/Manifest +++ b/sci-libs/bigdft/Manifest @@ -1,3 +1,6 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX bigdft-1.2.0.2-0001.patch 4991 RMD160 0341289986c2fb1e1d292f6f6f62798d15b01f5f SHA1 4d39856883911573d56f41fb6f5011b64d61bf7b SHA256 2af75ea82fd506e4e5871e948871f1c13b5bb33528750da2ed3d5647f7bb83aa AUX bigdft-1.2.0.2-0002.patch 557 RMD160 caefc2a1a789f5d8a9bc0349a975cfcb5330fef9 SHA1 fced52b9fcb0feff7b7e20be3c104b2da40c98e9 SHA256 55f108aa609bc93e359f7b3928334a5b147b50c7f7e99b58feae559bda3e3b09 AUX bigdft-1.2.0.2-0003.patch 620 RMD160 c2db417e0bf660fed15ebe79580afa9e60549497 SHA1 d12621e14c02c963937d14b12f9f5e02fdb98186 SHA256 d87ba1010e739e2d951b1a1a8208058a9c51ce28ed8e507e93ae36f215d3d237 @@ -5,5 +8,13 @@ AUX bigdft-1.2.0.2-0004.patch 833 RMD160 df98d7fcda945d11ea787b85bfaa79f457371f5 AUX bigdft-1.2.0.2-testH.patch 29091 RMD160 535dcd1c160863570991b26c194c707766233645 SHA1 682454d1986cc3963ee16b65f6d3a85f1642ec3a SHA256 dd7311f2ec7c4dde01131d8b22b375a74e0de73c7865172a79e83373e849fb52 DIST bigdft-1.2.0.2.tar.gz 944219 RMD160 fbd2fd53e4c684e560769d7aaf2ac9d17954bc62 SHA1 1a3754261c6229be17d3cecb70720fefaf843642 SHA256 3143e203879a2f8b1f05789336ceed91250960ef0681c1530868011fc16f56df DIST bigdft-1.3.2.tar.gz 1370869 RMD160 6967df2a837af540149aa452166ea16e25ee7aa7 SHA1 b219b4c2b4bee5a936eadcee0ea1faeb4f78b2cb SHA256 b18234c321bee98450ea0b6a3c249480ecec66d18dadcc32a7ba0d2d019c820d -EBUILD bigdft-1.2.0.2.ebuild 2176 RMD160 d88681bf612fddf41036309e32e4bdd001b84a99 SHA1 2038ef7b5de1ed57b2a75f7d5b127fccefd6d386 SHA256 49db71d8b9bd983e6c1b1c475be96d713a4e4eae274deda27ea0a349cc01289e -MISC ChangeLog 505 RMD160 464df1805eb7272e4b683a08e9bb2863af7f8df3 SHA1 809ea898cd5c262587c48d09a31a0557630f4f02 SHA256 91b92a6dcc0b230cd4dd9bba27b5fe8bb770d6eb518722050daf441238dc440e +EBUILD bigdft-1.2.0.2.ebuild 2108 RMD160 d0bb2cae6d7aaf77fef11e825024d64537659244 SHA1 d4819bd85ef42be39ac3ee659f0154519743b616 SHA256 737e34e6c0156dcaf1cd9b0b0d8a32af551d236c4b09b6a910a9362821485211 +MISC ChangeLog 734 RMD160 2166c49d4db729b39450adb2a13782ccde156c11 SHA1 0a1da767755f98a14d0796fc1eff4f76399f3d94 SHA256 b09e6933faa146d1bd2b0a7c73aa2158efb813f517074553ed8f948c0a5b0a6d +MISC metadata.xml 268 RMD160 a08ddac9bdb423a2a25e1a855118e1c1b7b4b1c3 SHA1 80806343ce9cacc256261167cc9a463c33b8f5b1 SHA256 8dc5093d7d2cd59f19de2421464b9d6ad5dff8526ec018d33c0f22874608938a +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ef10ACgkQgAnW8HDreRa5FACgsP/u0ke/9Y5V6Xt8m4SA/1Hh +k28AoK5MhscGwCLVg1dbLq73GO2Iz/ol +=zDmb +-----END PGP SIGNATURE----- diff --git a/sci-libs/bigdft/bigdft-1.2.0.2.ebuild b/sci-libs/bigdft/bigdft-1.2.0.2.ebuild index 55d34f59e..c81e7303c 100644 --- a/sci-libs/bigdft/bigdft-1.2.0.2.ebuild +++ b/sci-libs/bigdft/bigdft-1.2.0.2.ebuild @@ -1,36 +1,41 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 +# $Header: $ -EAPI="3" +EAPI=3 -inherit eutils toolchain-funcs +inherit eutils fortran-2 toolchain-funcs DESCRIPTION="A DFT electronic structure code using a wavelet basis set" HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/" -SRC_URI="http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz - http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz" +SRC_URI=" + http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz + http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="cuda doc mpi test" -RDEPEND="virtual/blas +RDEPEND=" + =sci-libs/libxc-1.0[fortran] + virtual/blas + virtual/fortran virtual/lapack mpi? ( virtual/mpi ) - cuda? ( dev-util/nvidia-cuda-sdk ) - =sci-libs/libxc-1.0[fortran]" + cuda? ( dev-util/nvidia-cuda-sdk )" DEPEND="${RDEPEND} dev-util/pkgconfig >=sys-devel/autoconf-2.59 doc? ( virtual/latex-base )" src_prepare() { - epatch ${FILESDIR}/${P}-0001.patch - epatch ${FILESDIR}/${P}-0002.patch - epatch ${FILESDIR}/${P}-0003.patch - epatch ${FILESDIR}/${P}-0004.patch - epatch ${FILESDIR}/${P}-testH.patch + epatch \ + "${FILESDIR}"/${P}-0001.patch \ + "${FILESDIR}"/${P}-0002.patch \ + "${FILESDIR}"/${P}-0003.patch \ + "${FILESDIR}"/${P}-0004.patch \ + "${FILESDIR}"/${P}-testH.patch rm -r src/PSolver/ABINIT-common mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/ @@ -44,11 +49,10 @@ src_configure() { if use mpi; then MY_FC="mpif90" MY_CC="mpicc" - else - MY_FC="$(tc-getFC)" - MY_CC="$(tc-getCC)" fi + tc-export FC CC + econf \ $(use_enable mpi) \ --enable-libpoissonsolver \ @@ -62,10 +66,7 @@ src_configure() { $(use_with cuda cuda-path /opt/cuda) \ $(use_with cuda lib-cutils /opt/cuda/lib) \ FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \ - FC="${MY_FC}" \ - CC="${MY_CC}" \ - LD="$(tc-getLD)" \ - || die "configure failed" + LD="$(tc-getLD)" } src_compile() { @@ -83,6 +84,5 @@ src_test() { src_install() { emake HAVE_LIBXC=1 DESTDIR="${D}" install || die "install failed" - dodoc README INSTALL COPYING ChangeLog AUTHORS NEWS || die "dodoc failed" + dodoc README INSTALL ChangeLog AUTHORS NEWS || die "dodoc failed" } - diff --git a/sci-geosciences/tcd-editor/metadata.xml b/sci-libs/bigdft/metadata.xml index cfa2ee264..4f728fd12 100644 --- a/sci-geosciences/tcd-editor/metadata.xml +++ b/sci-libs/bigdft/metadata.xml @@ -3,10 +3,7 @@ <pkgmetadata> <herd>sci</herd> <maintainer> -<email>timcera@earthlink.net</email> -<name>Tim Cera</name> + <email>sci@gentoo.org</email> </maintainer> -<longdescription lang="en"> -Tide editor is a graphical editor for Tidal Constituent Databases. -</longdescription> +<use><flag name='cuda'>Add cuda support</flag></use> </pkgmetadata> diff --git a/sci-libs/cgnsfoam/ChangeLog b/sci-libs/cgnsfoam/ChangeLog index 500216fe7..b78a9990b 100644 --- a/sci-libs/cgnsfoam/ChangeLog +++ b/sci-libs/cgnsfoam/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> cgnsfoam-1732.ebuild, + metadata.xml: + Fixed dep on openfoam + *cgnsfoam-1732 (10 Jan 2011) 10 Jan 2011; Oliver Borm (boroli) <oli.borm@web.de> +cgnsfoam-1732.ebuild, diff --git a/sci-libs/cgnsfoam/Manifest b/sci-libs/cgnsfoam/Manifest index 594123627..900e8c2fc 100644 --- a/sci-libs/cgnsfoam/Manifest +++ b/sci-libs/cgnsfoam/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + AUX cgnsfoam-compile.patch 2397 RMD160 3986d139f6e369d1aa540b1cb2edbad15c29936e SHA1 13edfd811fb4346ee6b3eb4cdd19a1340180aef1 SHA256 1571862813215bf2bc6c05999b96c6918b4c2c23c34b01808a1728debaa3f777 DIST cgnsfoam_1732.orig.tar.gz 48420 RMD160 2f3cd7076049a9e80d360383436879ea1c813c0b SHA1 f0864da7587ba0b429f117ce34a41f88ff8d364b SHA256 46a105bef7c068642f7eda66605b48f8d593b87f05369f3e397634a3c493fbae -EBUILD cgnsfoam-1732.ebuild 840 RMD160 acbb531f464dc65778accc92d9aebe75dff23cfb SHA1 4bfd252fac5ce38066991ca1103ca0793fde1a6d SHA256 dcfe43192ca83a3f3d74d61693d203abb6970a2e933f1bd945c5e277b1ab5992 -MISC ChangeLog 374 RMD160 4f174891aeddc141bd2c1db5eb2ce13423d8faee SHA1 d0ffa2dc2a0b7105f103ae639f12d03d29590ae6 SHA256 4f120148f42ed1961adc9622f88d74cb214de3294a029cd6b7ad4c32fc14f6f0 -MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 +EBUILD cgnsfoam-1732.ebuild 834 RMD160 051c5ce878f522064d667c864c60d57fbf8ac587 SHA1 146e95bd955a10dcf635e91dbde4b8b6bb766116 SHA256 2d914eaae1afd79fb073345b14c8ec5b9449ab69172d5c3ba66fa116c8f2c1a4 +MISC ChangeLog 484 RMD160 5a24f48ff8a43c2add4ff45661f94d54ef61ef27 SHA1 5e33a90ceb6e2e3eb4a05e28cf58af647099b642 SHA256 eb8e656697870dfb8aa7b5e6995a020ae69e7de42f15721c923c1d4c9cdfae3a +MISC metadata.xml 157 RMD160 ed43b99e7bf8bbf62cf4e46152138ab42d3a88c5 SHA1 2182a6de0b10959aad51af2990f1a6c69e34dd97 SHA256 750cb9e46ac2b77e1adf73de43c186a8c2d2234a9c6a89d9358d0969dc5cf8ac +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GCHEACgkQgAnW8HDreRb9MgCgoe2kRo2EWHEIOHEmNxcE50kq +HD0AoJY2YVkAYk2LVQq7C3+28UhlvlZe +=ehdt +-----END PGP SIGNATURE----- diff --git a/sci-libs/cgnsfoam/cgnsfoam-1732.ebuild b/sci-libs/cgnsfoam/cgnsfoam-1732.ebuild index f2789b51c..dee38ed6d 100644 --- a/sci-libs/cgnsfoam/cgnsfoam-1732.ebuild +++ b/sci-libs/cgnsfoam/cgnsfoam-1732.ebuild @@ -2,12 +2,12 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 inherit eutils multilib DESCRIPTION="cgnsfoam is a conversion tool from cgns to openfoam format" -HOMEPAGE="http://openfoam-extend.sourceforge.net" +HOMEPAGE="http://openfoam-extend.sourceforge.net/" SRC_URI="http://ppa.launchpad.net/cae-team/ppa/ubuntu/pool/main/c/${PN}/${PN}_${PV}.orig.tar.gz" LICENSE="GPL-2" @@ -15,12 +15,12 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -OF_PV="1.5" +OF_PV="1.7" -DEPEND="sci-libs/cgnslib +DEPEND=" + sci-libs/cgnslib sci-libs/libcgnsoo - =sci-libs/openfoam-src-${OF_PV}*" - + sci-libs/openfoam:${OF_PV}" RDEPEND="${DEPEND}" src_prepare() { diff --git a/sci-libs/cgnsfoam/metadata.xml b/sci-libs/cgnsfoam/metadata.xml index b229aec85..d369d068f 100644 --- a/sci-libs/cgnsfoam/metadata.xml +++ b/sci-libs/cgnsfoam/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> + <herd>sci</herd> </pkgmetadata> diff --git a/sci-libs/cgnslib/ChangeLog b/sci-libs/cgnslib/ChangeLog index 08604c499..400ad2532 100644 --- a/sci-libs/cgnslib/ChangeLog +++ b/sci-libs/cgnslib/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> cgnslib-2.5.4.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> cgnslib-2.5.4.ebuild: + Added fortran-2.eclass support + 10 Jan 2011; Oliver Borm (boroli) <oli.borm@web.de> -cgnslib-2.5.3.ebuild, -files/cgnslib-2.5.3_hdf5.patch, -files/cgnslib-2.5.3.patch, cgnslib-2.5.4.ebuild, files/cgnslib-2.5.4_hdf5.patch: diff --git a/sci-libs/cgnslib/Manifest b/sci-libs/cgnslib/Manifest index b9d77c1a3..f228e1749 100644 --- a/sci-libs/cgnslib/Manifest +++ b/sci-libs/cgnslib/Manifest @@ -1,6 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX cgnslib-2.5.4.patch 2730 RMD160 0d92b759686fc657bb1dce75ea64f35abda60516 SHA1 bf32f3294a3636f9f4fc3d24826642f9b5781477 SHA256 e601058b0641ad6646025156d7929fafdd17ec5c6ddaf688ac07a6fa30a47f4b AUX cgnslib-2.5.4_hdf5.patch 1889 RMD160 1fb75472109c51b7166f930891003901f4877c8b SHA1 1904fbc320b986642278f4e2df9d6ae09d81e601 SHA256 29cd5834f7adcb744575f1246ad4695df267cb8655acdd02bfba08189a63bb14 DIST cgnslib_2.5-4.tar.gz 398419 RMD160 1215e928bf5fe282637252661fd95e8a67dc89ed SHA1 d5f99f6df7409d923d8703fc3732b13bd1d89b20 SHA256 0485b32649f1e15de2e85a17f0cb2b5fe4d2522415eafe1f6c8cfa4820719964 -EBUILD cgnslib-2.5.4.ebuild 1089 RMD160 6c1dbd18557d8e6c748fe24cf755daaa415e5fae SHA1 322b0f39470dc3b63dc20b6cfcfa075e889a15a9 SHA256 b892dfc38b3ca6a806d29c9f4891d949f0aa40ffd884c2186e7af35225a4a584 -MISC ChangeLog 2073 RMD160 35e018c532c9dc7b5de2119efb0da5d31993ddeb SHA1 ac3087d0072b800e31fc542b6457424542a360f7 SHA256 a8c84d5948ee58e7aa970d490ae8e08431fcdaa03e51207651ad65e284be90c9 +EBUILD cgnslib-2.5.4.ebuild 1234 RMD160 3d7c6cc9fffb5a659956599be45882bd4cbc3964 SHA1 7eb9f33b3ce8d6dc8fb64d1aa175f861e097dc40 SHA256 6ba0fcd6dbe5accca6edb888ff1cd866b3127f0cb8fbfd4c7e5c52c3ace6dc9e +MISC ChangeLog 2283 RMD160 b641e4027fd91189dd8ffd96c2e069a43814e2d7 SHA1 a0866e43988ffee40ef65bfdc04707f36840c8b0 SHA256 61be0ed262f94c6522eb93ce59890251d1ae829238469a8f6e538da7dfc523d1 MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ef7QACgkQgAnW8HDreRbpswCfZfQcNDU02Km+o90mYu09aYtR +WiMAoNEJRUBZe6wW2DPkZye014W6+wAM +=PmAt +-----END PGP SIGNATURE----- diff --git a/sci-libs/cgnslib/cgnslib-2.5.4.ebuild b/sci-libs/cgnslib/cgnslib-2.5.4.ebuild index 17cff3bad..ce5ae6792 100644 --- a/sci-libs/cgnslib/cgnslib-2.5.4.ebuild +++ b/sci-libs/cgnslib/cgnslib-2.5.4.ebuild @@ -2,13 +2,14 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=2 -inherit toolchain-funcs versionator +inherit fortran-2 toolchain-funcs versionator MY_P="${PN}_$(replace_version_separator 2 '-')" +MY_S="${PN}_$(get_version_component_range 1-2)" -DESCRIPTION="The CFD General Notation System (CGNS) is a standard for CFD data." +DESCRIPTION="The CFD General Notation System (CGNS) is a standard for CFD data" HOMEPAGE="http://www.cgns.org/" SRC_URI="mirror://sourceforge/cgns/${MY_P}.tar.gz" @@ -17,15 +18,18 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="fortran hdf5 szip zlib" -DEPEND="hdf5? ( >=sci-libs/hdf5-1.8 ) - zlib? ( sys-libs/zlib ) - szip? ( sci-libs/szip )" - +DEPEND=" + fortran? ( virtual/fortran ) + hdf5? ( >=sci-libs/hdf5-1.8 ) + szip? ( sci-libs/szip ) + zlib? ( sys-libs/zlib )" RDEPEND="${DEPEND}" -MY_S="${PN}_$(get_version_component_range 1-2)" +S="${WORKDIR}"/${MY_S} -S=${WORKDIR}/${MY_S} +pkg_setup() { + use fortran && fortran-2_pkg_setup +} src_prepare() { epatch "${FILESDIR}"/${P}.patch @@ -35,7 +39,7 @@ src_prepare() { src_configure() { local myconf="--enable-gcc --enable-lfs --enable-shared=all --enable-64bit" - tc-export CC + tc-export CC FC econf \ ${myconf} \ @@ -47,5 +51,7 @@ src_configure() { src_install() { emake DESTDIR="${D}" install || die "install failed" - use hdf5 && fperms 755 /usr/bin/{hdf2adf,adf2hdf} + use hdf5 && \ + fperms 755 /usr/bin/{hdf2adf,adf2hdf} || \ + rm -f "${D}"/usr/bin/{hdf2adf,adf2hdf} } diff --git a/sci-libs/cgnstools/Manifest b/sci-libs/cgnstools/Manifest index cb3279450..5657dc0b1 100644 --- a/sci-libs/cgnstools/Manifest +++ b/sci-libs/cgnstools/Manifest @@ -1,7 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX cgnstools-2.5.4.patch 4068 RMD160 6d548f6e8ceed33034ae5c298e6fa87ff252493c SHA1 d6e5fd563eb86c5794ef5e80a77f5c746bcca597 SHA256 081480133aac5e0ab06fe9cde532df98eb2984aedc04b3b09f56e26e798620a7 AUX cgnstools-2.5.4_cgns_to_vtk2D.patch 1697 RMD160 a0d0a16aa0b05659f44fde0a8ac9a43c96f7924e SHA1 000493e4279438bd4bd8e9768df2de75a5e2d21d SHA256 a7c77cb5cc35d2ac7ef70eb924386e898049f52c10e31e586686ae3704bd2c9d AUX cgnstools-2.5.4_gcc4.4.patch 2616 RMD160 e8364cb7af8acfa1e681d48cb3aa38f21bd160c3 SHA1 06926f79890aa98757883017b83a94d76babf8f8 SHA256 5b7b04d0d72af24c80598603a931b57f80cc9a4a3878ef54a42607d98cb65213 DIST cgnstools-2-5-4.tar.gz 1339468 RMD160 4b0bab0fb8e080d92ec29b9f2fe6d17d3e7b21cc SHA1 2c4514b5e7d2a0a645d3672a837c066bc5c80e14 SHA256 28c263b8838da73eea6a497d1555f87391b44b5c917758d09176275a2a4130f5 -EBUILD cgnstools-2.5.4-r1.ebuild 1639 RMD160 e9646059cbfbb9ed429d55c86dba013b1bd4d1c2 SHA1 96d814d0372e9f41748056ac6f4d6fb35125f661 SHA256 ea906dc9d3fc5e086fb11b0b6400529e6c6c77f60f57b486db5ecd5ced75ceb9 +EBUILD cgnstools-2.5.4-r1.ebuild 1639 RMD160 d053a60b7ae15d9dbba146a55e6cddcb55846963 SHA1 f8b4aa49dcd32d50019b2c425ac110b425d079c2 SHA256 92f936ad2bbdfac5fd128b1851e13597701c295bed22fba89b1305b03adcb2b8 MISC ChangeLog 969 RMD160 4139ee7d15dd8c4bf90c3b1de7a4ee16b674e489 SHA1 f421671f28ccb991fc04ec0569c291d99c099b67 SHA256 5cd4279bfd6268d3209299cd6b387e4a90aa3a14d9ac92feb221e54861b3687b MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EpqkACgkQgAnW8HDreRYIhQCfR0gjWC/Vv5gYZjC/22WkLF4E +q8QAn33hDWiMinoVA2IsSjaStppQ9nmD +=y9NZ +-----END PGP SIGNATURE----- diff --git a/sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild b/sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild index d0f57dea5..f1526cd21 100644 --- a/sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild +++ b/sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild @@ -4,7 +4,7 @@ EAPI="2" -inherit eutils versionator multilib +inherit eutils multilib versionator MY_P="${PN}-$(replace_all_version_separators '-')" diff --git a/sci-libs/dcmtk/Manifest b/sci-libs/dcmtk/Manifest index 70ce8ed56..ef879394a 100644 --- a/sci-libs/dcmtk/Manifest +++ b/sci-libs/dcmtk/Manifest @@ -5,14 +5,14 @@ AUX dcmtk-asneeded.patch 3572 RMD160 301bf1f03e308d8b467cbf7e164bbb9bc09520f1 SH DIST dcmtk-3.5.4.tar.gz 3756374 RMD160 d1558c9c68e53e0ea3b080fd2fb50b9d8e30eeba SHA1 169056874947083e68eb941fcd53faaebc862ae5 SHA256 7b8575ba609516d76b681c0de8c1328cf23e57deb2c7085a6aa37d4292354d76 DIST dcmtk-3.5.5_20101008.tar.gz 4662578 RMD160 ccda8393aa1d27745832ed74635ef545f1fedab2 SHA1 29539987c042fd9c75f7628f49a03c49aecf5876 SHA256 f8eb25c76e078a387f86cd09ee27687f9860a1e9072b321ac8e070ccb85b1d90 DIST dcmtk_3.5.4-3.diff.gz 140253 RMD160 c06856a46513612c3a585bc3fea429d296ae6bb4 SHA1 75c14b8c6caa88155324b5bb8ed29363776ff7bf SHA256 8dd3ca447de4b0f1d553f672f36d5d88af86763604e2fc830667ce6fdd12677a -EBUILD dcmtk-3.5.4-r3.ebuild 1560 RMD160 f850c23a2f4bc04821e7665a2aeb55aa22150fcf SHA1 62055e4a292ebdebcd9462d776db9e95a6b13941 SHA256 9fa33e6e66dbc24a64dff2c6e2735479b4f1d44a7c61117903aba490b6680536 -EBUILD dcmtk-3.5.5_pre20101008.ebuild 1867 RMD160 4e2eaa0901059b4906b00dec60cb4806fa5418b5 SHA1 4d7d3b463382b73d54027c7c0bd53d699b798a34 SHA256 3611e83435242de1fe91731b8b4dca412ffc8e93711697d23622b7428f170f95 +EBUILD dcmtk-3.5.4-r3.ebuild 1560 RMD160 8f16de7502b23d1ce720e40d1d3829cf8a7fd693 SHA1 8b5202835eb82eac0a1907719f982641f2e17734 SHA256 6603a53cda3fa8cb95bab210d1d144267d5ce1f90de64f1df6ef27dab526564f +EBUILD dcmtk-3.5.5_pre20101008.ebuild 1867 RMD160 506f769ba3909ea7801e1c660b0086da452ef552 SHA1 2d2177cfa55bb29c24378cb783a1e622ff3c2781 SHA256 5a207ccc983b68cabfd8a149988ee98729f8bf294e6fcf4c0cb88f24e8672c87 MISC ChangeLog 1006 RMD160 f4e6fd915c9082e6c03999518c5c520c13fcb629 SHA1 e0e7730ad8a3fa27419373d19397f351f01d5eca SHA256 5edaa2c053ca9390a809f8f434b828ad591c2aaac6934371df34ff2f15c3c5d5 MISC metadata.xml 938 RMD160 e6451a136c100b3cafe90e2e1064dffb77aca7d9 SHA1 1a3b698c05897246eb73666f205ec7d873d20270 SHA256 3541a8cb00af24c3b785d021e1d15a94d9c0883d43a60228dd81ab7898534925 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk10v4EACgkQgAnW8HDreRZGCwCcCdqXjL5tfBFNBufg0r5930EA -LNIAnicjlmHM7d421UQM7YVeIQI7wQJC -=fiz4 +iEYEARECAAYFAk4Epq8ACgkQgAnW8HDreRb4fgCgl89Rowz/RJnYuMqeMgpC2OLL +Cy0An3yd5zdCBB6CH2BuetL55Az3I1dG +=ONRP -----END PGP SIGNATURE----- diff --git a/sci-libs/dcmtk/dcmtk-3.5.4-r3.ebuild b/sci-libs/dcmtk/dcmtk-3.5.4-r3.ebuild index cfa22d4ba..3e9bf07c3 100644 --- a/sci-libs/dcmtk/dcmtk-3.5.4-r3.ebuild +++ b/sci-libs/dcmtk/dcmtk-3.5.4-r3.ebuild @@ -16,7 +16,7 @@ SRC_URI=" LICENSE="BSD" KEYWORDS="~x86" SLOT="0" -IUSE="png ssl tcpd tiff xml zlib doc" +IUSE="doc png ssl tcpd tiff xml zlib" RDEPEND=" virtual/jpeg diff --git a/sci-libs/dcmtk/dcmtk-3.5.5_pre20101008.ebuild b/sci-libs/dcmtk/dcmtk-3.5.5_pre20101008.ebuild index 8e9c98ab7..85c20d3e6 100644 --- a/sci-libs/dcmtk/dcmtk-3.5.5_pre20101008.ebuild +++ b/sci-libs/dcmtk/dcmtk-3.5.5_pre20101008.ebuild @@ -15,7 +15,7 @@ LICENSE="BSD" KEYWORDS="~amd64 ~x86" SLOT="0" -IUSE="doc png ssl tcpd tiff +threads xml zlib" +IUSE="doc png ssl tcpd +threads tiff xml zlib" RDEPEND=" virtual/jpeg diff --git a/sci-libs/etsf_io/ChangeLog b/sci-libs/etsf_io/ChangeLog index e657c3e12..b4391ae02 100644 --- a/sci-libs/etsf_io/ChangeLog +++ b/sci-libs/etsf_io/ChangeLog @@ -2,6 +2,17 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> etsf_io-1.0.3.ebuild, + metadata.xml: + Fixed Malformed CVS Header on line: 3 + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> etsf_io-1.0.3.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> etsf_io-1.0.3.ebuild, + +metadata.xml: + Added fortran-2.eclass support + *etsf_io-1.0.3 (17 Jan 2011) 17 Jan 2011; Honza Macháček <Hloupy.Honza@centrum.cz> diff --git a/sci-libs/etsf_io/Manifest b/sci-libs/etsf_io/Manifest index 8c3064e59..b8f5878a8 100644 --- a/sci-libs/etsf_io/Manifest +++ b/sci-libs/etsf_io/Manifest @@ -1,3 +1,14 @@ -DIST etsf_io-1.0.3.tar.gz 453734 RMD160 df90acd34b0de104a07844ae2c9694edf27519c6 SHA1 ab3c4cb22ea2fc2498b396f186f221edd2463fcc SHA256 a02ead44b9634bdb6e47e50d76f35d56c10df468743e6fe5259c0dc478f7b32e -EBUILD etsf_io-1.0.3.ebuild 929 RMD160 0257864226359bac808ab9a108f19bb8495820c7 SHA1 6c1ccab966ede6f6468ee28414a3e759dc06dc93 SHA256 3d701906e2599221e493cae8149dfa5f4c2c3f63764a755d0ffea69f255bf09f -MISC ChangeLog 274 RMD160 31ff09d34ecd11d6deccdd8bd8045140429795a8 SHA1 59749fbcebdf10b6f6ad44a3046fc45b69bbed68 SHA256 8eafc2bb689f87f93df639b5fd7f7befe360c636f5eaf5e5a7bc3b0472ab5987 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +DIST etsf_io-1.0.3.tar 453734 RMD160 df90acd34b0de104a07844ae2c9694edf27519c6 SHA1 ab3c4cb22ea2fc2498b396f186f221edd2463fcc SHA256 a02ead44b9634bdb6e47e50d76f35d56c10df468743e6fe5259c0dc478f7b32e +EBUILD etsf_io-1.0.3.ebuild 830 RMD160 0958932454fbd1a2adb213bc4246a5ca5432a6cd SHA1 64a041e4db5dad588c4a0b70f123af11d5f8b91c SHA256 c595a76aaec90bf30dad3d2e6f4d62b7ad4b5be962ef9a6c420219423216fe29 +MISC ChangeLog 627 RMD160 77870c62494c0c7db1f02087e4c88ce2a9f36b96 SHA1 8d9f0b0d994dc95a8e2b78dce1e09a249c716522 SHA256 6a76c96c18a3107f897ea23325b3451dea56b5d9e036b1284bb3bcd29c73e712 +MISC metadata.xml 218 RMD160 5dcdfc9ffbff78c3625f6ee6cd8242c0130bba48 SHA1 e7d6721263f31430e0dd04b17f16c27ebac78a89 SHA256 45420c665fb7a061ce85d5300ea7ed5a034a812dc286e2c87540b90d1388d79d +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GCLEACgkQgAnW8HDreRbl5gCfcfQhUbjlMJJnHu0X9uozmGmC +euwAnRIrckyNiPLf/ha7zRpln9jKvtGG +=2T3e +-----END PGP SIGNATURE----- diff --git a/sci-libs/etsf_io/etsf_io-1.0.3.ebuild b/sci-libs/etsf_io/etsf_io-1.0.3.ebuild index 4392a2dd1..402389b9e 100644 --- a/sci-libs/etsf_io/etsf_io-1.0.3.ebuild +++ b/sci-libs/etsf_io/etsf_io-1.0.3.ebuild @@ -1,37 +1,33 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 +# $Header: $ -EAPI=3 -inherit autotools eutils flag-o-matic toolchain-funcs +EAPI=4 + +inherit fortran-2 multilib DESCRIPTION="A library of F90 routines to read/write the ETSF file format" -SRC_URI="http://www.etsf.eu/sites/default/files/${P}.tar.gz" -HOMEPAGE="http://www.etsf.eu/resources/software/libraries_and_tools" +HOMEPAGE="http://www.etsf.eu/resources/software/libraries_and_tools/" +SRC_URI="http://www.etsf.eu/sites/default/files/${P}.tar.gz -> ${P}.tar" -LICENSE="LGPL" +LICENSE="LGPL-2" SLOT="0" IUSE="examples" KEYWORDS="~amd64 ~x86" -RDEPEND="sci-libs/netcdf[fortran]" +RDEPEND=" + sci-libs/netcdf[fortran] + virtual/fortran" DEPEND="${RDEPEND}" -src_unpack() { - tar xf ${DISTDIR}/${A} -} +FORTRAN_STANDARD="90" src_configure() { # fortran 90 uses FCFLAGS export FCFLAGS="${FFLAGS:--O2}" econf \ - --prefix=/usr \ $(use_enable examples build-tutorials) \ - --with-netcdf-ldflags="-L/usr/lib -lnetcdff" \ - --with-moduledir=/usr/lib/finclude -} - -src_install() { - emake DESTDIR="${D}" install || die "emake install failed" - - dodoc README NEWS COPYING AUTHORS INSTALL ChangeLog || die "dodoc failed" + --prefix="${EPREFIX}/usr" \ + --with-netcdf-ldflags="-L${EPREFIX}/usr/$(get_libdir) -lnetcdff" \ + --with-moduledir="${EPREFIX}/usr/$(get_libdir)/finclude" } diff --git a/sci-biology/newbler/metadata.xml b/sci-libs/etsf_io/metadata.xml index 3302123e5..d747d72a2 100644 --- a/sci-biology/newbler/metadata.xml +++ b/sci-libs/etsf_io/metadata.xml @@ -1,9 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> + <herd>sci</herd> <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> + <email>sci@gentoo.org</email> </maintainer> - <herd>sci-biology</herd> </pkgmetadata> diff --git a/sci-libs/fftw/ChangeLog b/sci-libs/fftw/ChangeLog index cf0de9304..99038b101 100644 --- a/sci-libs/fftw/ChangeLog +++ b/sci-libs/fftw/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/fftw -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> fftw-3.3_alpha1.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> fftw-3.3_alpha1.ebuild: + Added fortran-2.eclass support + *fftw-3.3_alpha1 (12 Sep 2010) 12 Sep 2010; Christoph Junghans <kleiner_otti@gmx.de> diff --git a/sci-libs/fftw/Manifest b/sci-libs/fftw/Manifest index 45895319a..02b5c2872 100644 --- a/sci-libs/fftw/Manifest +++ b/sci-libs/fftw/Manifest @@ -3,13 +3,13 @@ Hash: SHA1 AUX fftw-3.2.1-as-needed.patch 3184 RMD160 fe4e353851780d1520cfa95cd4403ec7045d9c73 SHA1 c831f88d297579f6feed13a726184dea7f2362f8 SHA256 c70c4544a060f134d88930019562b4b4f413382e33b373e8389036be6aefb91c DIST fftw-3.3alpha1.tar.gz 3466915 RMD160 97abe5966b86193bbe52a550bb18d180fdaa8a5d SHA1 a782c2b2f17780bccf491090e80dee22994776cc SHA256 b5e64e261e0379deb165fa56ec61cfb0990b6a8963b8ebec9a0f3e6bfbc76e4b -EBUILD fftw-3.3_alpha1.ebuild 3747 RMD160 3d538eb87a33b6827cda63de51ad8add8cdcfadd SHA1 12c53c94385682dd7879cc102b749714f192ecb9 SHA256 32da3793a6c466e8bc7dbd229b9b3ee67dbd15909fea595d6fa8f460325a3d95 -MISC ChangeLog 289 RMD160 fb93d48c3a7db5fb589e1f8e50bb727653e96b2d SHA1 bee05e3bccc3de28fd49b8559dde224e0ae6dec2 SHA256 bd3aa0a63f45726af28f5c82ee946a55604c3cfde38150ddee49c4b7b9d0e848 +EBUILD fftw-3.3_alpha1.ebuild 3711 RMD160 0389cc2136512a271f0a3fa74dc635dad9965aa6 SHA1 25de1f6ae74c892ba53a6917ccf0df24a8de84f0 SHA256 454ff66802a231d649fbf9816416b0884bab5f64b842d618cf6152ec33163d0a +MISC ChangeLog 503 RMD160 1e17190d5aa7ab23b6c3ab1306b60483ff6f3590 SHA1 036156b5cdfcb586cfc14e867bbf00fd275417bc SHA256 6abf39e19cfad9b67372c0878064c2f58853c369f3d7851bbd6bc1f935ab2e66 MISC metadata.xml 637 RMD160 a7f1ab3fce5eae79531875234ca77532d0fd2cfa SHA1 b1cce6af4d119fc1b4f640b33e4ef1a8318a736c SHA256 a2798427fe8d4cbe97cf588e66bf54cc37d9650b9451290c2b6846cc6bb81e50 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkyNJaQACgkQy0OE/ans1/n96wCeNHj0tb5MEr3UMVrxwR245kMI -1LQAoIToghaV4qaZtrYecpZaJNrs9sir -=demm +iEYEARECAAYFAk4EgNkACgkQgAnW8HDreRYcFQCfXNfWxek5Rvr//yWrxkqbXEzj +QzMAn0r9MAeZY+IdSkaVE3t/fY7PPSCU +=wyTJ -----END PGP SIGNATURE----- diff --git a/sci-libs/fftw/fftw-3.3_alpha1.ebuild b/sci-libs/fftw/fftw-3.3_alpha1.ebuild index 2c6abddbc..3d9e309d5 100644 --- a/sci-libs/fftw/fftw-3.3_alpha1.ebuild +++ b/sci-libs/fftw/fftw-3.3_alpha1.ebuild @@ -1,37 +1,37 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=2 -inherit flag-o-matic eutils toolchain-funcs autotools + +inherit autotools eutils flag-o-matic fortran-2 toolchain-funcs DESCRIPTION="Fast C library for the Discrete Fourier Transform" HOMEPAGE="http://www.fftw.org/" SRC_URI="http://www.fftw.org/${P//_}.tar.gz" -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - LICENSE="GPL-2" SLOT="3.0" KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" IUSE="altivec doc fortran mpi openmp sse sse2 static-libs threads" +DEPEND=" + fortran? ( virtual/fortran ) + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + S="${WORKDIR}/${P//_}" pkg_setup() { + use openmp && FORTRAN_NEED_OPENMP="1" + use fortran && fortran-2_pkg_setup FFTW_THREADS="--disable-threads --disable-openmp" if use openmp; then FFTW_THREADS="--disable-threads --enable-openmp" elif use threads; then FFTW_THREADS="--enable-threads --disable-openmp" fi - if use openmp && - [[ $(tc-getCC)$ == *gcc* ]] && - [[ $(tc-getCC)$ != *apple* ]] && - ( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] || - ! has_version sys-devel/gcc[openmp] ) - then + if use openmp && ! tc-has-openmp; then ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 " ewarn "If you want to build fftw with OpenMP, abort now," ewarn "and switch CC to an OpenMP capable compiler" diff --git a/sci-libs/fgsl/ChangeLog b/sci-libs/fgsl/ChangeLog index e38e9a53a..9013e8077 100644 --- a/sci-libs/fgsl/ChangeLog +++ b/sci-libs/fgsl/ChangeLog @@ -1,7 +1,19 @@ # ChangeLog for sci-libs/fgsl -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*fgsl-0.9.4 (28 Jun 2011) + + 28 Jun 2011; Justin Lecher <jlec@gentoo.org> fgsl-0.9.3.ebuild, + +fgsl-0.9.4.ebuild: + Version Bump + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> fgsl-0.9.3.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> fgsl-0.9.3.ebuild: + Added fortran-2.eclass support + *fgsl-0.9.3 (17 Aug 2010) 17 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> +fgsl-0.9.3.ebuild, diff --git a/sci-libs/fgsl/Manifest b/sci-libs/fgsl/Manifest index 8953fdd51..93cea386e 100644 --- a/sci-libs/fgsl/Manifest +++ b/sci-libs/fgsl/Manifest @@ -1,5 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA512 + AUX fgsl-0.9.3-sharedlibs.patch 726 RMD160 91b13474678c68ae6539f58c4ccde108f28c62a7 SHA1 a4f750f13c8c8675aae0ae41b34ff62cc80ace1d SHA256 1c4a1bfb406e624f716c56c30345c56a49657148a10ce07ed573e0aed4e22ac3 DIST fgsl-0.9.3.tar.gz 293761 RMD160 159162527256408ecf210b382461794b71c4738c SHA1 96e0e0c6b538377bdbe043c8c064e5d60ba6e428 SHA256 ba6c7d95ea73ea81435b6960fa9dc1e6e11d2da7fa145117111352d873c71ce9 -EBUILD fgsl-0.9.3.ebuild 1294 RMD160 74b7d87cd557b9e6dd5da02e99b6bddef3b86026 SHA1 022d6c238abdf1928abb1a307e6480b31de87e4d SHA256 ab4e08836ec64a638b526dcb2675c1724fa1331cee7a7dced8fec88db1e698ac -MISC ChangeLog 309 RMD160 f017ad09f8b076d3b6dcb9175f622c8765d855fb SHA1 35185c2df55598aa2d448ce257d9c30f2550496a SHA256 7d98c6c919befb8e84a4edf0064f50dee6cffeccd0072ef9919aadd85525bed6 +DIST fgsl-0.9.4.tar.gz 999825 RMD160 7c12162b4fb64746d91715756c01e52dbb4e0e09 SHA1 82f3047a3b1b1970fae741946fd8479f15595362 SHA256 f589283f5b9df5df9ef39b108114df2ed740109fabb8956fe98eaaac20924ba7 +EBUILD fgsl-0.9.3.ebuild 1316 RMD160 3ac992686299b539a1939f1c41a39d26976a88e5 SHA1 72363962ae30dc54e817c9f40d7ea439f45b4615 SHA256 52be8cd8d78802b283c9c273b3dfff669e2c172aac9d6370b0876c03df788479 +EBUILD fgsl-0.9.4.ebuild 1317 RMD160 09e9bce3eceba940de76dc77c2a0c560f103a219 SHA1 6a67649eef90ed8c3968925532a37e35c261a47e SHA256 7004a1c19ec79542a6d6cf29e0451aaafb9800c408f37b2a5cfec36eab0ebfc2 +MISC ChangeLog 644 RMD160 3a678c9367fe1c668ccec699925348f3ce1ba53b SHA1 4f26ae484f8ef584e478b07cc69596a648f7e778 SHA256 84a2856b7a161cefc5560b92862f9ee1da5c906f2ea34f0704b974c49cb8e82a MISC metadata.xml 347 RMD160 52c569b75eaf0223827be9e12af42dd83e0df9e3 SHA1 af5df8f6d153077ca37f527ce46abbc49500dfca SHA256 5619b315d05f66962c028e3b5bdfa7dd5366d3e8e6853a9c680b0a71622a7b9b +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREKAAYFAk4KC+MACgkQgAnW8HDreRaInACeMQy5q+7lzdQR7cg6v6xUbli6 +VusAoKKovqEfPQ0yBLwAsj6AnAIqddSX +=kMpR +-----END PGP SIGNATURE----- diff --git a/sci-libs/fgsl/fgsl-0.9.3.ebuild b/sci-libs/fgsl/fgsl-0.9.3.ebuild index 2d7bbfc9b..cb37221d7 100644 --- a/sci-libs/fgsl/fgsl-0.9.3.ebuild +++ b/sci-libs/fgsl/fgsl-0.9.3.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 +EAPI=4 -inherit eutils multilib toolchain-funcs +inherit eutils fortran-2 multilib toolchain-funcs DESCRIPTION="A Fortran interface to the GNU Scientific Library" HOMEPAGE="http://www.lrz.de/services/software/mathematik/gsl/fortran/" @@ -15,10 +15,14 @@ SLOT="0" KEYWORDS="~amd64" IUSE="static-libs" -DEPEND=">=sci-libs/gsl-1.14" +DEPEND=" + >=sci-libs/gsl-1.14 + virtual/fortran" RDEPEND="${DEPEND}" #TODO: make docs +FORTRAN_STANDARD=90 + src_prepare() { epatch "${FILESDIR}"/${P}-sharedlibs.patch use amd64 && ln -s interface/integer_ilp64.finc integer.finc @@ -41,13 +45,13 @@ src_configure() { } src_install() { - dodoc NEWS README || die + dodoc NEWS README ln -s lib${PN}.so.0.0.0 lib${PN}.so.0 ln -s lib${PN}.so.0.0.0 lib${PN}.so - dolib.so lib${PN}.so* || die + dolib.so lib${PN}.so* insinto /usr/include - doins ${PN}.mod || die + doins ${PN}.mod if use static-libs ; then - newlib.a lib${PN}_$(tc-getFC).a lib${PN}.a || die + newlib.a lib${PN}_$(tc-getFC).a lib${PN}.a fi } diff --git a/sci-libs/fgsl/fgsl-0.9.4.ebuild b/sci-libs/fgsl/fgsl-0.9.4.ebuild new file mode 100644 index 000000000..792b0de6d --- /dev/null +++ b/sci-libs/fgsl/fgsl-0.9.4.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils fortran-2 multilib toolchain-funcs + +DESCRIPTION="A Fortran interface to the GNU Scientific Library" +HOMEPAGE="http://www.lrz.de/services/software/mathematik/gsl/fortran/" +SRC_URI="http://www.lrz.de/services/software/mathematik/gsl/fortran/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="static-libs" + +DEPEND=" + >=sci-libs/gsl-1.15 + virtual/fortran" +RDEPEND="${DEPEND}" +#TODO: make docs + +FORTRAN_STANDARD=90 + +src_prepare() { + epatch "${FILESDIR}"/${PN}-0.9.3-sharedlibs.patch + use amd64 && ln -s interface/integer_ilp64.finc integer.finc + use x86 && ln -s interface/integer_ilp32.finc integer.finc + cat <<- EOF > "${S}/make.inc" + F90 = $(tc-getFC) + CC = $(tc-getCC) + GSL_LIB = $(pkg-config --libs gsl) + GSL_INC = $(pkg-config --cflags gsl) + PREFIX = /usr + ARFLAGS = -csrv + FPP = -cpp + LIB = $(get_libdir) + EOF + use static-libs && echo "STATIC_LIBS = yes" >> "${S}/make.inc" +} + +src_configure() { +: +} + +src_install() { + dodoc NEWS README + ln -s lib${PN}.so.0.0.0 lib${PN}.so.0 + ln -s lib${PN}.so.0.0.0 lib${PN}.so + dolib.so lib${PN}.so* + insinto /usr/include + doins ${PN}.mod + if use static-libs ; then + newlib.a lib${PN}_$(tc-getFC).a lib${PN}.a + fi +} diff --git a/sci-libs/fox/ChangeLog b/sci-libs/fox/ChangeLog index 4355c8cd8..791c95e0e 100644 --- a/sci-libs/fox/ChangeLog +++ b/sci-libs/fox/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> fox-4.0.4.ebuild, + fox-4.1.0.ebuild: + Fix CVS Header , remove LICENSE from installation + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> +metadata.xml: + metadata.xml added + *fox-4.1.0 (17 Jan 2011) *fox-4.0.4 (17 Jan 2011) diff --git a/sci-libs/fox/Manifest b/sci-libs/fox/Manifest index e7544ce86..0ee4e56e8 100644 --- a/sci-libs/fox/Manifest +++ b/sci-libs/fox/Manifest @@ -1,6 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX 4.0.4-install-customizations.patch 993 RMD160 29b5a75de047adde3b3e468cab8d362fe591c240 SHA1 55b6987e80b7ff5e425ba140d2e44d088ed5ef1c SHA256 b8c283de0c6fe335c2bc524b988f5b46955fde7adca65d1da70ddfaa96f205c8 DIST FoX-4.0.4-full.tar.gz 503516 RMD160 856aaf50564dd0d35e86f133e4fb1fbe7aa11ed3 SHA1 01ee568543cd17f14b6a63de177e6796f189ccb2 SHA256 219db37dcda0b11fa602170d76da086fe140cbfcbd9f8620a00482398c48836e DIST FoX-4.1.0-full.tar.gz 1018847 RMD160 0eabc391c89ba5f132811f803c4dfe53e6fe5812 SHA1 0ebf95734aa4f6f656c8b7e73e4cd411d6fd2870 SHA256 8e7992ae6391178768bb58c230424a430ed57693a3cc7c4c22001ddc682910ff -EBUILD fox-4.0.4.ebuild 1373 RMD160 4d33339a5bbe926c5f4b2cd427621eb6c6056fad SHA1 bbbb178b57e400bc9d42f8dbea9c40a25ccca7e7 SHA256 d63a976dffaf701db9c7b48bde6efdd00738d0a3dd9c2056812187d4c867e9c4 -EBUILD fox-4.1.0.ebuild 1334 RMD160 e1c03022ec8ed3c134594e49116b9ef2af0c2d19 SHA1 d682f6b3d8366ec1db87ea6c957a18db6d2327d4 SHA256 e6233aaacebfd9c62cc797537062b76bafbf4ac7705279021aec5149f0dbf835 -MISC ChangeLog 346 RMD160 bf574dfda3242da520f587d10c1f9bb437074036 SHA1 bd1822703d2ce1b0ac929ac26de5a37af863907d SHA256 07115e849028f419895fc98f22359cf53103c6e256ba587ab7c6adbd0bb7a3d6 +EBUILD fox-4.0.4.ebuild 1349 RMD160 7c43fa7662b85da1340bafcfabab7652635b6dea SHA1 1fdfda43de956fe016e85caec5fdf56e037fc4b9 SHA256 edbda09ed598df641c8ab59dd220b7519b493477b306b90d76be95e6c7843707 +EBUILD fox-4.1.0.ebuild 1310 RMD160 a47a5008bb88571357ec8efb76c8e1774eb3ba94 SHA1 e0ff2f94fb122547ffc1344b2de0fc23ad315bad SHA256 ab16e96e768d3b8b197dd59ed3631345a0b1f467f0af774f6cb072f719db5d27 +MISC ChangeLog 568 RMD160 f23f14c9e86c0a1b781e636f1beda38cb5c7889b SHA1 ed1c1dd41d793f6d03a9722f932d07dae20cd969 SHA256 ebc1ac641f60db9d97b6264becdb37b53e8d20886ea189ce2498104688424efc +MISC metadata.xml 606 RMD160 3b91ea2266838d80fdfdbf6d712ba9671e84d538 SHA1 3cbe33a71397bc7fd727f8d4879030cfe018920d SHA256 8bb214fc57e40cbdd00f82a0c24ef64b86da3aa8dfbf69cb36593f3f1614b59d +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EpowACgkQgAnW8HDreRYuwwCgoKyUZnHwf3OT11d3StBEqDmR +cTUAnAonLIqptuWB4TZ1nCelO9NFnDdh +=FS4X +-----END PGP SIGNATURE----- diff --git a/sci-libs/fox/fox-4.0.4.ebuild b/sci-libs/fox/fox-4.0.4.ebuild index 0bb430de1..105d67bb9 100644 --- a/sci-libs/fox/fox-4.0.4.ebuild +++ b/sci-libs/fox/fox-4.0.4.ebuild @@ -1,5 +1,6 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 +# $Header: $ EAPI=3 @@ -12,12 +13,12 @@ DIRV="${PV/%[0-9]/X}" DESCRIPTION="A library designed to allow the easy use of XML from Fortran" HOMEPAGE="http://www1.gly.bris.ac.uk/~walker/FoX/" SRC_URI="http://www1.gly.bris.ac.uk/~walker/FoX/source/${MY_PN}-${DIRV}/${MY_P}-full.tar.gz" + LICENSE="BSD ZLIB" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="debug doc dom fast sax wcml wxml" -RDEPEND="" -DEPEND="${RDEPEND}" + S="${WORKDIR}/${MY_P}" src_prepare() { @@ -49,7 +50,7 @@ src_install() { -e's%comp_prefix/finclude%comp_prefix/lib/finclude%' \ FoX-config emake -j1 DESTDIR="${D}" install || die "make install failed" - dodoc README.FoX.txt Changelog LICENSE || die "dodoc failed" + dodoc README.FoX.txt Changelog || die "dodoc failed" if use doc; then dohtml -r DoX/ || die "installing the HTML docs failed" fi diff --git a/sci-libs/fox/fox-4.1.0.ebuild b/sci-libs/fox/fox-4.1.0.ebuild index ea50a3411..c57b61449 100644 --- a/sci-libs/fox/fox-4.1.0.ebuild +++ b/sci-libs/fox/fox-4.1.0.ebuild @@ -1,5 +1,6 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 +# $Header: $ EAPI=3 @@ -11,12 +12,12 @@ MY_P="${MY_PN}-${PV}" DESCRIPTION="A library designed to allow the easy use of XML from Fortran" HOMEPAGE="http://www1.gly.bris.ac.uk/~walker/FoX/" SRC_URI="http://www1.gly.bris.ac.uk/~walker/FoX/source/${MY_P}-full.tar.gz" + LICENSE="BSD ZLIB" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="debug doc dom fast sax wcml wxml" -RDEPEND="" -DEPEND="${RDEPEND}" + S="${WORKDIR}/${MY_P}" src_prepare() { @@ -48,7 +49,7 @@ src_install() { -e's%comp_prefix/finclude%comp_prefix/lib/finclude%' \ FoX-config emake -j1 DESTDIR="${D}" install || die "make install failed" - dodoc README.FoX.txt Changelog LICENSE || die "dodoc failed" + dodoc README.FoX.txt Changelog || die "dodoc failed" if use doc; then dohtml -r DoX/ || die "installing the HTML docs failed" fi diff --git a/sci-libs/fox/metadata.xml b/sci-libs/fox/metadata.xml new file mode 100644 index 000000000..0ad2e28c6 --- /dev/null +++ b/sci-libs/fox/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <maintainer> + <email>sci@gentoo.org</email> + </maintainer> + <use> + <flag name="dom">Automatically generated description for dom</flag> + <flag name="fast">Automatically generated description for fast</flag> + <flag name="sax">Automatically generated description for sax</flag> + <flag name="wcml">Automatically generated description for wcml</flag> + <flag name="wxml">Automatically generated description for wxml</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/ghmm/ChangeLog b/sci-libs/ghmm/ChangeLog new file mode 100644 index 000000000..a55592121 --- /dev/null +++ b/sci-libs/ghmm/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-libs/ghmm +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + diff --git a/sci-libs/ghmm/Manifest b/sci-libs/ghmm/Manifest index b9cca10ea..8181af87f 100644 --- a/sci-libs/ghmm/Manifest +++ b/sci-libs/ghmm/Manifest @@ -1,2 +1,13 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + EBUILD ghmm-9999.ebuild 809 RMD160 2045e42f6055e65c7c753b8b7d2908fa16d732b7 SHA1 73415292cdd81653704ce0ffc9722b1dc80476ae SHA256 bb6cb98074623588ba6db9865c8d407019ace59bead6bfd770ca8687d1b9fef0 -MISC metadata.xml 255 RMD160 184656009858e0a39b1c4f42399521e4464049a8 SHA1 dbd3a562b7cd7911378771015534077fc39c9484 SHA256 cc428331a6ed09c67a36af65ea5b384cb839fc6d68beb1b6c53abd383916fc75 +MISC ChangeLog 211 RMD160 e3224568832b531d2042a6478c7c8063651979c3 SHA1 904f9bd8807301db7e887a69991adf0c10cbde88 SHA256 7c189d40cc08eb996c8a4e03215ea11660c98a1f4bf7c5174a0fe790c3bfb7c3 +MISC metadata.xml 258 RMD160 fe5c0558a488959a837337ccacc520b7bad13cc3 SHA1 46d8c5eb1532c1ad40fb711e756ed0edb51019d8 SHA256 57d0a59f7455e7309389a052e7d93677a57b83e10fd22449736554f8f5069cdd +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4FkhMACgkQgAnW8HDreRay0QCeKDY5kUOSWMepyFUhnitAdLFS +Xy0An1udr72NMwDS3Fkej25Ykd90C9A/ +=P84z +-----END PGP SIGNATURE----- diff --git a/sci-libs/ghmm/metadata.xml b/sci-libs/ghmm/metadata.xml index 7c2c6e6d8..970013aea 100644 --- a/sci-libs/ghmm/metadata.xml +++ b/sci-libs/ghmm/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>science</herd> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci</herd> </pkgmetadata> diff --git a/sci-libs/gmsh/ChangeLog b/sci-libs/gmsh/ChangeLog index 86517a6d9..d60c82fe3 100644 --- a/sci-libs/gmsh/ChangeLog +++ b/sci-libs/gmsh/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> gmsh-2.5.0.ebuild, + gmsh-9999.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> gmsh-2.5.0.ebuild, + gmsh-9999.ebuild: + Added fortran-2.eclass support + 27 Mar 2011; Justin Lecher <jlec@gentoo.org> gmsh-2.5.0.ebuild, gmsh-9999.ebuild: Corrected slot of fltk, #360641 diff --git a/sci-libs/gmsh/Manifest b/sci-libs/gmsh/Manifest index 0f3269df8..55e59a67b 100644 --- a/sci-libs/gmsh/Manifest +++ b/sci-libs/gmsh/Manifest @@ -2,14 +2,14 @@ Hash: SHA1 DIST gmsh-2.5.0-source.tgz 3642009 RMD160 49ab2054d546e4549250119cec0453cd1cdfffef SHA1 b541fd9f1aadf1df7bf6fdd97a68ca41966ffeb6 SHA256 db1d3b92e56a85be9ec1c020aa2c705ccf5b7f0d00fa0f29b50efc73b378debc -EBUILD gmsh-2.5.0.ebuild 2513 RMD160 ba8aaf087c38f1bae49e950d8c958afd6f316651 SHA1 f095e2213661519f074173370a2d73f90d80d143 SHA256 899d014f97b9e535d83cc765fa5d58fa2d15daf8ad553bc7b659c90994b982d7 -EBUILD gmsh-9999.ebuild 2480 RMD160 6e1a39f15245158fd89d632d82a8a37da8eb5b8b SHA1 0321fc106fb1255e9ef0bc3061d6013d68e82f7b SHA256 c6f05f77a9a30d064c6dd6b89ec613e278b047d721637d0842521cdedaa7b3a7 -MISC ChangeLog 2989 RMD160 f9fe36714fe0299bd084d81de372dbedd2df71b4 SHA1 792738120af92460a4361c56f3be70638e1bbd2e SHA256 d51053ede111fa44d5fd7e3c19ae6d6b61f9083d3527b9f98922c5ccfa265d4a +EBUILD gmsh-2.5.0.ebuild 2585 RMD160 8c1570bdb1d64f80265f6ef712d2456fa3008551 SHA1 d1d7a377838fc2af54f8aa5f8540813b6e89c1e7 SHA256 9d425d927122f90c2937cfdf3c270feb4ed4d9e69294e4018bb52465389c8e34 +EBUILD gmsh-9999.ebuild 2305 RMD160 882c2fb7bed5d4fd21f11917ff919e65925a9912 SHA1 a6163b5c8b0d6e9018cb67d47dd13caf4eaff88a SHA256 1a56ff75ab5b22395ecd93782f2039fd70832e3cb3f86a431ff8258925f7f045 +MISC ChangeLog 3233 RMD160 773b5694e03fe72bde6200c85f47cf8ccf9e0f84 SHA1 e2a812e965695b0fd6d2e66a88a3076118f201e1 SHA256 8c44f424f4bacbab04be0af9a0c20ab8379e114836239ec7e29a332cab036595 MISC metadata.xml 733 RMD160 7d4b90e9579462bb19c80d1176bc02fa889b8844 SHA1 f1484dc55dace56aa3e546370382b5273f33c884 SHA256 58878c508258397ebe56dc3751b9c334a11f332ae732248a23ce454b880d266e -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2O7zUACgkQgAnW8HDreRbZ/wCfZyVWeCKU2pGqY9wZSYhvGO3Z -EmYAoLLvh4oE51z0W/6JVDNceqHC3u1V -=4v2a +iEYEARECAAYFAk4EgY8ACgkQgAnW8HDreRYUrgCgkLPfp6WdYdySnvyK/RJh4/Rk +ZjIAn3kSnPxGq0eSaFDBrJiIC9QCd41V +=ix8s -----END PGP SIGNATURE----- diff --git a/sci-libs/gmsh/gmsh-2.5.0.ebuild b/sci-libs/gmsh/gmsh-2.5.0.ebuild index 5a0f15d4f..349f98dca 100644 --- a/sci-libs/gmsh/gmsh-2.5.0.ebuild +++ b/sci-libs/gmsh/gmsh-2.5.0.ebuild @@ -2,11 +2,11 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=3 -inherit cmake-utils flag-o-matic toolchain-funcs +inherit cmake-utils flag-o-matic fortran-2 toolchain-funcs -DESCRIPTION="A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities." +DESCRIPTION="A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities" HOMEPAGE="http://www.geuz.org/gmsh/" SRC_URI="http://www.geuz.org/gmsh/src/${P}-source.tgz" @@ -15,9 +15,11 @@ LICENSE="GPL-3 free-noncomm" SLOT="0" KEYWORDS="~amd64 ~x86" ## cgns is not compiling ATM, maybe fix cgns lib first -IUSE="blas chaco cgns doc examples jpeg lua med metis mpi netgen opencascade png petsc taucs tetgen zlib X" +IUSE="blas cgns chaco doc examples jpeg lua med metis mpi netgen opencascade petsc png taucs tetgen X zlib" -RDEPEND="X? ( x11-libs/fltk:1 ) +RDEPEND=" + virtual/fortran + X? ( x11-libs/fltk:1 ) blas? ( virtual/blas virtual/lapack sci-libs/fftw:3.0 ) cgns? ( sci-libs/cgnslib ) jpeg? ( virtual/jpeg ) @@ -40,12 +42,19 @@ DEPEND="${RDEPEND} S=${WORKDIR}/${P}-source +pkg_setup() { + fortran-2_pkg_setup +} + src_configure() { local mycmakeargs="" - use blas && mycmakeargs="${mycmakeargs} - -DCMAKE_Fortran_COMPILER=$(tc-getF77)" - mycmakeargs="${mycmakeargs} $(cmake-utils_use_enable blas BLAS_LAPACK) + use blas && \ + mycmakeargs="${mycmakeargs} + -DCMAKE_Fortran_COMPILER=$(tc-getF77)" + + mycmakeargs="${mycmakeargs} + $(cmake-utils_use_enable blas BLAS_LAPACK) $(cmake-utils_use_enable cgns CGNS) $(cmake-utils_use_enable chaco CHACO) $(cmake-utils_use_enable X FLTK) diff --git a/sci-libs/gmsh/gmsh-9999.ebuild b/sci-libs/gmsh/gmsh-9999.ebuild index c32c95f5b..1a35dec25 100644 --- a/sci-libs/gmsh/gmsh-9999.ebuild +++ b/sci-libs/gmsh/gmsh-9999.ebuild @@ -2,42 +2,41 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=3 -inherit cmake-utils flag-o-matic subversion toolchain-funcs +inherit cmake-utils flag-o-matic fortran-2 subversion toolchain-funcs -DESCRIPTION="A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities." +DESCRIPTION="A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities" HOMEPAGE="http://www.geuz.org/gmsh/" ESVN_REPO_URI="https://geuz.org/svn/gmsh/trunk" ESVN_USER="gmsh" ESVN_PASSWORD="gmsh" -LICENSE="GPL-2" +LICENSE="GPL-3 free-noncomm" SLOT="0" KEYWORDS="" -IUSE="blas chaco cgns doc examples jpeg med metis mpi opencascade png taucs zlib X" - -RDEPEND="X? ( x11-libs/fltk:1 ) - blas? ( virtual/blas virtual/lapack sci-libs/fftw:3.0 ) - cgns? ( sci-libs/cgnslib ) - jpeg? ( virtual/jpeg ) - med? ( >=sci-libs/med-2.3.4 ) - mpi? ( sys-cluster/openmpi[cxx] ) - opencascade? ( sci-libs/opencascade ) - png? ( media-libs/libpng ) - zlib? ( sys-libs/zlib ) - taucs? ( sci-libs/taucs )" +IUSE="blas cgns chaco doc examples jpeg med metis mpi opencascade png taucs X zlib" + +RDEPEND=" + virtual/fortran + X? ( x11-libs/fltk:1 ) + blas? ( virtual/blas virtual/lapack sci-libs/fftw:3.0 ) + cgns? ( sci-libs/cgnslib ) + jpeg? ( virtual/jpeg ) + med? ( >=sci-libs/med-2.3.4 ) + mpi? ( sys-cluster/openmpi[cxx] ) + opencascade? ( sci-libs/opencascade ) + png? ( media-libs/libpng ) + zlib? ( sys-libs/zlib ) + taucs? ( sci-libs/taucs )" DEPEND="${RDEPEND} - dev-util/cmake - dev-vcs/subversion - doc? ( virtual/latex-base )" + dev-util/cmake + dev-vcs/subversion + doc? ( virtual/latex-base )" pkg_setup() { - ewarn "Put the F77 variable in env files to select your fortran compiler" - ewarn "example for gfortran:" - ewarn "echo \"F77=gfortran\" >> /etc/portage/env/sci-libs/gmsh" - + fortran-2_pkg_setup use taucs && ! use metis && \ die "taucs USE flag requires metis USE flag to be enabled" } @@ -45,19 +44,21 @@ pkg_setup() { src_configure() { local mycmakeargs="" - use blas && mycmakeargs="${mycmakeargs} - -DCMAKE_Fortran_COMPILER=$(tc-getF77)" - - mycmakeargs="${mycmakeargs} $(cmake-utils_use_enable blas BLAS_LAPACK) - $(cmake-utils_use_enable cgns CGNS) - $(cmake-utils_use_enable chaco CHACO) - $(cmake-utils_use_enable X FLTK) - $(cmake-utils_use_enable X FL_TREE) - $(cmake-utils_use_enable X GRAPHICS) - $(cmake-utils_use_enable med MED) - $(cmake-utils_use_enable metis METIS) - $(cmake-utils_use_enable taucs TAUCS) - $(cmake-utils_use_enable opencascade OCC)" + use blas && \ + mycmakeargs="${mycmakeargs} + -DCMAKE_Fortran_COMPILER=$(tc-getF77)" + + mycmakeargs="${mycmakeargs} + $(cmake-utils_use_enable blas BLAS_LAPACK) + $(cmake-utils_use_enable cgns CGNS) + $(cmake-utils_use_enable chaco CHACO) + $(cmake-utils_use_enable X FLTK) + $(cmake-utils_use_enable X FL_TREE) + $(cmake-utils_use_enable X GRAPHICS) + $(cmake-utils_use_enable med MED) + $(cmake-utils_use_enable metis METIS) + $(cmake-utils_use_enable taucs TAUCS) + $(cmake-utils_use_enable opencascade OCC)" # I'm not sure if this is needed, but it seems to help in some circumstances # see http://bugs.gentoo.org/show_bug.cgi?id=195980#c18 diff --git a/sci-libs/hdf5/ChangeLog b/sci-libs/hdf5/ChangeLog index 3f7eb7889..0c0ffd40b 100644 --- a/sci-libs/hdf5/ChangeLog +++ b/sci-libs/hdf5/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/hdf5 -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> hdf5-1.8.4-r2.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> hdf5-1.8.4-r2.ebuild: + Added fortran-2.eclass support + *hdf5-1.8.4-r2 (19 Jan 2010) 19 Jan 2010; Justin Bronder <jsbronder@gentoo.org> -hdf5-1.8.4-r1.ebuild, diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest index 2e2fc664a..fb87d001b 100644 --- a/sci-libs/hdf5/Manifest +++ b/sci-libs/hdf5/Manifest @@ -1,9 +1,19 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX hdf5-1.8.3-as-needed.patch 1909 RMD160 86c153a302d2730d94ab2c741fb71eb66de6b271 SHA1 aafc558d4a5bf58d78ff807f79a81b0f2ef8f8f3 SHA256 11d4fba2970b68666d65e31178f2a07630c0c1f46ef7b18bfa16d49de776a649 AUX hdf5-1.8.3-includes.patch 398 RMD160 5112dd05bebbc702f24fa22aeebc67209a4e6611 SHA1 339137d04a803e25a0cafaa4f4d167a4cbc9a7ae SHA256 cd82d8b3817d83d59054a2a32ce44aca060157095875f6e91c560ab830b32561 AUX hdf5-1.8.3-noreturn.patch 3222 RMD160 39285ba18447b0f8db22a5f8e9d51a3cd8a8e91e SHA1 c5d8f7528fbe5c0bde0cb0ac5c1dd189559ac140 SHA256 d902cfbda0382b8998506ea765d0795937485c44d8824051275ad668bcbd6565 AUX hdf5-1.8.4-gnutools.patch 4607 RMD160 a27fcd676bc3a04ac535dd55c48a72a5317b08a9 SHA1 8aa01c68f788bfedb490dafd0252970105810eac SHA256 d4f989f289e7fb3ee8e585b10232811c17588b730013698fc439cc0fdabcb252 AUX hdf5-1.8.4-scaleoffset.patch 1098 RMD160 4983755ff2d284c73f8479cbf11a19b1bf4ef7c2 SHA1 29be6d6cb7de5db5e10429879f9d6673b6af1519 SHA256 596568d5cf56eba73de4e88a3e7aa0c8c13f3660279ffda783e2074e846a9b2d DIST hdf5-1.8.4.tar.gz 7181176 RMD160 e448e2326b55aa89ff0bd7488cd4291d6c5485ee SHA1 37877e29c49a6af3e23aa9ad798ef12b8ba1c05c SHA256 a992fce9387a17f175b3b188dc2a42f545a3057aeb141beb3fc3361c7521f465 -EBUILD hdf5-1.8.4-r2.ebuild 2670 RMD160 2442b88a035bc26426009af831d37f2abbc8fd1f SHA1 6cdda08aa01f3b0ce5a2e9a60fbb11197384e56f SHA256 9431f0d0aa95e33de6f8e583fea2f5384d4c8f2f42deff3fa2b708836e0b868a -MISC ChangeLog 294 RMD160 0c8247e1be7d1f3bcfb6ae869ffa1c4d5ee59545 SHA1 6e47585dc89020ff07d8115280a7df2a9e50e360 SHA256 7f08fac34c8116df86273775ed2931fee24857928dbddacfa4fa502ed417a660 +EBUILD hdf5-1.8.4-r2.ebuild 2728 RMD160 27db0006c911203a32111207633659da1b2b518a SHA1 1f4b049d58124eea7f17c6b28e29feb343b7c219 SHA256 bf35f2dad2217fda9908999a9117e03e2220559a600219ddb693866672abdc32 +MISC ChangeLog 504 RMD160 8bc6ed8bfe9d2707c21de335b84654cfb85b00cc SHA1 70706361cbdac548ecdcf0916a366502157abc84 SHA256 3d75214ce3c1f5a336ef0536378d9b2c915089de0324ca50fa9cd0170813b173 MISC metadata.xml 445 RMD160 2df0c2fd89c734fbe2efbf51563ddad59bea4814 SHA1 4ae41352074e7b3fff16e5d1de312ffb00df2251 SHA256 e1dfcebd355f246f7f4b0d644e2914cebe3cf16cad2c135fe58a6985eefb61eb +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EgqEACgkQgAnW8HDreRYjWgCcCiMB0xoyDR3x9kU2DirmzLlx +VA8AoLofsoiCVBbslCPzeG05OwSGF3bf +=QDuq +-----END PGP SIGNATURE----- diff --git a/sci-libs/hdf5/hdf5-1.8.4-r2.ebuild b/sci-libs/hdf5/hdf5-1.8.4-r2.ebuild index be24acca9..71fc58ee0 100644 --- a/sci-libs/hdf5/hdf5-1.8.4-r2.ebuild +++ b/sci-libs/hdf5/hdf5-1.8.4-r2.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 +EAPI=3 MPI_PKG_USE_ROMIO=1 -inherit eutils autotools mpi +inherit autotools eutils fortran-2 mpi DESCRIPTION="General purpose library and file format for storing scientific data" HOMEPAGE="http://www.hdfgroup.org/HDF5/" @@ -18,15 +18,18 @@ KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86" IUSE="cxx examples fortran mpi szip threads zlib" -RDEPEND="mpi? ( $(mpi_pkg_deplist) ) +RDEPEND=" + fortran? ( virtual/fortran ) + mpi? ( $(mpi_pkg_deplist) ) szip? ( >=sci-libs/szip-2.1 ) zlib? ( sys-libs/zlib )" DEPEND="${RDEPEND} - >=sys-devel/libtool-2.2 + sys-devel/libtool:2 sys-process/time" pkg_setup() { + fortran && fortran-2_pkg_setup if use mpi; then if use cxx; then ewarn "Simultaneous mpi and cxx is not supported by ${PN}" @@ -40,19 +43,20 @@ pkg_setup() { } src_prepare() { - epatch "${FILESDIR}"/${PN}-1.8.3-as-needed.patch - epatch "${FILESDIR}"/${PN}-1.8.3-includes.patch - epatch "${FILESDIR}"/${PN}-1.8.3-noreturn.patch - epatch "${FILESDIR}"/${P}-gnutools.patch - epatch "${FILESDIR}"/${P}-scaleoffset.patch + epatch \ + "${FILESDIR}"/${PN}-1.8.3-as-needed.patch \ + "${FILESDIR}"/${PN}-1.8.3-includes.patch \ + "${FILESDIR}"/${PN}-1.8.3-noreturn.patch \ + "${FILESDIR}"/${P}-gnutools.patch \ + "${FILESDIR}"/${P}-scaleoffset.patch # respect gentoo examples directory - sed -i \ + sed \ -e 's:$(docdir)/hdf5:$(DESTDIR)/$(docdir):' \ - $(find . -name Makefile.am) || die - sed -i \ + -i $(find . -name Makefile.am) || die + sed \ -e '/docdir/d' \ - config/commence.am || die + -i config/commence.am || die eautoreconf # enable shared libs by default for h5cc config utility sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" tools/misc/h5cc.in \ diff --git a/sci-libs/iml/Manifest b/sci-libs/iml/Manifest index 50a692a26..f31d04a96 100644 --- a/sci-libs/iml/Manifest +++ b/sci-libs/iml/Manifest @@ -1,6 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX fix-undefined-symbol.patch 371 RMD160 eacff26ecc4c551d75a28bb803a2f7212974fdb2 SHA1 2a39ae5a6d7942dd9a3c771396b8393d6cd82c65 SHA256 d5d907e145ea859808d8a6e2083167f7d35548456df792ee1f85bd1e2dc4007a AUX iml-1.0.3-cblas.patch 1365 RMD160 37c1edb0fc7ca4d2d6d9cdfe5f48252b12ab0a79 SHA1 9098b0cb60e1981f6c4d33dcaa9047e16882a380 SHA256 15353191da84e3d7940982878a30c75ec440053416449544f52e46e9f971b70c DIST iml-1.0.3.tar.gz 395160 RMD160 6b845c476158ab977226a69fd8baa3e95bf8d3a8 SHA1 3783e6e0c5aacd0113f30eb731d12de981de6a5e SHA256 fc626debbf8f84689398f4b941a6c1ded0910eea4388e169bf63c48e257b0395 -EBUILD iml-1.0.3.ebuild 933 RMD160 7d095e4f183d299b8285131efc368b9dd213accb SHA1 bb0b623a496619875374f4b560a4154887ca7afe SHA256 eee27a4501218a3845f939d935c37e4f6ae51097af9a35aed14de5f8b3da0eca +EBUILD iml-1.0.3.ebuild 933 RMD160 8be4872d36787462ebfc2c8ac20faea2562e41f6 SHA1 a6ac3a910fcdeb9f244f50153ccc5e39030ebc96 SHA256 b4f1c6bdd6e8f9464623a4308142d34966015146c4958be5e9f2bce6f058c8e6 MISC ChangeLog 318 RMD160 6beb2c18b9914836fa1c6d10489a3852f70e415c SHA1 da611d76c5d8b5c7f4792f28c6b1b2638bfe787c SHA256 c1616b2ac3672e882d66f986700fcb678ab33f76002885111ddbb954fd5fe284 MISC metadata.xml 338 RMD160 e335411f4c21e57fb20107a6cd592fe4aeed2654 SHA1 795d76cd1ed1bff78c84e203bbae1553046d5999 SHA256 dad4bc6f829380868f8827b2bd046c3862783d4744c94e47c082634a7b66e1d9 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EprQACgkQgAnW8HDreRYzFQCgyLWf+wB6I6qboq5cclZJNe/J +CuIAmwcUVc5bJZM8VufTVE+4VkuUgCRe +=y4ew +-----END PGP SIGNATURE----- diff --git a/sci-libs/iml/iml-1.0.3.ebuild b/sci-libs/iml/iml-1.0.3.ebuild index e1dd2d0c7..92eab3436 100644 --- a/sci-libs/iml/iml-1.0.3.ebuild +++ b/sci-libs/iml/iml-1.0.3.ebuild @@ -4,7 +4,7 @@ EAPI=2 -inherit eutils autotools +inherit autotools eutils DESCRIPTION="Integer Matrix Library" HOMEPAGE="http://www.cs.uwaterloo.ca/~astorjoh/iml.html" diff --git a/sci-libs/libcmatrix/Manifest b/sci-libs/libcmatrix/Manifest index 4ade32e1f..0df32d3af 100644 --- a/sci-libs/libcmatrix/Manifest +++ b/sci-libs/libcmatrix/Manifest @@ -4,13 +4,13 @@ Hash: SHA1 AUX 3.2.1-gcc4.4.patch 286 RMD160 8b275ad714b6bedbff03e411187342406f5cf1a7 SHA1 52873e8ef3197148d6c4ddfe0155a3cbfe4fd3db SHA256 e6eff8c9be0f9ac9026d1c00841e81a3f2e00127cbb70bd6e117de262e262fb3 AUX 3.2.1-minuit2.patch 588 RMD160 7bfc835d79915342e6fdb209cfff29e0e8692bbc SHA1 374e8b92a1263ab488089303c6cbb46a28e7929f SHA256 099d47445e6efb340831b4a1f6210b02eb2a2ccf6f680f982761defcadfd1962 DIST libcmatrix-3.2.1.tar.gz 1151322 RMD160 d5f41d7fde34039482e3c971ecff84177ba5c064 SHA1 4612d4d0be34566bca83fe8b8a17033cd0457375 SHA256 6b4cb3ae4e1ed0a33190b09cd15a72c0938e3b598dbda39ca1557b482731b5c4 -EBUILD libcmatrix-3.2.1.ebuild 944 RMD160 1368d873f0e1ac14a4ac2a9b73c6393bc19a2613 SHA1 dc40f7a9d06946a7b18e0f84c14ec202a977dda0 SHA256 5b8815554a34f68e003c8f97a0d3cd549ef9c59845346b62ea98582968ff287d +EBUILD libcmatrix-3.2.1.ebuild 944 RMD160 7a3e0d62ae428c795f08604067d8bfcaa9e72e66 SHA1 78883565cf0f607451beecdeadea789efb24a4b3 SHA256 1a85078c61d53b5287a8c83a9151ef7b466c001337d701cc519ba787745f8c01 MISC ChangeLog 651 RMD160 c88318fc93f9fde3574d46810ff1a2b52b4f321b SHA1 ecae9b193aae911a853089bb6bd449b21a437bac SHA256 40156a04cffbb8b590c6b8d84aab489c62a20d8302f93e6147082507f0cf4a3c MISC metadata.xml 289 RMD160 f7c50f619a03ac5b5b26a51d70d2d39191105be6 SHA1 22712dad3f58dc9785e31641677156e9bde1f680 SHA256 e8611598809c2edefcdd6eaa8ab23448c45683a2a9ccfd4b8bfe0c7fd628d81c -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.11 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkruyZYACgkQgAnW8HDreRZcdACeP92sKWDbSccZhryjqqJm4r1f -rscAn3rqm0RM/UCe85nXvIzgd83KsPiY -=HZik +iEYEARECAAYFAk4EprkACgkQgAnW8HDreRYwFwCfb+CY6Haqwzo2I84c772FFoJ/ ++DYAn3X/nODppvcrxVuBnxdF5FPNAkoT +=gBSG -----END PGP SIGNATURE----- diff --git a/sci-libs/libcmatrix/libcmatrix-3.2.1.ebuild b/sci-libs/libcmatrix/libcmatrix-3.2.1.ebuild index ecfe08cb4..684fa1767 100644 --- a/sci-libs/libcmatrix/libcmatrix-3.2.1.ebuild +++ b/sci-libs/libcmatrix/libcmatrix-3.2.1.ebuild @@ -4,7 +4,7 @@ EAPI="2" -inherit eutils autotools +inherit autotools eutils MY_P="${PN}${PV}_lite" diff --git a/sci-libs/libfac/ChangeLog b/sci-libs/libfac/ChangeLog index bd7a01c57..5ec780e86 100644 --- a/sci-libs/libfac/ChangeLog +++ b/sci-libs/libfac/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-libs/libfac -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> libfac-3.1.0.ebuild, + libfac-3.1.1.ebuild, metadata.xml: + Cleaned ebuild and add USE description to metadata.xml + *libfac-3.1.1 (07 Jul 2010) 07 Jul 2010; Thomas Kahle <tom111@gmx.de> +libfac-3.1.1.ebuild: diff --git a/sci-libs/libfac/Manifest b/sci-libs/libfac/Manifest index 5502e6566..0459cd803 100644 --- a/sci-libs/libfac/Manifest +++ b/sci-libs/libfac/Manifest @@ -1,6 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST libfac-3-1-0.tar.gz 91544 RMD160 2500d402328ad532756c677015c1d01f8594e394 SHA1 d005ddd58a180b8a91fe5728b96bde515c5d9cc5 SHA256 fc3dda08f7ec039635f8d7f1629546f4ac7620a69cf9332ca39e29dd822aee7d DIST libfac-3-1-1.tar.gz 90104 RMD160 8ca086ad2dc1dfbf3d8824e244f0b1af087eef62 SHA1 3753363a6f56cfeb0d0be3bdf471d6bd55c14ede SHA256 4c463af2d22375aa62be4fb1f9a32cada6723ca5e3ddbd8a4f5cab72b675e33a -EBUILD libfac-3.1.0.ebuild 773 RMD160 2a74bd918c368b90390acc9eed8ab6229fd314f1 SHA1 66f3fe2a2f5f3bd6e69ffbb934d1bccce5afbcb9 SHA256 33486f00a13b78761d15c808c4f23393e4c767badbd6981893e7359bc446b457 -EBUILD libfac-3.1.1.ebuild 800 RMD160 fa8b7fd04f588991cb05ac209013b585a2e1c5ab SHA1 dc1cdd00016098a63c4b1a51467ee5bede01e085 SHA256 8ff26721c47cbebcfa49ff0d64d80bcb02e557b7eaefc85d34178b65aaaa1c28 -MISC ChangeLog 525 RMD160 dda8e981a681e9b43a893221f4f3fa864279023b SHA1 b4b02d6cf845c9a1aa86a06627a34f96af7fc092 SHA256 c4541bcbe2ec96c073bf1b3a2bc1612a00a54f4b161ba1668eaef23b8a6d7ef7 -MISC metadata.xml 345 RMD160 0710d4b1fc38dd54c329d2ab6050281a509d01d0 SHA1 e0501bc143413205459d24ce3f349467c111d0e9 SHA256 e154449982e54693b58f0aece8ee96100445981e98194e27c453559619babe60 +EBUILD libfac-3.1.0.ebuild 687 RMD160 4a1e24011cef3785b9e8a692f665ae10de630652 SHA1 ba4ce11646a5d804a630740a7d98202b94a8d1e5 SHA256 b9f5433f498e9c0decd0923f4052b4563d26bdcb8e4cce2dfca7a90e86f9d4a4 +EBUILD libfac-3.1.1.ebuild 687 RMD160 4a1e24011cef3785b9e8a692f665ae10de630652 SHA1 ba4ce11646a5d804a630740a7d98202b94a8d1e5 SHA256 b9f5433f498e9c0decd0923f4052b4563d26bdcb8e4cce2dfca7a90e86f9d4a4 +MISC ChangeLog 688 RMD160 7d0af838ca8a3955e50efa742a4ef7f76c07d3fc SHA1 b6c4887782761ec03096177b3993baa672f7ec4f SHA256 53f77d3e189faa4eb4cb6631178605fcd8d4e440190543e51c2693ed54aa356a +MISC metadata.xml 448 RMD160 1f67b3b38f8d95cfd33a71ad8d856fd5729add67 SHA1 d26896eb8764ba4b412cd789bcab468b330dca84 SHA256 44f52e08ec50381c7e8db8b0d7016b9244d9008d897733556fa5a3689fcd14c4 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F2pIACgkQgAnW8HDreRZVxACeJgrtTfuPSZBhDAWqs0uOJ1Ah +KNcAn1BbYbstt6X4UwKotugNTCeZKbDp +=qjdK +-----END PGP SIGNATURE----- diff --git a/sci-libs/libfac/libfac-3.1.0.ebuild b/sci-libs/libfac/libfac-3.1.0.ebuild index e49d00954..16a3ba378 100644 --- a/sci-libs/libfac/libfac-3.1.0.ebuild +++ b/sci-libs/libfac/libfac-3.1.0.ebuild @@ -1,36 +1,31 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=2 -inherit eutils -DESCRIPTION="libfac is an extension of Singular-factory to finite fields" +inherit eutils versionator -HOMEPAGE="ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/" +MY_PV=$(replace_all_version_separators '-') -SRC_URI="ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/libfac-3-1-0.tar.gz" +DESCRIPTION="libfac is an extension of Singular-factory to finite fields" +HOMEPAGE="ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/" +SRC_URI="ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/${PN}-${MY_PV}.tar.gz" LICENSE="GPL-2" SLOT="0" KEYWORDS="~x86 ~amd64" - IUSE="singular" -DEPEND="singular? ( sci-libs/factory[singular] ) - !singular? ( sci-libs/factory[-singular] )" - +DEPEND=">=sci-libs/factory-${PV}[singular=]" RDEPEND="${DEPEND}" -S="${WORKDIR}/libfac" +S="${WORKDIR}/${PN}" -src_compile() { +RESTRICT="mirror" + +src_configure() { econf --prefix="${D}/usr" \ - $(use_with singular Singular) || die "econf failed" + $(use_with singular Singular) - emake all || die "make failed" } - -src_install() { - emake install || die "Install failed" -}
\ No newline at end of file diff --git a/sci-libs/libfac/libfac-3.1.1.ebuild b/sci-libs/libfac/libfac-3.1.1.ebuild index eb44b9ea5..16a3ba378 100644 --- a/sci-libs/libfac/libfac-3.1.1.ebuild +++ b/sci-libs/libfac/libfac-3.1.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -10,30 +10,22 @@ MY_PV=$(replace_all_version_separators '-') DESCRIPTION="libfac is an extension of Singular-factory to finite fields" HOMEPAGE="ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/" - SRC_URI="ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/${PN}-${MY_PV}.tar.gz" LICENSE="GPL-2" SLOT="0" KEYWORDS="~x86 ~amd64" - IUSE="singular" DEPEND=">=sci-libs/factory-${PV}[singular=]" - RDEPEND="${DEPEND}" S="${WORKDIR}/${PN}" RESTRICT="mirror" -src_compile() { +src_configure() { econf --prefix="${D}/usr" \ - $(use_with singular Singular) || die "econf failed" + $(use_with singular Singular) - emake all || die "make failed" } - -src_install() { - emake install || die "Install failed" -}
\ No newline at end of file diff --git a/sci-libs/libfac/metadata.xml b/sci-libs/libfac/metadata.xml index 5530938b0..2808e858e 100644 --- a/sci-libs/libfac/metadata.xml +++ b/sci-libs/libfac/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> -<email>tom111@gmx.de</email> -<name>Thomas Kahle</name> -</maintainer> -<longdescription lang="en"> + <herd>sci</herd> + <maintainer> + <email>tom111@gmx.de</email> + <name>Thomas Kahle</name> + </maintainer> + <longdescription lang="en"> libfac is an extension of Singular-factory to finite fields </longdescription> + <use> + <flag name="singular">Automatically generated description for singular</flag> + </use> </pkgmetadata> diff --git a/sci-libs/libxc/ChangeLog b/sci-libs/libxc/ChangeLog index 21317e989..3b4cab98e 100644 --- a/sci-libs/libxc/ChangeLog +++ b/sci-libs/libxc/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> libxc-1.0.ebuild, + libxc-9999.ebuild: + Added fortran-2.eclass support + 15 Mar 2011; Justin Lecher <jlec@gentoo.org> libxc-1.0.ebuild, libxc-9999.ebuild, +metadata.xml: Remove fortran.eclass diff --git a/sci-libs/libxc/Manifest b/sci-libs/libxc/Manifest index 81b26589e..a05ee2553 100644 --- a/sci-libs/libxc/Manifest +++ b/sci-libs/libxc/Manifest @@ -2,14 +2,14 @@ Hash: SHA1 DIST libxc-1.0.tar.gz 502757 RMD160 0e48a6ab484d1c9f6e305dfc9c860e46c01aa330 SHA1 48a54c718bfb8784bf5e6aadf82d62ffb70bc5a2 SHA256 890544853fc8ff81d895fc973b5f1ed293f957b035301aad2d6caea1ce1efdaa -EBUILD libxc-1.0.ebuild 1210 RMD160 4f4136c711076fcc4db7bc63827f0609bab0c7d7 SHA1 f5e1fdb5ae80fe727c451bb424e91e7976f0e74f SHA256 4cf023aec988df62084a29a17c1709ba65a1150695da508ee3c4d46f62281595 -EBUILD libxc-9999.ebuild 943 RMD160 ff22af8d94aa716eeff045c7ac3806e67a56e1e6 SHA1 dd9f6fc0653d96be6436fa546378b2cba302449b SHA256 2edb825668bc3a13f7c37259cb6e4729c3412bd93180fe0254546bededfa6349 -MISC ChangeLog 544 RMD160 60919b013c5dd49e84b8bb60787648d088c491e4 SHA1 0a47dc1d503a03dde49ef89b1b7ab084c18b4d84 SHA256 1537205a815bf42ac7e846c8349656f56ae244040ecc9477de24798b76d9f721 +EBUILD libxc-1.0.ebuild 1162 RMD160 5674df7a4941c3b32c24244ba8ea753d7a3da1b1 SHA1 4378ca34fe816d5b05c9e2d13fa5228f5ad26367 SHA256 093d4e23b4990a1d8b5b0f651fb8f7ec47ea4220a7cb9c0d3843359dbc492c69 +EBUILD libxc-9999.ebuild 885 RMD160 13f5478d73d625aea9c382ddfeb5d18870c2fb82 SHA1 cfd09fb873970f87acc8d7a5ef3a72c403257162 SHA256 500d9aa1a88b7fdec449c387e2f95af8dc79a8f1c9921e6a0ee7d993bfaeaf01 +MISC ChangeLog 664 RMD160 540f87d17d93d72e703f2ca2c93cc91425b94be1 SHA1 2bf6bbd99b794b61e21db3a38c863d2539fa508b SHA256 448d453379d393c10f108f3a1c9784d8331744f7c522104d3d8e2dc21ce09686 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk1/PiYACgkQgAnW8HDreRZhoACgyQOpIOaj6sphn+PDlGML3Sod -aWgAnAngQ2GhNlviZ51rrG9jhFXg7MZk -=QInv +iEYEARECAAYFAk4Epr8ACgkQgAnW8HDreRaSNgCeP0txCpts+nC6aVEeCQ/0JmIs +16YAnRilcdP6156yILIDeXQ+Zs+ter8O +=vszm -----END PGP SIGNATURE----- diff --git a/sci-libs/libxc/libxc-1.0.ebuild b/sci-libs/libxc/libxc-1.0.ebuild index a7520b1d8..576307c38 100644 --- a/sci-libs/libxc/libxc-1.0.ebuild +++ b/sci-libs/libxc/libxc-1.0.ebuild @@ -2,14 +2,14 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=3 -inherit multilib toolchain-funcs +inherit fortran-2 multilib toolchain-funcs MY_P=${P//_/-} DESCRIPTION="A library of exchange-correlation functionals for use in DFT" -HOMEPAGE="http://www.tddft.org/programs/octopus/wiki/index.php/Libxc" +HOMEPAGE="http://www.tddft.org/programs/octopus/wiki/index.php/Libxc/" SRC_URI="http://www.tddft.org/programs/octopus/download/${PN}/${P}.tar.gz" LICENSE="LGPL-3" @@ -17,13 +17,7 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="fortran" -S=${WORKDIR}/${MY_P} - -pkg_setup() { - if use fortran ; then - tc-export FC - fi -} +S="${WORKDIR}"/${MY_P} src_configure() { econf \ diff --git a/sci-libs/libxc/libxc-9999.ebuild b/sci-libs/libxc/libxc-9999.ebuild index 14fdb4026..761f43f3f 100644 --- a/sci-libs/libxc/libxc-9999.ebuild +++ b/sci-libs/libxc/libxc-9999.ebuild @@ -2,26 +2,20 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=3 -inherit eutils multilib toolchain-funcs flag-o-matic autotools subversion +inherit autotools eutils flag-o-matic fortran-2 multilib subversion toolchain-funcs -DESCRIPTION="The ETSF library of exchange-correlation functionals" +DESCRIPTION="A library of exchange-correlation functionals" HOMEPAGE="http://www.tddft.org/programs/octopus/wiki/index.php/Libxc" ESVN_REPO_URI="http://www.tddft.org/svn/octopus/trunk/${PN}/" ESVN_BOOTSTRAP="eautoreconf -i" LICENSE="LGPL-3" SLOT="0" -IUSE="fortran debug" +IUSE="debug fortran" KEYWORDS="~amd64 ~x86" -pkg_setup() { - if use fortran ; then - tc-export FC - fi -} - src_configure() { econf \ $(use_enable fortran) \ diff --git a/sci-libs/lpsolve/Manifest b/sci-libs/lpsolve/Manifest index 1abd39ee4..77f6e2655 100644 --- a/sci-libs/lpsolve/Manifest +++ b/sci-libs/lpsolve/Manifest @@ -1,23 +1,13 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA1 DIST lp_solve_5.5.2.0_source.tar.gz 799623 RMD160 23a69c71062747ddf4cbc57120cd7db5f9378ac2 SHA1 e2830053cf079839b9ce21662cbc886ac6d31c80 SHA256 5827a30b143105283f398a09419ea608719a2d7699ecea165a66d521803bcc9c -EBUILD lpsolve-5.5.2.0.ebuild 1192 RMD160 dbd4c04433038874030a499b6547729c9609a4b1 SHA1 7e93271b555cd245bbbad825b92dfcf84e131583 SHA256 6f95a46c8d0494519a9515603791fd4acb4e8b3ed4bda12e9096d6b9ac77ce95 +EBUILD lpsolve-5.5.2.0.ebuild 1192 RMD160 02eea6deb92a6efd156128f7a91d39b98aa1a43d SHA1 4191160324fd756a03317188563a3da706db1145 SHA256 e08475e973b514805c8cdb2c2f19453d1f7a8624998b7d62120ae86494fc72f0 MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBCAAGBQJNLFHAAAoJEOf+E+/4L5LmPdMP/A9LuXK0vCaIYdn52sFyjL0I -txG7LGjwP1gJXLT/97H1tNWlVcYd9CN86cxJ8mCdl/8KWK+UcU/pfsIeJRJiVUJD -PRxq9/UVZQeT8QVvNExD0gIDDqa+4T9f8/yQhYUEC1MZ9/nAcXy2VP4d8R9Wzf+s -nWYmGMFGebQ9LFdQdEn4sHnseAXAgjMSqFFIoP3MquR+7QiFgYITgYmrlLtxNekI -JuBCMCysxAJHeeA1prEOiPoCgYrKGUlkX98S9QZdiSd52KY2giqEFgPBB5GAfWZC -Emd1iwMo8jSyMfuyCEfLbqRkQ6SVoRFjVfbYIfG2kLnTIxze0Sb/wkRIPozr2P5P -nh+LYlE57BaTh8wGaKF/e0oZ8rX+GwJ7Dz25JTHwqlc/VgD4Iv8Rs5E1MiLjFC9w -8Fvh9bTggMiVrQ1mEXv7Am9Ew1w+hb/cktqcH+kjM+NU60KUe7PFymlcQRBm9zHz -IJyO4TX5qdexuU2DnYW9l5xlGW5Q+87Ja3EdZ9bxVHMNOuKsNCSnew7HaJoHeRt6 -Vi0ipfjIEp9X5SWXL++3kOppNfbrqyj6yvfKrBUYgsUqSO8mO/DzXc4f472SKPS3 -Jpm0JKw4Ee/sI4n8D1rvmRS8KRRGCbgvwsXul4uxheNOAO0zx/mm8dmpl28lZOuW -1yJPtawJY5NVAGOd3l8w -=d7al +iEYEARECAAYFAk4EpsQACgkQgAnW8HDreRYscwCgoVB2b8u08en/66nveFmt62EM +OFoAnRaIuv3nudxbGM2+PFeVGF6V/Hn+ +=Zt0G -----END PGP SIGNATURE----- diff --git a/sci-libs/lpsolve/lpsolve-5.5.2.0.ebuild b/sci-libs/lpsolve/lpsolve-5.5.2.0.ebuild index 6a1782077..423e29f9b 100644 --- a/sci-libs/lpsolve/lpsolve-5.5.2.0.ebuild +++ b/sci-libs/lpsolve/lpsolve-5.5.2.0.ebuild @@ -15,7 +15,7 @@ LICENSE="LGPL-2.1" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="static-libs examples" +IUSE="examples static-libs" DEPEND="" RDEPEND="${DEPEND}" diff --git a/sci-libs/matio/ChangeLog b/sci-libs/matio/ChangeLog index 37c11651a..620f108b5 100644 --- a/sci-libs/matio/ChangeLog +++ b/sci-libs/matio/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/matio -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> matio-1.3.4.ebuild: + Added fortran-2.eclass support + *matio-1.3.4 (10 Aug 2010) 10 Aug 2010; Sébastien Fabbro <bicatali@gentoo.org> -matio-1.3.3.ebuild, diff --git a/sci-libs/matio/Manifest b/sci-libs/matio/Manifest index 0edd5d54d..5ad9bae84 100644 --- a/sci-libs/matio/Manifest +++ b/sci-libs/matio/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX matio-1.3.4-autotools.patch 1087 RMD160 996771a8d033247fb701356a96b71ea56c5cb97f SHA1 0ae3f6e5e75ae0c211ab43ef4b7ac6d3948d107e SHA256 37a572925ae026e42b682b1a816ed0094e7e906b76bdde098e775b5d1c203f7c DIST matio-1.3.4.tar.gz 450343 RMD160 3a0f2fe1260e48af0fb9e501d0af1383cefe5dd3 SHA1 721b9b57f2437850dd114acca1f422622e2c47e2 SHA256 7261880b18a661e5d206b4e479d4334b47549f093130df42f7204fd05dfe0bc5 -EBUILD matio-1.3.4.ebuild 1127 RMD160 98bb6afc3c1361a100b3f392102f3ed8d618b1e5 SHA1 88d02c1c3f5a5a2de6e54f377e3f23befa584ebc SHA256 4d5c6ae5206abfb30d2831c2d53577b2ccc5b0dae41c8fd349e769e26f20ba07 -MISC ChangeLog 1144 RMD160 4d8c5db6e907cc1e57914ab22403d11cd56abdf7 SHA1 3ca196ded85f063d56f837c129d3504fdcfdba36 SHA256 a713f381d19c65654805b02e2b2e5f5699bf3aada7f07c931ca4e81d588a7f4e +EBUILD matio-1.3.4.ebuild 1137 RMD160 31af7426cc36f49b7bc8c7520c9dd8b86b9e131b SHA1 61aa6153a4e60a28de3804b7774b23ddd7c8c5c7 SHA256 4336d02f6576e965ecded9063b23feae429b4d765275d2f24050ef76622e48f4 +MISC ChangeLog 1245 RMD160 0abc9f5d822021fd74a82ab2c063477f966cb255 SHA1 c77af000c7a63636683baf33ebd7f6f57d2caf55 SHA256 63c0d11c15a3410fa960c87304195ff6f144b1133665cbd20f9cc1f9b2a9aa12 MISC metadata.xml 313 RMD160 974b1335daa5b99cc1afc3d1592ca45e64b12259 SHA1 0e01789e32462b40a3d646d9de831a5987de65d2 SHA256 d7d339f2978f3b717d87eeffa70343181e30d19b42a74a498291bf641353e9aa +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EpskACgkQgAnW8HDreRa51wCdE/DlmjYo113U0yrTVmMZJ0RN +iWgAn33gXhWNaLFpNNcgFX0n237pi1St +=eY9P +-----END PGP SIGNATURE----- diff --git a/sci-libs/matio/matio-1.3.4.ebuild b/sci-libs/matio/matio-1.3.4.ebuild index 9cd4fc1aa..a04795358 100644 --- a/sci-libs/matio/matio-1.3.4.ebuild +++ b/sci-libs/matio/matio-1.3.4.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=3 -inherit eutils autotools +inherit autotools eutils fortran-2 DESCRIPTION="Library for reading and writing matlab files" HOMEPAGE="http://sourceforge.net/projects/matio/" diff --git a/sci-libs/modglue/Manifest b/sci-libs/modglue/Manifest index 4b15dad8f..56989d6be 100644 --- a/sci-libs/modglue/Manifest +++ b/sci-libs/modglue/Manifest @@ -5,13 +5,13 @@ AUX modglue-1.16-ldflags.patch 687 RMD160 32369f6aebc57f065dffc41942e45f4b9e6789 AUX modglue-1.16-lib64.patch 2145 RMD160 704320cca279e61366268675b0cca3af69843c26 SHA1 14a670705faa25ed4f59cf31cb6d0cb12a15e131 SHA256 2c3526bc68405feaba50caa00c7e04f1ea2579cdcc4565532085b90c2480ee95 AUX modglue-1.16-parallelmake.patch 1475 RMD160 57d087fa3d8cda09bf9bc420a01196e928f5c4c5 SHA1 1deb19735157281c22b8f17251c67f4053917c92 SHA256 110d385e42b4013b0cf8cdb1c7b74d1c103e12ad79eb7264b367d6a126b8e5ec DIST modglue-1.16.tar.gz 89987 RMD160 46e0ee58004dfbdcc34862d73ec85d699b2dece0 SHA1 3f47c261c81fdd0ff4ba2dc7958dd4d83dcffd1b SHA256 1da62910d7171cb5547c0757c366e5338f889c0155c33375e891df75e2ee429e -EBUILD modglue-1.16.ebuild 1166 RMD160 c9279fdb40d9d3b0c4e0c0220d4d1ea352250997 SHA1 25e3f23fa9ed7324a859a3d0681695a2e506581a SHA256 4c70b3afa9999d95217fb56c4442b531035ef1f91a422ea0336310c3c4f38775 +EBUILD modglue-1.16.ebuild 1166 RMD160 f1638397c70ac1bb01b32661b895aa7fa06cd011 SHA1 faeb71bb9b63aa7f284eac30cd493745b0fcd40c SHA256 b1708a068b5415069814c6ee19c91c80408e6e89581f2ab33501fb0024d61cee MISC ChangeLog 1366 RMD160 52187fd93e1d5350c430c986f3828d6b281da87b SHA1 17959b6a615465c02d9064dc621895867f6ba9b2 SHA256 6802a422573bb7890c3924d0563685e16e49a82cac9bfd79838ca322764320d7 MISC metadata.xml 885 RMD160 34165bffafd7c55b7d84155b39bd32a1251e6aa7 SHA1 6386d45d76662564b2f064fe1379d7cf69b83c3f SHA256 930e55dd4ad9b6e93ca69134cd181210c6bf6c114a4b9a7a6200ea47ee465eb4 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk10vJwACgkQgAnW8HDreRZFyQCg0itc+rEp+xEcvu0IoHAIkNHE -FtkAoMAEEXq2xT4Njo92BchLtsXgpQ8x -=oeFx +iEYEARECAAYFAk4Eps8ACgkQgAnW8HDreRb2bgCgoIdouTClW2ITnVmDUIuulQ1n +lAAAniUnusqLRWsIqLWzu+a7dDiQSBgQ +=g/jD -----END PGP SIGNATURE----- diff --git a/sci-libs/modglue/modglue-1.16.ebuild b/sci-libs/modglue/modglue-1.16.ebuild index 8a83cce7c..aea46ea38 100644 --- a/sci-libs/modglue/modglue-1.16.ebuild +++ b/sci-libs/modglue/modglue-1.16.ebuild @@ -4,7 +4,7 @@ EAPI="3" -inherit eutils autotools-utils +inherit autotools-utils eutils DESCRIPTION="C++ library for handling of multiple co-processes" HOMEPAGE="http://cadabra.phi-sci.com" diff --git a/sci-libs/nfft/Manifest b/sci-libs/nfft/Manifest index bb28e126f..667b06d5a 100644 --- a/sci-libs/nfft/Manifest +++ b/sci-libs/nfft/Manifest @@ -4,13 +4,13 @@ Hash: SHA1 AUX nfft-3.1.3-install.patch 455 RMD160 5acbfcddfe923036e5e47c2317a017b30a31a838 SHA1 6e19ec569811996efe2f1955bbb090b0efe20a75 SHA256 6e5e0d9c5c839e228109fc1386e146bb8ba6a549701eaaf527b5aa60a2b369fa AUX nfft-3.1.3-remove-maintainer-mode.patch 2810 RMD160 70925c0a1583b651383369edc2ae4934e282005c SHA1 26a1febeca6a2e729e2796068b7964c3b49e55c2 SHA256 acecf6ed6fda98fd7d104908036a1f4f166721f68469f54e9267c9ea349f7b6f DIST nfft-3.1.3.tar.gz 1659745 RMD160 fd43df4bf42e464caccdf10eeb5b9c55e9c7920e SHA1 45ce0e0ae3eeb49ccb2f3ba37b8ad427f08cf9ac SHA256 e4f65f0d1aa81cf76a506f10a9ac68bdcd770a4426671274d372101dca497382 -EBUILD nfft-3.1.3.ebuild 941 RMD160 1fff109b30c70561218f5adf02049455e8f3290b SHA1 4c2deadc3c0dc0e10eff5b610a3d183307ceeef7 SHA256 21d38aa8e255dc686f15e006720a17e971d9a56a0b302efbf300a274e11c713c +EBUILD nfft-3.1.3.ebuild 941 RMD160 858b0d9dcc60120f0886240a0619fcbb0fcb6c3a SHA1 1712b642f148151f100945652e79b9082a0fe6c8 SHA256 4a286c77ae114f8eac79facf21fc519bc61e0c08757f9b7569e38375ae9aa293 MISC ChangeLog 335 RMD160 6808f9942e76ad6aa56ea371e9f83c07e48efeec SHA1 b409a433b292634ceb5bf370a3df56bfb389d8d8 SHA256 8a56adce98da9d02bb579988a4c54ad08707a130009cc5128d4ddf5de499d13b MISC metadata.xml 256 RMD160 53a5d04f6246118e052c9cae27b7070de9b88529 SHA1 563e3277f01cc3bf484d46a6da50719855a5a689 SHA256 e683c0d7d2051297085cdbb7444ce887044c7ed0ba02cf04be170cdf62919c74 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkyNIaoACgkQy0OE/ans1/l8HQCdGwMClhqdXoVpBEid/WvjEzJ2 -iaMAn0RIgpVD5dSLeaCTqG6O76v/KoNX -=aYE3 +iEYEARECAAYFAk4EptQACgkQgAnW8HDreRZCRgCeLFPdA+mbFMf5wYkUL9WTsk9/ +kJ4Ani90i/r8NL5LO5LZnlYWiIjKPSqI +=y2R8 -----END PGP SIGNATURE----- diff --git a/sci-libs/nfft/nfft-3.1.3.ebuild b/sci-libs/nfft/nfft-3.1.3.ebuild index 18714bec0..eb5f5a4f9 100644 --- a/sci-libs/nfft/nfft-3.1.3.ebuild +++ b/sci-libs/nfft/nfft-3.1.3.ebuild @@ -4,7 +4,7 @@ EAPI="3" -inherit eutils autotools +inherit autotools eutils DESCRIPTION="library for nonequispaced discrete Fourier transform" HOMEPAGE="http://www-user.tu-chemnitz.de/~potts/nfft" diff --git a/sci-libs/omalloc/Manifest b/sci-libs/omalloc/Manifest index cbc818bd6..ca12225de 100644 --- a/sci-libs/omalloc/Manifest +++ b/sci-libs/omalloc/Manifest @@ -1,6 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX omalloc-0.9.6-gentoo.diff 4699 RMD160 1ccc067a58957b24b02f80cb0629892179a87205 SHA1 452e8a90d7bd34207e0bec260310244c98cfd57e SHA256 00b1e2b0de32f2cf99ffc443fa2e37f0e514b790bf248238698b4bbe5cc8a113 AUX parallel-build.patch 900 RMD160 1236c0c03b5209d782edf33bde30e10cefb71636 SHA1 f8aef60f60b890a63680d0276bce03b7070ba19d SHA256 f48cf0af887189c4a427e1b65d4b13962e11987b57d6b82eee06e85f85828f3e DIST Singular-3-1-1-2.tar.gz 19397418 RMD160 205671f1ea2e2f22c025defc3d85c762362c7e3f SHA1 217af7a4e9b36b769a145bf81fb27c49d64333f6 SHA256 4e5929b324f952c69de1dedddbeca1c51a3733a0f63e026d3e7b61a7e469d5a7 -EBUILD omalloc-0.9.6.ebuild 953 RMD160 6724842392978fa39e77b95d2d510eb2d3365fd0 SHA1 8f866ee5c5273ccee84b31bebfb22eb40af3cfa6 SHA256 a150c6abc6c9839423016b1aceb766652b56ceaa3998b0922e5a2f4350b070a7 +EBUILD omalloc-0.9.6.ebuild 953 RMD160 a30d804671a7b61f5e9934d54081c303775f8feb SHA1 3698a71ab0566c0e33b52c837c29fc2515f3cd36 SHA256 01a31b93084f7257df5b3de0deb41a2e4b05a52d5513fdd693721c7a89034ae7 MISC ChangeLog 544 RMD160 b9826ba26f551059127b5caf3917d5629a1a4d3c SHA1 f2e0c529445d02f600ee6b533cbca86f960af72c SHA256 fc2bfee3785cb54079f95aef9fad121707bedfacc04031e151294330aa03dfcb MISC metadata.xml 330 RMD160 c8055f309c938468c7c0af9279c734fe40c7ac0d SHA1 2f4244a2e40645277e94692be694f5feac2c2c6c SHA256 802e41cbccd2d4b549736141e341590687775e678bf3ace3524027ff5beed136 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EptsACgkQgAnW8HDreRZgjwCgihG16ABrq6u01G19UzLWmvnD +mewAnRQMejhzFNLGDX0Js0JW1ATiO9lZ +=zzXy +-----END PGP SIGNATURE----- diff --git a/sci-libs/omalloc/omalloc-0.9.6.ebuild b/sci-libs/omalloc/omalloc-0.9.6.ebuild index b860d2c95..b3ac452a8 100644 --- a/sci-libs/omalloc/omalloc-0.9.6.ebuild +++ b/sci-libs/omalloc/omalloc-0.9.6.ebuild @@ -4,7 +4,7 @@ EAPI="2" -inherit eutils versionator toolchain-funcs +inherit eutils toolchain-funcs versionator Sing_PV=$(replace_all_version_separators -) Sing_DIR=$(get_version_component_range 1-3 ${MY_PV}) diff --git a/sci-libs/pagmo/ChangeLog b/sci-libs/pagmo/ChangeLog new file mode 100644 index 000000000..87b76c3fb --- /dev/null +++ b/sci-libs/pagmo/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-libs/pagmo +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> pagmo-9999.ebuild, metadata.xml: + migrate from 'git' to 'git-2' + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> pagmo-9999.ebuild, + +metadata.xml: + metadata.xml added + diff --git a/sci-libs/pagmo/Manifest b/sci-libs/pagmo/Manifest index 0a62ed106..4fe340408 100644 --- a/sci-libs/pagmo/Manifest +++ b/sci-libs/pagmo/Manifest @@ -1 +1,13 @@ -EBUILD pagmo-9999.ebuild 887 RMD160 4c9f301299d663468dfc64b13fa76c1db1c559c3 SHA1 2c608caa9a20559de1c53fb7d5bd015707e3f443 SHA256 f836edbbdaaf3072b8a0b3e5247b2f02c1be4564425a379ead3804ff9643e841 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +EBUILD pagmo-9999.ebuild 890 RMD160 e6997925ce6379837eab3cd1a33bcd322a6f88f6 SHA1 fbbbd77964277ff3c096f3d3c4e74d963093678f SHA256 c7b02a82518a67d637fad9af830e4f5531a3f628c8cceab7543276931d754d2a +MISC ChangeLog 333 RMD160 ddc8ce772542d69b067086c84c87e6abc4917cc2 SHA1 e40795fa388cfb808cdbd4e4a2397e4ae3dd74db SHA256 9c1eeee3511049645345e099fa99dda7f908e5c7a4202bd7e345c653ecd6f3a2 +MISC metadata.xml 383 RMD160 fd20dd12e672349610a84e35fde5af73bf996e84 SHA1 dae88f0d10064f7a4a79763b9ef7bf9e25e81f6d SHA256 0bfb42bea7e0e4040b308dae16a2973e4cb5a1d5bb084b1b583d488823fceb19 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GCNUACgkQgAnW8HDreRbZ/wCgqc+FhLOF9/xOOxzgCYG5zZTO +aNwAnA5+MzaL3AGymWIqtm8V8aIpM4jp +=Qj6R +-----END PGP SIGNATURE----- diff --git a/sci-libs/pagmo/metadata.xml b/sci-libs/pagmo/metadata.xml new file mode 100644 index 000000000..ce5ca8e2f --- /dev/null +++ b/sci-libs/pagmo/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <maintainer> + <email>sci@gentoo.org</email> + </maintainer> + <use> + <flag name="kepler">Automatically generated description for kepler</flag> + <flag name="nlopt">Automatically generated description for nlopt</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/pagmo/pagmo-9999.ebuild b/sci-libs/pagmo/pagmo-9999.ebuild index 8a898fc1e..cd1bca3b1 100644 --- a/sci-libs/pagmo/pagmo-9999.ebuild +++ b/sci-libs/pagmo/pagmo-9999.ebuild @@ -1,23 +1,25 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" -inherit cmake-utils git +EAPI=4 + +inherit cmake-utils git-2 DESCRIPTION="Parallelization engine for optimization problems" HOMEPAGE="http://pagmo.sourceforge.net/" -EGIT_REPO_URI="git://pagmo.git.sourceforge.net/gitroot/pagmo/pagmo" SRC_URI="" +EGIT_REPO_URI="git://pagmo.git.sourceforge.net/gitroot/pagmo/pagmo" LICENSE="GPL-3" SLOT="0" -IUSE="gsl kepler mpi nlopt python test" KEYWORDS="~amd64 ~x86" +IUSE="gsl kepler mpi nlopt python test" -RDEPEND="dev-libs/boost[mpi?,python?] - gsl? ( sci-libs/gsl ) - nlopt? ( sci-libs/nlopt )" +RDEPEND=" + dev-libs/boost[mpi?,python?] + nlopt? ( sci-libs/nlopt ) + gsl? ( sci-libs/gsl )" DEPEND="${RDEPEND}" src_configure() { diff --git a/sci-libs/pfft/ChangeLog b/sci-libs/pfft/ChangeLog index 0de13e649..4ba70e34b 100644 --- a/sci-libs/pfft/ChangeLog +++ b/sci-libs/pfft/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/pfft -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> pfft-1.0_alpha1.ebuild: + Fixed Manifest and cleaned ebuild + 15 Sep 2010; Christoph Junghans <kleiner_otti@gmx.de> pfft-1.0_alpha1.ebuild, files/pfft-1.0alpha1-Makefile.am, files/pfft-1.0alpha1-configure.ac, +files/pfft-1.0alpha1-libpfft.pc.in: diff --git a/sci-libs/pfft/Manifest b/sci-libs/pfft/Manifest index ee4d1d5b7..2a9c461fe 100644 --- a/sci-libs/pfft/Manifest +++ b/sci-libs/pfft/Manifest @@ -5,13 +5,13 @@ AUX pfft-1.0alpha1-Makefile.am 594 RMD160 52dd29a74c0449e08e3a0ed901b20d0ee1dfa1 AUX pfft-1.0alpha1-configure.ac 1166 RMD160 44e2c18eb5cd41c51c263ede72cb2e6e10b5dbc7 SHA1 a805dee3a82968fd453ae3c8845fec34256398a7 SHA256 bde312db82ab7f4c90f73749baef4affbf3b69650feb78e9f23fff25c131dfaf AUX pfft-1.0alpha1-libpfft.pc.in 286 RMD160 06fae27f51eda49d3fb5d51b3871080a192dcd49 SHA1 dd61a3fab7df5901f608c8d836b551dbf27955ac SHA256 596058e43e945bbc06752161dbd94ed11b2e2b3b751fbd43fd0c5da705a0625d DIST pfft-1.0alpha1.tar.gz 29635 RMD160 b17066560d267f2b58a7b10a7db47c8c72e5c545 SHA1 bdd35a2dae1e1a1d9177f1e5a238fe6ce38f4b64 SHA256 83e201717506e0857bb4c6f986a6b9e98ea418d05454a34914175e61d0b3b395 -EBUILD pfft-1.0_alpha1.ebuild 912 RMD160 6c69c58da70f499dc5e6ab040c56f98e2f80a1d1 SHA1 ff0a79dab2d6092d8127b978f76d25e2a2c678e1 SHA256 3397c2779b86e9c81ded4264658bd8537c39a2f7402b82509be02aa98e369509 -MISC ChangeLog 576 RMD160 1dfeab5d7166efa32d85943ee00a333fb949a59a SHA1 f2870e245178acb697bdfc9b311ee4d20723d940 SHA256 77253e68892931283d2df888295e171169049be95681a88a70d2e4528deea670 +EBUILD pfft-1.0_alpha1.ebuild 734 RMD160 c49d0574d604ab1ecd9894e0912ea6fd327919fe SHA1 65ee04189477b796c57afdb15da7aaac1b3af85c SHA256 935ea0cd703087c1861eea4c31b6b2f99a4d27df18221739259e0274b7007025 +MISC ChangeLog 684 RMD160 d5e23e815d622469bfd037534e24d21ff5a1465e SHA1 2dfcf97a053777ed4fac82b5a4357aa3823be3df SHA256 76fdc805f0690132d746cf6badf4e13444d47479c68b76cac131354307365537 MISC metadata.xml 256 RMD160 53a5d04f6246118e052c9cae27b7070de9b88529 SHA1 563e3277f01cc3bf484d46a6da50719855a5a689 SHA256 e683c0d7d2051297085cdbb7444ce887044c7ed0ba02cf04be170cdf62919c74 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkyRGdwACgkQy0OE/ans1/mR0gCePuhvT1g7i/lYsp+qoQzIMOgk -jygAoIAK9GPnmzee5w420gUXc5d+7vfN -=c/mF +iEYEARECAAYFAk4EwoQACgkQgAnW8HDreRbq2QCgjoRODMj2FA9BRnIZfFBDg4Mj +eHMAoLSg72EDmXXHLu6sxBEh9VhznnCE +=4pA3 -----END PGP SIGNATURE----- diff --git a/sci-libs/pfft/pfft-1.0_alpha1.ebuild b/sci-libs/pfft/pfft-1.0_alpha1.ebuild index a8f94c5ab..d44f96acf 100644 --- a/sci-libs/pfft/pfft-1.0_alpha1.ebuild +++ b/sci-libs/pfft/pfft-1.0_alpha1.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 -inherit eutils autotools +inherit autotools eutils -DESCRIPTION="parallel 3d FFT" +DESCRIPTION="Parallel 3d FFT" HOMEPAGE="http://www-user.tu-chemnitz.de/~mpip/software.php" SRC_URI="http://www-user.tu-chemnitz.de/~mpip/software/${P//_}.tar.gz" @@ -15,9 +15,9 @@ SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="static-libs" -RDEPEND="=sci-libs/fftw-3.3*[mpi] +RDEPEND=" + =sci-libs/fftw-3.3*[mpi] virtual/mpi" - DEPEND="${RDEPEND}" S="${WORKDIR}/${P//_}" @@ -28,17 +28,9 @@ src_prepare() { cp "${FILESDIR}"/"${PF//_}"-"${i}" "${i}" || die "cp of ${i} failed" done - eautoreconf || die "eautoreconf failed" + eautoreconf } src_configure() { - econf --disable-la-files "$(use_enable static-libs static)" || die "econf failed" -} - -src_compile() { - emake || die "emake failed" -} - -src_install() { - emake install DESTDIR="${D}" || die "emake install failed" + econf --disable-la-files "$(use_enable static-libs static)" } diff --git a/sci-libs/votca-tools/ChangeLog b/sci-libs/votca-tools/ChangeLog index a374af189..7c03d65c4 100644 --- a/sci-libs/votca-tools/ChangeLog +++ b/sci-libs/votca-tools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> votca-tools-9999.ebuild: + Sort inherit and/or USE + 03 Jun 2011; Christoph Junghans <ottxor@gentoo.org> votca-tools-9999.ebuild: use default instead of tip diff --git a/sci-libs/votca-tools/Manifest b/sci-libs/votca-tools/Manifest index 59390c06a..d68071c77 100644 --- a/sci-libs/votca-tools/Manifest +++ b/sci-libs/votca-tools/Manifest @@ -1,17 +1,13 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 -EBUILD votca-tools-9999.ebuild 1587 RMD160 229cad1900bde3d6692a32263295a032668ca60e SHA1 3ea5c4dc558692c6e495c4dd920274ed161b5b89 SHA256 7255a454e1fd43ecfbc93398d92cb4ad57c9c2073ab81ae4e0df66be338be9a3 -MISC ChangeLog 3000 RMD160 0cae94d8aca35c7a7d4ae727f612f42cf2202ea9 SHA1 02f4cb2f57cd44688cb36f121f6f7f7d81185807 SHA256 bf46d9da5b1d29572c041e9ab8ab8aa40818f7a8f70b115592ce2961843b708d +EBUILD votca-tools-9999.ebuild 1587 RMD160 0f5539bcc811e6fe92782f0689e27eed24c691d3 SHA1 071693d54b69caaea5f3554b319c4a7618f300e4 SHA256 acbfe8e8d36913ae65cb535fd1b19b5bbeff6a54d0819f573d1d3e0f4414e94f +MISC ChangeLog 3099 RMD160 2cad07e41d4fda666adffacf6a9723694937c06f SHA1 f2e366596cc2c95d6a622de7e3a14b763aeeddaa SHA256 cd7174dae3f59779150c402c42e989051164f73f153a1a3fd11beb0b72218808 MISC metadata.xml 364 RMD160 f5b24d257b77c1729805134ab10a0220746adabd SHA1 9d96df2a755efaf921cccf34456b8e5fc3e964e9 SHA256 0d446730e41f7ace28e9f7d974483b906f1eabadaed42b4b34bc8756ffff50fb -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iQEcBAEBAgAGBQJN6VeTAAoJEOeBhlrCAAWGwZUH/0qjxmDZZ6B7Tt56dnH7Js/F -BpYfCbI9XQK+AM5PmqdbUDpxPdsaF/cgMRXJWE5RHu42qO76E+OxGTsOc8bz+gn1 -IcFOMIezjEIWRLR/mYyc077mps7vL61ulqMDntII+PT1SPnVmj2h8f0vCMG18Zzy -i7sAe2UWiEjM8/NsI35PNUOGuYRJZfp68UaWvG//iaivkgVZrAeRDIVOBezdFm3z -a0gxYYTJrFJeNsPDKZObMYU+ZhT1Au5NyJHLaMS/iWrs2TAg5f4RySR0cGpYhJKj -pVXr0aJDIc64ifJMUBKXrRDuTMGgMyIc1+xmngP6sbkXhAgEYv6YpgZSaBtnjgw= -=SGb9 +iEYEARECAAYFAk4EhR0ACgkQgAnW8HDreRa76QCfYJkSIoCj+/uwlA+goVxEoYNg +hUwAniSQffo0iBzRISyH5iO4dTBYN9Jj +=DumX -----END PGP SIGNATURE----- diff --git a/sci-libs/votca-tools/votca-tools-9999.ebuild b/sci-libs/votca-tools/votca-tools-9999.ebuild index 931a919a4..94d99d577 100644 --- a/sci-libs/votca-tools/votca-tools-9999.ebuild +++ b/sci-libs/votca-tools/votca-tools-9999.ebuild @@ -4,7 +4,7 @@ EAPI="3" -inherit eutils cmake-utils +inherit cmake-utils eutils if [ "${PV}" != "9999" ]; then SRC_URI="boost? ( http://votca.googlecode.com/files/${PF}_pristine.tar.gz ) diff --git a/sci-libs/wannier90/ChangeLog b/sci-libs/wannier90/ChangeLog index 7958732ce..ee6673415 100644 --- a/sci-libs/wannier90/ChangeLog +++ b/sci-libs/wannier90/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> wannier90-1.2.ebuild, + +metadata.xml: + Added fortran-2.eclass support + 18 Jan 2011; Honza Macháček <Hloupy.Honza@centrum.cz> wannier90-1.2.ebuild: Corrected the sources location. Thanks to jerome.borme@laposte.net from bug 329429. diff --git a/sci-libs/wannier90/Manifest b/sci-libs/wannier90/Manifest index 00eb9c868..c06406c54 100644 --- a/sci-libs/wannier90/Manifest +++ b/sci-libs/wannier90/Manifest @@ -1,5 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX wannier90-1.1-0001.patch 616 RMD160 b92b6bf4f80dab94bc560325a8cde388a6c7a844 SHA1 375d6a8ff738e6e6ba55009802e2b651e95fa6e8 SHA256 05398424121dbe53f35559b0e0e372ea841f5dd5a9ede53df66afb805b5ef22a AUX wannier90-1.1-0002.patch 5596 RMD160 36dd891904566fef47f601cc436bf0c89e10fcc3 SHA1 8dc7ff37147530a3a63484ef2695d2141bd20433 SHA256 2476ccf3090cbab54b699327df20b81c5aa75bd2b5c0b203841d5ec6128c620a DIST wannier90-1.2.tar.gz 5643731 RMD160 4a8035ed4faf5256ad66aa9fe23ac32a86b3abf4 SHA1 b4caaddb6e91afe673c122507e92c6b5fbc7689f SHA256 a76f88eef01c5a40aaa2c74ee393ede8a57bd9085f6b7f2ab656b50c1a30ece4 -EBUILD wannier90-1.2.ebuild 1669 RMD160 8e3f198473aa1d3f46669fdce9af7b00544f1c88 SHA1 c0d58e15d785204be60bd7be6d241ac5bf049d94 SHA256 76b5015828c708be18b19ad9947d08999d2c179bb11b7854ec57748b80caacab -MISC ChangeLog 514 RMD160 7f19f9584d3d6263e51d288cb308f63183a89d3a SHA1 ab60bf5ab8ed2523e7d4d05cbdcea7ffeef0e0c7 SHA256 b0f0e32be111fa76eadf05b8e42465b8f480104188b0e5b1d722f013e69a3b6a +EBUILD wannier90-1.2.ebuild 1689 RMD160 31a4753d5270699e0e2cfb185d878d928c878e9d SHA1 67fd03a525cfa5e35b6d21508bc08196149b46ac SHA256 407918ff9614646097ba15eee9ab73aacd43a5fdf956613bc04d888c29fb712f +MISC ChangeLog 634 RMD160 d11e401c8ef02e97415a0ff41973e9fa644fa2f9 SHA1 b2dbf5181fee326e0dd44a8d3b1757e33afea79d SHA256 1c271b6f28bb41041ca92a72b0a74b11a705bca566233ee8f389ad46cc89a661 +MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4AfAQACgkQgAnW8HDreRZEwgCgwWZmFgEfN4pjBPbnRYZGhoyj +0GsAn1WlAyPvWCe+DV7FlPwj2mLht4Wh +=66T6 +-----END PGP SIGNATURE----- diff --git a/sci-libs/wannier90/metadata.xml b/sci-libs/wannier90/metadata.xml new file mode 100644 index 000000000..efb490d78 --- /dev/null +++ b/sci-libs/wannier90/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +<maintainer> + <email>sci@gentoo.org</email> +</maintainer> +</pkgmetadata> diff --git a/sci-libs/wannier90/wannier90-1.2.ebuild b/sci-libs/wannier90/wannier90-1.2.ebuild index 9e6c95627..ad19243ba 100644 --- a/sci-libs/wannier90/wannier90-1.2.ebuild +++ b/sci-libs/wannier90/wannier90-1.2.ebuild @@ -1,22 +1,26 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 +# $Header: $ -EAPI="3" +EAPI=3 -inherit eutils multilib +inherit eutils fortran-2 multilib DESCRIPTION="Calculates maximally localized Wannier functions (MLWFs)" HOMEPAGE="http://www.wannier.org/" SRC_URI="http://wannier.org/code/${P}.tar.gz" + LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc examples perl test" -RDEPEND="virtual/blas + +RDEPEND=" + virtual/blas virtual/lapack perl? ( dev-lang/perl )" DEPEND="${RDEPEND} - doc? ( virtual/latex-base + doc? ( virtual/latex-base || ( dev-texlive/texlive-latexextra app-text/tetex @@ -26,8 +30,9 @@ DEPEND="${RDEPEND} src_prepare() { # Patch taken from sci-physics/abinit-5.7.3 bundled version - epatch "${FILESDIR}"/${PN}-1.1-0001.patch - epatch "${FILESDIR}"/${PN}-1.1-0002.patch + epatch \ + "${FILESDIR}"/${PN}-1.1-0001.patch \ + "${FILESDIR}"/${PN}-1.1-0002.patch } src_configure() { @@ -63,11 +68,11 @@ src_install() { insinto /usr/$(get_libdir)/finclude doins src/*.mod || die if use examples; then - mkdir -p ${D}/usr/share/${PN} - cp -r examples ${D}/usr/share/${PN}/; + mkdir -p "${D}"/usr/share/${PN} + cp -r examples "${D}"/usr/share/${PN}/; fi if use doc; then (cd doc; dodoc *.pdf ) fi - dodoc README README.install LICENCE CHANGE.log + dodoc README README.install CHANGE.log } diff --git a/sci-mathematics/acl2/ChangeLog b/sci-mathematics/acl2/ChangeLog index 48176d913..5a37fb3b9 100644 --- a/sci-mathematics/acl2/ChangeLog +++ b/sci-mathematics/acl2/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/acl2 -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> acl2-4.2.ebuild: + Some ebuild cleaning + *acl2-4.2 (13 Apr 2011) 13 Apr 2011; Dongxu Li <dongxuli2011@gmail.com> -files/set-booksdir.patch: diff --git a/sci-mathematics/acl2/Manifest b/sci-mathematics/acl2/Manifest index 1cb5a906a..02b00d2d7 100644 --- a/sci-mathematics/acl2/Manifest +++ b/sci-mathematics/acl2/Manifest @@ -1,4 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +AUX set-booksdir.patch 591 RMD160 a4775c520b3756e8b33de8bc38b54e4873c57a39 SHA1 37ccf5718c75a6e4f45fdbfe8876ec8acf625e5b SHA256 2b6e65de0d25705444f6d75dc2e8658433bd79d5c180026da34b230bf9808bea DIST acl2.tar.gz 11699557 RMD160 622dbef91b3af8d75a99cc482ca240a20cc8af0a SHA1 75c24b3fc6b1ca0e7a4163fd47088eca3b0c1104 SHA256 0f727b44257640346dc6eecc046f339b171676e79c31883535281e61bbfca077 -EBUILD acl2-4.2.ebuild 1171 RMD160 3ecf0b3b40ef64fce05872335970b92b9307e12f SHA1 ac2d708e05176d8484e5a87bc9cd57ea1b89bcae SHA256 eb0e42bfabbdece0aa7d1c1978c21ab6835b3a7485882a39a5de865a0b8c8e03 -MISC ChangeLog 508 RMD160 2561e715a5e033265726b6b21ad0b54a5ea3aa9c SHA1 f7edc4c6d898cf0a2843957cfb339c90ddde2441 SHA256 1fe5549394c3acb062e710f4dca45ebf0173b0c705d9864a000234055c1e504b +EBUILD acl2-4.2.ebuild 1146 RMD160 28e3c9501699fa1762d85d4bca4cafa3abf7c817 SHA1 f92b0fbdba8fc28fdc017059dce601aba6f7bf94 SHA256 e1b6bffb596791dc65de391f32a5f984cc409fd95ed743430df990d7439e85b6 +MISC ChangeLog 596 RMD160 452638339debc95a94e58be2983a922cbf479649 SHA1 b211120f5fe33a8ebe50c3de8b964d71634220ea SHA256 108b88ef5f447139afccb57e9ee9f458aad86b4efd8194391668ac1365c20df0 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4E8SAACgkQgAnW8HDreRYVsQCgn6D5WwElrrTFwgfr4bMItbQu +PL0AoNAu4WmDjMSiiXA4kgX4Mjzsw2B3 +=voYN +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/acl2/acl2-4.2.ebuild b/sci-mathematics/acl2/acl2-4.2.ebuild index 9c1396593..bf7d91955 100644 --- a/sci-mathematics/acl2/acl2-4.2.ebuild +++ b/sci-mathematics/acl2/acl2-4.2.ebuild @@ -5,23 +5,15 @@ inherit eutils DESCRIPTION="ACL2 industrial strength theorem prover" - HOMEPAGE="http://www.cs.utexas.edu/users/moore/acl2/" - SRC_URI="http://www.cs.utexas.edu/users/moore/acl2/v${PV/\./-}/distrib/acl2.tar.gz" -LICENSE="GPL-2" - SLOT="0" - +LICENSE="GPL-2" KEYWORDS="~amd64 ~x86" - IUSE="" -#RESTRICT="strip" - DEPEND="dev-lisp/sbcl" - RDEPEND="${DEPEND}" S="${WORKDIR}/${PN}-sources" diff --git a/sci-mathematics/algae/ChangeLog b/sci-mathematics/algae/ChangeLog index 9bb58696e..079bc8992 100644 --- a/sci-mathematics/algae/ChangeLog +++ b/sci-mathematics/algae/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-mathematics/algae -# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> algae-4.3.6.ebuild, + metadata.xml: + Tweak the ebuild + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> algae-4.3.6.ebuild: + Added fortran-2.eclass support + *algae-4.3.6 (7 June 2006) 7 June 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su> diff --git a/sci-mathematics/algae/Manifest b/sci-mathematics/algae/Manifest index d49ccfb12..c13e8ca71 100644 --- a/sci-mathematics/algae/Manifest +++ b/sci-mathematics/algae/Manifest @@ -1,7 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX Makefile.in-doc.patch 235 RMD160 5074f322864ebf809aba80ed5020a18ff24b0864 SHA1 882777e78dfcdeb866c5d941ddef548e97b0c6e0 SHA256 0d181144a83ebd9dd912e58be81fe18fc003935ed656a8e31cec70761d4eb889 AUX Makefile.in-src.patch 193 RMD160 23f3389914dab1b15c2c9821c6b37800afde408e SHA1 d7bc9639c4053911076440e7cf5470aa15d66455 SHA256 dd5204e6eaff31c655cc543443d4c204b929bb3d27646b37e0422dc7f54f7024 AUX configure.in.patch 466 RMD160 fc73794fed429776e6e90e3949f38e038a29cc63 SHA1 89a06bf3a3220c810e50a4bd28c38ffee62c4dce SHA256 b2f13f41937c36bf2332e96b8e19cc5e37e1af077dc83aed55201b31934563ab DIST algae-4.3.6.tar.gz 1790061 RMD160 0dfee737c3eccb59563fd85da8d7772937d5795c SHA1 f935540e8479b543d51cf04fc38e6c573679e19c SHA256 b456e8ab32eda24a1c0dde44f75455e6b5a8a7604ce8cd7ff9419651d93c0ec1 -EBUILD algae-4.3.6.ebuild 1761 RMD160 a31061b50178ca76da9672e485aa78718339ae72 SHA1 b9e68cc83a4ff292bb697fe4a99553d662cdc023 SHA256 8c7951020fdbf0c22926de4392d5b10c71e391246421a6af1171f2bc9f961fe7 -MISC ChangeLog 421 RMD160 32ac2dfea015132c07494868a357581e710b289b SHA1 1d6987ba3b1086afe1cf85c6e1fad1d0a844ce35 SHA256 83daa6f83c7c6c73f577fa3fd1ee291353efeab82aa73e6e46f47f7f3ddfff94 -MISC metadata.xml 565 RMD160 d83d2d9d8b55deb308465e41bbb7a955e73094af SHA1 f9613cf772743872f01789f5f056b25f2e1e1c4b SHA256 d54042b12c6336d8c359655ccefc3e5c82d2a121afaf2eede113abd39dc41e76 +EBUILD algae-4.3.6.ebuild 1270 RMD160 c15687f66ff2992ebb5d6947e3b878fe8abaea15 SHA1 4275e42adb9a1ccd2aa2ecf113702f19bfa66e30 SHA256 ef2faf3511cf55f9cfcf7798461439cf9e449c7ec07a52b641e44b50468e4343 +MISC ChangeLog 625 RMD160 f11a45bca44cda7b3e62869d70632a41264e9e81 SHA1 6afd7f41d759fcb418fdefc3dd6252d280c3f625 SHA256 96ab71667a17455a5b1724e61251dbb976caf3b65d616d32ddf526a5c16633d6 +MISC metadata.xml 624 RMD160 9398614645d38f7fc4479329d0c9644ec671e263 SHA1 17098234c2520361f4a5ea33c19460edaafb3ac6 SHA256 336b4da1efeb1c0f9df43348e8c8d429032ed58151c10c3b8c33be4d2e3dd446 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EqAoACgkQgAnW8HDreRa+oACePXmnKFkkT4AuIPxFin1ztwkm +xr8An0X88T8KOTJ+SuF4/f9kXhT8BhZh +=Ajdq +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/algae/algae-4.3.6.ebuild b/sci-mathematics/algae/algae-4.3.6.ebuild index 06cfc37bc..eeeaaae5d 100644 --- a/sci-mathematics/algae/algae-4.3.6.ebuild +++ b/sci-mathematics/algae/algae-4.3.6.ebuild @@ -1,70 +1,55 @@ -# Copyright 1999-2006 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit eutils +EAPI=4 -DESCRIPTION="high-level interpreted language for numerical analysis" +inherit autotools eutils fortran-2 +DESCRIPTION="High-level interpreted language for numerical analysis" HOMEPAGE="http://algae.sourceforge.net/" - SRC_URI="mirror://sourceforge/algae/${P}.tar.gz" -LICENSE="GPL-2" +LICENSE="GPL-2" SLOT="0" - KEYWORDS="~x86" +IUSE="blas intel lapack" -IUSE="icc blas lapack" - -DEPEND="sci-libs/fftw \ - icc? ( dev-lang/icc dev-lang/ifc ) \ +DEPEND=" + sci-libs/fftw \ + intel? ( dev-lang/icc dev-lang/ifc ) blas? ( virtual/blas ) lapack? ( virtual/lapack )" - -src_unpack() { - unpack ${A} - cd "${S}" - epatch "${FILESDIR}/configure.in.patch" || die "epatch configure.in failed" - epatch "${FILESDIR}/Makefile.in-src.patch" || die "epatch src/Makefile.in failed" - epatch "${FILESDIR}/Makefile.in-doc.patch" || die "epatch doc/Makefile.in failed" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/configure.in.patch + "${FILESDIR}"/Makefile.in-src.patch + "${FILESDIR}"/Makefile.in-doc.patch + eautoreconf } -src_compile() { - autoconf - if use icc; then - F77="ifort" FFLAGS="-O3 -axKWNBP -ip" \ - CC="icc" CFLAGS="-O3 -axKWNBP -ip" \ +src_configure() { + if use intel; then + F77="ifort" \ + CC="icc" \ LDFLAGS="-L/opt/intel/compiler80/lib" LIBS="-latlas" \ econf \ --with-readline --with-fftw \ $(use-enable blas ) $(use-enable lapack ) \ - --with-fortran-libs="-limf -lifcore -lifport" \ - || die "econf failed" + --with-fortran-libs="-limf -lifcore -lifport" else - FLAGS="${CFLAGS}" econf --with-readline --with-fftw \ - $(use-enable blas ) $(use-enable lapack ) \ - || die "econf failed" + FLAGS="${FCFLAGS}" econf --with-readline --with-fftw \ + $(use-enable blas ) $(use-enable lapack ) fi - - emake htmldir="/usr/share/doc/${P}/html" || die "emake failed" } -src_install() { - dodoc INSTALL NEWS PROBLEMS README VERSION doc/FAQ - dodir /usr/share/doc/${P}/html - make install prefix="${D}usr" htmldir="${D}usr/share/doc/${P}/html" \ - || die "make install failed" - insinto /usr/share/doc/${P} - doins doc/*ps -} - -pkg_postinst() { - ln -s "/usr/bin/${P}" "/usr/bin/${PN}" - ln -s "/usr/share/doc/${P}/html" "/usr/share/${PN}/html" +src_compile() { + emake htmldir="/usr/share/doc/${P}/html" } -pkg_prerm() { - rm -f "/usr/bin/${PN}" - rm -f "/usr/share/${PN}/html" +src_install() { + emake install prefix="${D}usr" htmldir="${D}usr/share/doc/${P}/html" + dodoc INSTALL NEWS PROBLEMS README VERSION doc/FAQ doc/*ps } diff --git a/sci-mathematics/algae/metadata.xml b/sci-mathematics/algae/metadata.xml index 0cbe82f94..5b73e554a 100644 --- a/sci-mathematics/algae/metadata.xml +++ b/sci-mathematics/algae/metadata.xml @@ -12,4 +12,5 @@ Boeing because they needed a fast and versatile tool, capable of handling large systems. Algae has been applied to interesting problems in aerospace and related fields for more than a decade. </longdescription> +<use><flag name='intel'>Use icc as c compiler</flag></use> </pkgmetadata> diff --git a/sci-mathematics/aribas/ChangeLog b/sci-mathematics/aribas/ChangeLog index 5aff76b30..9f1b03455 100644 --- a/sci-mathematics/aribas/ChangeLog +++ b/sci-mathematics/aribas/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/aribas -# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> aribas-1.63.ebuild: + RDEPEND is not explicitly assigned -> fixed + *aribas-1.63 (06 Oct 2008) 06 Oct 2008; Andrey Grozin <grozin@gentoo.org> +files/64aribas-gentoo.el, diff --git a/sci-mathematics/aribas/Manifest b/sci-mathematics/aribas/Manifest index 792f6bbe4..881b309ef 100644 --- a/sci-mathematics/aribas/Manifest +++ b/sci-mathematics/aribas/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + AUX 64aribas-gentoo.el 101 RMD160 80e8ef65ba255ee8f9a00ec74dda0b60882eaddd SHA1 b557bdba9d2885843b0d8c578d63d6108b6467eb SHA256 a98d5b298714ba33759658c84b6b290faffb18ff72c667508647e5621eea64b7 DIST aribas-1.63.tar.gz 291939 RMD160 f377eac5fa6da2aa2411f7e75eca426e539ad2aa SHA1 280d71a7ecaa8f1ce6c62efa61118e2f48b63353 SHA256 60d5367057780ded5bab012a5d55f192c3f98f315e1c8475092791ce216c9543 -EBUILD aribas-1.63.ebuild 1624 RMD160 1ffae812a752a6e6562bda5f920418c631fa9a2f SHA1 d9afa265ff7d4e605061ba11a528fd8bb4bc09db SHA256 90b1f489e4c13133897d8db7e5611704642dc2993cd451555c8e531ae2f752ef -MISC ChangeLog 411 RMD160 45f962d44794d34a0549ba36d4f62251bf7be45f SHA1 4f587d605c63c4f4235e3f6a4f6736f3b406d356 SHA256 1b1c21d99aa0a64095310f98396bcea9d36677492138f6385b987d47469c08e7 +EBUILD aribas-1.63.ebuild 1537 RMD160 a4c4dd6143fe5d9343ce382df1fb08c10d6bef10 SHA1 b50820c7e7fcaf22c33aa860a76f66031c5a3fe1 SHA256 71db77442d21358ad51d022a6a57b34fad9de30687944db8c906e8383cf4902c +MISC ChangeLog 525 RMD160 6a4f4ba6ec4fa6b55d2a31007525b860b4ee7437 SHA1 70fffceda60d6c12aed0d0db7c1eb251be4fd63b SHA256 54a6d5535ac11264d050df3bbcf8ce071bf1677d416682fefeb8101545f2226c MISC metadata.xml 372 RMD160 5ea712b2662b9a8559f2b0074b3acf09cdb48590 SHA1 6b2093b4002ce4015b29a8932a8a7c13e3941fa7 SHA256 35d67b958db4069cb66a1b5fddfb9b1b67690ac01458c1b1ba8d52463b6ef270 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F5kgACgkQgAnW8HDreRa/fwCgwUfcLs6N+AIGbnCd1o76yOTV +q6cAoJ6wrZmGJSZ4XpPcDY2xvyrF/+of +=o4x/ +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/aribas/aribas-1.63.ebuild b/sci-mathematics/aribas/aribas-1.63.ebuild index 9fe836746..fa8af4769 100644 --- a/sci-mathematics/aribas/aribas-1.63.ebuild +++ b/sci-mathematics/aribas/aribas-1.63.ebuild @@ -1,6 +1,9 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ + +EAPI=4 + inherit elisp-common versionator DESCRIPTION="Interpreter for big integer and multi-precision floating point arithmetic" @@ -10,17 +13,15 @@ SRC_URI="ftp://ftp.mathematik.uni-muenchen.de/pub/forster/${PN}/UNIX_LINUX/${P}. LICENSE="GPL-2" SLOT="0" KEYWORDS="~x86" -IUSE="doc examples emacs" +IUSE="doc emacs examples" DEPEND="emacs? ( virtual/emacs )" +RDEPEND="${DEPEND}" SITEFILE=64${PN}-gentoo.el CH_PV=$(delete_all_version_separators) -src_unpack() { - unpack ${A} - cd "${S}"/src - +src_prepare() { # Linux x86 assembly piece if use x86; then mv LINUX/arito386.S . @@ -34,9 +35,9 @@ src_unpack() { src_compile() { cd src if use x86; then - emake CFLAGS="-DLiNUX -DPROTO ${CFLAGS}" || die "emake failed" + emake CFLAGS="-DLiNUX -DPROTO ${CFLAGS}" else - emake CC=gcc CFLAGS="-DUNiX -DPROTO ${CFLAGS}" || die "emake failed" + emake CC=gcc CFLAGS="-DUNiX -DPROTO ${CFLAGS}" fi if use emacs; then @@ -48,10 +49,10 @@ src_compile() { src_install() { dobin src/${PN} doman doc/*.1 - dodoc CHANGES${CH_PV}.txt || die "dodoc failed" + dodoc CHANGES${CH_PV}.txt if use doc; then - dodoc doc/${PN}.doc doc/${PN}.tut || die "dodoc failed" + dodoc doc/${PN}.doc doc/${PN}.tut fi if use examples; then diff --git a/sci-mathematics/axiom/ChangeLog b/sci-mathematics/axiom/ChangeLog index 2a1ba00eb..a8d64e4cd 100644 --- a/sci-mathematics/axiom/ChangeLog +++ b/sci-mathematics/axiom/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-mathematics/axiom -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/axiom/ChangeLog,v 1.22 2008/08/30 13:17:33 markusle Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> axiom-201009.ebuild, + metadata.xml: + RDEPEND is not explicitly assigned -> fixed + *axiom-201009 (11 Oct 2010) 11 Oct 2010; Thomas Kahle <tom111@gmx.de> -axiom-201005.ebuild, diff --git a/sci-mathematics/axiom/Manifest b/sci-mathematics/axiom/Manifest index 586ef0c89..9f044c08c 100644 --- a/sci-mathematics/axiom/Manifest +++ b/sci-mathematics/axiom/Manifest @@ -1,6 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + AUX noweb-2.9-insecure-tmp-file.Makefile.patch 439 RMD160 16cdc72fab65bab45c7728d374da60f7b4cccc65 SHA1 428d4380a17535939a59b5efd12556ab4cafde06 SHA256 3c4b5bea61620cb545e576d2e82dd8daa0478fc6c40ae0a93dbdac432aa9531d AUX noweb-2.9-insecure-tmp-file.patch.input 4819 RMD160 2afe80731bd3fcfa23e0ee799649886ce3fdd0af SHA1 23aff1cf0862618c7450704d0d47fcec2497de0b SHA256 68bf232fd91b94fc9d08373d079afcb890a6af6991373da81089560ce21889a9 DIST axiom-sept2010-src.tgz 119714986 RMD160 acb5fee41b5216e59119ff3708ac8869835b881e SHA1 e9c0b7b26a98c884b830f1356cfb748fa4b45fc1 SHA256 b750350f065ad5db3edda228908728b83bf5fec100052a83eeebc628bc3ef4bf -EBUILD axiom-201009.ebuild 3733 RMD160 7693b3478d9aaf72dff163fed94ea5a677be80eb SHA1 e6e35af2ae832385794c5c3df17ef4207eb8437d SHA256 91bdabd980c507b48f9b5892926df190ce4850197e3e7b3e19545f26b9efa2dc -MISC ChangeLog 4337 RMD160 60e58691f87d5c12c9fd4460b2c5a87ae88d96e3 SHA1 c62e19bb7cb477fe0ae5a6cc90575b260a396be9 SHA256 2206c2944f69add37d5cd9178a61bd8b4ede2558033b2b29820efdfce0039526 -MISC metadata.xml 168 RMD160 d98790cf055dc0f820c63d65f485b9dcfa8950f4 SHA1 95c9e4f7368f82053d631bbcd469612c92ca13cb SHA256 c0cc8d6ab9385750af753ddc504299ed90a70b5c4c655f6c77d865917a8829c9 +EBUILD axiom-201009.ebuild 3756 RMD160 e3a4e966b4283d50ffdcb8e2648fb43b1e9f44d1 SHA1 7b437570f2692e09ea8d9358892dd6d321090a7a SHA256 cc103d5516ea6bce3f66402f6f7e1c573d32d86bce3bccf7dde4ab84bd3dfb98 +MISC ChangeLog 4468 RMD160 1189eb2d3f1f8e5ce8f1046043ec935a79d41a91 SHA1 ecbdcdc367b1d18ec89aa3a5b63bc20ea756df7d SHA256 b2b795068558ccd13b901e07f5ae20d3fef6acf46b885adf92daad5c2cd3e083 +MISC metadata.xml 169 RMD160 a8b2671842bbec7d36e587fbf53c4eb111498347 SHA1 604114857745acb6253b121cda619e3c35771cc7 SHA256 7a9f25879c1299572cfaf2a3efb47313412564a1ef12c828224194f4e96edcd0 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F5swACgkQgAnW8HDreRacZQCfRVqfKdGh4nX6F6zWkipKxIgJ +aUUAn3gxLtSEHGUyBkfA/Lew0ag0QQI+ +=EuLS +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/axiom/axiom-201009.ebuild b/sci-mathematics/axiom/axiom-201009.ebuild index 93427f01b..69fbb715c 100644 --- a/sci-mathematics/axiom/axiom-201009.ebuild +++ b/sci-mathematics/axiom/axiom-201009.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/axiom/axiom-200805.ebuild,v 1.6 2008/08/30 13:17:33 markusle Exp $ -inherit eutils multilib flag-o-matic +inherit eutils flag-o-matic multilib DESCRIPTION="Axiom is a general purpose Computer Algebra system" HOMEPAGE="http://axiom.axiom-developer.org/" @@ -19,13 +19,15 @@ RESTRICT="strip" # Seems to need a working version of pstricks package these days Bummer: <gmp-5 is needed for the # interal gcl, otherwise axiom will try to build an internal copy of gmp-4 which fails. -DEPEND="virtual/latex-base +RDEPEND=" + dev-libs/gmp + x11-libs/libXaw" +DEPEND="${RDEPEND} app-text/dvipdfm dev-texlive/texlive-pstricks - x11-libs/libXaw sys-apps/debianutils sys-process/procps - dev-libs/gmp" + virtual/latex-base" S="${WORKDIR}"/${PN} diff --git a/sci-mathematics/axiom/metadata.xml b/sci-mathematics/axiom/metadata.xml index 5a2f1c7b8..2b0bd5314 100644 --- a/sci-mathematics/axiom/metadata.xml +++ b/sci-mathematics/axiom/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-mathematics</herd> + <herd>sci-mathematics</herd> </pkgmetadata> diff --git a/sci-mathematics/cipi/ChangeLog b/sci-mathematics/cipi/ChangeLog index 7aeb4a10a..54e03ff9a 100644 --- a/sci-mathematics/cipi/ChangeLog +++ b/sci-mathematics/cipi/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-mathematics/cipi -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> cipi-1.0.ebuild: + migrate from 'git' to 'git-2' + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> cipi-1.0.ebuild, metadata.xml: + RDEPEND is not explicitly assigned -> fixed + *cipi-1.0 (20 Jul 2010) 20 Jul 2010; Thomas Kahle <tom111@gmx.de> +cipi-1.0.ebuild, +metadata.xml: diff --git a/sci-mathematics/cipi/Manifest b/sci-mathematics/cipi/Manifest index 6a3e98085..c8ebd9d50 100644 --- a/sci-mathematics/cipi/Manifest +++ b/sci-mathematics/cipi/Manifest @@ -1,3 +1,13 @@ -EBUILD cipi-1.0.ebuild 799 RMD160 cb6909955cb4a63a632e92430d771b699b3c88a2 SHA1 b2056fbc05435cc00ba44275b7deb71a18570bae SHA256 608e3e5e915da9afa396ee4c21a95fe491a7b01b28983de36501439181974843 -MISC ChangeLog 256 RMD160 41008a342ed2556becffcd1f27de3b8bd21cdfa2 SHA1 6fcba3c185f96d73440d55ab2771115cc78d2cf7 SHA256 a408f473131cc2ea862285d6ba83c7c1913deac8dad0547cff5443dc22fb783e -MISC metadata.xml 429 RMD160 3e6d840b453b9727a910b55817a10ca791291005 SHA1 11a41885d99172fa32e90a6e1b3da2ee71fd4a13 SHA256 8cdbca433ec6c0c2ffdb52fb8b494a00ab9f56bd24bc1fd90e5ffcc4995878ae +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +EBUILD cipi-1.0.ebuild 815 RMD160 2c1e2cab7482a0f7c67edc44e18c8682ab4f6d36 SHA1 02268b9daa1e35035d08c427b2fdd202bfdc9374 SHA256 758266fa28eb39b49da0eeda5ba6fdfde5bf1312e1faad6592b54f33dc9b6d43 +MISC ChangeLog 478 RMD160 974c3e22b3c10fcb1a9acd9127a2ec64c3ddd9c5 SHA1 51d85554f3120f203b4e1f16f322c56a585d8a20 SHA256 71493d0412f348da081c48a3a3df9b23605421d66424a53e073ecaa189714eb1 +MISC metadata.xml 433 RMD160 b2b35cf3a37c660b71abe052b9b051892f80bd35 SHA1 31360c9ced491acd0264f7356836ae6e67f350d2 SHA256 9af678a14427419b57161636a463939469c115f1e936d667dab1391a3085ff20 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F57oACgkQgAnW8HDreRbE+QCfUjY/lijv7jVG2Tb1SmZCOEq0 +4i8AoIzSl6o7yMfHnkRJRQRUwIWIZ6fO +=pTPX +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/cipi/cipi-1.0.ebuild b/sci-mathematics/cipi/cipi-1.0.ebuild index ca0bc1afe..200b79391 100644 --- a/sci-mathematics/cipi/cipi-1.0.ebuild +++ b/sci-mathematics/cipi/cipi-1.0.ebuild @@ -1,26 +1,30 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 +EAPI=4 -inherit cmake-utils git +inherit cmake-utils git-2 -DESCRIPTION="cipi is computing information projections iteratively" +DESCRIPTION="Computing information projections iteratively" HOMEPAGE="http://github.com/tom111/cipi" EGIT_REPO_URI="git://github.com/tom111/cipi.git" EGIT_COMMIT="${PV}" -CMAKE_IN_SOURCE_BUILD="yes" + LICENSE="GPL-3" SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="doc" -DEPEND="dev-libs/boost - doc? ( virtual/latex-base )" +DEPEND=" + dev-libs/boost + doc? ( virtual/latex-base )" +RDEPEND="${DEPEND}" DOCS="AUTHORS README" +CMAKE_IN_SOURCE_BUILD="yes" + src_configure() { mycmakeargs=( $(cmake-utils_use_enable doc) @@ -30,10 +34,10 @@ src_configure() { } pkg_postinst() { - elog " " + echo "" elog "The sample PARAM file has been installed to /usr/share/${PN}-${PV}" - elog " " + echo "" if use doc; then elog "A pdf manual has been installed to /usr/share/${PN}-${PV}" fi -}
\ No newline at end of file +} diff --git a/sci-mathematics/cipi/metadata.xml b/sci-mathematics/cipi/metadata.xml index 462f8208d..7b5155f27 100644 --- a/sci-mathematics/cipi/metadata.xml +++ b/sci-mathematics/cipi/metadata.xml @@ -1,12 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-mathematics</herd> -<maintainer> - <email>tom111@gmx.de</email> - <name>Thomas Kahle</name> -</maintainer> -<longdescription lang="en"> + <herd>sci-mathematics</herd> + <maintainer> + <email>tom111@gmx.de</email> + <name>Thomas Kahle</name> + </maintainer> + <longdescription lang="en"> cipi is a threaded implementation of iterative proportional fitting. It is used to compute information projections iteratively. </longdescription> diff --git a/sci-mathematics/flocq/ChangeLog b/sci-mathematics/flocq/ChangeLog index 28ee4ccf1..23ceec7f0 100644 --- a/sci-mathematics/flocq/ChangeLog +++ b/sci-mathematics/flocq/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> flocq-1.4.0.ebuild: + Define EAPI after inherit + 06 May 2011; J.-C. Demay <jcdemay@gmail.com> -flocq-1.2.ebuild, +flocq-1.4.0.ebuild: version bump diff --git a/sci-mathematics/flocq/Manifest b/sci-mathematics/flocq/Manifest index 62714161c..9e6d66900 100644 --- a/sci-mathematics/flocq/Manifest +++ b/sci-mathematics/flocq/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST flocq-1.4.0.tar.gz 129022 RMD160 04944a466bf1df71389eec5dbda0969b7c6f79c2 SHA1 bebe3cdbfb2308312c757f5205fc53d4a5c21954 SHA256 9cda6786f79bf4f826d0b48a5601c292a065472b31f3717bb0045ac6414ec023 -EBUILD flocq-1.4.0.ebuild 614 RMD160 8d244238667572ff8662cc6d25288848c0cdedc6 SHA1 b5ea8c707c6cb7f63a45af58a499c9252131a94b SHA256 0abc28abcca68c953343d41cd503ba6553cb9e099405ee0fde33878659580d41 -MISC ChangeLog 315 RMD160 8cebc4c880fd2bc3d090c717c708a36f22aedfc5 SHA1 e6a6b92aac62e84a66819614c26f18716a0e0504 SHA256 f73302279648b8d77b28273da4b0962cbedb4e7183fc146d775dc677faabde3b +EBUILD flocq-1.4.0.ebuild 488 RMD160 537e3860301cf4fbfe81e54115b1e23f00cc4b06 SHA1 c973f79c4f04db83b29050bb5b0e0bff9a9e514f SHA256 d3acd508844ef450c896051216fe304492b18f7246980010b84bc981b38272db +MISC ChangeLog 411 RMD160 ebd74444d2bbfffa67532df5a52b1af93c9a2b9f SHA1 3e8b0ded6a089484d14664285854c3156450e2ff SHA256 0f7807fee2a6f1880a2bc81f47aa3ee83ece8e3d16f6c3ce16e6169a47aaa5d9 MISC metadata.xml 497 RMD160 9a76fe39578db3ce4e7fcaaec6bcff9c38ff40ed SHA1 a7ba11329f3269f949be97f4f44ca7e4ea5a2d8d SHA256 888cc1091b03da5c749d586bccafc4eaa063c08a9273458b17026a6c8c91626a +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Fk1UACgkQgAnW8HDreRY/0gCglaCsMydQUNeQqisucQ5D+0OD +WuAAoLZwYoiuSeUqSgVK2+5Mhfkk1hA4 +=c4rI +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/flocq/flocq-1.4.0.ebuild b/sci-mathematics/flocq/flocq-1.4.0.ebuild index 734992fd5..44074f5a2 100644 --- a/sci-mathematics/flocq/flocq-1.4.0.ebuild +++ b/sci-mathematics/flocq/flocq-1.4.0.ebuild @@ -2,27 +2,20 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit autotools +EAPI=4 -EAPI="2" - -DESCRIPTION="A floating-point formalization for the Coq system." +DESCRIPTION="A floating-point formalization for the Coq system" HOMEPAGE="http://flocq.gforge.inria.fr/" SRC_URI="https://gforge.inria.fr/frs/download.php/28389/${P}.tar.gz" LICENSE="LGPL-3" SLOT="0" -KEYWORDS="~amd64 ~ppc ~sparc ~x86" +KEYWORDS="~amd64 ~ppc ~x86" IUSE="" DEPEND="sci-mathematics/coq" +RDEPEND="${DEPEND}" src_configure() { econf --libdir="`coqc -where`/user-contrib/Flocq" } - -src_install() { - emake install DESTDIR="${D}" || die "emake install failed" - dodoc NEWS README AUTHORS ChangeLog -} - diff --git a/sci-mathematics/freefem++/Manifest b/sci-mathematics/freefem++/Manifest index eae724460..15dea7aea 100644 --- a/sci-mathematics/freefem++/Manifest +++ b/sci-mathematics/freefem++/Manifest @@ -7,14 +7,14 @@ AUX freefem++-no-doc-autobuild.patch 1155 RMD160 39cc42211934298ec1dea2bb68fced6 AUX freefem++-path.patch 5244 RMD160 47ef29ac13194b1bedf47a6395eab3c392f1e87d SHA1 29b26f21cbbcd84f08b6c683125800ef21c36149 SHA256 1d47be7c24bc321a48e279fdfa9bf9b032241ebf0c553644a5681ff519197f10 DIST freefem++-3.5.tar.gz 18472428 RMD160 3eccdd385566d470778d5a1fab494638f5bb1b85 SHA1 301fd85e72e7b4ca001fe20459ccde6d899b4895 SHA256 c67c859dc7e5b498fa52b5f7cf99e3325f6c2facf42afd5eb77e16f83192c687 DIST freefem++-3.8.tar.gz 21848854 RMD160 31e3b23ede5c0097cbd7c36bd79d8c95be4ea868 SHA1 791783afb35f76b3638180b89a4cf39c6b91d545 SHA256 4ea6d754eb3914f20b1fe7620d562e95461b7206f289108e2fc803baecf70e6c -EBUILD freefem++-3.5.ebuild 3819 RMD160 06f08cd31232c2ae1f0c6a257e5a9d74acebae02 SHA1 0edf3e1e9b7c09c173ba7885691158f22a05821b SHA256 662e4ae35a3ab318959adf5e20b2a30738b51fac867cd34cc9e603f7c790e8e3 -EBUILD freefem++-3.8.ebuild 3170 RMD160 25bf480d7ee17b006e8e08fa49fe269bec46a851 SHA1 39c51e20939fbbb7095d72db766bd1e99c6136ce SHA256 cc8bd7ed689656188c2443c42b99b3bacf0dee88933767a325c80fe2627b24b3 +EBUILD freefem++-3.5.ebuild 3819 RMD160 ae528d9510eca07b38970fd04bad0f21b3ca1a85 SHA1 87bc5266ddfb2e9ca6268c10f95d5dbc4597e9d3 SHA256 22b590b1feb5fe44f66dce736ec88be77808f11f4f29fdce870a35d5f91cf6f1 +EBUILD freefem++-3.8.ebuild 3170 RMD160 cdc000396be8e7c3834abcd6d038118133a5fb05 SHA1 dd515ed7595f6749a2b623e0603251fed6a10333 SHA256 bbbfb737c10067e4252232a071e6418e1e54209cefacc278a0fbdfd623d43a39 MISC ChangeLog 3816 RMD160 651ad4d4723cdeb3949d18beb13a6811dcb0a54f SHA1 24e6a0d1fd34ec622f70d6125f0f094a3f7767f2 SHA256 cc1364af9ee3baf126bdc78bf499c4dea3036a522008c1631f4f22682b876ff8 MISC metadata.xml 381 RMD160 17dca0ed77bf65c0d2d8aa2148243f67c4a05edf SHA1 f583b125502b06a151f200849e2892bd08dbc70e SHA256 d7569d977d779a55533651e01e4d45e5ae7a1ada36b634e8b988ae4db86cdb83 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkyV6HIACgkQgAnW8HDreRaRAgCginvYexuzefatA4otnSEc5cev -FTMAni8dSm5UBJ0yYN67uUrvEiDqPJRg -=ggQx +iEYEARECAAYFAk4EqBEACgkQgAnW8HDreRYKtgCgjiQgvsRoEBDBF6H3kV1cBpUL +MRoAoMpnBs2JIm7SeJNB+SE8Lr3q6WhF +=vS+7 -----END PGP SIGNATURE----- diff --git a/sci-mathematics/freefem++/freefem++-3.5.ebuild b/sci-mathematics/freefem++/freefem++-3.5.ebuild index ae1ab1773..fd8d32d11 100644 --- a/sci-mathematics/freefem++/freefem++-3.5.ebuild +++ b/sci-mathematics/freefem++/freefem++-3.5.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit eutils autotools versionator flag-o-matic mpi +inherit autotools eutils flag-o-matic mpi versionator MY_PV=$(replace_version_separator 2 '-') diff --git a/sci-mathematics/freefem++/freefem++-3.8.ebuild b/sci-mathematics/freefem++/freefem++-3.8.ebuild index 510348814..0b1eef451 100644 --- a/sci-mathematics/freefem++/freefem++-3.8.ebuild +++ b/sci-mathematics/freefem++/freefem++-3.8.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit eutils autotools versionator flag-o-matic mpi +inherit autotools eutils flag-o-matic mpi versionator MY_PV=$(replace_version_separator 2 '-') diff --git a/sci-mathematics/gambit/ChangeLog b/sci-mathematics/gambit/ChangeLog index 6953686a8..c3d9a0e3d 100644 --- a/sci-mathematics/gambit/ChangeLog +++ b/sci-mathematics/gambit/ChangeLog @@ -1,7 +1,11 @@ -# ChangeLog for sci-misc/gambit +# ChangeLog for sci-mathematics/gambit # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> gambit-0.2010.09.01.ebuild, + metadata.xml: + Cleaned ebuild + 16 Apr 2011; Dongxu Li <dongxuli2011@gmail.com> ChangeLog: Moved the the sci-mathematics category. diff --git a/sci-mathematics/gambit/Manifest b/sci-mathematics/gambit/Manifest index 44e4b2e01..fce904bf0 100644 --- a/sci-mathematics/gambit/Manifest +++ b/sci-mathematics/gambit/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST gambit-0.2010.09.01.tar.gz 1400267 RMD160 c1d8c171bdfd93c159cdbc53764740da129a8414 SHA1 9edf09c74a1745b753d67eea921bf80651ab8039 SHA256 a224851e56302d345a3c6e9dfa5366d2edcd24b694ef532f0ad253bc9e5290e2 -EBUILD gambit-0.2010.09.01.ebuild 831 RMD160 e6f0bd1223e7523c975e970c98906b999ddd07cb SHA1 2de9d0998ba9f2b6756d9c27254928e63cf82290 SHA256 96744bd116b0b9a49f848f4747a53099f4bd657598bb68c09c61849b71e024ba -MISC ChangeLog 359 RMD160 61a088980ca674bb4d51b1d50416ffc9b17fd6b8 SHA1 7d8af04987f157b826c65077924200cdbac1435b SHA256 89e1927bd763729ecf0f19f48b2f0a42f38b95f5d34c44a9b67573496b8bb3d3 -MISC metadata.xml 328 RMD160 a1513a276c503da0d2973ef2fc64827ab3c478f4 SHA1 431a58575f79b0c8d78d67c82c0ec46630addb3d SHA256 36b55920635d72ec65047c2a925e9724808e66af74996bc120cbbe9aecb43c76 +EBUILD gambit-0.2010.09.01.ebuild 727 RMD160 55d767582d60fdbbfbb4e33e6752b8780943d609 SHA1 d3019f3056855dd91365c358b4c3f512ed8900ef SHA256 6a54e7b6b6ee14f6b3ec251198fd45923bcff71a7dd47914a36777df6684c1a0 +MISC ChangeLog 475 RMD160 0e62465d7c6c63d21cbb702e9cf09d924855669b SHA1 35426332fc8f1d0d73d4671f3e1434ef5d89f262 SHA256 bfef0f8c33685d74423072094f180ecb965baf8b62bfc580198681dd564ee474 +MISC metadata.xml 333 RMD160 7c6f3c7a8c2f1fc4e53dbbea7535ab23c8b96afd SHA1 8597e2ed2eff785cbd94bfbdbd0c272ef604aba4 SHA256 40f8d20bac359daa69a2745564eda564b77c8d1f737158b49d4c60e822423a3e +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F3xYACgkQgAnW8HDreRYJMQCeK0e68CUQ7VO+YMF9cGQgu24g +tT0AmgJhkolF5lamwSFjSagUENm/iAIz +=DVh1 +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/gambit/gambit-0.2010.09.01.ebuild b/sci-mathematics/gambit/gambit-0.2010.09.01.ebuild index 132a798a2..9eea1b2bb 100644 --- a/sci-mathematics/gambit/gambit-0.2010.09.01.ebuild +++ b/sci-mathematics/gambit/gambit-0.2010.09.01.ebuild @@ -2,44 +2,34 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -DESCRIPTION="Gambit: Software Tools for Game Theory" +EAPI=4 -HOMEPAGE="http://www.gambit-project.org/doc/index.html" +WX_GTK_VER="2.8" + +inherit wxwidgets -SRC_URI="mirror://sourceforge/gambit/${P}.tar.gz - " +DESCRIPTION="Gambit: Software Tools for Game Theory" +HOMEPAGE="http://www.gambit-project.org/doc/index.html" +SRC_URI="mirror://sourceforge/gambit/${P}.tar.gz" #http://econweb.tamu.edu/gambit/doc/${PN}-manual-${PV}.pdf #http://econweb.tamu.edu/gambit/doc/${PN}-manual-${PV}.tar.gz LICENSE="GPL-2" - SLOT="0" - KEYWORDS="~amd64 ~x86" +IUSE="X" -#IUSE="wxwindows" -IUSE="X" - -DEPEND="X? ( >=x11-libs/wxGTK-2.6 - =x11-libs/gtk+-1.2* ) - " - -RDEPEND="" +DEPEND=" + X? ( + x11-libs/wxGTK:2.8[X] + x11-libs/gtk+:2 )" +RDEPEND="${DEPEND}" -src_compile() { - # disable +src_configure() { local myconf - if use amd64 - then + if use amd64; then myconf='--disable-enumpoly' - fi + fi econf "${myconf}" \ - "$(use_enable X gui)" ||die - emake ||die + $(use_enable X gui) } - -src_install() { - emake DESTDIR="${D}" install ||die - dodoc NEWS README* AUTHORS ChangeLog -} - diff --git a/sci-mathematics/gambit/metadata.xml b/sci-mathematics/gambit/metadata.xml index f29201e6a..48126bd9b 100644 --- a/sci-mathematics/gambit/metadata.xml +++ b/sci-mathematics/gambit/metadata.xml @@ -1,14 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>dongxuli2011@gmail.com</email> - <name>Dongxu Li</name> -</maintainer> -<use> - <flag name="X"> + <herd>sci</herd> + <maintainer> + <email>dongxuli2011@gmail.com</email> + <name>Dongxu Li</name> + </maintainer> + <use> + <flag name="X"> Enable gui support using wxWidgets. </flag> -</use> + </use> </pkgmetadata> diff --git a/sci-mathematics/gap/ChangeLog b/sci-mathematics/gap/ChangeLog index 5f022efb9..2c0b18866 100644 --- a/sci-mathematics/gap/ChangeLog +++ b/sci-mathematics/gap/ChangeLog @@ -1,7 +1,10 @@ -# ChangeLog for sci-mathematics/yorick -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# ChangeLog for sci-mathematics/gap +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> gap-4.4.12.ebuild: + Cleaned ebuild + *gap-4.4.12 (16 Jan 2009) 16 Jan 2009; Sébastien Fabbro <bicatali@gentoo.org> +gap-4.4.12.ebuild, diff --git a/sci-mathematics/gap/Manifest b/sci-mathematics/gap/Manifest index 072d2de11..6c64b4e03 100644 --- a/sci-mathematics/gap/Manifest +++ b/sci-mathematics/gap/Manifest @@ -1,6 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX 64gap-gentoo.el 372 RMD160 64bfc282eff91a40b46e602f4d91a81d2910d8c8 SHA1 009075a2d4e365e90ab7e095cf3b4c405d766764 SHA256 52aadba56bb25d064c850ee9eb0e8bbc1ea043587b5a7e6d84c9a68e9cead6a3 DIST gap4r4p12.tar.bz2 47715810 RMD160 124f78de675b952032a50c5bc19a49b870410964 SHA1 b6b6b809c0a2ec5ed202fa672517a2199b0bf91e SHA256 5ff56c5eb89b1fd0da9f216dbe1dce8fe44674858b6ad06cb277d36b7960be4d DIST xtom1r1p4.tar.bz2 11480845 RMD160 85db22d9af4e4029e82b5ad213cc9cf4de194041 SHA1 544d738afc3086be93ef2729e85a40f938c8be96 SHA256 5591dfa222d2fb6c4596c3e5c5347db339e08f209798e4a332a0d902035d4f66 -EBUILD gap-4.4.12.ebuild 2007 RMD160 9a92a04d20333525a717f17aa6a5deb232d616fe SHA1 b51eedb49d012de6d220464409f109bb57857885 SHA256 7196bfb90feea9543f1ba9fdfc248ab104b0dfbfe4a30e213fbb53452695d94e -MISC ChangeLog 411 RMD160 0f3fad17a54686427ba6439265cb6c65c0b9424a SHA1 082e314704520a9ec04eb0b3ae7cd13e49ca2236 SHA256 5097281fd76626f84965ecf2e4b9c4f6f3f3cadc1ede1d1097b2130f8932b856 -MISC metadata.xml 792 RMD160 8044670e7dd061b3f5edd4d640216274217ef2c6 SHA1 f21b06eacbe806e8caad323c1a7b2f193d3567a9 SHA256 d4145b4a649e5b35a0d4b7b533308a5df2e156b842f2c64203f8ab1bb9310034 +EBUILD gap-4.4.12.ebuild 1948 RMD160 f3252674a8479786077fca62fd405fd25ea80e0f SHA1 037615f117d4a26a4afd2a51ad277043e1f8ecd0 SHA256 bc22e02c9d1eef1d4ae7876827913fb9f1b3a0954e159d29f44d6485123423c2 +MISC ChangeLog 492 RMD160 198cffe9d67d84563c3d9e15f28629b6db221ac1 SHA1 2fba9cc02b9243fc6bd59a4836a3711f6ed2e0e3 SHA256 012f85fe0617d08ae7ac4599421a56d81a450d730f408e7869e1e3ae2806e5d0 +MISC metadata.xml 887 RMD160 43218e4dbae4867e654810df67c10735f783e296 SHA1 fd76046fe70103bf9271c98c150bd79d054234d7 SHA256 a52507374271a04eaafeb6a55f318986d458f0965f8004c31dc746094505b480 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EwwgACgkQgAnW8HDreRZSdACfRegpxODDGDtk7NDfvOnYiX3N +kMcAoIcswp+H4opK/2TIVFg2Do4qZEV+ +=y2gR +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/gap/gap-4.4.12.ebuild b/sci-mathematics/gap/gap-4.4.12.ebuild index 916df83da..d45ce3a4c 100644 --- a/sci-mathematics/gap/gap-4.4.12.ebuild +++ b/sci-mathematics/gap/gap-4.4.12.ebuild @@ -1,14 +1,10 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit versionator elisp-common -DESCRIPTION="System for computational discrete algebra" -HOMEPAGE="http://www.gap-system.org/" -SLOT="0" -IUSE="emacs vim-syntax xtom" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86" +EAPI=3 + +inherit elisp-common versionator XTOM_VERSION=1r1p4 @@ -17,19 +13,25 @@ PV2=$(get_version_component_range 3 ) PV1=$(replace_version_separator 1 'r' ${PV1} ) PV2=${PV1}p${PV2} -SRC_URI="ftp://ftp.gap-system.org/pub/gap/gap4/tar.bz2/${PN}${PV2}.tar.bz2 +DESCRIPTION="System for computational discrete algebra" +HOMEPAGE="http://www.gap-system.org/" +SRC_URI=" + ftp://ftp.gap-system.org/pub/gap/gap4/tar.bz2/${PN}${PV2}.tar.bz2 xtom? ( ftp://ftp.gap-system.org/pub/gap/gap4/tar.bz2/xtom${XTOM_VERSION}.tar.bz2 )" -RDEPEND="emacs? ( virtual/emacs ) - vim-syntax? ( || ( app-editors/vim app-editors/gvim ) )" +SLOT="0" +IUSE="emacs vim-syntax xtom" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86" -#### delete the next line when moving this ebuild to the main tree! -RESTRICT=mirror +RDEPEND=" + emacs? ( virtual/emacs ) + vim-syntax? ( || ( app-editors/vim app-editors/gvim ) )" +DEPEND="${RDEPEND}" S="${WORKDIR}"/${PN}${PV1} src_compile() { - econf emake CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" compile || die "emake failed" } diff --git a/sci-mathematics/gap/metadata.xml b/sci-mathematics/gap/metadata.xml index 8173924cd..b4fd03a58 100644 --- a/sci-mathematics/gap/metadata.xml +++ b/sci-mathematics/gap/metadata.xml @@ -1,12 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>A.G.Grozin@inp.nsk.su</email> - <name>Andrey Grozin</name> -</maintainer> -<longdescription lang="en"> + <herd>sci</herd> + <maintainer> + <email>A.G.Grozin@inp.nsk.su</email> + <name>Andrey Grozin</name> + </maintainer> + <longdescription lang="en"> Groups, Algorithms, Programming is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands @@ -16,4 +16,5 @@ representations, rings, vector spaces, algebras, combinatorial structures, and more. </longdescription> + <use><flag name="xtom">Automatically generated description for xtom</flag></use> </pkgmetadata> diff --git a/sci-mathematics/gappa/ChangeLog b/sci-mathematics/gappa/ChangeLog index 8175f6985..c5da9beb7 100644 --- a/sci-mathematics/gappa/ChangeLog +++ b/sci-mathematics/gappa/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*gappa-0.15.0 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -gappa-0.14.0.ebuild, + +gappa-0.15.0.ebuild: + Version Bump + 13 Feb 2011; J.-C. Demay <jcdemay@gmail.com> +gappa-0.14.0.ebuild, -gappa-0.13.0.ebuild: version bump diff --git a/sci-mathematics/gappa/Manifest b/sci-mathematics/gappa/Manifest index f8b83264f..f35722f3e 100644 --- a/sci-mathematics/gappa/Manifest +++ b/sci-mathematics/gappa/Manifest @@ -1,4 +1,14 @@ -DIST gappa-0.14.0.tar.gz 388606 RMD160 68807095b69e36d078174b76f355a07623c359fe SHA1 87e7d92499b7d2f3541f3cac43f60bf41fe00b64 SHA256 5b18e9365faef9f53d232c928fec76609fdcdae0268206f922461de7e63d9448 -EBUILD gappa-0.14.0.ebuild 1319 RMD160 8307a6a9f67fd7dce79b5ad750fa865164ed2d88 SHA1 c8654c4f8dd00f98eefac9cb809fca202fc80a43 SHA256 a7f293571b3c3e7db18f5cc6f610394edf9b939535f7a8d8b5b8ff6410cce3f7 -MISC ChangeLog 614 RMD160 1fdbd205aae6bd2912d67bde1f661d95d6e4012d SHA1 6e4b0f0ddc2ca9117e5c5305be5567823b06ea0f SHA256 6cdfe8f8fd83235509cf140bec6784d0de34b238f31fc3acde0495d025cdcbed +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +DIST gappa-0.15.0.tar.gz 396853 RMD160 d88d4554d3a37e8709ca20e726c2140125b178d9 SHA1 c34f0f5864307c572577cd67878d25a2fd57230c SHA256 358c00667ba2cf021cf41103f4013f50dc1428e4125624cdac2007bd022f376a +EBUILD gappa-0.15.0.ebuild 1154 RMD160 5c60e80a560ecd31dd94f63a55a90f6e4198e6df SHA1 c7b2e400cfeb26c327d3d2bc4a8ce250f885957b SHA256 485a03b2f172b2396c1912e139acb87d856db0bed8b2c0c598ef8a229d833749 +MISC ChangeLog 752 RMD160 4e52bae5645ce56ef6cc2211bab5105f11cb321f SHA1 27bbc7244500fef6b2122806fc5196c84514de6c SHA256 9fb1de9e29cb21bf38e927ab752507d08d6f0bede0c0b320bbf504bd219fa16f MISC metadata.xml 542 RMD160 9e7e7c72c403c90ed49ad797d4810b3cdef4b1d1 SHA1 e164614670cda7a42656824856e56297e5b4e85a SHA256 3ec0a6e959d961e8eb7c8a357c7cdd563c4fcff7ed717b2d7c734c76fa0b7cd7 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GC3IACgkQgAnW8HDreRYVywCfYSJuDzqZJnppqkQsGBe5DnDa +Qk0AoMzZDkv44464Sv56vmtEoOZKbQEC +=vaK1 +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/gappa/gappa-0.14.0.ebuild b/sci-mathematics/gappa/gappa-0.14.0.ebuild deleted file mode 100644 index 1339151e9..000000000 --- a/sci-mathematics/gappa/gappa-0.14.0.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -DESCRIPTION="A tool to help verifying and proving properties on floating-point or fixed-point arithmetic." -HOMEPAGE="http://gappa.gforge.inria.fr/" -SRC_URI="http://gforge.inria.fr/frs/download.php/26856/${P}.tar.gz" - -LICENSE="|| ( CeCILL-2.0 GPL-2 )" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~sparc ~x86" -IUSE="doc" - -RDEPEND="dev-libs/gmp - dev-libs/mpfr - dev-libs/boost" -DEPEND="${RDEPEND} - doc? ( app-text/texlive - app-text/ghostscript-gpl - app-doc/doxygen )" - -src_unpack() { - unpack ${A} - mv ${S/%0.14.0/0.13.0} ${S} - cd ${S} -} - -src_prepare() { - sed -i doc/doxygen/Doxyfile \ - -e "s/GENERATE_LATEX = NO/GENERATE_LATEX = YES/g" \ - -e "s/USE_PDFLATEX = NO/USE_PDFLATEX = YES/g" \ - -e "s/PDF_HYPERLINKS = NO/PDF_HYPERLINKS = YES/g" -} - -src_compile(){ - emake DESTDIR="/" || die "emake failed" - - if use doc; then - cd doc/doxygen - doxygen Doxyfile || die "doxygen failed" - cd "${S}" - emake -C doc/doxygen/latex || die "emake doc failed" - fi -} - -src_install(){ - emake install DESTDIR="${D}" || die "emake install failed" - dodoc AUTHORS NEWS README - - if use doc; then - mv doc/doxygen/latex/refman.pdf ./gappa.pdf - dodoc ./gappa.pdf - fi -} diff --git a/sci-mathematics/gappa/gappa-0.15.0.ebuild b/sci-mathematics/gappa/gappa-0.15.0.ebuild new file mode 100644 index 000000000..525651f73 --- /dev/null +++ b/sci-mathematics/gappa/gappa-0.15.0.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +ID=28594 + +DESCRIPTION="Verifying and proving properties on floating-point or fixed-point arithmetic" +HOMEPAGE="http://gappa.gforge.inria.fr/" +SRC_URI="https://gforge.inria.fr/frs/download.php/${ID}/${P}.tar.gz" + +LICENSE="|| ( CeCILL-2.0 GPL-2 )" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~sparc ~x86" +IUSE="doc" + +RDEPEND=" + dev-libs/boost + dev-libs/gmp + dev-libs/mpfr" +DEPEND="${RDEPEND} + doc? ( + app-text/texlive + app-text/ghostscript-gpl + app-doc/doxygen )" + +src_prepare() { + if use doc; then + sed \ + -i doc/doxygen/Doxyfile \ + -e "s/GENERATE_LATEX = NO/GENERATE_LATEX = YES/g" \ + -e "s/USE_PDFLATEX = NO/USE_PDFLATEX = YES/g" \ + -e "s/PDF_HYPERLINKS = NO/PDF_HYPERLINKS = YES/g" || die + fi +} + +src_compile(){ + emake DESTDIR="/" + + if use doc; then + cd doc/doxygen + doxygen Doxyfile || die "doxygen failed" + cd "${S}" + emake -C doc/doxygen/latex + fi +} + +src_install(){ + default + + if use doc; then + mv doc/doxygen/latex/refman.pdf ./gappa.pdf + dodoc ./gappa.pdf + fi +} diff --git a/sci-mathematics/gappalib-coq/ChangeLog b/sci-mathematics/gappalib-coq/ChangeLog index db6238ae6..b4d33094c 100644 --- a/sci-mathematics/gappalib-coq/ChangeLog +++ b/sci-mathematics/gappalib-coq/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-mathematics/gappalib-coq -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*gappalib-coq-0.16.0 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -gappalib-coq-0.14.1.ebuild, + +gappalib-coq-0.16.0.ebuild: + Version Bump + 04 Jul 2010; J.-C. Demay <jcdemay@gmail.com> +gappalib-coq-0.14.1.ebuild, -gappalib-coq-0.13.ebuild: version bump diff --git a/sci-mathematics/gappalib-coq/Manifest b/sci-mathematics/gappalib-coq/Manifest index cf504fbf0..eeb3c1422 100644 --- a/sci-mathematics/gappalib-coq/Manifest +++ b/sci-mathematics/gappalib-coq/Manifest @@ -1,4 +1,14 @@ -DIST gappalib-coq-0.14.1.tar.gz 110155 RMD160 a9cc0a6c0400b2675cc7c8caddc5a4a5af3351d0 SHA1 3fdd4ba1b03619548a2c0345b3035503c9aee764 SHA256 4a17321854d9ce3737d02ad5c3c8f1fbb30521ee6dce2e7af814b604eff3efd6 -EBUILD gappalib-coq-0.14.1.ebuild 849 RMD160 7a1f294bd89c04b6ef5fa66d0b866ef833101967 SHA1 0e629e3e4250ce53e8f10928f9c19f75fcb3079c SHA256 2da7e24a8362eb04bc1e5d3bcab20eb5ddf4eae1005d2910db1afb08671501db -MISC ChangeLog 459 RMD160 6f0b6dcb03ddc498f5e92a989ddf098ce71e46fc SHA1 3b5e90dae0d5bd82d08f078730433358085564f5 SHA256 15915817ec8908eda3d7777c217de65849414862e6cef3d43ea0d15b0e8d7c7d +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +DIST gappalib-coq-0.16.0.tar.gz 111747 RMD160 6e59d50be1b178da78a7a950e15e4c6f926861e1 SHA1 da7f54a7d839e8bee1fd8e2acedcc1dbd061f0ad SHA256 63c98fda2ef70de13de7bc8a0b5de243a1d75020fe767494f5c2c79a171a8ef6 +EBUILD gappalib-coq-0.16.0.ebuild 704 RMD160 2e9dc302fa3d571abbf2a26046756c5d5d715e79 SHA1 2daad7730bb66ee43f2b75936a29ac62a440da0d SHA256 a74842748439c2641cca16f940da70d0182806a4ee2b7cb811b2751ad8deed18 +MISC ChangeLog 618 RMD160 84c39048274ec8df7beb6b2019d57d9d4eedb9ff SHA1 96708b8e5de3c9d4755c7b28f78ac870f3231e6a SHA256 70a5a0aa23fac75a1eae971c9fc56a5ddc193090e4628b7362f26abac0497c62 MISC metadata.xml 443 RMD160 55e58c43af6e41bc5601ca2543b2f474d102a59f SHA1 75fdfc8f6a45175d41b6edfc537e857a205ce3ab SHA256 f799ef0a949ecbc8353f099966b0b11a2022cf812c4c80a331a40356773561fe +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GD0IACgkQgAnW8HDreRZLKACgtPmKGEPrxTDa2dqm61KhNfKF +3kYAoLaDTEiXRBgcW/fMVChDBdNpFPxx +=jenJ +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/gappalib-coq/gappalib-coq-0.14.1.ebuild b/sci-mathematics/gappalib-coq/gappalib-coq-0.14.1.ebuild deleted file mode 100644 index 71a67fab0..000000000 --- a/sci-mathematics/gappalib-coq/gappalib-coq-0.14.1.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -DESCRIPTION="This library allows the certificates Gappa generates to be imported by the Coq." -HOMEPAGE="http://gappa.gforge.inria.fr/" -SRC_URI="http://gforge.inria.fr/frs/download.php/28157/${P}.tar.gz" - -LICENSE="LGPL-2" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~sparc ~x86" -IUSE="" - -DEPEND="sci-mathematics/gappa - sci-mathematics/coq - sci-mathematics/flocq" -RDEPEND="${DEPEND}" - -src_prepare(){ - sed -i configure -e "s/if test \"\$libdir\" = '\${exec_prefix}\/lib';/ \ - if test \"\$libdir\" = '\${exec_prefix}\/lib' -o "\$libdir" = \"\${prefix}\/lib64\";/g" -} - -src_compile(){ - emake DESTDIR="/" || die "emake failed" -} - -src_install(){ - emake install DESTDIR="${D}" || die "emake install failed" - dodoc NEWS README AUTHORS -} - diff --git a/sci-mathematics/gappalib-coq/gappalib-coq-0.16.0.ebuild b/sci-mathematics/gappalib-coq/gappalib-coq-0.16.0.ebuild new file mode 100644 index 000000000..f0b130cef --- /dev/null +++ b/sci-mathematics/gappalib-coq/gappalib-coq-0.16.0.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +ID=28596 + +DESCRIPTION="Gappa certificate generator to be imported by the Coq" +HOMEPAGE="http://gappa.gforge.inria.fr/" +SRC_URI="http://gforge.inria.fr/frs/download.php/${ID}/${P}.tar.gz" + +LICENSE="LGPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="" + +DEPEND=" + sci-mathematics/gappa + sci-mathematics/coq + sci-mathematics/flocq" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed \ + -i configure \ + -e "s/if test \"\$libdir\" = '\${exec_prefix}\/lib';/ \ + if test \"\$libdir\" = '\${exec_prefix}\/lib' -o "\$libdir" = \"\${prefix}\/lib64\";/g" +} + +src_compile(){ + emake DESTDIR="/" +} diff --git a/sci-mathematics/giac/ChangeLog b/sci-mathematics/giac/ChangeLog index b9938a583..65e10b10e 100644 --- a/sci-mathematics/giac/ChangeLog +++ b/sci-mathematics/giac/ChangeLog @@ -1,7 +1,10 @@ -# ChangeLog for sci-mathematics/frama-c +# ChangeLog for sci-mathematics/giac # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> giac-0.9.2.ebuild: + Cleaned ebuild + 16 May 2011; J.-C. Demay <jcdemay@gmail.com> giac-0.9.2.ebuild, +metadata.xml: QA fixes diff --git a/sci-mathematics/giac/Manifest b/sci-mathematics/giac/Manifest index c01b7aa39..2ef3e1f83 100644 --- a/sci-mathematics/giac/Manifest +++ b/sci-mathematics/giac/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST giac-0.9.2.tar.gz 22657411 RMD160 58264abf8b15c9a4f9f612f871787d08f754af56 SHA1 7eb0af9eab7bdfacd97942a952657cf47a250e21 SHA256 dbbb8b4996aa79ecedee8ca5406a92f69c8da7d868e5b4fba2aa5f8745b4d6bf -EBUILD giac-0.9.2.ebuild 1523 RMD160 96efee50fb222f10a1845b9445d6503eac2b08fd SHA1 00caca74c3f80533e8de0789fad468288ff11e56 SHA256 1ec86cf9531ca7a4ee9068ed3ee500acc10ff84b304e96f4aa29af33af98d30b -MISC ChangeLog 219 RMD160 2609a7a2328b01fe8089f82b8d73e1d16d67bfac SHA1 73d54afa9e8f8808d6d4c7432b043d2b1580885d SHA256 f45a491256c85857a1235decfd7ebc8513007934de9b455779f7e6ff47175665 +EBUILD giac-0.9.2.ebuild 1428 RMD160 25cca2d95ee890b611fc42c3f49f5ac7c7d2b99b SHA1 2832afc047ac27570823778ea95fafc6bb52c608 SHA256 3c6b97fb96284aae81163c19abd8020575d4cdb504d97a3caef4424470a274ef +MISC ChangeLog 300 RMD160 fc18beba9adf312ad9163b42e8f1cef2f84cf502 SHA1 97af6727e002085ec9c4b54072d6d72ee8525a06 SHA256 83389e202903be8d142c61108ca0040503fed7de3b2b24cb31a2ca8a7622ff80 MISC metadata.xml 662 RMD160 6211873854a7b62f46485b68f52a1aefbc5c2dc9 SHA1 8c80b6346f56ad5250095e5fea5bf80c08864e8f SHA256 412112d6e9cf060c5d2a46e5197e026371e700a1a5cae7a2dfbf0320388ec4ed +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GEG8ACgkQgAnW8HDreRZXmwCgu3Doa2zgJOhwHSJkqnC5Tkh4 +ZgkAoJcXmS8D8eE+tLSrSUkh/5F5Pd+R +=bzbL +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/giac/giac-0.9.2.ebuild b/sci-mathematics/giac/giac-0.9.2.ebuild index 428faaefe..a1e4f23d6 100644 --- a/sci-mathematics/giac/giac-0.9.2.ebuild +++ b/sci-mathematics/giac/giac-0.9.2.ebuild @@ -2,27 +2,30 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="4" +EAPI=4 DESCRIPTION="A free C++ CAS (Computer Algebra System) library and its interfaces" HOMEPAGE="http://www-fourier.ujf-grenoble.fr/~parisse/giac.html" SRC_URI="ftp://ftp-fourier.ujf-grenoble.fr/xcas/${P}.tar.gz" -LICENSE="GPL-2" +LICENSE="GPL-2" SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="doc examples fltk" -RDEPEND=">=dev-libs/gmp-3 - >=sys-libs/readline-4.2 - fltk? ( >=x11-libs/fltk-1.1.9 ) - dev-libs/mpfr - sci-libs/gsl - >=sci-mathematics/pari-2.3 - >=dev-libs/ntl-5.2" +DEPEND=" + dev-libs/gmp + sys-libs/readline + dev-libs/mpfr + sci-libs/gsl + >=sci-mathematics/pari-2.3 + >=dev-libs/ntl-5.2 + fltk? ( x11-libs/fltk:1 )" +RDEPEND="${DEPEND}" src_prepare(){ - sed -e "s:\$(prefix)/share:\$(DESTDIR)\$(prefix)/share:g" \ + sed \ + -e "s:\$(prefix)/share:\$(DESTDIR)\$(prefix)/share:g" \ -e "s:config.h \$(includedir)/giac:config.h \$(DESTDIR)\$(includedir)/giac:g" \ -e "s:\$(DESTDIR)\$(DESTDIR):\$(DESTDIR):g" \ -i `find -name Makefile\*` @@ -32,26 +35,24 @@ src_prepare(){ } src_install() { - emake DESTDIR="${D}" install || die "emake install failed" - mv ${D}/usr/bin/{aide,giac-help} - rm ${D}/usr/bin/*cas_help - dodoc AUTHORS ChangeLog COPYING INSTALL NEWS README TROUBLES + default + mv "${D}"/usr/bin/{aide,giac-help} + rm "${D}"/usr/bin/*cas_help if use !fltk; then - rm ${D}/usr/bin/x* + rm "${D}"/usr/bin/x* fi if use !doc; then - rm -R ${D}/usr/share/doc/giac ${D}/usr/share/giac/doc/ + rm -R "${D}"/usr/share/doc/giac "${D}"/usr/share/giac/doc/ else for LANG in el en es fr pt; do if echo ${LINGUAS} | grep -v $LANG &> /dev/null; then - rm -R ${D}/usr/share/giac/doc/$LANG + rm -R "${D}"/usr/share/giac/doc/$LANG else - ln ${D}/usr/share/giac/doc/aide_cas ${D}/usr/share/giac/doc/$LANG/aide_cas + ln "${D}"/usr/share/giac/doc/aide_cas "${D}"/usr/share/giac/doc/$LANG/aide_cas fi done fi if use !examples; then - rm -R ${D}/usr/share/giac/examples + rm -R "${D}"/usr/share/giac/examples fi } - diff --git a/sci-mathematics/hypre/ChangeLog b/sci-mathematics/hypre/ChangeLog index 140692c5c..305a54ee2 100644 --- a/sci-mathematics/hypre/ChangeLog +++ b/sci-mathematics/hypre/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> hypre-2.6.0b.ebuild, + hypre-2.7.0b.ebuild: + Added fortran-2.eclass support + *hypre-2.7.0b (19 Mar 2011) 19 Mar 2011; Jens-Malte Gottfried <jmgottfried@web.de> diff --git a/sci-mathematics/hypre/Manifest b/sci-mathematics/hypre/Manifest index 736fee136..409872108 100644 --- a/sci-mathematics/hypre/Manifest +++ b/sci-mathematics/hypre/Manifest @@ -1,7 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX makefile-mpicxx.patch 425 RMD160 286af0f70526b19937dfa4408ad555bb02860cf4 SHA1 ad712f84c5232ecb4dd8ad957562c4b5a684bfc4 SHA256 2410c1dfc8cc991ac61eb7d741ef8c3c1bcbc54f5f2ced949f7c61c9d5c5ab84 DIST hypre-2.6.0b.tar.gz 9599317 RMD160 4d683b41eb142b8aaf224ff5742d781a0c8ccea4 SHA1 7ef8ff0e980c3e78a0f55e3944f6d13c44ff7046 SHA256 b36a6c885d4ecf152ff476b23c83ef9f2dcb1a4c7661f80939fd1dae7590409c DIST hypre-2.7.0b.tar.gz 9819362 RMD160 a29fcf7f370108a1c3420887a96b7dfce8a9a99e SHA1 4f8468f23e2a7bc9b964dbae27840858de8e3f80 SHA256 76415c586028a986a2294267c7448bdddd4191005288b45458c1d5b3ceacf572 -EBUILD hypre-2.6.0b.ebuild 1175 RMD160 7a920c65067e03d00a4fd26c9b70c528e123accc SHA1 84046f3ea877c0d7dae2dae577e740a5d36ea7a5 SHA256 d6a93d023d4b7ab2baa805365ca75c3658e1d806657d2dd7df774680fd549be7 -EBUILD hypre-2.7.0b.ebuild 1175 RMD160 7a920c65067e03d00a4fd26c9b70c528e123accc SHA1 84046f3ea877c0d7dae2dae577e740a5d36ea7a5 SHA256 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c0cc8d6ab9385750af753ddc504299ed90a70b5c4c655f6c77d865917a8829c9 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4AhCUACgkQgAnW8HDreRaXDwCgw8t0A/IJW2kH88v1gtLK35df +EUAAn1WbyZmjTAXedQXmmu1sIe0FElw4 +=3KHd +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/hypre/hypre-2.6.0b.ebuild b/sci-mathematics/hypre/hypre-2.6.0b.ebuild index 80be0c344..ab36140be 100644 --- a/sci-mathematics/hypre/hypre-2.6.0b.ebuild +++ b/sci-mathematics/hypre/hypre-2.6.0b.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit eutils +inherit eutils fortran-2 DESCRIPTION="Parallel High Performance Preconditioners library for scalable solution of linear systems" diff --git a/sci-mathematics/hypre/hypre-2.7.0b.ebuild b/sci-mathematics/hypre/hypre-2.7.0b.ebuild index 80be0c344..ab36140be 100644 --- a/sci-mathematics/hypre/hypre-2.7.0b.ebuild +++ b/sci-mathematics/hypre/hypre-2.7.0b.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit eutils +inherit eutils fortran-2 DESCRIPTION="Parallel High Performance Preconditioners library for scalable solution of linear systems" diff --git a/sci-mathematics/lattE-macchiato/Manifest b/sci-mathematics/lattE-macchiato/Manifest index d322a51a4..8adff9d46 100644 --- a/sci-mathematics/lattE-macchiato/Manifest +++ b/sci-mathematics/lattE-macchiato/Manifest @@ -3,23 +3,13 @@ Hash: SHA1 AUX buildpackages.patch 10897 RMD160 1d208b64ae14e8806883cf062bcb02682ecdc01d SHA1 142ac3fc4b61fea53a9c39c7c2983d3f6743e2a2 SHA256 afc48c1ccb7081722096e27c33aa5979b4c46beb1bdf268a9049ccef9bb76927 DIST latte-for-tea-too-1.2-mk-0.9.3.tar.gz 12782533 RMD160 c8577dad33e0c7c23166fec4d931429577eb4339 SHA1 79bf3d2c5ae8036a934b03b7758e0794c1808a9e SHA256 3096587528f6012ee4545d51610a989f03447dc103734352cacd37182a499f48 -EBUILD lattE-macchiato-0.9.3.ebuild 1306 RMD160 9a283098933b7a429e71711ba9ea32577bc01191 SHA1 475f5559d825cf066a9fafae0e27b80708e13bf6 SHA256 3e9e79bc8e5ae7155904fec9bd98305ca9d57eeb04694d9f78cf236bbc4ea5b2 +EBUILD lattE-macchiato-0.9.3.ebuild 1306 RMD160 f5771c63f1dce41ba13ac5023af16eff35d7a3f8 SHA1 f1552f5c7641369ae546f8812ab2e34d3123a244 SHA256 ac8a5714b4e914cd9060c6052b346ff5efbfc8f6c07164f9624660ea9be5251b MISC ChangeLog 468 RMD160 a638f93d2543901b113f9f3dd1de8c287dfbf25c SHA1 1392eaf16ac16c05eb48c7d77a5de599e3eaae41 SHA256 a48797144bf642cb9b4df17a2492fd3198665df25a339720887331e8dedd4307 MISC metadata.xml 361 RMD160 273db3a009b85938f85e60ea0d34d6fc625f9477 SHA1 7f6e903d81af55b08c7dbb9feb4f7ad39852a23e SHA256 71a0f19b08b1e752e754bbc5faf15880601d00c5b9df2bc5ca5a3b8e93e83b7f -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMISV2AAoJENwGBM22xffepKoP/0iMH2/+1tzEalAKE6gpHWzh -wCkjVNpyKhTKBrWdved4QaC16POD9IbDg/HrBsG9KOQZkKiOFs/ImQD9FTs5liuQ -Ls3EKKSJJAJBYoo8eDkCaPu2Q9wQuibzwU7Q7X+q9+rsYTy7pJ3DcYJrmyKqFut2 -CSApRxrH6OF1noMBhyNmk/jhTpXUjBewWRqqSMMIQLdzBV//YcW8MSBh+kDuKCqu -ZYLn3uZ4ID/1RQY4Er5YIK23jj7qY+sX/pLSQ0zObN03FAC2fCegMQklwUHmUQ+M -XrUeWri1iZhcWBKunpnLplvavD7i19X4MVMHedeRQm25SfIaAS6vYLxIa9thjJH/ -RuSicDQ3jpEzBb1eJvOBvYzDF8vamx5Dw7mfmiWgzFpQgdvUIEAcUeGeUxo2vvA7 -ZyGtsQohFwOLEVwBSGPDzUkS4G7EcIhDrBHc/IbjWSp7yMp94pagMJNwIVMEm3no -mfPG+9eXTKPaKZN0JRuDxDx5HmqVfTrpMUm7+v19GWgunVMO6WhD9MRznGG3A0Mh -eHLEhjba2OTRqBmJzkcaoKDX1XDamijEWxb/Vqo/vr0TfIUZ0hUhdWZvNP9MPrAw -Jx7TOfUiqWeA7tBQj363iX/JyN8HD7j4IJgkHWMJZormoKh4ZzRfdK3VADgXVXyz -/UMXtZUaJgpnwnkZVr8g -=zVz4 +iEYEARECAAYFAk4EqK0ACgkQgAnW8HDreRZ5JwCffiCSq4isd4rw1CQAuX09Js+X +PGIAoIwnkHQEC8ZTMfyWr2JjGO3MDgpk +=d206 -----END PGP SIGNATURE----- diff --git a/sci-mathematics/lattE-macchiato/lattE-macchiato-0.9.3.ebuild b/sci-mathematics/lattE-macchiato/lattE-macchiato-0.9.3.ebuild index 7e59439ec..0df012b68 100644 --- a/sci-mathematics/lattE-macchiato/lattE-macchiato-0.9.3.ebuild +++ b/sci-mathematics/lattE-macchiato/lattE-macchiato-0.9.3.ebuild @@ -4,7 +4,7 @@ EAPI="2" -inherit eutils flag-o-matic autotools +inherit autotools eutils flag-o-matic DESCRIPTION="lattE-macchiato consists of tools for lattice point enumeration" SRC_URI="http://www.math.ucdavis.edu/~mkoeppe/latte/download/latte-for-tea-too-1.2-mk-0.9.3.tar.gz" diff --git a/sci-mathematics/netgen/Manifest b/sci-mathematics/netgen/Manifest index 309c1b72b..dcaa0c271 100644 --- a/sci-mathematics/netgen/Manifest +++ b/sci-mathematics/netgen/Manifest @@ -4,13 +4,13 @@ Hash: SHA1 AUX netgen.desktop 175 RMD160 f801118f44d826b1b6335a07fcb1706f6e9fd502 SHA1 daf39d365fe782b5dc1416e427e813fb74ab1e29 SHA256 bfffdfe0a573ef80e689001a8864e3691b9c3e53aabdb235c9be3682c0461c07 AUX netgen.png 4220 RMD160 05fb7ef5da0075c7ccc77e7b6084974d2309e798 SHA1 eee96e5b55c62379580bfe3cd873d7ddc87dba05 SHA256 4db00f0c652265728d994fc5b9ab8d65a91b2704d1b939c334c789d358b10dd3 DIST netgen-4.9.13.tar.gz 1829916 RMD160 36553ee92e943bf9857de1880857f6618ce77228 SHA1 95eab8ab2f8ead3737586755b0f8100ce8301531 SHA256 a5f188bb0fafc0536389314efb8fe6d294b93512b54f2b67c9a3e5431c3b0412 -EBUILD netgen-4.9.13.ebuild 2139 RMD160 8b008d4d8cffbc6bb764015b40fc0c724605e0ac SHA1 af84c90f3613fef81b3ecd98f8e0d01eb623afd1 SHA256 7636ed875004b755c42cb90e1a2b58a1874f739cac578726d2b6f4e0903a1187 +EBUILD netgen-4.9.13.ebuild 2139 RMD160 ba4e218965d25c7068717163be26c04cb8e11d39 SHA1 6054273538b4e4967fd640560b384f80e676f135 SHA256 bf0452f5a14be05b08e2713953f5e7e16fca0c6678037813687a4395e881c54a MISC ChangeLog 2623 RMD160 678c5997fbaf3fdc85df86880ab3f8720fbdba6b SHA1 210670fc69137f37cdecccc48473ff47858a7d72 SHA256 44abc7617041aada77a85c260d133ace47d1d86b95863684517fef65ffcfa25f MISC metadata.xml 233 RMD160 258648efcb3283d6b5b57e0f83f5b7e70e2e8934 SHA1 7ffea1043099218d27a7d14fa7650a23f730597c SHA256 778cb286d3500e67c946ae599348456970be42cddc9e6a5f683633e46d244066 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk196noACgkQgAnW8HDreRbHtQCfcEnn3qv6WhQWE2YQPAxpvs5r -7/oAoJj0MCmF5Nyt1qybK1kbnVuHZkL+ -=g2LI +iEYEARECAAYFAk4EqLIACgkQgAnW8HDreRapWACgmdLeEjUN7K2WjLfi+EV+dT/X +aX4AoNHomcff/rzB8bIfa82M6mqx0oXi +=MYI5 -----END PGP SIGNATURE----- diff --git a/sci-mathematics/netgen/netgen-4.9.13.ebuild b/sci-mathematics/netgen/netgen-4.9.13.ebuild index 7b4639ec5..367f84cdb 100644 --- a/sci-mathematics/netgen/netgen-4.9.13.ebuild +++ b/sci-mathematics/netgen/netgen-4.9.13.ebuild @@ -4,7 +4,7 @@ EAPI="2" -inherit eutils versionator multilib flag-o-matic +inherit eutils flag-o-matic multilib versionator DESCRIPTION="NETGEN is an automatic 3d tetrahedral mesh generator" HOMEPAGE="http://www.hpfem.jku.at/netgen/" @@ -12,7 +12,7 @@ SRC_URI="mirror://sourceforge/netgen-mesher/${P}.tar.gz" LICENSE="LGPL-2.1" KEYWORDS="~amd64 ~x86" -IUSE="opencascade jpeg -mpi -ffmpeg" +IUSE="-ffmpeg jpeg -mpi opencascade" SLOT="0" DEPEND="dev-tcltk/tix diff --git a/sci-mathematics/normaliz/ChangeLog b/sci-mathematics/normaliz/ChangeLog index feef2bf21..4f1814921 100644 --- a/sci-mathematics/normaliz/ChangeLog +++ b/sci-mathematics/normaliz/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-mathematics/normaliz -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> normaliz-2.2.ebuild, + metadata.xml: + Cleaned ebuild, unused local USE-description + 03 Nov 2010; Thomas Kahle <tomka@gentoo.org> -normaliz-2.5.ebuild, -normaliz-2.5-r1.ebuild, -files/normaliz-2.5-makefile.patch: moved to main tree, 2.2 version stays for macaulay2 diff --git a/sci-mathematics/normaliz/Manifest b/sci-mathematics/normaliz/Manifest index 4e45c1b4c..552d45fe6 100644 --- a/sci-mathematics/normaliz/Manifest +++ b/sci-mathematics/normaliz/Manifest @@ -2,15 +2,13 @@ Hash: SHA256 DIST Normaliz2.2Linux32.zip 3712125 RMD160 0b223dc7996c5b3d1d4b2d009c718043ee7647e9 SHA1 e3b518164c8c6d22f6303b357a337fdc7dadae77 SHA256 9588942dc63a999070341f5b84e4eeab318bf5c610a5403d909793f9931f1263 -EBUILD normaliz-2.2.ebuild 781 RMD160 2a3e08479875f799f85a8116648c5f432903a2d9 SHA1 8db64bfd896ef270ce28be7ae23a2156f589a654 SHA256 d028cf3aa12706dd608512b7c847824bc9195d0cf8988eb6b18cda9b268779ec -MISC ChangeLog 945 RMD160 d7c637255d3e275df7971e07dde3b855df9e19c8 SHA1 1101075e894b4eea64ec359a24428e9e0db832bf SHA256 8de677a73da9c3fa180e30078a956d7702cca68bc3a93964d2d0fefb4884584d -MISC metadata.xml 622 RMD160 061c75168a8d9b3ba45c3540c8a237f11dfd2870 SHA1 59cf06140e04d754796ef4f1c776ddb3fb57fde4 SHA256 d6a6dd3aa1f8749303d3072a15504b2fe5900cc947a16a14d9c3f61e06612075 +EBUILD normaliz-2.2.ebuild 711 RMD160 0a6a78f84ffcd360aab4b73bb3ae3334ece425d6 SHA1 705364715b3db9606d1924ae2644386d166916a4 SHA256 d87e8239cd8f88450f7f5f2c1229e445c91fd6147f9204818ee0cec1777509c7 +MISC ChangeLog 1077 RMD160 0dcaa7ea2ae72902d9c7cf455e91e7f940d8bff0 SHA1 5f3296b66987650ed9e5845afdb04235322eefa8 SHA256 b7ecc17a0ea681b45f12fe2dde6ac5488370d8d7d11d237f9e612e8017f47e19 +MISC metadata.xml 425 RMD160 33f71761120b6561fcf6f6b56a401c52ca50fd98 SHA1 52e23a5956e77d66bb9af553fc5c9904cfbaed30 SHA256 7c92bd211c37fbd4395b790e4fb1481482316c6202f02d1b26c5ed9d59df4dbb -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iJwEAQEIAAYFAkzRHT8ACgkQQYXt1pFHaaH6zAP/TrvIQi5VTcUHnqq4EVmM8/sO -11I5HjGTD11uquGvG5C7/+6pNhYEQNL+v5hUTvkvPPmcSiM2ZK35jFdy5Xu22Q90 -Z5cVV4HD9YgvzGvevnfoqAPMV+dw37657QC7mCf2MNpoomIh8tc6z8/fx1BoSy7Y -dQuh8VE8KLSXVZ8vBls= -=eU33 +iEYEAREIAAYFAk4GCXcACgkQgAnW8HDreRZA8ACdEClfr27yjEbp7sXerFlzCYBO +CPMAnjhdDCYyEZAeWBCyy3Celgk6lZmA +=I6T6 -----END PGP SIGNATURE----- diff --git a/sci-mathematics/normaliz/metadata.xml b/sci-mathematics/normaliz/metadata.xml index 2ec8c8221..9ca68fe61 100644 --- a/sci-mathematics/normaliz/metadata.xml +++ b/sci-mathematics/normaliz/metadata.xml @@ -1,16 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>tom111@gmx.de</email> - <name>Thomas Kahle</name> -</maintainer> -<use> - <flag name="extras"> Install the java-gui and Macaulay2/Singular packages.</flag> - <flag name="optimization">Accept upstream's choices for -O option, i.e. -O3 almost everywhere.</flag> -</use> -<longdescription lang="en"> + <herd>sci</herd> + <maintainer> + <email>tom111@gmx.de</email> + <name>Thomas Kahle</name> + </maintainer> + <longdescription lang="en"> Normaliz is a (command line) tool for computations in affine monoids, vector configurations, lattice polytopes, and rational cones. </longdescription> diff --git a/sci-mathematics/normaliz/normaliz-2.2.ebuild b/sci-mathematics/normaliz/normaliz-2.2.ebuild index de4b90b93..d8943d459 100644 --- a/sci-mathematics/normaliz/normaliz-2.2.ebuild +++ b/sci-mathematics/normaliz/normaliz-2.2.ebuild @@ -1,14 +1,15 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 +EAPI=4 inherit eutils -DESCRIPTION="Normaliz is a tool for computations in affine monoids and more" +DESCRIPTION="Computations in affine monoids and more" HOMEPAGE="http://www.mathematik.uni-osnabrueck.de/normaliz/" SRC_URI="http://www.mathematik.uni-osnabrueck.de/normaliz/Normaliz2.2/Normaliz2.2Linux32.zip" + LICENSE="GPL-3" SLOT="0" KEYWORDS="~x86 ~amd64" @@ -17,15 +18,15 @@ IUSE="doc" DEPEND="dev-libs/gmp[-nocxx]" RDEPEND="${DEPEND}" -S="${WORKDIR}/Normaliz2.2Linux/source" +S="${WORKDIR}"/Normaliz2.2Linux/source src_prepare () { sed -i "s/-O3/${CXXFLAGS}/" Makefile || die "sed on Makefile failed" } src_install() { - dobin norm32 norm64 normbig || die "install failed" + dobin norm32 norm64 normbig if use doc; then - dodoc "../doc/Normaliz2.2Documentation.pdf" || die "install failed" + dodoc "../doc/Normaliz2.2Documentation.pdf" fi } diff --git a/sci-mathematics/pest/ChangeLog b/sci-mathematics/pest/ChangeLog index c884fe164..b9fe96e7a 100644 --- a/sci-mathematics/pest/ChangeLog +++ b/sci-mathematics/pest/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/pest -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> pest-12.1.ebuild: + Added fortran-2.eclass support + 16 Dec 2010; Justin Lecher <jlec@gentoo.org> pest-12.1.ebuild: Removal of fortran.eclass, #348851 diff --git a/sci-mathematics/pest/Manifest b/sci-mathematics/pest/Manifest index f69d1e7a8..97a41ea6b 100644 --- a/sci-mathematics/pest/Manifest +++ b/sci-mathematics/pest/Manifest @@ -4,13 +4,13 @@ Hash: SHA1 DIST addendum.pdf 1029933 RMD160 2d0f620559ead34aace3dc3cc4e8bf8b92882be4 SHA1 d806bd3603d39e2ab0cdecce58325f93898d64d0 SHA256 e4a8d050020bec968a6526e4aa6a7dc3cc01c51d118c773b5930d1d9a3260569 DIST pest-12.1.tar.zip 1065554 RMD160 d0b8164cfeda65213bfd76bd46a1042a933bb6b1 SHA1 46b82fdf56ed6a47a76c05ebf3f2de941c4bf511 SHA256 b84b95551d839636433db7eb719a11ef37c0d89a736f2cfdf27b37e7a81833c6 DIST pestman.pdf 1743872 RMD160 13fa38e0c5885db7bbacebc43afa718a11bd7ede SHA1 0a2243298332f4a19504e0983fb42e744a302911 SHA256 48a9f657c2a49b9e4a231a9573871a497f79634ac614587af82b0dbb41fbf893 -EBUILD pest-12.1.ebuild 2081 RMD160 33493ea1f0b66ae63cc754e6b9c8bc4bfc0023b5 SHA1 f293998be1b7e012832a8bf89099ef11ea9586c9 SHA256 67f00c5f5cb4e18d3c9bfabd5a3e070ec3bd7a6943a5bbdab6e7873f79fa222a -MISC ChangeLog 1165 RMD160 8a1b2124ab92d2a0e0bc132b0a8fd6c2dbd09af0 SHA1 1f6d2262f584f9b26f219c57e9a27b0dcdc0a1db SHA256 b02cb60c77e972098ae076e230ca6a3a1b2eb41d40f09208719751f45c360cc6 +EBUILD pest-12.1.ebuild 2074 RMD160 5f8f7e901e2734e39bf16d41ebbb0caf97793f92 SHA1 349cdd2f08c39d83599cb34daa8d74996d0193ce SHA256 654b0f609db8528e9439d02ccd13409646e74a9159222439e114e4dcb36a2ece +MISC ChangeLog 1264 RMD160 826e6be8cbe225671963000008a72c6dcdd43528 SHA1 8998752c8a60a086ae0d43c375466800acb5d5bd SHA256 8d4f3512188ba5f5b28c272a7e2149b403a1134ac29a5aaa6d9ebb4afd64ec14 MISC metadata.xml 382 RMD160 582743add3713788f6b66839dbb323f4f4c317cf SHA1 09bb79f2ccc27ed21f72496cb8f727eeb586ee2b SHA256 6f81bf54599563d6ae7525ac3212a0c6f52a0ec6a2611322cdabf0c167c61757 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk0KOM4ACgkQgAnW8HDreRaLIwCgrKCVkoY7ccCl37ExRK6nLzuf -NAUAnjGXa+QfQtZKSeFMs4gjmjBKX082 -=IDkG +iEYEARECAAYFAk4EqLUACgkQgAnW8HDreRbQIgCghdX9HKD6MrHp6u/UCAArT50M +cFIAniaCohyZyjpuabZzZRsN3MFs+P/m +=+qno -----END PGP SIGNATURE----- diff --git a/sci-mathematics/pest/pest-12.1.ebuild b/sci-mathematics/pest/pest-12.1.ebuild index 0fa4614bc..381dea81d 100644 --- a/sci-mathematics/pest/pest-12.1.ebuild +++ b/sci-mathematics/pest/pest-12.1.ebuild @@ -1,19 +1,20 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=2 -inherit versionator toolchain-funcs +inherit fortran-2 toolchain-funcs versionator MY_P="${P/-/}" -DESCRIPTION="Model-independent Parameter ESTimation for model calibration and -predictive uncertainty analysis." -HOMEPAGE="http://www.pesthomepage.org" -SRC_URI="http://www.pesthomepage.org/getfiles.php?file=${MY_P}.tar.zip -> ${P}.tar.zip - doc? ( http://www.pesthomepage.org/files/pestman.pdf - http://www.pesthomepage.org/files/addendum.pdf )" +DESCRIPTION="Model-independent Parameter ESTimation for calibration and predictive uncertainty analysis" +HOMEPAGE="http://www.pesthomepage.org/" +SRC_URI=" + http://www.pesthomepage.org/getfiles.php?file=${MY_P}.tar.zip -> ${P}.tar.zip + doc? ( + http://www.pesthomepage.org/files/pestman.pdf + http://www.pesthomepage.org/files/addendum.pdf )" # License is poorly specified on the SSPA web site. It only says that # Pest is freeware. @@ -21,12 +22,13 @@ LICENSE="public-domain" SLOT="0" KEYWORDS="~amd64" IUSE="doc" + DEPEND="app-arch/unzip" RDEPEND="" -MAKEOPTS="${MAKEOPTS} -j1" +FORTRAN_STANDARD="90" -# Need a Fortran 90 compiler. +MAKEOPTS="${MAKEOPTS} -j1" S="${WORKDIR}/${PN}" diff --git a/sci-mathematics/petsc/ChangeLog b/sci-mathematics/petsc/ChangeLog index 52f6b1a69..0604c7fa4 100644 --- a/sci-mathematics/petsc/ChangeLog +++ b/sci-mathematics/petsc/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> petsc-3.1_p4.ebuild, + petsc-3.1_p5-r2.ebuild, petsc-3.1_p7.ebuild, petsc-3.1_p8.ebuild, + petsc-3.1_p8-r1.ebuild, metadata.xml: + Added fortran-2.eclass support + *petsc-3.1_p8-r1 (19 Apr 2011) 19 Apr 2011; Thomas Kahle <tomka@gentoo.org> +petsc-3.1_p8-r1.ebuild: diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest index 5fc9c5bd9..4ecbe61c4 100644 --- a/sci-mathematics/petsc/Manifest +++ b/sci-mathematics/petsc/Manifest @@ -1,3 +1,6 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX petsc-3.1_p8-configure-pic.patch 550 RMD160 cdcdd5ed4a32f9ea6210491bf8c902d79c612694 SHA1 8590519ac8559400d3b0ae81fc3c72fcc851b839 SHA256 b7fbe00a12eec17d6bbf3d56c5c892ed79e10e867b943785fded71350c5cec2a AUX petsc-configure-pic.patch 533 RMD160 f24a17f653d67f42cb13701b0798704bcae95ec0 SHA1 3508bdce47619f3b29d86da4792e63c152a8314c SHA256 cfe886eb1343841e6f1b47a8a7c9ad7be66616af48eff6fce9efab64ecfb2589 AUX petsc-disable-rpath.patch 783 RMD160 ed962b20b7cabc6b554b1d9cde3de5c8a120523b SHA1 59ccf94388185c8e54aa7d9772f7616ecc84fe94 SHA256 f92814bf71e6615f8bd0e185c8c9fb06304de705d73a84f234a3f855c104400e @@ -5,10 +8,17 @@ DIST petsc-3.1-p4.tar.gz 15455558 RMD160 42d1c587ab1a2676f62de866afe8c43365a1b23 DIST petsc-3.1-p5.tar.gz 15456384 RMD160 c97e6cf9e000c6eb635a5c76d006b7f8b84b3320 SHA1 e884e3f670093fff66fe1a3964b2f6bfc58543ce SHA256 193c7f8a5826a2bfd47a915f74e87d31a67339f89129aadb16e7b4b9e9dbf7e1 DIST petsc-3.1-p7.tar.gz 15458474 RMD160 a22f839ae76ad262ff4fa2070fe256fa77a96f06 SHA1 aaee2ddeceb162699ab1b942de6a98c87dcb0b5e SHA256 c13c5eb18955d9c42413406dce8784d8c305d8ed33dcf107db736c309ac20175 DIST petsc-3.1-p8.tar.gz 15460606 RMD160 7d2bdc1bb5eda1d3fee39fe96d9edb2ce0e21afe SHA1 bfd083a85753366bc349808eb72eab1b8cc66944 SHA256 eba776e3cebf187f96ef5c638bd769602e27b5f5341be7eadb48dcad33072282 -EBUILD petsc-3.1_p4.ebuild 4102 RMD160 6dbe234a3b77a1c123df8892352a5c3810e5003d SHA1 46dc5828b917b510a65b72012a88fe2d350559ca SHA256 ec1a91c2025aca456a113702bd4fef0973e61c2fec90c3a413fde12b94b2ae81 -EBUILD petsc-3.1_p5-r2.ebuild 4881 RMD160 2294d4569b98bb6db0903e92c99d641143b241dd SHA1 6ed44e1417e88973c575bbdb8afe65a4d5176dc9 SHA256 02465efaf67fd0b8a0ff12e750ccbac7bb76432b399b67528f699c61d8cbd581 -EBUILD petsc-3.1_p7.ebuild 4881 RMD160 ef5a6585d776f5db34e956754177c24b3d97bd9a SHA1 c0ef05217cba012ae7a54cda908353510d553e00 SHA256 111d150b4243d6a4be72601c99704f1eb7692845ba70069ddbcea795aace197b -EBUILD petsc-3.1_p8-r1.ebuild 5750 RMD160 8aa2890ce6e424ac8f2df33bf8f8e853477aeeec SHA1 12919e67ea1c92708c3c8bcd15bb69029449b523 SHA256 b2894ea85c8939f440bfe29bd0cff496cbb9af547815e849c10ec8ba65fc8034 -EBUILD petsc-3.1_p8.ebuild 4880 RMD160 ac0078f38be42553853945dab348321e2dbe3906 SHA1 cb3c7625abd4bd660651abf9969a552a6114084f SHA256 e7c9fb3f339717367393f0583dedc1e94b1e4f0510a9206e5e561957643446e1 -MISC ChangeLog 2649 RMD160 833ac07759fdef4dccee5fe7fa070fa42c01e8e7 SHA1 c165c8d802fb32346241a624cdcadeca6ce198d1 SHA256 9c268c813ebb933269c380f99147b020ac1e6304455b2a524ba87489030d9324 -MISC metadata.xml 338 RMD160 7bb392dfe214a3ed4048d083323cf5ee5cb10bdb SHA1 e2b7a8a4963ff82d009e5ffcb1a444caaea4262e SHA256 efafc54fd365ea7eee3a0140b197068c8aa2168fefb3a196c091699bf6d18e53 +EBUILD petsc-3.1_p4.ebuild 4112 RMD160 a5987f1d62c3100c8ffd2d4de787d34e0f5519a7 SHA1 46893bddd0a27a8f295d1e8078df4a84f9fd2e85 SHA256 dff13b8cfbce68a903f05e13072f10082ae47405be8668adddc754bf41a84a95 +EBUILD petsc-3.1_p5-r2.ebuild 4891 RMD160 787e20de85c64bc669e302030b3509417aee05ed SHA1 1a45b02d95b399c229f4f4c337b7b9cb10617ed2 SHA256 775a1acf1e710553227c83112365cc7aa7d1ffe7c834bd2f4de325fd94cdd233 +EBUILD petsc-3.1_p7.ebuild 4891 RMD160 787e20de85c64bc669e302030b3509417aee05ed SHA1 1a45b02d95b399c229f4f4c337b7b9cb10617ed2 SHA256 775a1acf1e710553227c83112365cc7aa7d1ffe7c834bd2f4de325fd94cdd233 +EBUILD petsc-3.1_p8-r1.ebuild 5770 RMD160 a137300f9c9cea3a7f07b5702701edeb8b0ca944 SHA1 866de2d01dc7fdc691275417de64f9613262e7f4 SHA256 142f14c57ba0c1ff8d6dc8b37d5e3e1b1ba3b698c926c4de7867a2864a93d9d1 +EBUILD petsc-3.1_p8.ebuild 4890 RMD160 a7d2853f3af44163e17b43266856131b3ffcc8bc SHA1 5f591ec81a5b9d2a53aff6ea4ab3824fe1a16ce0 SHA256 5d9334887c3a6cb61afa35dafd23c6bc4357233a6cca894d1f4b9d6705abe9fa +MISC ChangeLog 2859 RMD160 9ffe9cbbb2e7fe75f3e9c63b2f2c075e11031035 SHA1 56169ef9fcdf02ce1deae4e5422bd8251a84a2e4 SHA256 9cc89e59866d218e303bfd775292f56d7e5f70b73def47ea00ba5754bec6b5f9 +MISC metadata.xml 397 RMD160 f2ad9763aa7800518279a830a3e654498a70c1e5 SHA1 e322129efe4914746543f189838bdd6c19729924 SHA256 3064af413e451a4447af7a20ec7577f4fa12b142832e483c0db9a3210012adc0 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EqLwACgkQgAnW8HDreRYlxwCeIpRI3mhvSyUCpf3ySW2oqcWI +t7YAoML0OuX/MQWpQ1TxFb2a+an+1MVw +=wstd +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/petsc/metadata.xml b/sci-mathematics/petsc/metadata.xml index 15bb0c366..079f8ffb7 100644 --- a/sci-mathematics/petsc/metadata.xml +++ b/sci-mathematics/petsc/metadata.xml @@ -5,5 +5,6 @@ <use> <flag name="hypre">Use HYPRE (sci-mathematics/hypre) for preconditioning</flag> <flag name="metis">Use METIS (sci-libs/parmetis) for partitioning</flag> + <flag name="complex-scalars">Make scalars complex</flag> </use> </pkgmetadata> diff --git a/sci-mathematics/petsc/petsc-3.1_p4.ebuild b/sci-mathematics/petsc/petsc-3.1_p4.ebuild index 38d922389..6adee0a83 100644 --- a/sci-mathematics/petsc/petsc-3.1_p4.ebuild +++ b/sci-mathematics/petsc/petsc-3.1_p4.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=3 -inherit flag-o-matic toolchain-funcs +inherit flag-o-matic fortran-2 toolchain-funcs MY_P="${PN}-${PV/_/-}" @@ -15,7 +15,7 @@ SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" LICENSE="petsc" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="mpi X cxx debug static-libs fortran doc" +IUSE="cxx debug doc fortran mpi static-libs X" RDEPEND="mpi? ( virtual/mpi[cxx?,fortran?] ) X? ( x11-libs/libX11 ) diff --git a/sci-mathematics/petsc/petsc-3.1_p5-r2.ebuild b/sci-mathematics/petsc/petsc-3.1_p5-r2.ebuild index 1284a8f03..f3165c269 100644 --- a/sci-mathematics/petsc/petsc-3.1_p5-r2.ebuild +++ b/sci-mathematics/petsc/petsc-3.1_p5-r2.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=3 -inherit flag-o-matic toolchain-funcs +inherit flag-o-matic fortran-2 toolchain-funcs MY_P="${PN}-${PV/_/-}" @@ -15,7 +15,7 @@ SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" LICENSE="petsc" SLOT="0" KEYWORDS="~x86 ~amd64" -IUSE="mpi hypre metis hdf5 X cxx debug static-libs fortran doc" +IUSE="cxx debug doc fortran hdf5 hypre metis mpi static-libs X" RDEPEND="mpi? ( virtual/mpi[cxx?,fortran?] ) X? ( x11-libs/libX11 ) diff --git a/sci-mathematics/petsc/petsc-3.1_p7.ebuild b/sci-mathematics/petsc/petsc-3.1_p7.ebuild index b76ae93df..f3165c269 100644 --- a/sci-mathematics/petsc/petsc-3.1_p7.ebuild +++ b/sci-mathematics/petsc/petsc-3.1_p7.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit flag-o-matic toolchain-funcs +inherit flag-o-matic fortran-2 toolchain-funcs MY_P="${PN}-${PV/_/-}" @@ -15,7 +15,7 @@ SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" LICENSE="petsc" SLOT="0" KEYWORDS="~x86 ~amd64" -IUSE="mpi hypre metis hdf5 X cxx debug static-libs fortran doc" +IUSE="cxx debug doc fortran hdf5 hypre metis mpi static-libs X" RDEPEND="mpi? ( virtual/mpi[cxx?,fortran?] ) X? ( x11-libs/libX11 ) diff --git a/sci-mathematics/petsc/petsc-3.1_p8-r1.ebuild b/sci-mathematics/petsc/petsc-3.1_p8-r1.ebuild index 5f2eaa7fc..a1876283b 100644 --- a/sci-mathematics/petsc/petsc-3.1_p8-r1.ebuild +++ b/sci-mathematics/petsc/petsc-3.1_p8-r1.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit flag-o-matic toolchain-funcs +inherit flag-o-matic fortran-2 toolchain-funcs MY_P="${PN}-${PV/_/-}" @@ -15,7 +15,7 @@ SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" LICENSE="petsc" SLOT="0" KEYWORDS="~x86 ~amd64" -IUSE="mpi hypre metis hdf5 X cxx debug static-libs fortran doc complex-scalars" +IUSE="complex-scalars cxx debug doc fortran hdf5 hypre metis mpi static-libs X" RDEPEND="mpi? ( virtual/mpi[cxx?,fortran?] ) X? ( x11-libs/libX11 ) @@ -169,11 +169,11 @@ src_install(){ dosed "s:${PETSC_ARCH}/lib:$(get_libdir):g" /usr/include/"${PN}/${PETSC_ARCH}"/include/petscconf.h dosed "s:INSTALL_DIR =.*:INSTALL_DIR = /usr:" /usr/include/"${PN}/${PETSC_ARCH}"/conf/petscvariables - cat > ${T}/99petsc <<EOF -PETSC_ARCH=${PETSC_ARCH} -PETSC_DIR=/usr/include/${PN} -EOF - doenvd ${T}/99petsc + cat >> "${T}"/99petsc <<- EOF + PETSC_ARCH=${PETSC_ARCH} + PETSC_DIR=/usr/include/${PN} + EOF + doenvd "${T}"/99petsc if ! use mpi ; then insinto /usr/include/"${PN}"/mpiuni diff --git a/sci-mathematics/petsc/petsc-3.1_p8.ebuild b/sci-mathematics/petsc/petsc-3.1_p8.ebuild index a7566db65..aca7776bf 100644 --- a/sci-mathematics/petsc/petsc-3.1_p8.ebuild +++ b/sci-mathematics/petsc/petsc-3.1_p8.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit flag-o-matic toolchain-funcs +inherit flag-o-matic fortran-2 toolchain-funcs MY_P="${PN}-${PV/_/-}" @@ -15,7 +15,7 @@ SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" LICENSE="petsc" SLOT="0" KEYWORDS="~x86 ~amd64" -IUSE="mpi hypre metis hdf5 X cxx debug static-libs fortran doc" +IUSE="cxx debug doc fortran hdf5 hypre metis mpi static-libs X" RDEPEND="mpi? ( virtual/mpi[cxx?,fortran?] ) X? ( x11-libs/libX11 ) diff --git a/sci-mathematics/pff/ChangeLog b/sci-mathematics/pff/ChangeLog index 0c2af77c8..612adcf89 100644 --- a/sci-mathematics/pff/ChangeLog +++ b/sci-mathematics/pff/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/pff -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> pff-8.2.1.2.ebuild: + Cleaned ebuild + 04 Jul 2010; J.-C. Demay <jcdemay@gmail.com> +metadata.xml, +ChangeLog: QA fixes diff --git a/sci-mathematics/pff/Manifest b/sci-mathematics/pff/Manifest index b55996981..a41e4ee0b 100644 --- a/sci-mathematics/pff/Manifest +++ b/sci-mathematics/pff/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST Float8.2-1.2.tgz 322949 RMD160 5ef8a68e4c10d8cffe4cd8d3eb5d5d2c1394fb60 SHA1 ab9b01cf953e32c100ed21e9980adf68553aaed1 SHA256 df61debf5afb2cbf44be6a605622b1645ba07be1912bb154ef79009d7eb235b2 -EBUILD pff-8.2.1.2.ebuild 754 RMD160 9b5756e657d7c9a2fb44b089e282285f7cedf496 SHA1 c109b256d784a95f40acfec7e4c393104a9e4279 SHA256 9160ba0f01b3e83f8c4af08980d371f6fa1e7d8ccde68b1162829b91c912ea99 -MISC ChangeLog 208 RMD160 7ae0226788e62a6b71e3ae9c151ee15459fedbf7 SHA1 927352d079d68f605465f2807acb46997e5ea6d5 SHA256 585784f5cc7288f01b3b187445279e76806d43af18b1e1d1345f95e023114d0b +EBUILD pff-8.2.1.2.ebuild 675 RMD160 157d4cd76666f11758394a45ac61da190d3bf814 SHA1 245a11863b5a91067da561d888417633913c7f6a SHA256 b6e92e960e16459b81003d274fe9164d3a7dc4dff4970306c037e926e23d2eb2 +MISC ChangeLog 293 RMD160 a27db59b52b8bd47a9ebec70dd8b821859deb0b7 SHA1 5de056188f4a024364518c1fdeaad60f5bfd4f33 SHA256 c1b047b53e5ee337aa8e0dbe6a62a7ca71c278ec7451e4f6eae9e39d1ba29da0 MISC metadata.xml 497 RMD160 c5e6a8eb0b3db8e1ebd6545bc94ae10fc07411c4 SHA1 267286d8696a8eb1163a3e79917c4bc5626f0cee SHA256 3ba778defe74a0a683099bd44b6f279b64bd6860c0c9ea53b5be8bb60c1b4340 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GEOYACgkQgAnW8HDreRY67gCfSHckYRfgnTdHI8J7mLuhSo6d +9wsAoI6a2bMhqAO387qKtI9NGnAjcL/m +=8ivt +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/pff/pff-8.2.1.2.ebuild b/sci-mathematics/pff/pff-8.2.1.2.ebuild index 3e4189d12..359274571 100644 --- a/sci-mathematics/pff/pff-8.2.1.2.ebuild +++ b/sci-mathematics/pff/pff-8.2.1.2.ebuild @@ -1,16 +1,16 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 -DESCRIPTION="Library for reasoning about floating point numbers in coq." +DESCRIPTION="Library for reasoning about floating point numbers in coq" HOMEPAGE="http://lipforge.ens-lyon.fr/www/pff/" SRC_URI="http://lipforge.ens-lyon.fr/frs/download.php/147/Float${PV/%????/}-${PV/#????/}.tgz" LICENSE="LGPL-2" SLOT="0" -KEYWORDS="~amd64 ~ppc ~sparc ~x86" +KEYWORDS="~amd64 ~ppc ~x86" IUSE="" DEPEND="sci-mathematics/coq" @@ -19,15 +19,11 @@ RDEPEND="${DEPEND}" S="${WORKDIR}/Float" src_prepare() { - sed -i -e "s|\`\$(COQC) -where\`/user-contrib| \ - \$(DESTDIR)/\`\$(COQC) -where\`/user-contrib|g" Makefile + sed \ + -e "s|\`\$(COQC) -where\`/user-contrib|\$(DESTDIR)/\`\$(COQC) -where\`/user-contrib|g" \ + -i Makefile || die } src_compile(){ emake DESTDIR="/" || die "emake failed" } - -src_install(){ - emake install DESTDIR="${D}" || die "emake install failed" -} - diff --git a/sci-mathematics/scilab/ChangeLog b/sci-mathematics/scilab/ChangeLog index e742125d3..084c3f21d 100644 --- a/sci-mathematics/scilab/ChangeLog +++ b/sci-mathematics/scilab/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> scilab-5.2.1.ebuild, + scilab-5.3.2.ebuild: + Sort inherit and/or USE + 16 Jun 2011; Guillaume Horel <guillaume.horel@gmail.com> scilab-5.3.2.ebuild, +files/scilib-5.3.2-scilib-fix.patch: Fixed jgraphx version dependency and disabled mpi support in hdf diff --git a/sci-mathematics/scilab/Manifest b/sci-mathematics/scilab/Manifest index 288888524..c20fba9b0 100644 --- a/sci-mathematics/scilab/Manifest +++ b/sci-mathematics/scilab/Manifest @@ -13,11 +13,11 @@ AUX scilab-5.2.1-java-heap.patch 438 RMD160 7f63afd4b8bc56f6f5ca496524d0047a0145 AUX scilab-5.2.1-no-redef-exp10.patch 2126 RMD160 cd50b646441ebe9426cd3e8dc5c388f70b66c894 SHA1 62c7934045db41d3c8ce4318d859ebf3f7785ee9 SHA256 47e892b65050d719ed356cd0219a37f372c3ac5cb379a37fc3b5560f86a340b5 AUX scilab-5.2.1-nojavacheckversion.patch 633 RMD160 a8ebc801a17083f18343bdb2250016f3ea7b8291 SHA1 24a2bde08da02dcc7f77ce6ef5349e0b6971a6a6 SHA256 e7ae10f8b7f979b87ba971903bfbab2e1a9cdea617b3ce06e5770dad25cf9ef8 AUX scilab-5.2.1-scilib-fix.patch 368 RMD160 d2106819b9ed8e221aff4cddb11c1102c3a77e07 SHA1 869e143f064c3325d260a5f5f602da859e5fe8dc SHA256 ace8712acdc15ddffc1811f29ac8b3d53a760f23b8270f60857750fc6a548911 -AUX scilib-5.3.2-scilib-fix.patch 368 RMD160 d2106819b9ed8e221aff4cddb11c1102c3a77e07 SHA1 869e143f064c3325d260a5f5f602da859e5fe8dc SHA256 ace8712acdc15ddffc1811f29ac8b3d53a760f23b8270f60857750fc6a548911 +AUX scilab-5.3.2-scilib-fix.patch 368 RMD160 d2106819b9ed8e221aff4cddb11c1102c3a77e07 SHA1 869e143f064c3325d260a5f5f602da859e5fe8dc SHA256 ace8712acdc15ddffc1811f29ac8b3d53a760f23b8270f60857750fc6a548911 AUX sparc64.diff 1011 RMD160 86849042292bcd7a195e6745bb06d84fbe4af3e5 SHA1 602a3e3a9c8551e043f66d1cf81dcdd3292b7f0e SHA256 1c309296a003edfbb917df3e2948df117bc02b79c421232e971d14a966a25af6 DIST scilab-5.2.1-src.tar.gz 54855137 RMD160 312ccc62f44bc3dbf8f25260a7090f62dc70818e SHA1 6fad986beb03a42cee6e8ef9bfa0b8976236b3f6 SHA256 f85aa3b7fde0e523f7f0159613da7cca7bd2d125860b50fa2ed00394c97075e0 DIST scilab-5.3.2-src.tar.gz 47356102 RMD160 18cff3bbf0dd7e901de8879355b243c4c16fe9fb SHA1 c0d7a7db6ea3a6a35722b451c6ef99b799079896 SHA256 6b33aace70b0889a71a417a28530ff58b96042ea35cb033c37bb1ac7c9a4ec15 -EBUILD scilab-5.2.1.ebuild 3626 RMD160 425cc158c8cce598e63b8fd3baeb3086e3672f96 SHA1 c9085fcd5f99fa7ea18483f4adcb8a60cb806863 SHA256 befb38c6998a6b44d2443d0dcbc6ab1d13da7d129f4676700bb789fe168ab896 -EBUILD scilab-5.3.2.ebuild 3437 RMD160 dbbe08c188945038c3f07cfff7e6533fe4547454 SHA1 cbaa22f8481955afb70bb89d4bf64029512490e6 SHA256 279d269f406cf73dc9ccd6456b36875ff929b12fcf16071659f929bfaab3a4b4 -MISC ChangeLog 2514 RMD160 045e14cc047c6e931fece9200e2bb9662e9a10a3 SHA1 636ed9672bc662ba7fa037b47c240dec4d67bfd9 SHA256 ecd7394bb0c46c79544ca6d8fe0d43c7b3e3e4e55045850a23f4b4710c639852 +EBUILD scilab-5.2.1.ebuild 3626 RMD160 e712ac5b2300982cc328523d7cbc5f10d8647c3b SHA1 315888f4e31bd868412a830da031117b65c6a542 SHA256 d9dc4d7085bff7953e854895ed24ce9573e1e744e6659284cad68f67d4c8025c +EBUILD scilab-5.3.2.ebuild 3431 RMD160 29eaca323817257ff15cfd1322502b31d4e95ea4 SHA1 2c98cda4bce89ab3e55fff02d24671f401f84c44 SHA256 76124c45f5b5e72c268acc42f65a55d2aef5fc537a25803368dcd491b885bf08 +MISC ChangeLog 2632 RMD160 1d85f0d807ba3405930c6d2ab47fc0d288d5ae8d SHA1 5b1261d3469dcc3eb817e920a16a3b8bfbb92b9e SHA256 01c833c3328e7b2376cef74575035f046582169b66eaed76caca9a126c7688b3 MISC metadata.xml 872 RMD160 aef8847644f734faba3b42b9028690664612c8e6 SHA1 4686ca608887e1d9fea6ee4e11f4aa54c8eff150 SHA256 43da74dcf0ae13eb0987c33f397a9b9d7abe187196107d50814a3104466b90ee diff --git a/sci-mathematics/scilab/files/scilib-5.3.2-scilib-fix.patch b/sci-mathematics/scilab/files/scilab-5.3.2-scilib-fix.patch index 6d3c2e1cb..6d3c2e1cb 100644 --- a/sci-mathematics/scilab/files/scilib-5.3.2-scilib-fix.patch +++ b/sci-mathematics/scilab/files/scilab-5.3.2-scilib-fix.patch diff --git a/sci-mathematics/scilab/scilab-5.2.1.ebuild b/sci-mathematics/scilab/scilab-5.2.1.ebuild index c120969aa..52c331dc7 100644 --- a/sci-mathematics/scilab/scilab-5.2.1.ebuild +++ b/sci-mathematics/scilab/scilab-5.2.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=2 -inherit eutils autotools java-pkg-2 check-reqs +inherit autotools check-reqs eutils java-pkg-2 DESCRIPTION="Scientific software package for numerical computations" LICENSE="CeCILL-2" diff --git a/sci-mathematics/scilab/scilab-5.3.2.ebuild b/sci-mathematics/scilab/scilab-5.3.2.ebuild index 295c30f14..1a6db4869 100644 --- a/sci-mathematics/scilab/scilab-5.3.2.ebuild +++ b/sci-mathematics/scilab/scilab-5.3.2.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI=3 -inherit eutils autotools java-pkg-2 check-reqs flag-o-matic +inherit autotools check-reqs eutils flag-o-matic java-pkg-2 DESCRIPTION="Scientific software package for numerical computations" LICENSE="CeCILL-2" @@ -29,7 +29,7 @@ RDEPEND="virtual/lapack >=dev-java/flexdock-0.5.2 >=dev-java/jeuclid-core-3.1 >=dev-java/jlatexmath-0.9.4 - =dev-java/jgraphx-1.4.1* + =dev-java/jgraphx-1.4.1.0 dev-java/jogl dev-java/jgoodies-looks dev-java/jrosetta @@ -101,7 +101,7 @@ src_configure() { $(use_with matio) \ $(use_with umfpack) \ $(use_with tk) \ - $(use_with xcos scicos) \ + $(use_with xcos) \ ${myopts} } diff --git a/sci-mathematics/why/ChangeLog b/sci-mathematics/why/ChangeLog index 4820f8b40..2a1bf9c66 100644 --- a/sci-mathematics/why/ChangeLog +++ b/sci-mathematics/why/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> why-2.29.ebuild: + EAPI bump + 06 May 2011; J.-C. Demay <jcdemay@gmail.com> -why-2.28.ebuild, +why-2.29.ebuild: version bump diff --git a/sci-mathematics/why/Manifest b/sci-mathematics/why/Manifest index 35d623525..59cc05df6 100644 --- a/sci-mathematics/why/Manifest +++ b/sci-mathematics/why/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX why_jessie-carbon.patch 1651 RMD160 66796b81d7f047312f941a826e99296e1522c955 SHA1 2a4de59dea9a6ce5e960e0729e388a6b3e851948 SHA256 b04c7434176e85da5de15f86417ed01a2a79c6c978beae2af234fc683b1bae96 DIST why-2.29.tar.gz 2962977 RMD160 2438151fd7ecb309b1a1fb79f09db032b9338c08 SHA1 2b649673964d3273eb995f2e70797c5a2b10925d SHA256 f1d09d64468592db4ccfb0fad7fcaec928a26e0b90a74e5818edb52ae707a905 -EBUILD why-2.29.ebuild 1464 RMD160 643ad7bf50f510bb3f10882b302ea7b4590e16be SHA1 608e583872abab481ac6e9223831ea63834ba4e9 SHA256 5c79c57844828c8a60a4bcd78f4d9553b87cbb877a9d3895e118065afe6fb6c3 -MISC ChangeLog 704 RMD160 30784599b3d6b0112c93a5ed927e8ca721732eac SHA1 864eccf86954ceb018a05a6efabdbcb683a2f291 SHA256 ddff26d6271ac115e1e3053f4f49a2365f3d1e34a19b48aa54887a8d000ec068 +EBUILD why-2.29.ebuild 1355 RMD160 5e763e52fd86a77dac9969d690536ddd628b324d SHA1 e5505a1f29c3a6d64f1210c3d0ec58f3c8033e13 SHA256 ab9cf61991c1049f0babf46ac555bcc4b32f4e8cd6c28234cbf63197ed1f824a +MISC ChangeLog 781 RMD160 c228e8346a09e01f32cdbeb5c47e6ee00e250eb8 SHA1 981f1a965d9f599451a19a9c672035a31b69249b SHA256 1f0dda94c66a129f889f32ff45d13411dc282d9d3b036db06039007adccf978d MISC metadata.xml 835 RMD160 38717707edcc9cd836d5f13bbfd38ae7a26114e2 SHA1 c7eb904790b811b3e9393a40440dc24c917f8b39 SHA256 fe7c99c8ec56d17c9fe627e4e2b7edbb2b97a81b33d27fcf2d64a7254d3fe8de +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EqvsACgkQgAnW8HDreRbhxQCgyhCnGEJGJr0sEW6NgNuu9VCP +3zIAn1lvuzSO6A/jEl6VEOFbsPq3yWgQ +=ic/x +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/why/why-2.29.ebuild b/sci-mathematics/why/why-2.29.ebuild index 2095e82df..c8cc38d38 100644 --- a/sci-mathematics/why/why-2.29.ebuild +++ b/sci-mathematics/why/why-2.29.ebuild @@ -1,57 +1,61 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 inherit autotools eutils -DESCRIPTION="Why is a software verification platform." +DESCRIPTION="Software verification platform" HOMEPAGE="http://why.lri.fr/" SRC_URI="http://why.lri.fr/download/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~ppc ~x86" -IUSE="apron coq doc examples gappa jessie gtk pff" +IUSE="apron coq doc examples gappa gtk jessie pff" -DEPEND=">=dev-lang/ocaml-3.09 - >=dev-ml/ocamlgraph-1.2 - gtk? ( >=dev-ml/lablgtk-2.14 ) - apron? ( sci-mathematics/apron ) - coq? ( sci-mathematics/coq ) - gappa? ( sci-mathematics/gappalib-coq ) - pff? ( sci-mathematics/pff ) - jessie? ( >=sci-mathematics/frama-c-20100401 )" +DEPEND=" + >=dev-lang/ocaml-3.09 + >=dev-ml/ocamlgraph-1.2 + apron? ( sci-mathematics/apron ) + coq? ( sci-mathematics/coq ) + gappa? ( sci-mathematics/gappalib-coq ) + gtk? ( >=dev-ml/lablgtk-2.14 ) + jessie? ( >=sci-mathematics/frama-c-20100401 ) + pff? ( sci-mathematics/pff )" RDEPEND="${DEPEND}" src_prepare() { - sed -i Makefile.in \ + sed \ -e "s/DESTDIR =.*//g" \ - -e "s/@COQLIB@/\$(DESTDIR)\/@COQLIB@/g" + -e "s/@COQLIB@/\$(DESTDIR)\/@COQLIB@/g" \ + -i Makefile.in || die #to build with apron-0.9.10 - sed -i configure.in \ + sed \ -e "s/pvs/sri-pvs/g" \ -e "s/oct_caml/octMPQ_caml/g" \ -e "s/box_caml/boxMPQ_caml/g" \ - -e "s/polka_caml/polkaMPQ_caml/g" - + -e "s/polka_caml/polkaMPQ_caml/g" \ + -i configure.in || die + epatch "${FILESDIR}"/${PN}_jessie-carbon.patch eautoreconf } src_configure() { - econf $(use_enable apron) PATH="/usr/bin:$PATH" || die "econf failed" + econf \ + $(use_enable apron) } src_compile(){ - emake -j1 DESTDIR="/" || die "emake failed" + emake -j1 DESTDIR="${EROOT}" || die "emake failed" } src_install(){ - DESTDIR="${D}" emake install || die "emake install failed" - dodoc CHANGES README Version + default + doman doc/why.1 if use doc; then diff --git a/sci-mathematics/yorick/Manifest b/sci-mathematics/yorick/Manifest index adacef67e..f290dd953 100644 --- a/sci-mathematics/yorick/Manifest +++ b/sci-mathematics/yorick/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX yorick-2.1.06.patch 2226 RMD160 8fa290925df2965512b0f74613a448b2e85a9504 SHA1 28e6a47baaf46968c385f90cebc66062cf15d63f SHA256 c9c45abc3c10df80321503b03510a03049e534e25f53d03f969ee30e774e1da8 DIST yorick-2.1.06.tgz 2275314 RMD160 f9380c97953f2a7d9ba941ee4c43d73e2f41ad3f SHA1 779b432d53b1f9ce21a44285fbccdd3f8083c219 SHA256 8387d01201641fc1350d8be10e73cabb984c7909a8a9c20fea993bcf0e5be749 -EBUILD yorick-2.1.06.ebuild 1297 RMD160 c3f835ed573e78ca2cfddb4cea422e0c9b1c360c SHA1 f5556b966bb2ab00d990a42382375ceae59a5fbe SHA256 ddd04019930075e8208ec5a6f472edb1b9d992d147cb86433bac427d7e98e8f1 +EBUILD yorick-2.1.06.ebuild 1297 RMD160 da7cba7417d46ed4b9b7afb53162f8aa3bb44682 SHA1 d5b3062d9e0a3e12af6ebff97affaad23b6bcaed SHA256 6afb8ef6eb5d33a8c41e7c3822f5c806f5a0c721e172faaf3099d1e138034bcc MISC ChangeLog 758 RMD160 af6e46646b61e6dbde6674e36800473cd6a2fb13 SHA1 2a9cddabecd2f1179346126b772b92b3ab25c10d SHA256 fa74aba2c6fa27f1d11718c34838d3ad52acddb0811c6643ed1a7013f6749b3d MISC metadata.xml 485 RMD160 116d161add231d6d5d0333bf596e021c308d032a SHA1 6d818632bca16d17378d45d28f108eb888c29a8c SHA256 6bbb40a8d3ed52bbe61106ca858b6d7e5e5ebad47ce4604db80e3477fd0e6e3b +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EqdkACgkQgAnW8HDreRbg3QCgy6934Vc4bTGVBaTqga4aB18I +4QgAoNHeWpn0f5X8aocedtqM3x+5oHAE +=fagB +-----END PGP SIGNATURE----- diff --git a/sci-mathematics/yorick/yorick-2.1.06.ebuild b/sci-mathematics/yorick/yorick-2.1.06.ebuild index 0f87f48e3..1e478d519 100644 --- a/sci-mathematics/yorick/yorick-2.1.06.ebuild +++ b/sci-mathematics/yorick/yorick-2.1.06.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI=2 -inherit eutils versionator elisp-common +inherit elisp-common eutils versionator DESCRIPTION="Language for scientific computing and rapid prototyping" HOMEPAGE="http://yorick.sourceforge.net/" diff --git a/sci-misc/emu/ChangeLog b/sci-misc/emu/ChangeLog deleted file mode 100644 index b46038656..000000000 --- a/sci-misc/emu/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-electronics/linsmith -# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -* emu-1.10 (16 Nov 2005) - - 16 Nov 2005; Lucas Chiesa <lucas.chiesa@gmail.com> emu-1.10.ebuild: - Initial import of sci-misc/emu. Thanks Flammie Pirinen - <flammie@gentoo.org> for the ebuild. Closes bug #98051. diff --git a/sci-misc/emu/Manifest b/sci-misc/emu/Manifest deleted file mode 100644 index ff658c7cb..000000000 --- a/sci-misc/emu/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST emu-1.10-src.tar.gz 1725276 RMD160 1c7e6da80572160e3add42f1b4bb84e4faed21ae SHA1 50c670d69b42ed0e63833d9a4a3404429b398be8 SHA256 1d962642a3042bc4caa5cf9bd57efb7d4911a664f6acefb6dd17cc277cfd4042 -EBUILD emu-1.10.ebuild 1470 RMD160 b4261fb0a28a0378081246384e626a1182cbcb62 SHA1 38f39d9775f204887a11df68317ea4efed2b15f0 SHA256 f96ffaa3a56a1cd5265e0544da8a51788ec57befbbc2c8ddf6f5d77aa5f432e6 -MISC ChangeLog 337 RMD160 ec7e95ff1fe110b074b4d0af204a5e6ff90ec73a SHA1 fa4ec140311a16b7fdfe00ec422647c239a1b928 SHA256 1aabc0413177c0f66cabe860ae4c3fda5a9df5664a4173817d51e62e0f350c91 -MISC metadata.xml 379 RMD160 1db8292c88b280e4c0b0e6aa4125e4843f737fda SHA1 3e0e8755351024b6cd30ee78010ba18917477751 SHA256 fae1027a22fc5e6a45ca480e8a8a8f70566c843d95386cd379e1a52428ca25c4 diff --git a/sci-misc/emu/emu-1.10.ebuild b/sci-misc/emu/emu-1.10.ebuild deleted file mode 100644 index dec703bf1..000000000 --- a/sci-misc/emu/emu-1.10.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="EMU Speech Database System" -HOMEPAGE="http://emu.sourceforge.net" -SRC_URI="mirror://sourceforge/${PN}/${P}-src.tar.gz" - -LICENSE="as-is" # or EMU? -SLOT="0" -KEYWORDS="~x86" -IUSE="R esps estools nist-sphere nas X" - -DEPEND=">=dev-lang/tcl-8.4 - X? ( virtual/x11 )" -RDEPEND=">=dev-lang/tcl-8.3 - >=dev-lang/tk-8.3 - dev-tcltk/bwidget - dev-tcltk/tcllib - R? ( dev-lang/R ) - X? ( virtual/x11 )" -# !R? ( splus ) -# esps? ( esps ) -# estools? ( estools ) -# nist-sphere? ( nist-sphere ) - -S=${WORKDIR}/${P}-src - -src_unpack() { - unpack ${A} - # This tcl install script is partially braindamaged - cd ${S} - sed -i "s:\$(WISH) ./doinstall.tcl$:\0 --prefix=${D}/usr/ \ - --tcl_prefix=${D}/usr/ --bin=${D}/usr/bin/ --auto:g" Makefile.in -} - -src_compile() { - myconf="--with-tcl=/usr/lib/ --with-tk=/usr/lib/" - # --without selectors do not work here: - # $(use_with esps) $(use_with estools) $(use_with nist-sphere nist) \ - # $(use_with nas)" - use esps && myconf="$myconf --with-esps" - use estools && myconf="$myconf --with-estools" - use nist-sphere && myconf="$myconf --with-nist" - use nas && myconf="$myconf --with-nas" - - econf $myconf || die "econf failed" - emake || die "emake failed" -} - -src_install() { - - make DESTDIR="${D}" install || die "install failed" - for f in ${D}/usr/bin/* ; do - sed -i "s|${D}||g" $f - done - dodoc README TODO - rm ${D}/usr/COPYING -} - diff --git a/sci-misc/emu/metadata.xml b/sci-misc/emu/metadata.xml deleted file mode 100644 index 8309cd46b..000000000 --- a/sci-misc/emu/metadata.xml +++ /dev/null @@ -1,14 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>flammie@gentoo.org</email> - <name>Flammie Pirinen</name> - </maintainer> - <longdescription lang="en"> - EMU is a speech signal database handling and analysis tool - collection. - </longdescription> -</pkgmetadata> - diff --git a/sci-misc/finomaton/ChangeLog b/sci-misc/finomaton/ChangeLog index 7226b0ef0..f8b90a82d 100644 --- a/sci-misc/finomaton/ChangeLog +++ b/sci-misc/finomaton/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/finomaton -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> finomaton-1.0.ebuild: + Some ebuild cleaning + 04 Jul 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> ChangeLog: Silence repoman; fix metapost dependency diff --git a/sci-misc/finomaton/Manifest b/sci-misc/finomaton/Manifest index 57c6703e4..2353493a6 100644 --- a/sci-misc/finomaton/Manifest +++ b/sci-misc/finomaton/Manifest @@ -2,23 +2,13 @@ Hash: SHA1 DIST finomaton-1.0.tar.gz 69681 RMD160 ff25e28299a27f50f89d22c88895c4717e9cec2b SHA1 9f79441eaf11b92e353c6ee22ac63c9198a6a15f SHA256 a4aed3796e4803f569a7e638faa5a143811af88b4e7ab4ac92d26b90d357d390 -EBUILD finomaton-1.0.ebuild 730 RMD160 b121de93543c3843fbde19c0562b88d091d0e565 SHA1 54609605e7151e9c0548fd97b988f5ae83541b8a SHA256 f9d78d8bd41bfbeed2a0bc0f7458349279515b9062f8ca685e117836fadad008 -MISC ChangeLog 243 RMD160 637ae03b5a9639f886dc263816fdcd2114f7b8d4 SHA1 033d9a89d523caefe6812d7a744f4fb05a06a752 SHA256 c37216e1799a9cee13dbebf597fc5c10e64f0c70b7d064d1119470d122ad0d23 +EBUILD finomaton-1.0.ebuild 703 RMD160 08d6603773a761d6938c393bf0e2969c6289f168 SHA1 05836a2141b56f6136f3f216820e544b24de73cd SHA256 9b7ff08d630cd31778d719d8f8689510cda83e1fdbb469562ebcd1f527f2da3c +MISC ChangeLog 457 RMD160 acdc764a3f18bdb16312ba34b491601c373fd5a7 SHA1 d843c9e098c7e34f697f14a8dfa5510f69991e6f SHA256 3cc7f4caba3582dcd99a1883535a49bbf949d059267c3737d4119afe05ad3f91 MISC metadata.xml 223 RMD160 754bf1189c9d51090f3e0439f6e7d6f603b93df0 SHA1 54348ca01c174e03ff3318b2a9da50d970db6695 SHA256 5c57a999484660ea4a3e55f9c526bb38097d5c1cb2356353133ec4d7e89f1f88 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMMKl3AAoJENwGBM22xffezNkP/i1ibcxGSAo/pp7UGKnWrBKe -0EUsrBsoDBsLUrqUIDXnOD2FCiLoL6awq1mICQBVGufqseIpeyGpRtpdtzY80X4v -8nV/Tjn7O2qKkL6jiWp5iAEhnVn+8qNtFott3B3Vd+n01Y2/lEoJM5/JGayHGXAk -av6hzDEfmjaGQxHUaEmXvKOEF+y9/5pWeEvhlo3JQQLGK7HNFPcaigyn7UJNMAsD -sPC9POKgDOwjDdv/YCD5S0A8X1QRBu0AP3Qm8SDQb38Za4+wMDR66T0/z2Sj7RIn -OoCeQa7dIzFA3c7iDprPoAK32+HsMryGbGdodSsvY4UDUGxKKmB0Hif0w5t8e5Dj -dWrnCADw0cXVUK6evuP5LDBTbVOlVGXkYTacjujL3i0UXtQFVqeIkZKzQB9IE4/C -FTxluB7hlMCHo3b/8MpvZ5DmXhHxjHYybasvnFYmoovkM7/3MT7rYA9UZ2j1ktvY -AIUYdr0n3vYAnR4/MytjCAo6QvBAb+B64Cg3f0ZvGWqMxFwAqKg/rhX8OuyYJs9w -86bVx4rH34vWZMDX6A+N2S1lsOldbZJ1WYsLQgMC1WgWyFRmDOn58IRE35Mm7opy -vYEl1a49C5I3/tuiDLtPizK1NFSNcvyD6cJ5tmHOzc475oGHClTJ3155hOB7OGZs -izOJ58S1tdyWVgCxWwfl -=9Ff0 +iEYEARECAAYFAk4E8f4ACgkQgAnW8HDreRZ4jQCeLtKK3P/geA09TZhFNLloP4wV +JlgAn0cHIhXlLl7BZ/JROk1BMdURbo9N +=3OuL -----END PGP SIGNATURE----- diff --git a/sci-misc/finomaton/finomaton-1.0.ebuild b/sci-misc/finomaton/finomaton-1.0.ebuild index b51403ddf..c13e06823 100644 --- a/sci-misc/finomaton/finomaton-1.0.ebuild +++ b/sci-misc/finomaton/finomaton-1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -9,19 +9,16 @@ HOMEPAGE="http://stud4.tuwien.ac.at/~e0225855/finomaton/finomaton.html" SRC_URI="http://stud4.tuwien.ac.at/~e0225855/finomaton/${P}.tar.gz" LICENSE="GPL-2" - SLOT="0" - KEYWORDS="~x86" - IUSE="examples" # script only DEPEND="" # tex for metapost -RDEPEND="dev-texlive/texlive-metapost - >=dev-lang/tcl-8.3 - >=dev-lang/tk-8.3" +RDEPEND=" + dev-lang/tk + dev-texlive/texlive-metapost" src_install() { dobin finomaton.tcl diff --git a/sci-misc/foma/ChangeLog b/sci-misc/foma/ChangeLog index e97a7c426..73e5b46ba 100644 --- a/sci-misc/foma/ChangeLog +++ b/sci-misc/foma/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -foma-0.9.1_alpha.ebuild, + -foma-0.9.4_alpha.ebuild, foma-0.9.14_alpha.ebuild, metadata.xml: + Cleaned ebuild + *foma-0.9.14_alpha (09 May 2011) 09 May 2011; <flammie@gentoo.org> +foma-0.9.14_alpha.ebuild: diff --git a/sci-misc/foma/Manifest b/sci-misc/foma/Manifest index 49521b8c8..68d9f725b 100644 --- a/sci-misc/foma/Manifest +++ b/sci-misc/foma/Manifest @@ -1,8 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST foma-0.9.14alpha.tar.gz 306549 RMD160 f5fc03910a76bb0e95b3e0a0008cae5d369dca16 SHA1 85947de3c71ad06448dc7848945ff1deef4e540c SHA256 8ae2f9681e1ecd8c1bc5b1914e755736a839c620b6111c5ab38e2e253ef3255f -DIST foma-0.9.1alpha.tar.gz 238601 RMD160 971e8d5990c85ee78e34fb9b64424030f16b556a SHA1 7c2127e30f12bc3330d3c49c27020b69aadcdfe4 SHA256 5b72417a4654e62959f4e52e7c1db391b3c2058b4054fb197fa763c7999bd70e -DIST foma-0.9.4alpha.tar.gz 92640 RMD160 8e93b00e8407be5f8a44f1cba040526a4c4179b6 SHA1 df272ad99ec442d23c0ed143da8e05d422f52607 SHA256 ec29fa86ed8e386743fec43b8f53f93274a9642aab8060c12e7712fea295a83a -EBUILD foma-0.9.14_alpha.ebuild 902 RMD160 c9f95684be92b2074e5ea85e0cee15a3f2eb6cd3 SHA1 2983f570c3a73d149f59c107572498bbabbb427b SHA256 883a259fe6a1e2271e6102730e25276cddec3ae29d32df950d0c83f80396462e -EBUILD foma-0.9.1_alpha.ebuild 625 RMD160 e4666a074b47cda1639d93211ca0b9d3e1d7ee19 SHA1 d4d5f0cd5908df1177933252c153cc91f4928092 SHA256 fd670315f134d04cd6a6b6dff817364214e2835f421548f26b93caad4ba0d6dd -EBUILD foma-0.9.4_alpha.ebuild 722 RMD160 f8ac33f80c77cc4420a96f941e0e11c6bd12849b SHA1 83b2d8c104277d1416410e1ce20a3af049d87026 SHA256 e1655f7e5d73c19051997f1ec7a70b69f1eb2f8f50eda2afa5d294dcdaf5b6e6 -MISC ChangeLog 485 RMD160 a97238238ea33358f64e1335ad31dc6a69e0def8 SHA1 c3255f9987e71223c71f1835c11fab11a25eba43 SHA256 3fb96e2713dc3a4d73f7309ce18b1eebe2fc16f8b14e66267cce42e5b542fda5 -MISC metadata.xml 223 RMD160 754bf1189c9d51090f3e0439f6e7d6f603b93df0 SHA1 54348ca01c174e03ff3318b2a9da50d970db6695 SHA256 5c57a999484660ea4a3e55f9c526bb38097d5c1cb2356353133ec4d7e89f1f88 +EBUILD foma-0.9.14_alpha.ebuild 788 RMD160 923b300eaa28fa8ad17be50efbd73080ec4b9cdb SHA1 d5dcfbc8f9d08f6f27464a179f7ed6eb28c09ee7 SHA256 93db12caadec5348c3e2a9ae29a066cb8ace69adaf3bcae75af80ed815ee7c02 +MISC ChangeLog 644 RMD160 0647d38bd45d4ea441016ce4e00bfba5071ea29a SHA1 8b4ea29427c26d33b3703a9bfeda32da3f3cf8a3 SHA256 8ae6253161c7eff667e1ad385a8f73effbac610bce1509b0ff276d1ae8eeb998 +MISC metadata.xml 226 RMD160 1c7ce9a688f707139f29f88e7c855bf92ec72191 SHA1 f2a77147c65f180e50735c60939cd1f5d94bb249 SHA256 393c34db7f76c24fa19ace290f2b842696abffb363b7316976ca41e00f8f22f0 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GEocACgkQgAnW8HDreRa+nwCgg1EoOX+J+RclV6ECDDhaBRaW +nXoAoJ4WzLjEl748Ogu5eDBeGzEI7WjZ +=HQkd +-----END PGP SIGNATURE----- diff --git a/sci-misc/foma/foma-0.9.14_alpha.ebuild b/sci-misc/foma/foma-0.9.14_alpha.ebuild index 93616abe6..e0c455ce9 100644 --- a/sci-misc/foma/foma-0.9.14_alpha.ebuild +++ b/sci-misc/foma/foma-0.9.14_alpha.ebuild @@ -2,46 +2,43 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ +EAPI=4 + MY_P=${P/_alpha/alpha} DESCRIPTION="Finite state toolkit compatible with Xerox tools" - HOMEPAGE="http://foma.sf.net/" - SRC_URI="http://dingo.sbs.arizona.edu/~mhulden/${MY_P}.tar.gz" LICENSE="GPL-2" - SLOT="0" - KEYWORDS="~x86" - IUSE="" -DEPEND=">=sys-devel/bison-2.3 - >=sys-devel/flex-2.5.35 - sys-libs/readline - sys-libs/libtermcap-compat" - -RDEPEND="${DEPEND}" +RDEPEND=" + sys-libs/libtermcap-compat + sys-libs/readline" +DEPEND="${RDEPEND} + >=sys-devel/bison-2.3 + >=sys-devel/flex-2.5.35" S="${WORKDIR}/${PN}" -src_unpack() { - unpack ${A} - cd ${S} - sed -i -e "s/^CFLAGS =/CFLAGS = ${CFLAGS} -fPIC/" \ +src_prepare() { + sed \ + -e "s/^CFLAGS =/CFLAGS = ${CFLAGS} -fPIC/" \ -e 's/ltermcap/lcurses/' \ - -e 's/ldconfig/true/g' Makefile + -e 's/ldconfig/true/g' \ + -i Makefile || die } src_compile() { - emake || die "make failed" - emake libfoma || die "library failed" + emake + emake libfoma } src_install() { - dobin foma || die "installing binaries failed" + dobin foma dolib.so libfoma.so.0.9.14 - dodoc README README.symbols || die "installing docs failed" + dodoc README README.symbols } diff --git a/sci-misc/foma/foma-0.9.1_alpha.ebuild b/sci-misc/foma/foma-0.9.1_alpha.ebuild deleted file mode 100644 index ab8c63309..000000000 --- a/sci-misc/foma/foma-0.9.1_alpha.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -MY_P=${P/_alpha/alpha} - -DESCRIPTION="Finite state toolkit compatible with Xerox tools" - -HOMEPAGE="http://foma.sf.net/" - -SRC_URI="http://dingo.sbs.arizona.edu/~mhulden/${MY_P}.tar.gz" - -LICENSE="GPL-2" - -SLOT="0" - -KEYWORDS="~amd64" - -IUSE="" - -DEPEND=">=sys-devel/bison-2.3 - >sys-devel/flex-2.5.4 - sys-libs/readline - dev-libs/boehm-gc" - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -src_install() { - dobin foma || die "installing binaries failed" - dodoc README README.symbols || die "installing docs failed" -} diff --git a/sci-misc/foma/foma-0.9.4_alpha.ebuild b/sci-misc/foma/foma-0.9.4_alpha.ebuild deleted file mode 100644 index e3063f90b..000000000 --- a/sci-misc/foma/foma-0.9.4_alpha.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -MY_P=${P/_alpha/alpha} - -DESCRIPTION="Finite state toolkit compatible with Xerox tools" - -HOMEPAGE="http://foma.sf.net/" - -SRC_URI="http://dingo.sbs.arizona.edu/~mhulden/${MY_P}.tar.gz" - -LICENSE="GPL-2" - -SLOT="0" - -KEYWORDS="~amd64" - -IUSE="" - -DEPEND=">=sys-devel/bison-2.3 - >=sys-devel/flex-2.5.35 - sys-libs/readline - dev-libs/boehm-gc" - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -src_unpack() { - unpack ${A} - cd ${S} - sed -i -e "s/^CFLAGS =/CFLAGS = ${CFLAGS} /" Makefile -} - -src_install() { - dobin foma || die "installing binaries failed" - dodoc README README.symbols || die "installing docs failed" -} diff --git a/sci-misc/foma/metadata.xml b/sci-misc/foma/metadata.xml index 0ad3ea858..fcf844dd8 100644 --- a/sci-misc/foma/metadata.xml +++ b/sci-misc/foma/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>no-herd</herd> -<maintainer> - <email>flammie@gentoo.org</email> -</maintainer> + <herd>no-herd</herd> + <maintainer> + <email>flammie@gentoo.org</email> + </maintainer> </pkgmetadata> diff --git a/sci-misc/hfst/ChangeLog b/sci-misc/hfst/ChangeLog index 05b5cfd25..6f9b6ac9b 100644 --- a/sci-misc/hfst/ChangeLog +++ b/sci-misc/hfst/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> hfst-2.2.ebuild, + hfst-3.0.2.ebuild: + EAPI bump + *hfst-3.0.2 (09 May 2011) 09 May 2011; <flammie@gentoo.org> +hfst-3.0.2.ebuild, metadata.xml: diff --git a/sci-misc/hfst/Manifest b/sci-misc/hfst/Manifest index 019c595ee..bd18b6349 100644 --- a/sci-misc/hfst/Manifest +++ b/sci-misc/hfst/Manifest @@ -1,6 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST hfst-2.2.tar.gz 3608685 RMD160 d10006421670ce3f1c9d44115b6916a84f4b0063 SHA1 51f9ad1008124c310047e79798d76498bc01dbab SHA256 0b63d60dd331f7bcf32908015cada8920127215564735036696a0e877ab69337 DIST hfst-3.0.2.tar.gz 1110799 RMD160 f068c8a70528201e2b76c9ff406316cadbf486e1 SHA1 1bfc94590fde4ee6ff70466edeae5f983005db4f SHA256 8d02fa5b2ee490c9a6bdf62b7b98918b94cea080c41e8c404a6bce6d123c0a31 -EBUILD hfst-2.2.ebuild 485 RMD160 d605b9d3730b94eaeffbdc4f3b1e29d9b4867d28 SHA1 cadadc321ac90ff7c8361a20eaf1f9dabc552fb8 SHA256 884aaddd7449ecdf4492681d8b35e789ba30afa471deda57857663ac4312b909 -EBUILD hfst-3.0.2.ebuild 718 RMD160 c635db30da9b689fb0b9cc8ec4d4481949c7b231 SHA1 6c7015785ad9109b239adeb7eb4f1e0215b66e04 SHA256 006c1279881a8d7c77e6037e36fb415e831c29aefa664e1d6897b5e1363bec63 -MISC ChangeLog 349 RMD160 585e568676a431e5be0779896fb13753f30dc204 SHA1 d061981ca7f276a54a142d19019a0699b298ddd6 SHA256 f0a257d413ad62eebdce22cfcc607e889d962c0acdd7d416402f56ace6f55b63 +EBUILD hfst-2.2.ebuild 339 RMD160 838b761bacc5d67831f84b9e2879610adbe93754 SHA1 7c59244d6c3969fd420a483c3fa5a89767a08dc1 SHA256 ef969bd58e99247618157276e1eb3bf900e0b19001644d522a09b94d4161f04b +EBUILD hfst-3.0.2.ebuild 593 RMD160 ae393576f86cb7dc4a266ae8724f6990b1a8eca1 SHA1 f0955861d119b6dd49deec5575b6fafc9a10589e SHA256 028fa5ade8aabf795799503c53dd4ba7893db982804fcd01ba02666e8dd55108 +MISC ChangeLog 447 RMD160 10c4d26250ebd41f838ccb57a6f332c6e6c8b955 SHA1 50a1dd9caf5eb7f53e8201389d7f00ede3570a5f SHA256 00318db61b7b4b6c62515a76cd775c3985930daccdc8746ccd0fe4949a8f0724 MISC metadata.xml 673 RMD160 c88e78868c478be019d8b9580d81544c03b43552 SHA1 6bcd5819a40eaff92d05932be82e242f6bf9a7f6 SHA256 0f90d150b1b080e28b6bb95030d901d37c997394ec3c6fd2b5746ed27adf5bb0 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EwzkACgkQgAnW8HDreRaIegCeJe3Dc3hk4p6DFr9hOgYrKycq +4LgAoIYFeBrr4goaNKGs2MJgB7Q5iaO9 +=IBSe +-----END PGP SIGNATURE----- diff --git a/sci-misc/hfst/hfst-2.2.ebuild b/sci-misc/hfst/hfst-2.2.ebuild index a688b29d6..7e7d56fbb 100644 --- a/sci-misc/hfst/hfst-2.2.ebuild +++ b/sci-misc/hfst/hfst-2.2.ebuild @@ -1,21 +1,14 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ +EAPI=4 + DESCRIPTION="Helsinki Finite State Transducer API and tools" HOMEPAGE="http://hfst.sourceforge.net/" SRC_URI="mirror://sourceforge/hfst/hfst-2.2.tar.gz" LICENSE="GPL-3" SLOT="0" -KEYWORDS="~x86" +KEYWORDS="~amd64 ~x86" IUSE="" - -DEPEND="" -RDEPEND="" - -src_install() -{ - emake DESTDIR="${D}" install || die "install failed" - dodoc AUTHORS ChangeLog NEWS README THANKS || die "docs missing" -} diff --git a/sci-misc/hfst/hfst-3.0.2.ebuild b/sci-misc/hfst/hfst-3.0.2.ebuild index 3049c4de5..9ed89b652 100644 --- a/sci-misc/hfst/hfst-3.0.2.ebuild +++ b/sci-misc/hfst/hfst-3.0.2.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 +EAPI=4 DESCRIPTION="Helsinki Finite State Transducer API and tools" HOMEPAGE="http://hfst.sourceforge.net/" @@ -13,20 +13,16 @@ SLOT="0" KEYWORDS="~x86" IUSE="+openfst sfst" # foma" -DEPEND="openfst? ( >sci-misc/openfst-1.2 ) -sfst? ( >sci-misc/sfst-1.3 ) -" -# foma? ( >sci-misc/foma-0.9.13 ) +DEPEND=" + openfst? ( >sci-misc/openfst-1.2 ) + sfst? ( >sci-misc/sfst-1.3 )" +# foma? ( >sci-misc/foma-0.9.13 ) RDEPEND="${DEPEND}" -src_configure() -{ - econf $(use_with openfst) $(use_with sfst) --without-foma - # $(use_with foma) -} - -src_install() -{ - emake DESTDIR="${D}" install || die "install failed" - dodoc AUTHORS ChangeLog NEWS README THANKS || die "docs missing" +src_configure() { + econf \ + $(use_with openfst) \ + $(use_with sfst) \ + --without-foma +# $(use_with foma) } diff --git a/sci-misc/jwnl/Manifest b/sci-misc/jwnl/Manifest index 8d6507911..3210094e4 100644 --- a/sci-misc/jwnl/Manifest +++ b/sci-misc/jwnl/Manifest @@ -3,23 +3,13 @@ Hash: SHA1 DIST jwnl13rc3.zip 640112 RMD160 798ce5c8a20df08d6adde44255677b5ee71708e6 SHA1 720bfd4632f0efc47b185aa06aa1da41dca342a9 SHA256 6c0cbfa0dfc19e5d773255c684398cf38970312ae955a99a128c826830a785ad DIST jwnl13rc3_src.zip 109993 RMD160 b091421cf771e13a2758715e888d533124b5e776 SHA1 a7755e3710287d4462dfce3ee171bad885e17b08 SHA256 d00d1102ab6c9731c48570583d6f7d21faba50a670e1d44d17fb994fd2a9e912 -EBUILD jwnl-1.3_rc3.ebuild 1209 RMD160 b4ef0750a5ffab1dc53f0f76d30c6f6c1a374c3f SHA1 64624cc76f9b6291eafdcc3d702f5325b1dd933c SHA256 557378f75f807a263460b0e37449933108c4cda97aacd27724133e0257a7f4ee +EBUILD jwnl-1.3_rc3.ebuild 1209 RMD160 d81c91db0ab7dc362bc595bc1209853044302aaf SHA1 7db614a8b7a9b5643c785407d8e031eb83f52b29 SHA256 05388408e6612bebce13bc64f103aa8820d7d97a470f493f27f4966db6189806 MISC ChangeLog 337 RMD160 e1e18c0232c1230e984b6c611d5fa127d1c9a476 SHA1 ce97f2f885edaa6a00ea502ebed5771c8b1c74d3 SHA256 bc813606194d803d768aad310710bebf9ccdc2fb4a558f608a4997c1d0bef8d0 MISC metadata.xml 342 RMD160 fd059c7c999945259f1a29c60776136f08cd1072 SHA1 0052cee54eba1992a1aed3d74935116e99030cdf SHA256 6d5a15f68717cdfcea236046f217cc527e6a655c39d996127b86974a6b994171 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMISXWAAoJENwGBM22xffeUbAP/jko8OqXrNqsSMh2ZbhYrLF3 -PXf6tr7PWCca/BB9b/e2EelxGy53b9pizu7zbV+a3sOwpZ9QcXZ92oW4CklYycFN -Or7kxjJHsVPWib+oq1DwLPegSL6waeFA8DV6c0GwH19jP3U7J/olmpBdZDd6N6N3 -HNphi3mcnbXYsKnx/9Zw6yKSQ8RYiSnkS+OWChevLQPW2s4hRdZHRyK6c+XZq2UD -wUUayhWL5S8LJkAruNy7t6JAWkw4pdOVchJsO7nAiDiaA1pb8tqI2F1qEf2beItp -ZlLLnYBsDvGVVxTj3ws2+1VJFl/BVRqEEnPgMFroOxnJnhry3APJwhsaMR6YgMLc -ovLvhUPWN4/rOdr4okL65z7/gOo8cBjkwgSob22Pk74hu3GBAJG1+5Fvu8KRq+JS -NvDKfriaOV93wvCv1Yp125JCwKxDqSpASibolapvRjkgcI+SKMTEBWQr7kTIIaqR -Mh6h6qThIpnObiKizYHqKKV5/asN9yvP88xUZFKds5I0rE2kCoCpfsJcvfzNt9IK -F5Cd8Eq5TNajMbKO9nlCHYxf2wdMJIG+OajO3rhHa/q1ztwLJ9kmAblK2rNiazAX -nm2ZFOyX0Wm77QjKLwbZbv5/vUDe/Z7GWwpUj22DfgihVJ7tZEgBPy3t+jK1IX4D -u+reUGwOxazOFx8xPa9u -=QJkc +iEYEARECAAYFAk4ErSEACgkQgAnW8HDreRawagCfQh+IKUsDC+hSwWYbFw2ahakn +KKoAoNBAOfz7H7hgOp12lDVDLWPR4hp7 +=OpX6 -----END PGP SIGNATURE----- diff --git a/sci-misc/jwnl/jwnl-1.3_rc3.ebuild b/sci-misc/jwnl/jwnl-1.3_rc3.ebuild index 37f1943ab..cb6c319e5 100644 --- a/sci-misc/jwnl/jwnl-1.3_rc3.ebuild +++ b/sci-misc/jwnl/jwnl-1.3_rc3.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit eutils versionator java-pkg-2 java-utils-2 +inherit eutils java-pkg-2 java-utils-2 versionator MY_P=${PN}$(delete_all_version_separators) DESCRIPTION="Java interface to WordNet dictionary data" diff --git a/sci-misc/nco/.#Manifest.1.21 b/sci-misc/nco/.#Manifest.1.21 deleted file mode 100644 index 13c63f15e..000000000 --- a/sci-misc/nco/.#Manifest.1.21 +++ /dev/null @@ -1,6 +0,0 @@ -DIST nco-3.9.9.tar.gz 4109201 RMD160 e1721bf3f9ad1473dc0120651b6130830cd7c77c SHA1 f8e62993423cdf3c444637a8c280a8a62e725651 SHA256 cdfd7cf47aef49b32e4e581bc7d2d6cdd05312ed88a2a0cfaf83c520e665b142 -DIST nco-4.0.7.tar.gz 4859089 RMD160 baadd326b0d5088639d8baa53c7888781308a244 SHA1 d0586b9c386152ace2d8d15138ad35850b78d34f SHA256 fbff6e8f316efbdc55a39ee1da0a38cddc7005c624facb7c82f632dea629c0de -EBUILD nco-3.9.9.ebuild 1708 RMD160 f3280c3ee9e8f74f9e87bd9df18a08559ae8f8fa SHA1 cefa7b344e7c7e636c0d72f1286ec2fbd48aac7d SHA256 a112f3f00b462aa4aa02e4176745c3d3233c3f87ad70e74137f74d874b313b4a -EBUILD nco-4.0.7.ebuild 1394 RMD160 a83f8387eac44f1ea1713ddd4249c477f44ce5ce SHA1 73e3c05f7e0adb7d4a87e8ac35b34e5ae525cc66 SHA256 b2ed3dde7ae9165044ed5f2bac7dc854bb4172fc20cfdaee56c51052845ed175 -MISC ChangeLog 3301 RMD160 404390d3cba52c8010b1df88f0a78fa663902148 SHA1 f67405e0f58d378bd9e3a1374441b2c77a128e93 SHA256 7745a9680fbba3f76e05891068b119c60623666c79a68aa59a4158761f2156b7 -MISC metadata.xml 866 RMD160 054c53be984a3638a603ddbe88aa24466272664c SHA1 63fd9f687572d71a006cd51deb648e764c52b543 SHA256 804e9546205b2965cda0cd1b81547aeb1b9fdc561526c5078d066af3a79b296f diff --git a/sci-misc/nco/Manifest b/sci-misc/nco/Manifest index a920759d2..30e60e0e4 100644 --- a/sci-misc/nco/Manifest +++ b/sci-misc/nco/Manifest @@ -1,3 +1,3 @@ DIST nco-4.0.7.tar.gz 4859089 RMD160 baadd326b0d5088639d8baa53c7888781308a244 SHA1 d0586b9c386152ace2d8d15138ad35850b78d34f SHA256 fbff6e8f316efbdc55a39ee1da0a38cddc7005c624facb7c82f632dea629c0de -EBUILD nco-4.0.7.ebuild 1454 RMD160 5965c02e611389d12c877a12dc8b6a05aedb281f SHA1 2f79ccc6beb47a908a9dbe587a6ddc399fc1c769 SHA256 d4647b296089505e217bdc3fb1d4ee6e8344dc36c21b883d0802386eac310374 +EBUILD nco-4.0.7.ebuild 1455 RMD160 811905e272ae170b7b13da76d0fac224ca5089b9 SHA1 2581d9f5709d036e77113f48d82ef712d6295c00 SHA256 c8b3e37728a31a3eec8cb0bec23aa5ba3a84727fdc4f9ec6f229005e6b526209 MISC metadata.xml 866 RMD160 054c53be984a3638a603ddbe88aa24466272664c SHA1 63fd9f687572d71a006cd51deb648e764c52b543 SHA256 804e9546205b2965cda0cd1b81547aeb1b9fdc561526c5078d066af3a79b296f diff --git a/sci-misc/nco/nco-4.0.7.ebuild b/sci-misc/nco/nco-4.0.7.ebuild index 486844daa..6da2897fc 100644 --- a/sci-misc/nco/nco-4.0.7.ebuild +++ b/sci-misc/nco/nco-4.0.7.ebuild @@ -3,6 +3,7 @@ # $Header: $ EAPI=4 + inherit eutils DESCRIPTION="Command line utilities for operating on netCDF files" @@ -12,14 +13,13 @@ SRC_URI="http://dust.ess.uci.edu/nco/src/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~ppc ~x86" - IUSE="doc gsl mpi ncap2 static-libs udunits" -RDEPEND=">=sci-libs/netcdf-4 +RDEPEND=" + >=sci-libs/netcdf-4 gsl? ( sci-libs/gsl ) mpi? ( virtual/mpi ) udunits? ( >=sci-libs/udunits-2 )" - DEPEND="${RDEPEND} ncap2? ( !mpi? ( dev-java/antlr:0 ) ) doc? ( virtual/latex-base )" diff --git a/sci-misc/nltk/ChangeLog b/sci-misc/nltk/ChangeLog index 1803c90ea..e0d694500 100644 --- a/sci-misc/nltk/ChangeLog +++ b/sci-misc/nltk/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-misc/nltk -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*nltk-2.0.1_rc1 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -nltk-0.9.5.ebuild, + +nltk-2.0.1_rc1.ebuild, metadata.xml: + Version Bump, cleaned old + 04 Jul 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> nltk-0.9.5.ebuild: Silence repoman, drop ~amd64 since dependencies cannot be fulfilled. No diff --git a/sci-misc/nltk/Manifest b/sci-misc/nltk/Manifest index f62e39668..d1cf02071 100644 --- a/sci-misc/nltk/Manifest +++ b/sci-misc/nltk/Manifest @@ -1,25 +1,14 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 -DIST nltk-0.9.5.tar.gz 1177059 RMD160 079ccaf078405310028d2d1e93f0d46486d313ca SHA1 2267ac50c6c2cede9286c3b502ead98045678d80 SHA256 2dc56cccff566177d7f1e86df055852ebfa821b46f94920b81e0a80c0626bd02 -DIST nltk-data-0.9.5.zip 104049679 RMD160 0a06a0750236d5d2ab7c094fb3c73e979f62e3c4 SHA1 b04f3d1466cc0c2ccda2c320760a0ec443ccaf7b SHA256 dffe745f2615d7baa6112ce03d3fdb1e3949f9cda36db146eb32093b557ee87b -EBUILD nltk-0.9.5.ebuild 816 RMD160 1885b83c959fe6794b121cade5dfad2f90fe92aa SHA1 6485366aeacd95b1e1d080a5b8dfc4a51a37ae4c SHA256 18742142c1d7cf76b2e0223f8d6d864d92831a5e68ced0741f2dfca824598c2a -MISC ChangeLog 869 RMD160 6a5e628a92bf1a4c987a3524422c94de76693019 SHA1 84d83c752b988bc43ab6bca86aa593e35cf482f5 SHA256 518f46beacc6898730feadf9b9557ef98a0e7bc83ddabd9a59be22920bb0baa3 -MISC metadata.xml 364 RMD160 aff2bdd66780e4c75fb9b6ae3d736b26cc955c9e SHA1 7e21481f5ba1c24eb28c17dd91a609fe176da3a6 SHA256 9660ff37111b5f36e3020fcc257a7bf52c9f3c8c1020da7be578393363197e96 +DIST nltk-2.0.1rc1.zip 1095096 RMD160 7548789676c355caaa0f04feb82cccaa4ca19b81 SHA1 8985c3aeb2ec0d183b2df80319853122247c1ee6 SHA256 ab26d1a93b783c26bd234ecaeef250b8a5f35b601810d0b78e24c52e749627e7 +EBUILD nltk-2.0.1_rc1.ebuild 641 RMD160 4bb8e07c7e90fce25054dc1e96784a61038646a4 SHA1 d8e01721477eb307251ab7c6db695f6c01657941 SHA256 5f4c268b6711a497a51827cad8e01ac056f71aaba3f025ac5c928542d3026579 +MISC ChangeLog 1036 RMD160 460ab1bc2255ff4eff2b25a72a519e452f332c75 SHA1 91c8974ce0637a03e0440653fd7349249b5e2f28 SHA256 e0a3bd061f731a42943573c46759070fa54746b5dae11ef9d5bdd8d9154b1048 +MISC metadata.xml 368 RMD160 2d8e538d51e402538d27e83802e1287507ad4608 SHA1 7ff5f8609bbdcb811907a914970b06c30b57ca0f SHA256 cb29427987e6baf23b0d4621f0e9d690c5795cef427d9758ffdbea2b6b6d1fa0 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMMKh7AAoJENwGBM22xffeiDkP/inOhq6QBexKEZI5gIwvU4a7 -iyJmpo9coQW1C333d7wmLEUGWy7MDG6WkFS564UEWrIME6n49Me1I+0qBlk3f0Bk -gmXdVAyM1uwt3TP9Z+imQPSfRDWOFNhC4R0AD6zHA2XR8hzUKL2p1BJzAX0o/9IL -HELU/t2FCMQcxAdgxWeGbVw0p02mcY8VkFdzRhqBZ/BdDkfnr0gJSPkarc2fDuUu -oHZ+urq6AwaCYwR4/laq2l7Tl6vZF1tAF4tlQ08+73e1mm+gvXfJcEFzejh1IC3e -J9LMwUEgoSRvBCtBw4ZPb5ZkSs9lrOsxm7BgsM8cL3aKpc6cFMgIncQ3g5/Yaam7 -1ZeR1S6MUbHJASc+Ygo4yEjeVMxf7NliFdGgNGvaQ+5PdYqF2giqPiCeZL942O+d -UhNDsyXQASHzkOi6qnK3Gi5zp1vI0d4kr89fMegX61eJXCqcrDGvTiQ4px0ON0d5 -XyZ48W1+QXapZWT/cFh49x/2S3Y34RNL39hJd8n8xbhsJbB77ha11LY9a/vqx+QS -Ta5cpWtrG1rd/Xh+qySxyBH/TmfzrSE8Fq/UTmX1/2rP/JwySZvqKht+yo0MrcVU -ZGt8nJ1+d+i1Icun2f/g+evS9GFUUrWb0CeZRHqnTxPN6EqeuMsFaWPZXfkGPheT -vrhpZLJB5yII0yYw3Y0x -=MYtm +iEYEAREIAAYFAk4F43QACgkQgAnW8HDreRaRrgCeMT79DrH0nCFWEZ9KqLVUFvLD +1VkAoMI6AK5b/XweVMPn295A9SVvXnNC +=6MnT -----END PGP SIGNATURE----- diff --git a/sci-misc/nltk/metadata.xml b/sci-misc/nltk/metadata.xml index 498cc9d45..d1ecb4ffd 100644 --- a/sci-misc/nltk/metadata.xml +++ b/sci-misc/nltk/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>no-herd</herd> -<maintainer> - <email>flammie@gentoo.org</email> -</maintainer> -<longdescription> + <herd>no-herd</herd> + <maintainer> + <email>flammie@gentoo.org</email> + </maintainer> + <longdescription> NLTK is collection of natural language tools written in python language. It also contains huge corpora. </longdescription> diff --git a/sci-misc/nltk/nltk-0.9.5.ebuild b/sci-misc/nltk/nltk-2.0.1_rc1.ebuild index 80fe7f448..ca32ec655 100644 --- a/sci-misc/nltk/nltk-0.9.5.ebuild +++ b/sci-misc/nltk/nltk-2.0.1_rc1.ebuild @@ -1,40 +1,32 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=3 PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" PYTHON_USE_WITH="tk" RESTRICT_PYTHON_ABIS="3.*" -PYTHON_MODNAME="yaml nltk_contrib nltk" +PYTHON_MODNAME="nltk_contrib nltk" -inherit eutils distutils +inherit distutils eutils DESCRIPTION="Natural language processing tool collection" HOMEPAGE="http://www.nltk.org/" -SRC_URI=" - mirror://sourceforge/${PN}/${P}.tar.gz - mirror://sourceforge/${PN}/${PN}-data-${PV}.zip" +SRC_URI="http://${PN}.googlecode.com/files/${P/_rc/rc}.zip" LICENSE="GPL-2" SLOT="0" KEYWORDS="" IUSE="" -DEPEND="${DEPEND} - dev-python/numarray +DEPEND=" dev-python/numpy dev-python/matplotlib + dev-python/pyyaml >=app-dicts/wordnet-2.0 sci-misc/pywordnet" RDEPEND="${DEPEND}" -NLTK_DATA="${WORKDIR}/data/" - -src_install() { - distutils_src_install - insinto /usr/share/nltk/data - doins -r "${WORKDIR}"/${PN}_data/* || die -} +S="${WORKDIR}"/${P/_rc/rc} diff --git a/sci-misc/openfst/Manifest b/sci-misc/openfst/Manifest index 6874f56d5..c7bf98705 100644 --- a/sci-misc/openfst/Manifest +++ b/sci-misc/openfst/Manifest @@ -1,5 +1,15 @@ -MISC ChangeLog 739 RMD160 6be6fed5ff79ddee9a8872f4884da075300d29e7 SHA1 4a4c12d31bea9f11e6ebc80099b0a5a409bb49e5 SHA256 15b110959e4cf87ab976d40f7cf0060e1eaf65e1b420d88675c563838b40aafc +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX openfst-20080422_beta-gcc-4.3.patch 2918 RMD160 0aeceeb049614182f2e83fa3a149ba5aa54cffaa SHA1 64bb951888f83a3ba9f780b4ec4dec46d9d20303 SHA256 8aab92d28f806074916d76245de4c46b15c9ac302a8417e4cb168aa8d755cb12 -MISC metadata.xml 223 RMD160 754bf1189c9d51090f3e0439f6e7d6f603b93df0 SHA1 54348ca01c174e03ff3318b2a9da50d970db6695 SHA256 5c57a999484660ea4a3e55f9c526bb38097d5c1cb2356353133ec4d7e89f1f88 -EBUILD openfst-1.2.7.ebuild 715 RMD160 81f44c1e6407f9c04c7e744b577ac593d2096b47 SHA1 11c8797f15469653b7051b70f1c2b31b9c688fa5 SHA256 7487360f5df0d0705daa65d9cec6cd2f85da757094e7cbd064d697066be6b4e4 DIST openfst-1.2.7.tar.gz 668134 RMD160 a24279f4deb85f79875b237c548f0b600c3a6af8 SHA1 75aa24fe050c295e16aaeb31a216c1d97952c84e SHA256 a38b10a7a1b6c054fb15035f3197f566ac6b23bc2acd5958052165ae7ce5c11c +EBUILD openfst-1.2.7.ebuild 715 RMD160 a1e01034f8532cf312079d84e77db9e229d98fcd SHA1 d7111ccea8b2be3519fd477d10caee2bf4ce1698 SHA256 84fe16dba0e133d4618ffb9ef261b62b29fa0167716c672392274d7d559f1a1c +MISC ChangeLog 739 RMD160 6be6fed5ff79ddee9a8872f4884da075300d29e7 SHA1 4a4c12d31bea9f11e6ebc80099b0a5a409bb49e5 SHA256 15b110959e4cf87ab976d40f7cf0060e1eaf65e1b420d88675c563838b40aafc +MISC metadata.xml 223 RMD160 754bf1189c9d51090f3e0439f6e7d6f603b93df0 SHA1 54348ca01c174e03ff3318b2a9da50d970db6695 SHA256 5c57a999484660ea4a3e55f9c526bb38097d5c1cb2356353133ec4d7e89f1f88 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4ErSUACgkQgAnW8HDreRaqcwCfSTt8XOijnzhJdVIaEjvtrVF6 +czwAn1c5uBRH2+xQUGVVjMwU6KCyBCYI +=xcaI +-----END PGP SIGNATURE----- diff --git a/sci-misc/openfst/openfst-1.2.7.ebuild b/sci-misc/openfst/openfst-1.2.7.ebuild index 4ccb69f2c..b1813c722 100644 --- a/sci-misc/openfst/openfst-1.2.7.ebuild +++ b/sci-misc/openfst/openfst-1.2.7.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit eutils multilib flag-o-matic +inherit eutils flag-o-matic multilib DESCRIPTION="Finite State Transducer tools by Google et al." HOMEPAGE="http://www.openfst.org" diff --git a/sci-misc/opennlp-tools/ChangeLog b/sci-misc/opennlp-tools/ChangeLog index e3c6e80e4..13ead5057 100644 --- a/sci-misc/opennlp-tools/ChangeLog +++ b/sci-misc/opennlp-tools/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-misc/opennlp-tools -# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> opennlp-tools-1.3.0.ebuild, + metadata.xml: + Cleaned ebuild and add USE description to metadata.xml + *opennlp-tools-1.3.0 (03 Jan 2008) 02 Jan 2008; Flammie Pirinen <flammie@gentoo.org> diff --git a/sci-misc/opennlp-tools/Manifest b/sci-misc/opennlp-tools/Manifest index d32badedb..0066cf9ac 100644 --- a/sci-misc/opennlp-tools/Manifest +++ b/sci-misc/opennlp-tools/Manifest @@ -1,3 +1,6 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST EnglishChunk.bin.gz 2529886 RMD160 442b1b2d4e3e88f620d6dcbce855ff38a2c88370 SHA1 1f57f19f13d51bf1584e1ba978158de36a39b351 SHA256 c2311f3d2e69aa13fa7c0c8e8b0d18b765a79a118da92bcfedc0702e63279c61 DIST EnglishSD.bin.gz 105687 RMD160 f8d438ecca941da9d8e56d51709c6af1b4d87bca SHA1 35bc048f7efac92abb6d9d95820671babe875c6a SHA256 e7192ae62454b73cf8e708e170c2416415529b9336889f3851dcae79b026e67f DIST EnglishTok.bin.gz 436785 RMD160 8fe7edaa45f946fabbdd1f8f897630d292d6e26b SHA1 12e8446a7a58a93972b4a45852be67aee66b1eaa SHA256 4d565ec5504f8b5fce80831050940374d8c179171b744aef14380ecc92c07bc9 @@ -42,6 +45,13 @@ DIST tagdict 213785 RMD160 a56cd181c58114d4a5758ce79569c97770a5e834 SHA1 89462ba DIST time.bin.gz 3622921 RMD160 71926ba19cdadc8ad50b528c6bae909d4cceb5db SHA1 8369ce6e14cb1bc2477e4d1fdbfccc09043ac5bd SHA256 c3dda43a836ee38c9d71ab55f6965a3d9d0fc174b276f96dd5df15895e435c53 DIST tmodel.bin.gz 4809 RMD160 3e757e0634bf3757e6224a7daecfe6ef57f2ca74 SHA1 582b476d315cce15e5fb9722908da410e6e108f5 SHA256 0eacf313641d851bec8044838b9350a70bfa96332e00e115744ff0a84df08937 DIST tmodel.nr.bin.gz 588 RMD160 44d334cc38f4c6af4ea354af995ac4875e151d2e SHA1 7ab75dbafd5e043f986c3b6b0cf4d78517b50c3c SHA256 850637e0cd688ee4dfada0840bdb0b12d5c6e72cc16fdd0b53043a7b4d03e2f5 -EBUILD opennlp-tools-1.3.0.ebuild 4614 RMD160 20cbed13b3f350aaf0005faeda5afd342e34e795 SHA1 85e4be61a994809309a058d18497757d0d98be4f SHA256 a978071f8e721f9f735e9cbee1ad53489f0d8fc0aaa7eeb4cebe1d9db51fec89 -MISC ChangeLog 255 RMD160 16639164faf36a0ad36defb9b366c8d6ac95a2b0 SHA1 49145763c76749e54738e62cd0d20b69a5625c92 SHA256 a09e5c7af482bf12d455054363a9c69b47904c83afb2585944f1c35e5087525a -MISC metadata.xml 377 RMD160 002a9f073642160e9ba8ab7ed46639247f911ba4 SHA1 4de2b1aa4e393e410f109ed612f73d729e0de1bf SHA256 4c1d671fe6396c31a9cd966083d6a817e143abea7e2b7250189484f8203b8e1a +EBUILD opennlp-tools-1.3.0.ebuild 4617 RMD160 930d696ca732b0e6cd91947ff0d5b8628fcab323 SHA1 afac0609adda9401c5dc576577def9d92cfd3e9f SHA256 3c7c3eb8675a7b70500c36c1b3b8aebbfa976e95f8ecf1b9775bcbc1c04848b5 +MISC ChangeLog 404 RMD160 7910ba88cbf1638aba8f8ac7a6e3360762e3aa88 SHA1 d804b7b0cb282484df7aee415109cd57cd7a55e9 SHA256 ba0c80cc26286af76240b088cf016addf5dc33c117f5d16ccfab1ea907ae05d8 +MISC metadata.xml 472 RMD160 cdfc748640854b7f3f71269ebddc4dee9cad9b3c SHA1 f6ec1c8c04ee89df7a121ebbaa020765a0684904 SHA256 44943217770bf31d2f4776db0014a06e9ed93085664e0d50367f3a7cb52c1904 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F2ugACgkQgAnW8HDreRYABgCfUvaSlixKQw8U54mTJ9glNxbg +tjAAn0odjq4lzrXJmEsMbiz3M7ZRVOLH +=tLzH +-----END PGP SIGNATURE----- diff --git a/sci-misc/opennlp-tools/metadata.xml b/sci-misc/opennlp-tools/metadata.xml index f9fa22d2e..66b2255cf 100644 --- a/sci-misc/opennlp-tools/metadata.xml +++ b/sci-misc/opennlp-tools/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>no-herd</herd> -<maintainer> - <email>flammie@gentoo.org</email> -</maintainer> -<longdescription> + <herd>no-herd</herd> + <maintainer> + <email>flammie@gentoo.org</email> + </maintainer> + <longdescription> Open source natural language processing toolkit containing lots of differents text processing tools and an API. </longdescription> + <use> + <flag name="models">Automatically generated description for models</flag> + </use> </pkgmetadata> diff --git a/sci-misc/opennlp-tools/opennlp-tools-1.3.0.ebuild b/sci-misc/opennlp-tools/opennlp-tools-1.3.0.ebuild index b5569b5e5..8703d120f 100644 --- a/sci-misc/opennlp-tools/opennlp-tools-1.3.0.ebuild +++ b/sci-misc/opennlp-tools/opennlp-tools-1.3.0.ebuild @@ -1,14 +1,16 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ JAVA_PKG_IUSE="doc source" + inherit java-pkg-2 java-ant-2 DESCRIPTION="Natural Language Programming API and tool suite" HOMEPAGE="http://opennlp.sf.net/" -MODELS="english/chunker/EnglishChunk.bin.gz +MODELS=" + english/chunker/EnglishChunk.bin.gz english/coref/acronyms english/coref/cmodel.bin.gz english/coref/cmodel.nr.bin.gz @@ -60,13 +62,12 @@ models? ( ${MODELS_SRC_URI} )" # Toolkit is all LGPL-2.1 LICENSE="LGPL-2.1" - SLOT="0" - KEYWORDS="~x86" - IUSE="${IUSE} models" -COMMON_DEP="dev-java/trove + +COMMON_DEP=" + dev-java/trove >=sci-misc/jwnl-1.3_rc3 >=app-dicts/wordnet-2.0 sci-misc/opennlp-maxent" diff --git a/sci-misc/praat/ChangeLog b/sci-misc/praat/ChangeLog index 5c219462e..eade52d56 100644 --- a/sci-misc/praat/ChangeLog +++ b/sci-misc/praat/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-misc/praat -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -praat-5.0.38.ebuild, + -praat-5.0.45.ebuild, praat-5.1.00.ebuild, praat-5.1.15.ebuild, metadata.xml: + Cleaned ebuild + *praat-5.1.15 (07 Sep 2009) 07 Sep 2009; Flammie Pirinen <flammie@gentoo.org> +praat-5.1.15.ebuild: diff --git a/sci-misc/praat/Manifest b/sci-misc/praat/Manifest index b744b6bda..f2800922e 100644 --- a/sci-misc/praat/Manifest +++ b/sci-misc/praat/Manifest @@ -1,10 +1,16 @@ -DIST praat5038_sources.tar.gz 6797859 RMD160 8bbd5a82c05491b669c8a5a7fda44277e8245ac3 SHA1 9b7a8acd9912e76ef7e8cb46b11fddaf6bd8aa3c SHA256 dd9d444b5e96f372e3bcddf02e0556ef075fcd192d71c1417d0d02af856654ec -DIST praat5045_sources.tar.gz 7133779 RMD160 887cc542ab8c99caf2371b8499b5fbb8d5d7dc72 SHA1 9ddeec51bb086dc7993105f4106b7e3da6323ccc SHA256 adffb8ae04ef45f34181042dd3f130f08f1ae1e098717c235ec91cfaffa141d1 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST praat5100_sources.tar.gz 5389639 RMD160 a6b497e0e433a0d2a9f6a13f6bf432824c8de767 SHA1 d611773696f6810266a312cf9e8f8426e82604c7 SHA256 0483badf3a0fd78134595cc868c14c77402bc432b184406557399467a50ba543 DIST praat5115_sources.tar.gz 5643423 RMD160 04b49e5459f9712d99c821ed6a83524f2a089d2b SHA1 64b382ee3ac75cb6128bbce751532a90a2a9c341 SHA256 680491b18e6f1c083bc74f7544dfa95d9c86d81af2f298331683074cc8cd1d65 -EBUILD praat-5.0.38.ebuild 1173 RMD160 ca35e12b4391d8b20b67d37f4b6f4300d43b5978 SHA1 d90f663833d8a5e06f92317087fbd8c878a2ec9b SHA256 e26b68fae0716c70b576d423a945abbd03b1be52690071aeea7e30826a19db8b -EBUILD praat-5.0.45.ebuild 1263 RMD160 15c807a2fa87d73420f0b8faffdc6453fcca755b SHA1 31aedf001402e15d7f2eac32e80988caa65fa993 SHA256 d7c65df08df822770190a53ffee85b3a62d8a200fc5e79c146b84de768bafa50 -EBUILD praat-5.1.00.ebuild 1263 RMD160 ecfe5bf16acba16b923dc5b9724e33e811931a62 SHA1 32dc08a5d87acfc4c9ddd76b82e51fbbfcd6636f SHA256 e5a2b462f780e47d7ec0d9efa120d42cc84a473e229aa4d88520a9b8103f59d8 -EBUILD praat-5.1.15.ebuild 1261 RMD160 6c8b52ae5dfc6c56d7deffc8de7eed99fa4ecc70 SHA1 2ee6fe3adcf293417d2e4d9511193777135c2378 SHA256 56f8f02926c6ba7b36d3feca72c0a9ad6ead3d15f9af7e31ae80dd528679663b -MISC ChangeLog 716 RMD160 6554916f99b0054c373f7579717f979b73078362 SHA1 9a87250de190591cc06ddf36e7d65db2d2c52f44 SHA256 8a07dc99eabf02dd9ff191364a6cbc8eeb3004731c37e94acd68b60dc5e1e0bf -MISC metadata.xml 367 RMD160 43af5fc696b058396bb82094438443b3801277ac SHA1 7e2a76f4325309c85c22e90a0665bda421827cf9 SHA256 e98b570f7a01d7e2f8c39efd7732a2adb115ab0a2f3117a6c921c9e1fa1f0bab +EBUILD praat-5.1.00.ebuild 1255 RMD160 a76a82fae9f059ddce7ac4585c4523ef43f3a8b3 SHA1 2076ce4a65efb3e4fd1b10503b5a673c0c8ad445 SHA256 0bcf0a2a5da732289923a04220787a789bab3883a75155af62942a981764e236 +EBUILD praat-5.1.15.ebuild 1255 RMD160 a76a82fae9f059ddce7ac4585c4523ef43f3a8b3 SHA1 2076ce4a65efb3e4fd1b10503b5a673c0c8ad445 SHA256 0bcf0a2a5da732289923a04220787a789bab3883a75155af62942a981764e236 +MISC ChangeLog 883 RMD160 598cef68474483d602f58f5ff17bb91843a8f032 SHA1 71ce5142808ee7a2edd67816335db5b6f038ccbc SHA256 80392fcd252ca909ab77c237de635a5d54f6e4e6db5b0fb2c1079a24ea5d64e9 +MISC metadata.xml 374 RMD160 ef33198e50344900d47588387d0fa0b6dad101bd SHA1 b72e128783793ac2a317b92fd9926272f43e3384 SHA256 9cf6525055efd4aade2a587b34e78c2b1115d2f5d0c093403321cb4f838204f5 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GE64ACgkQgAnW8HDreRYedgCfbxg5Nh4th2Ri9P9ujWphq5ML +dG8AnjsDxbcTS50+uxrKlbJqXJ2Rs9kT +=tDSD +-----END PGP SIGNATURE----- diff --git a/sci-misc/praat/metadata.xml b/sci-misc/praat/metadata.xml index aab6dfb75..c8cb1bb82 100644 --- a/sci-misc/praat/metadata.xml +++ b/sci-misc/praat/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>no-herd</herd> -<maintainer><email>flammie@gentoo.org</email></maintainer> -<longdescription lang="en"> + <herd>no-herd</herd> + <maintainer> + <email>flammie@gentoo.org</email> + </maintainer> + <longdescription lang="en"> Praat is a phonetic program for computer. It includes speech synthesis, analysis and other tools. </longdescription> </pkgmetadata> - diff --git a/sci-misc/praat/praat-5.0.38.ebuild b/sci-misc/praat/praat-5.0.38.ebuild deleted file mode 100644 index e3d3932d4..000000000 --- a/sci-misc/praat/praat-5.0.38.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit versionator -# FIXME: for versions with last part < 10 pad with zeroes -MY_PV=$(delete_all_version_separators) - -DESCRIPTION="Speech analysis and synthesis" -SRC_URI="http://www.fon.hum.uva.nl/praat/${PN}${MY_PV}_sources.tar.gz" -HOMEPAGE="http://www.fon.hum.uva.nl/praat/" -DEPEND="|| ( ( x11-libs/libXmu - x11-libs/libXt - x11-libs/libX11 - x11-libs/libICE - x11-libs/libXext - x11-libs/libSM - x11-libs/libXp - ) - virtual/x11 - ) - x11-libs/openmotif" -RDEPEND="${DEPEND}" -KEYWORDS="~amd64" -IUSE="" -LICENSE="GPL-2" -SLOT="0" - -S="${WORKDIR}/sources_${MY_PV}" - -src_compile() { - # TODO: following line should be updated for non-linux etc. builds - cp "${S}/makefiles/makefile.defs.linux.dynamic" "${S}/makefile.defs" - emake || die "emake failed" -} - -src_install() { - dobin praat - dodir /usr/share/${PN} - insinto /usr/share/${PN} - doins test/* - dodir /usr/share/${PN}/texio - insinto /usr/share/${PN}/texio - doins test/texio/* - dodir /usr/share/${PN}/logisticRegression - insinto /usr/share/${PN}/logisticRegression - doins test/logisticRegression/* -} - diff --git a/sci-misc/praat/praat-5.0.45.ebuild b/sci-misc/praat/praat-5.0.45.ebuild deleted file mode 100644 index 27c6bff66..000000000 --- a/sci-misc/praat/praat-5.0.45.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit versionator -# FIXME: for versions with last part < 10 pad with zeroes -# e.g 4 => 4000, 5.1 => 5100, 5.2.7 => 5207. -MY_PV=$(delete_all_version_separators) - -DESCRIPTION="Speech analysis and synthesis" -SRC_URI="http://www.fon.hum.uva.nl/praat/${PN}${MY_PV}_sources.tar.gz" -HOMEPAGE="http://www.fon.hum.uva.nl/praat/" -DEPEND="|| ( ( x11-libs/libXmu - x11-libs/libXt - x11-libs/libX11 - x11-libs/libICE - x11-libs/libXext - x11-libs/libSM - x11-libs/libXp - ) - virtual/x11 - ) - x11-libs/openmotif" -RDEPEND="${DEPEND}" -KEYWORDS="~amd64" -IUSE="" -LICENSE="GPL-2" -SLOT="0" - -S="${WORKDIR}/sources_${MY_PV}" - -src_compile() { - # TODO: following line should be updated for non-linux etc. builds - # (Flammie does not have testing equipment) - cp "${S}/makefiles/makefile.defs.linux.dynamic" "${S}/makefile.defs" - emake || die "emake failed" -} - -src_install() { - dobin praat - dodir /usr/share/${PN} - insinto /usr/share/${PN} - doins test/* - dodir /usr/share/${PN}/texio - insinto /usr/share/${PN}/texio - doins test/texio/* - dodir /usr/share/${PN}/logisticRegression - insinto /usr/share/${PN}/logisticRegression - doins test/logisticRegression/* -} - diff --git a/sci-misc/praat/praat-5.1.00.ebuild b/sci-misc/praat/praat-5.1.00.ebuild index 25ae8d384..a71a7d372 100644 --- a/sci-misc/praat/praat-5.1.00.ebuild +++ b/sci-misc/praat/praat-5.1.00.ebuild @@ -1,7 +1,9 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ +EAPI=4 + inherit versionator # FIXME: for versions with last part < 10 pad with zeroes # e.g 4 => 4000, 5.1 => 5100, 5.2.7 => 5207. @@ -10,7 +12,16 @@ MY_PV=$(delete_all_version_separators) DESCRIPTION="Speech analysis and synthesis" SRC_URI="http://www.fon.hum.uva.nl/praat/${PN}${MY_PV}_sources.tar.gz" HOMEPAGE="http://www.fon.hum.uva.nl/praat/" -DEPEND="|| ( ( x11-libs/libXmu + +KEYWORDS="~amd64 ~x86" +IUSE="" +LICENSE="GPL-2" +SLOT="0" + +DEPEND=" + || ( + ( + x11-libs/libXmu x11-libs/libXt x11-libs/libX11 x11-libs/libICE @@ -22,18 +33,13 @@ DEPEND="|| ( ( x11-libs/libXmu ) x11-libs/openmotif" RDEPEND="${DEPEND}" -KEYWORDS="~amd64" -IUSE="" -LICENSE="GPL-2" -SLOT="0" S="${WORKDIR}/sources_${MY_PV}" -src_compile() { +src_prepare() { # TODO: following line should be updated for non-linux etc. builds # (Flammie does not have testing equipment) cp "${S}/makefiles/makefile.defs.linux.dynamic" "${S}/makefile.defs" - emake || die "emake failed" } src_install() { @@ -48,4 +54,3 @@ src_install() { insinto /usr/share/${PN}/logisticRegression doins test/logisticRegression/* } - diff --git a/sci-misc/praat/praat-5.1.15.ebuild b/sci-misc/praat/praat-5.1.15.ebuild index 7009e2aa6..a71a7d372 100644 --- a/sci-misc/praat/praat-5.1.15.ebuild +++ b/sci-misc/praat/praat-5.1.15.ebuild @@ -1,7 +1,9 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ +EAPI=4 + inherit versionator # FIXME: for versions with last part < 10 pad with zeroes # e.g 4 => 4000, 5.1 => 5100, 5.2.7 => 5207. @@ -10,7 +12,16 @@ MY_PV=$(delete_all_version_separators) DESCRIPTION="Speech analysis and synthesis" SRC_URI="http://www.fon.hum.uva.nl/praat/${PN}${MY_PV}_sources.tar.gz" HOMEPAGE="http://www.fon.hum.uva.nl/praat/" -DEPEND="|| ( ( x11-libs/libXmu + +KEYWORDS="~amd64 ~x86" +IUSE="" +LICENSE="GPL-2" +SLOT="0" + +DEPEND=" + || ( + ( + x11-libs/libXmu x11-libs/libXt x11-libs/libX11 x11-libs/libICE @@ -22,18 +33,13 @@ DEPEND="|| ( ( x11-libs/libXmu ) x11-libs/openmotif" RDEPEND="${DEPEND}" -KEYWORDS="~x86" -IUSE="" -LICENSE="GPL-2" -SLOT="0" S="${WORKDIR}/sources_${MY_PV}" -src_compile() { +src_prepare() { # TODO: following line should be updated for non-linux etc. builds # (Flammie does not have testing equipment) cp "${S}/makefiles/makefile.defs.linux.dynamic" "${S}/makefile.defs" - emake || die "emake failed" } src_install() { @@ -48,4 +54,3 @@ src_install() { insinto /usr/share/${PN}/logisticRegression doins test/logisticRegression/* } - diff --git a/sci-misc/salome-med/Manifest b/sci-misc/salome-med/Manifest index e53e2c117..b3d143d49 100644 --- a/sci-misc/salome-med/Manifest +++ b/sci-misc/salome-med/Manifest @@ -15,14 +15,14 @@ AUX salome-med-5.1.4-med_int.patch 15420 RMD160 46314924e3f8fbf1347f736f47a92727 AUX salome-med-5.1.4-scotch.patch 411 RMD160 1a096ab3ba71c5e7c0f2e654022255af8f30f4dc SHA1 9fc334b2a4d5b75a7457e56157f5b2a1537d8adb SHA256 79d3e87c52bebc2a6a7fb06fcd4fed4fe366aa8403615d3e60c9790068734fb4 DIST src5.1.3.tar.gz 106470135 RMD160 f46ac847ab57c76df524ddf358b887662fc862cf SHA1 643c775f90277314983747e002918ee5b826db90 SHA256 78ce2acc9cfa474e030723674f4420c420fd2de926b1939455c3716f1fd48a2b DIST src5.1.4.tar.gz 120063320 RMD160 c309cebcc4808071d72b5a335185002d69d1420f SHA1 a8b922424af634bda35269e6049a1262e27fc260 SHA256 dd59384ad4fbbbe49c72e946eed9e0f6144a01c799efab62033113a3db46eeae -EBUILD salome-med-5.1.3.ebuild 3790 RMD160 dab4579f85b15523a60ae992b8a39f0128ec5b72 SHA1 8915c574c6aa024e0dace7db24762e1d210e1885 SHA256 2cd610c0be8056031727656ab56c62cae34f083bc2e77b3df160b53733c75d96 -EBUILD salome-med-5.1.4.ebuild 3834 RMD160 6e6acbbb2d61baff29438d0d516cc7e174f808f0 SHA1 aa5cba1ba694548783942ad447781146d3a5ee71 SHA256 ed412525c9a32427a19ec69b844e7cfed7d1f78a168b0db44e67ec92a03da207 +EBUILD salome-med-5.1.3.ebuild 3790 RMD160 31aa2074d560194323f5fe259ae7e76619024390 SHA1 b2f5e9ee413a1ddff0e8c10863dc128b1f8153b1 SHA256 b64c1a3967cec7676d4e4491d66cfcbe722091c833e9c074145d4903b2d42cd8 +EBUILD salome-med-5.1.4.ebuild 3834 RMD160 a79595431026db022ffcde26cf99e51969190418 SHA1 8bcf10ce7d5a819cdf2ac563a4bc1e76854cc613 SHA256 aa1e8d35212944298537325a167ebd7733d470f0af10239e6910bb1ccb1f9b05 MISC ChangeLog 3118 RMD160 0292a5eb43e045df97c162fa9ca42c902e88b62d SHA1 b01fb4cba1a896165b9bb01863ca14432dd407de SHA256 6d5ab1cbcd954ecb6acd84f872ab37ed1c854862ef7401d626d5ba280dec5a0b MISC metadata.xml 274 RMD160 81f0dbbb32fd2de80832c9872616b0a48b2d4c04 SHA1 72f2c4ce931ef27e7f913218049757f318f0415d SHA256 49d1680ffc0598f56db8198488dc66263eef05571d59bb3875e0a8858f54f5e4 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk10xJ8ACgkQgAnW8HDreRYY4gCgzV1SMmhvVxhLH8NmE4IoLfXa -OjoAn3LpghhM5tp6vLWyH0KyhOc/1bxA -=+coR +iEYEARECAAYFAk4ErSsACgkQgAnW8HDreRZimACeOuE0Q/K6JQmxXsfbTQSNrbdB +HYMAn0WYHa0ScA9mfA3IVG7qv59hqk7f +=gPET -----END PGP SIGNATURE----- diff --git a/sci-misc/salome-med/salome-med-5.1.3.ebuild b/sci-misc/salome-med/salome-med-5.1.3.ebuild index 41709d78a..e099e9525 100644 --- a/sci-misc/salome-med/salome-med-5.1.3.ebuild +++ b/sci-misc/salome-med/salome-med-5.1.3.ebuild @@ -14,7 +14,7 @@ SRC_URI="http://files.opencascade.com/Salome/Salome${PV}/src${PV}.tar.gz" LICENSE="GPL-2" KEYWORDS="~amd64 ~x86" SLOT="0" -IUSE="debug doc mpi metis opengl scotch" +IUSE="debug doc metis mpi opengl scotch" RDEPEND=" >=sci-misc/salome-kernel-${PV} diff --git a/sci-misc/salome-med/salome-med-5.1.4.ebuild b/sci-misc/salome-med/salome-med-5.1.4.ebuild index e649ce257..a1137ffa7 100644 --- a/sci-misc/salome-med/salome-med-5.1.4.ebuild +++ b/sci-misc/salome-med/salome-med-5.1.4.ebuild @@ -14,7 +14,7 @@ SRC_URI="http://files.opencascade.com/Salome/Salome${PV}/src${PV}.tar.gz" LICENSE="GPL-2" KEYWORDS="~amd64 ~x86" SLOT="0" -IUSE="debug doc mpi metis opengl scotch" +IUSE="debug doc metis mpi opengl scotch" RDEPEND=" >=sci-misc/salome-kernel-${PV} diff --git a/sci-misc/sfst/ChangeLog b/sci-misc/sfst/ChangeLog index f2e64acf2..b9ed4f737 100644 --- a/sci-misc/sfst/ChangeLog +++ b/sci-misc/sfst/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -sfst-1.1.ebuild, + -sfst-1.2.ebuild, -sfst-1.3.ebuild, sfst-1.4.2.ebuild, metadata.xml: + Cleaned ebuild + *sfst-1.4.2 (09 May 2011) 09 May 2011; <flammie@gentoo.org> +sfst-1.4.2.ebuild: diff --git a/sci-misc/sfst/Manifest b/sci-misc/sfst/Manifest index 8cc0a4e86..8e86a68d6 100644 --- a/sci-misc/sfst/Manifest +++ b/sci-misc/sfst/Manifest @@ -1,15 +1,19 @@ -MISC ChangeLog 1014 RMD160 2c2501bcce89760a14ed39b8b426400dbda4ddd2 SHA1 198c994649f8eb66064f29aa6ae51f5410947026 SHA256 6a3e5a302797de075265a2e1d2346a7d3b6b6f6b3cd0b867185338c7f750a13e +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + AUX 50sfst-gentoo.el 215 RMD160 80bbc30f9e67a4a065d521593fa2a598dd721494 SHA1 f5c7c4e6a13ad8178465876f706cb42eeecf1be2 SHA256 d8207a2fb7d0d4d3c81b014cd0e5501b8efcfb196d18e100ac011776cc34addf AUX SFST-1.3-gcc43.patch 1404 RMD160 b5b6e0c54a7dded1009fcd7aa06d09738fae2b96 SHA1 496fbe1a5ce5241c042614e920f4da5cb6f5f112 SHA256 0e25d451d9e7a7108492c59e4d605ea2c6909eba6f7677ad1f8d158be05180b8 AUX ftdetect-sfst.vim 83 RMD160 13bac861a8cd65f7896274c979a719795b8a69aa SHA1 15a75ae33e048a72bc00bd7ebb8f7d7db2811775 SHA256 8e48a335cebddc3f82af95bd826717b30e53164559f92124c20442eafac869e0 -MISC metadata.xml 493 RMD160 ea55577c02d3767473d78e1e2b00cd8b556b9a13 SHA1 2a237598bbecb05fe3f58923c084cf8b12cbe52e SHA256 7b452c2e5e1db167cf8064c8620a80101a4f5e8c655efff6e3e34de20ed98e73 -EBUILD sfst-1.1.ebuild 1835 RMD160 3e64bed7598acbd3ae730080aa5aa7b48f13985a SHA1 0b51f9ecf32c4f95fc9b262de3ddf51571b3e63d SHA256 e0bafa4204212c14209a663d856ffe69e93779f12533345472e1abf120dda4ce -EBUILD sfst-1.2.ebuild 1841 RMD160 b03952bc60a390b63bcec031e878c41742293965 SHA1 0fea341e08390c19ed62c1dd69589e4a817cc832 SHA256 6f108c3339c03f2373838fb7c228c6dcd9a973a13fc137314c683b2934259315 -EBUILD sfst-1.3.ebuild 1909 RMD160 4316e8bde69e402c7f8fdb011450eaab2bce039c SHA1 2d08380736d4a5f3c21ff18bfa7ab9afc2a57b1c SHA256 f5e8c12e258b1fba49f1bfcdffcc8ea2f577feb12a740b789a21c24dc044843c -EBUILD sfst-1.4.2.ebuild 2085 RMD160 5d8637d811003d355a71b6ac9d2f0709e8639b3d SHA1 a171c197eb44b1dddf4a5ba2f4fc6706183ddad0 SHA256 604947782c6b2551fa7881ee76939fd271539a75ff138adb02598786be1686ce -DIST SFST-1.1.tar.gz 474747 RMD160 91c7bf5f39d97225ff6fb315f4308e584380d882 SHA1 6aec4935b6479990199b2ec8b6ff75c382fb6236 SHA256 10792517303cdae430c13990e655c8332fe78fed177623e52746fd51074e0be9 -DIST vim-mode.tar.gz 1104 RMD160 c7e3f79fb5bd466724c3d456a92fbeb07d355515 SHA1 83b9651a7e4ca9642b16be416e616734e8c3f88c SHA256 a62ba91c40da75be389a334db62cc2b4904bedfac657b185012b10f3f55dfe09 -DIST sfst.el 4752 RMD160 b322b17fc4a0b9d22938af5438524cfac18f7a02 SHA1 779b36a5f60ea6ff6894950f82cce186397a6802 SHA256 b47ff59f5ff24482dbbb2f1e71a8b9ca234c4154487f83eb2118f1a62bb9eb5f -DIST SFST-1.2.tar.gz 470537 RMD160 00674aac48bd7d69ab19a247ce74b07b1159740b SHA1 527d13c6526f212ac036c32d0a0343309e92350a SHA256 4c3e99d1250e969904b21114b1d5cb30f6f9f1141455639047ff8289b3b3bb26 -DIST SFST-1.3.tar.gz 470992 RMD160 ae767b482d453fc8ca78f36ae6340fdea545064c SHA1 642f9c0cacc9a248aae05b2e87ed4cd58b936ffa SHA256 4a6ef3e0dab446598b7471de8d45550e2e131e96cde714df47b4070d4c1326b2 DIST SFST-1.4.2.tar.gz 490458 RMD160 77b0fd451026067ce91f6837d16cd6f55064ba35 SHA1 948f73fb6e66f30aadfb12311cbd4a8c7101494d SHA256 0f3040f9e79faa7fee083d3344a87db533dfd84340b43eb86e79a208c70ad7be +DIST sfst.el 4752 RMD160 b322b17fc4a0b9d22938af5438524cfac18f7a02 SHA1 779b36a5f60ea6ff6894950f82cce186397a6802 SHA256 b47ff59f5ff24482dbbb2f1e71a8b9ca234c4154487f83eb2118f1a62bb9eb5f +DIST vim-mode.tar.gz 1104 RMD160 c7e3f79fb5bd466724c3d456a92fbeb07d355515 SHA1 83b9651a7e4ca9642b16be416e616734e8c3f88c SHA256 a62ba91c40da75be389a334db62cc2b4904bedfac657b185012b10f3f55dfe09 +EBUILD sfst-1.4.2.ebuild 2006 RMD160 cf05b1605e9bfc7590c2e4e33e5a39d5a09e9ac1 SHA1 d0a59a97d498df6401e0c21c7a8f53de83b9ec67 SHA256 675801be3feb19e31a691491b35cdab3bdb306ad2517c16676d6d294f123f395 +MISC ChangeLog 1168 RMD160 f01cf9b7b1d2829720725f26bccacec4d0876649 SHA1 b35ed0389e472eb94e551336128bcb0c766d2c5f SHA256 ab244f9e3f15a47650efa899c0ce2d5bf503f17cb75cfe806ef7a5db866121c1 +MISC metadata.xml 497 RMD160 0ef821b2a7bab621a959c7a021e851aff35a238b SHA1 b0cf3723f544a94e3e238863c485994c63d501cb SHA256 46240ab2b0ffdce64dfc703181f202108da06030291692169417d2015cae0d43 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GFB8ACgkQgAnW8HDreRalpACgikOwdweGqycr2Bfa31/sqNG7 +3VgAn1nqJdorzDrzj7mtXEZH5bMTtsWc +=lnv+ +-----END PGP SIGNATURE----- diff --git a/sci-misc/sfst/metadata.xml b/sci-misc/sfst/metadata.xml index 913dfd00e..2ec953e0d 100644 --- a/sci-misc/sfst/metadata.xml +++ b/sci-misc/sfst/metadata.xml @@ -1,12 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>no-herd</herd> -<maintainer> - <email>flammie@gentoo.org</email> - <description>N.B. This is used in my master’s thesis project</description> -</maintainer> -<longdescription> + <herd>no-herd</herd> + <maintainer> + <email>flammie@gentoo.org</email> + <description>N.B. This is used in my master’s thesis project</description> + </maintainer> + <longdescription> SFST is open source package for compiling and using Finite State Transducers, mainly for linguistic uses, made in university of Stuttgart, Germany. diff --git a/sci-misc/sfst/sfst-1.1.ebuild b/sci-misc/sfst/sfst-1.1.ebuild deleted file mode 100644 index f33fb36c5..000000000 --- a/sci-misc/sfst/sfst-1.1.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2008 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit elisp - -MY_PN="SFST" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="Uni Stuttgart Finite State Transducer tools" -HOMEPAGE="http://www.ims.uni-stuttgart.de/projekte/gramotron/SOFTWARE/SFST.html" -SRC_URI="ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/${MY_P}.tar.gz -vim-syntax? ( ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/vim-mode.tar.gz ) -emacs? ( http://www.cis.uni-muenchen.de/~wastl/emacs/sfst.el )" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86" -IUSE="vim-syntax emacs" - -DEPEND="sys-libs/readline -sys-devel/bison -sys-devel/flex -sys-apps/sed" -RDEPEND="sys-libs/readline" - -S="${WORKDIR}/${MY_PN}" - - -src_unpack() { - unpack ${A} - cd "${S}" - sed -i -e 's_/usr/local_$(destdir)/usr_g' -e 's/= install/= install -D/g' \ - -e 's/^strip:/all:/g' -e 's/strip $(ALLPROGRAMS)/echo/g' \ - -e "s/^CFLAGS = -O4 \(.*\)/CFLAGS = ${CFLAGS} \1/g" \ - src/Makefile || die "sed failed" - if use emacs ; then - cp "${DISTDIR}/sfst.el" "${S}" - fi - if use vim-syntax ; then - mv "${WORKDIR}"/INSTALL "${S}"/INSTALL-vim-syntax - mv "${WORKDIR}"/sfst.vim "${S}"/ - fi -} - -src_compile() { - cd "${S}/src" - emake || die "make failed" - if use emacs ; then - cd "${S}" - elisp_src_compile - fi -} - -src_install() { - cd "${S}/src" - emake destdir="${D}" install maninstall || die "install failed" - cd "${S}" - dodoc README || die "doc failed" - insinto /usr/share/doc/${PF}/ - doins doc/SFST-Manual.pdf doc/SFST-Tutorial.pdf || die "doc failed" - insinto /usr/share/${PN} - doins -r data/* - if use vim-syntax ; then - insinto /usr/share/vim/vimfiles/syntax/ - doins sfst.vim - insinto /usr/share/vim/vimfiles/ftdetect/ - newins "${FILESDIR}"/ftdetect-sfst.vim sfst.vim - dodoc INSTALL-vim-syntax - fi - if use emacs ; then - elisp_src_install - fi -} - diff --git a/sci-misc/sfst/sfst-1.2.ebuild b/sci-misc/sfst/sfst-1.2.ebuild deleted file mode 100644 index 8ea3ac5db..000000000 --- a/sci-misc/sfst/sfst-1.2.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2008 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit elisp - -MY_PN="SFST" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="Uni Stuttgart Finite State Transducer tools" -HOMEPAGE="http://www.ims.uni-stuttgart.de/projekte/gramotron/SOFTWARE/SFST.html" -SRC_URI="ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/${MY_P}.tar.gz -vim-syntax? ( ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/vim-mode.tar.gz ) -emacs? ( http://www.cis.uni-muenchen.de/~wastl/emacs/sfst.el )" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="vim-syntax emacs" - -DEPEND="sys-libs/readline -sys-devel/bison -sys-devel/flex -sys-apps/sed" -RDEPEND="sys-libs/readline" - -S="${WORKDIR}/${MY_PN}" - - -src_unpack() { - unpack ${A} - # settings in makefile are a bit hacky - sed -i -e "s/^CFLAGS = -O3/CFLAGS = ${CFLAGS}/g" \ - -e "s/local//g" \ - -e 's/strip/echo strip removed: /g' \ - "${S}"/src/Makefile || die "sed failed" - cd "${S}" - if use emacs ; then - cp "${DISTDIR}/sfst.el" "${S}" - fi - if use vim-syntax ; then - mv "${WORKDIR}"/INSTALL "${S}"/INSTALL-vim-syntax - mv "${WORKDIR}"/sfst.vim "${S}"/ - fi -} - -src_compile() { - cd "${S}/src" - emake || die "make failed" - if use emacs ; then - cd "${S}" - elisp_src_compile - fi -} - -src_install() { - cd "${S}/src" - # destdir works but prefix fails - emake DESTDIR="${D}" install maninstall || die "install failed" - cd "${S}" - dodoc README || die "doc failed" - insinto /usr/share/doc/${PF}/ - doins doc/SFST-Manual.pdf doc/SFST-Tutorial.pdf || die "doc failed" - insinto /usr/share/${PN} - doins -r data/* - if use vim-syntax ; then - insinto /usr/share/vim/vimfiles/syntax/ - doins sfst.vim - insinto /usr/share/vim/vimfiles/ftdetect/ - newins "${FILESDIR}"/ftdetect-sfst.vim sfst.vim - dodoc INSTALL-vim-syntax - fi - if use emacs ; then - elisp_src_install - fi -} - diff --git a/sci-misc/sfst/sfst-1.3.ebuild b/sci-misc/sfst/sfst-1.3.ebuild deleted file mode 100644 index df0fa574c..000000000 --- a/sci-misc/sfst/sfst-1.3.ebuild +++ /dev/null @@ -1,78 +0,0 @@ -# Copyright 1999-2008 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit eutils elisp - -MY_PN="SFST" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="Uni Stuttgart Finite State Transducer tools" -HOMEPAGE="http://www.ims.uni-stuttgart.de/projekte/gramotron/SOFTWARE/SFST.html" -SRC_URI="ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/${MY_P}.tar.gz -vim-syntax? ( ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/vim-mode.tar.gz ) -emacs? ( http://www.cis.uni-muenchen.de/~wastl/emacs/sfst.el )" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="vim-syntax emacs" - -DEPEND="sys-libs/readline -sys-devel/bison -sys-devel/flex -sys-apps/sed" -RDEPEND="sys-libs/readline" - -S="${WORKDIR}/${MY_PN}" - - -src_unpack() { - unpack ${A} - # settings in makefile are a bit hacky - #epatch "${FILESDIR}"/SFST-1.3-gcc43.patch || die "patch failed" - sed -i -e "s/^CFLAGS = -O3/CFLAGS = ${CFLAGS}/g" \ - -e "s/local//g" \ - -e 's/strip/echo strip removed: /g' \ - "${S}"/src/Makefile || die "sed failed" - cd "${S}" - if use emacs ; then - cp "${DISTDIR}/sfst.el" "${S}" - fi - if use vim-syntax ; then - mv "${WORKDIR}"/INSTALL "${S}"/INSTALL-vim-syntax - mv "${WORKDIR}"/sfst.vim "${S}"/ - fi -} - -src_compile() { - cd "${S}/src" - emake || die "make failed" - if use emacs ; then - cd "${S}" - elisp_src_compile - fi -} - -src_install() { - cd "${S}/src" - # destdir works but prefix fails - emake DESTDIR="${D}" install maninstall || die "install failed" - cd "${S}" - dodoc README || die "doc failed" - insinto /usr/share/doc/${PF}/ - doins doc/SFST-Manual.pdf doc/SFST-Tutorial.pdf || die "doc failed" - insinto /usr/share/${PN} - doins -r data/* - if use vim-syntax ; then - insinto /usr/share/vim/vimfiles/syntax/ - doins sfst.vim - insinto /usr/share/vim/vimfiles/ftdetect/ - newins "${FILESDIR}"/ftdetect-sfst.vim sfst.vim - dodoc INSTALL-vim-syntax - fi - if use emacs ; then - elisp_src_install - fi -} - diff --git a/sci-misc/sfst/sfst-1.4.2.ebuild b/sci-misc/sfst/sfst-1.4.2.ebuild index e74fa6df9..73d5664b6 100644 --- a/sci-misc/sfst/sfst-1.4.2.ebuild +++ b/sci-misc/sfst/sfst-1.4.2.ebuild @@ -2,43 +2,46 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit eutils elisp +EAPI=4 + +inherit elisp eutils MY_PN="SFST" MY_P="${MY_PN}-${PV}" DESCRIPTION="Uni Stuttgart Finite State Transducer tools" HOMEPAGE="http://www.ims.uni-stuttgart.de/projekte/gramotron/SOFTWARE/SFST.html" -SRC_URI="ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/${MY_P}.tar.gz -vim-syntax? ( ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/vim-mode.tar.gz ) -emacs? ( http://www.cis.uni-muenchen.de/~wastl/emacs/sfst.el )" +SRC_URI=" + ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/${MY_P}.tar.gz + vim-syntax? ( ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/vim-mode.tar.gz ) + emacs? ( http://www.cis.uni-muenchen.de/~wastl/emacs/sfst.el )" LICENSE="GPL-2" SLOT="0" KEYWORDS="~x86" -IUSE="vim-syntax emacs" +IUSE="emacs vim-syntax" -DEPEND="sys-libs/readline -sys-devel/bison -sys-devel/flex -sys-apps/sed" +DEPEND=" + sys-libs/readline + sys-devel/bison + sys-devel/flex + sys-apps/sed" RDEPEND="sys-libs/readline" S="${WORKDIR}/${MY_PN}" - -src_unpack() { - unpack ${A} +src_prepare() { # settings in makefile are a bit hacky #epatch "${FILESDIR}"/SFST-1.3-gcc43.patch || die "patch failed" - sed -i -e "s/^CFLAGS = -O3/CFLAGS = ${CFLAGS}/g" \ + sed \ + -e "s/^CFLAGS = -O3/CFLAGS = ${CFLAGS}/g" \ -e "s/local//g" \ -e 's/strip/echo strip removed: /g' \ -e 's/# FPIC/FPIC/' \ -e 's/ $(PREFIX/ $(DESTDIR)$(PREFIX/g' \ -e 's/ldconfig/true/' \ -e 's/$(INSTALL_LIBS)/$(INSTALL_DIR) $(DESTDIR)$(PREFIX)\/lib\n\t\0/' \ - "${S}"/src/Makefile || die "sed failed" + -i "${S}"/src/Makefile || die "sed failed" cd "${S}" if use emacs ; then cp "${DISTDIR}/sfst.el" "${S}" @@ -50,8 +53,7 @@ src_unpack() { } src_compile() { - cd "${S}/src" - emake || die "make failed" + emake -C "${S}/src" if use emacs ; then cd "${S}" elisp_src_compile @@ -61,11 +63,11 @@ src_compile() { src_install() { cd "${S}/src" # destdir works but prefix fails - emake DESTDIR="${D}" install maninstall libinstall || die "install failed" + emake DESTDIR="${D}" install maninstall libinstall cd "${S}" - dodoc README || die "doc failed" + dodoc README insinto /usr/share/doc/${PF}/ - doins doc/SFST-Manual.pdf doc/SFST-Tutorial.pdf || die "doc failed" + doins doc/SFST-Manual.pdf doc/SFST-Tutorial.pdf insinto /usr/share/${PN} doins -r data/* if use vim-syntax ; then @@ -79,4 +81,3 @@ src_install() { elisp_src_install fi } - diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog index c3d770043..fea065779 100644 --- a/sci-physics/abinit/ChangeLog +++ b/sci-physics/abinit/ChangeLog @@ -2,6 +2,25 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*abinit-6.8.1 (29 Jun 2011) + + 29 Jun 2011; Honza Macháček <Hloupy.Honza@centrum.cz> +abinit-6.8.1.ebuild: + Yet another quick version bump, no improvement to the ebuild. Compiles well + for me but has problems testing. The fault may be just in my openmpi + installation but use with caution. + + 29 Jun 2011; Honza Macháček <Hloupy.Honza@centrum.cz> abinit-6.6.3.ebuild: + Restored the support for threaded fftw. Works for me. NEVER DISABLE FEATURES + FOR OTHERS. + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> -abinit-6.6.2.ebuild, + abinit-6.6.3.ebuild: + Dropped ~ppc as many deps aren't keyworded + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> abinit-6.6.2.ebuild, + abinit-6.6.3.ebuild: + Added fortran-2.eclass support + *abinit-6.6.3 (10 May 2011) 11 May 2011; Dongxu Li <dongxuli2011@gmail.com> abinit-6.6.3.ebuild abinit-6.6.2.ebuild: diff --git a/sci-physics/abinit/Manifest b/sci-physics/abinit/Manifest index 4c5522312..2ee9c036a 100644 --- a/sci-physics/abinit/Manifest +++ b/sci-physics/abinit/Manifest @@ -1,9 +1,9 @@ AUX 6.0.3-fftw.patch 571 RMD160 b15b2905fd46a1c0f6fcc99c317b1b52a327ef12 SHA1 b518c2db591d93a425598e780d1edd971fe38e0d SHA256 ad8e1810dcdd19a23baf7d951ce0c7af1b47e19e934c5cc6cb598431cfd2e21c AUX 6.2.2-change-default-directories.patch 1006 RMD160 ba252ecc7f5592f4df762716582c6e331a5e994f SHA1 4d79a7a261211c44692c09e63197261bfdb2c06e SHA256 8865966dd0d94b00443faae62b58e9938a5ba5d15bc32b59f79f815922f91c44 AUX 6.6.1-openmp.patch 19735 RMD160 6e6e42a5f030bdfb859583dd5e72ea434e980bcf SHA1 51c032ca7f52fe4e1c4afe86f2cb019166d4afbb SHA256 9568ace3732159ae395a3eef069338ded1d734becde1b8b382a58adf2f254933 -DIST abinit-6.6.2.tar.gz 41103295 RMD160 d231811cb393c4cd1a51447f924715b8f617f56f SHA1 b3710bad16535a0eac6d7924b2a0d44b871de71d SHA256 c2d8e132591bbf96fa2f868fae4e39df92050b63090023ef561a163ca568a05b DIST abinit-6.6.3.tar.gz 41161321 RMD160 f9169812cfb2dc30f752bf0ab0ffc41250ea0bbb SHA1 02c9fd6abe1b73164b804b6e0b1f829ec9fd286e SHA256 fad84d3e774e3b4ba16f2a2924e60b8ba42ab21fefd89d8ce4848f9a9e03f774 -EBUILD abinit-6.6.2.ebuild 6498 RMD160 a9d7d765250aa1d40663c280719b5b9fae9ad509 SHA1 1f3f3a11b41d9ebe981cda82dfd14eec19a927d0 SHA256 c492abaccfa2a269278832b17d5034e9d3cabcf0fe276d89e48be858832b01c7 -EBUILD abinit-6.6.3.ebuild 5742 RMD160 2ac569eac21714e1bfb0c244e8567409a184dc01 SHA1 836e7a5e71c45360689516538ebd17dac62f5eae SHA256 1e6ed77ec63e8764c2f32ce0fcc57836b806a0362b5e40e5cd7aaeedf9765580 -MISC ChangeLog 2478 RMD160 eb660f69e179ff048956e1d07840c9dd18cc81d5 SHA1 de803e05449a9b17c30d141c53e8f717e0239365 SHA256 b2d0fdcd5fc76a0a8498f69254f61d6e3aebf79c37753c2814cbdb27fbae35c4 +DIST abinit-6.8.1.tar.gz 43548991 RMD160 320de2b02862ba5ebf2e0ac209e4f63bf457345f SHA1 00b78334fc6f2859665a720c98cf318eed0d57b2 SHA256 6a8ff5f88ee765b8c71fc80a171c61213f1143399f3de66364d32a9560f22689 +EBUILD abinit-6.6.3.ebuild 6256 RMD160 88bf466811c42d04a57c1ddc6d3949d3ca6cdabf SHA1 3bdf27623990cb4e2131d333c6e5f690742e034a SHA256 fef385cfc374e619c12918ddcfe3c4c6e9e72eb297c1663e948eedfc2a6e675c +EBUILD abinit-6.8.1.ebuild 6256 RMD160 88bf466811c42d04a57c1ddc6d3949d3ca6cdabf SHA1 3bdf27623990cb4e2131d333c6e5f690742e034a SHA256 fef385cfc374e619c12918ddcfe3c4c6e9e72eb297c1663e948eedfc2a6e675c +MISC ChangeLog 3210 RMD160 eeddead33ca6afe11e62929ada84041be20c4d16 SHA1 5406bff86fd67dc8cd834c303c02cb2073e9ffa8 SHA256 28f5b197338358b150b3bf8d35dcb0777efef9382bc3c9ba0f4c6dbe626a0655 MISC metadata.xml 1225 RMD160 bebdbae077b05fe05bac5665b5b4d1f654620366 SHA1 464ff6d71e8b44df92c421a984c1f6a9cae38299 SHA256 71e7a9928f03914c9c5e6c45e6a6185a50f5c3dda7fbf791d3ca238dbee6727e diff --git a/sci-physics/abinit/abinit-6.6.3.ebuild b/sci-physics/abinit/abinit-6.6.3.ebuild index fb8c9967b..3799d0578 100644 --- a/sci-physics/abinit/abinit-6.6.3.ebuild +++ b/sci-physics/abinit/abinit-6.6.3.ebuild @@ -1,9 +1,10 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 +# $Header: $ EAPI="3" -inherit autotools eutils multilib toolchain-funcs +inherit autotools eutils fortran-2 multilib toolchain-funcs DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory" HOMEPAGE="http://www.abinit.org/" @@ -11,8 +12,8 @@ SRC_URI="http://ftp.abinit.org/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86" -IUSE="cuda -debug +fftw +fox gsl +hdf5 mpi +netcdf python +threads -test -vdwxc" +KEYWORDS="~amd64 ~x86" +IUSE="cuda -debug +fftw +fox gsl +hdf5 mpi +netcdf python -test +threads -vdwxc" RDEPEND=">=sci-libs/bigdft-1.2.0.2 sci-libs/etsf_io @@ -44,6 +45,7 @@ DEPEND="${RDEPEND} S=${WORKDIR}/${P%[a-z]} pkg_setup() { + fortran-2_pkg_setup # Doesn't compile with gcc-4.0, only >=4.1 if [[ $(tc-getFC) == *gfortran ]]; then if [[ $(gcc-major-version) -eq 4 ]] \ @@ -69,8 +71,20 @@ src_configure() { local netcdff_libs="-lnetcdff" use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" local fft_flavor="fftw3" - #fft_flavor="fftw3-threads" causes a ./configure error - local fft_libs="-L/usr/$(get_libdir) $(pkg-config --libs fftw3)" + local fft_libs="-L/usr/lib" + # Since now, fftw threads support is protected by black magick. + # Anybody removes it again, dies. + # If it does not work FOR YOU, disable the "threads" USE flag + # for the package at YOUR box. If YOU want it disabled selectively + # for fftw use in abinit, you may consider adding a special USE flag + # for that. NEVER REMOVE AN OPTION FOR OTHERS, at least if there is + # anybody it works for. + if use threads; then + fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)" + fft_flavor="fftw3-threads" + else + fft_libs="${fft_libs} $(pkg-config --libs fftw3)" + fi if use mpi; then MY_FC="mpif90" MY_CC="mpicc" diff --git a/sci-physics/abinit/abinit-6.6.2.ebuild b/sci-physics/abinit/abinit-6.8.1.ebuild index a879cd149..3799d0578 100644 --- a/sci-physics/abinit/abinit-6.6.2.ebuild +++ b/sci-physics/abinit/abinit-6.8.1.ebuild @@ -4,7 +4,7 @@ EAPI="3" -inherit autotools eutils multilib toolchain-funcs +inherit autotools eutils fortran-2 multilib toolchain-funcs DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory" HOMEPAGE="http://www.abinit.org/" @@ -13,9 +13,9 @@ SRC_URI="http://ftp.abinit.org/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="cuda -debug +fftw +fox gsl +hdf5 mpi +netcdf python -smp +threads -test -vdwxc" +IUSE="cuda -debug +fftw +fox gsl +hdf5 mpi +netcdf python -test +threads -vdwxc" -RDEPEND="=sci-libs/bigdft-1.2.0.2 +RDEPEND=">=sci-libs/bigdft-1.2.0.2 sci-libs/etsf_io =sci-libs/libxc-1.0[fortran] sci-physics/atompaw[libxc] @@ -37,24 +37,15 @@ RDEPEND="=sci-libs/bigdft-1.2.0.2 ) mpi? ( virtual/mpi ) python? ( dev-python/numpy ) - x86? ( - cuda? ( dev-util/nvidia-cuda-sdk ) - ) - amd64? ( - cuda? ( dev-util/nvidia-cuda-sdk ) - ) - " - + cuda? ( dev-util/nvidia-cuda-sdk )" DEPEND="${RDEPEND} dev-util/pkgconfig dev-perl/Text-Markdown" -#WANT_AUTOCONF="latest" -#WANT_AUTOMAKE="latest" - S=${WORKDIR}/${P%[a-z]} pkg_setup() { + fortran-2_pkg_setup # Doesn't compile with gcc-4.0, only >=4.1 if [[ $(tc-getFC) == *gfortran ]]; then if [[ $(gcc-major-version) -eq 4 ]] \ @@ -62,20 +53,11 @@ pkg_setup() { die "Requires gcc-4.1 or newer" fi fi - if use smp; then - ewarn "OpenMP support mostly broken. Apparently some developers \ - have used OpenMP semaphors !$ as comment delimiters. Not yet solved \ - upstream, patch incomplete." - if use mpi && has_version sys-cluster/openmpi; then - ewarn "Combined with openMPI, OpenMP support is especially likely to crash." - fi - fi } src_prepare() { epatch "${FILESDIR}"/6.2.2-change-default-directories.patch epatch "${FILESDIR}"/6.0.3-fftw.patch - epatch "${FILESDIR}"/6.6.1-openmp.patch eautoreconf } @@ -89,8 +71,20 @@ src_configure() { local netcdff_libs="-lnetcdff" use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" local fft_flavor="fftw3" - # fft_flavor="fftw3-threads" causes error in ./confgure - local fft_libs="/usr/$(get_libdir) $(pkg-config --libs fftw3)" + local fft_libs="-L/usr/lib" + # Since now, fftw threads support is protected by black magick. + # Anybody removes it again, dies. + # If it does not work FOR YOU, disable the "threads" USE flag + # for the package at YOUR box. If YOU want it disabled selectively + # for fftw use in abinit, you may consider adding a special USE flag + # for that. NEVER REMOVE AN OPTION FOR OTHERS, at least if there is + # anybody it works for. + if use threads; then + fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)" + fft_flavor="fftw3-threads" + else + fft_libs="${fft_libs} $(pkg-config --libs fftw3)" + fi if use mpi; then MY_FC="mpif90" MY_CC="mpicc" @@ -100,26 +94,15 @@ src_configure() { MY_CC="$(tc-getCC)" MY_CXX="$(tc-getCXX)" fi - if use smp; then - MY_FC="${MY_FC} -fopenmp" - MY_CC="${MY_CC} -fopenmp" - MY_CXX="${MY_CXX} -fopenmp" - fi - #enable bindings for ab6 header and libraries - # --enable-bindings - #--with-fc-version=f90 --enable-bindings \ - local my_cuda - if use cuda; then - if use x86 || use amd64; then - my_cuda="--enable-gpu --with-gpu-flavor=cuda-single --with-gpu-prefix=/opt/cuda/" - fi - fi MARKDOWN=Markdown.pl econf \ $(use_enable debug debug enhanced) \ $(use_enable mpi) \ $(use_enable mpi mpi-io) \ - $(use_enable smp) \ + --disable-smp \ $(use_enable vdwxc) \ + $(use_enable cuda gpu) \ + "$(use cuda && echo "--with-gpu-flavor=cuda-single")" \ + "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" \ "$(use gsl && echo "--with-math-flavor=gsl")" \ "$(use gsl && echo "--with-math-incs=$(pkg-config --cflags gsl)")" \ "$(use gsl && echo "--with-math-libs=$(pkg-config --libs gsl)")" \ @@ -150,8 +133,7 @@ src_configure() { CC="${MY_CC}" \ CXX="${MY_CXX}" \ LD="$(tc-getLD)" \ - FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include" \ - "${my_cuda}" + FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include" } src_compile() { diff --git a/sci-physics/atompaw/ChangeLog b/sci-physics/atompaw/ChangeLog index 4c273869c..ebf5c9300 100644 --- a/sci-physics/atompaw/ChangeLog +++ b/sci-physics/atompaw/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> atompaw-3.0.1.ebuild, + +metadata.xml: + Added fortran-2.eclass support + *atompaw-3.0.1 (25 Feb 2011) 25 Feb 2011; Honza Macháček <Hloupy.Honza@centrum.cz> diff --git a/sci-physics/atompaw/Manifest b/sci-physics/atompaw/Manifest index 3b5d49c2c..fe68cc103 100644 --- a/sci-physics/atompaw/Manifest +++ b/sci-physics/atompaw/Manifest @@ -1,6 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST atompaw-3.0.1.tar.gz 3785332 RMD160 68c8f80be0f86fab7373f299fee54f0b5680ead3 SHA1 86d1259a516e7daa0902e259d07a4de93021de2a SHA256 ec1cf11d72227e16ada9b695c1cdd160fee8d58a10b10ba903029779bc5ea73f DIST atompaw-usersguide.pdf 164947 RMD160 41a3e4691a33820ce566cd99b9c0bc1f9a4a5f0f SHA1 304788ec317ecda0472a767fd001f885e677982c SHA256 cdd33185faa37bde41a875b02d62e05ac647ccec4bd800fc15848135b1c5a426 DIST atompaw.pdf 334715 RMD160 63ad12eecbfeca830eac57ea70d38e94ded3db6b SHA1 5d7d4a420dfb2f222cc3c441323a130f59e772f8 SHA256 10a70f0c31e4a0a06e31b2b922b938742daf8635c87b95f5a48609555d9397ed DIST atompawEqns.pdf 198480 RMD160 8f0c5a5f4b75f9527fbec368243d6059968c1188 SHA1 5bf54dd4a67a02cd7698bdd1d1c84202b5b0beba SHA256 181af33190b77b630c1fb94882d0cbc5f79281346f93c25ef4d645806f2c1dc6 -EBUILD atompaw-3.0.1.ebuild 1567 RMD160 213c5803e4998619d19f426eb21396ee9fed7ea8 SHA1 5d76e53952244152dd0368e4b9226b2ab665b270 SHA256 391570833b460e9ae48870a6ff247d3c49bf99da4a2bad44435242770866a8b0 -MISC ChangeLog 369 RMD160 0b7667d3c7f1958c1fe21ba50bcb6bfb438d52fb SHA1 1f992011cec899bc942bf8bf9a7a42f8ff9e78b4 SHA256 d93eb96d02caf3b5510ad5548aa43d1c9ec0f4fc8663f7c3cb4696f58d60073a +EBUILD atompaw-3.0.1.ebuild 1610 RMD160 1ab02dde5e4a031f08a677019caea5d0f5d145e8 SHA1 5c2f77116f4a2f81f6e8035babc218b29adb2fff SHA256 4979553af18fd06d7b24dc1f0bf11d0ab61e0e45374c562adc00995467400715 +MISC ChangeLog 489 RMD160 260fc389c038c2a74efa20f2ead2ed1873107e38 SHA1 1f75957c5e65f66b251ea71b40b1d2e618844b69 SHA256 b5284be3694ea98f241a1b5f3451c9577f0ab4b338ea4823ab8054bb31d266fe +MISC metadata.xml 276 RMD160 a25096484f1bc1725d690365c1e34c9db122ba7a SHA1 c4f45385788f2c6564c74ffebb021c80b15d127d SHA256 4ef0c357c4c532c67c0f818a263e305493db24c8ce3abdd9f01ac39dcb5eb070 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Afc8ACgkQgAnW8HDreRaHcACdEY9+gg8AlXsX2FtTL1EqOi5G +TM8AniodLXjx55RK7VPTJGCSeFKcyLtt +=9FZJ +-----END PGP SIGNATURE----- diff --git a/sci-physics/atompaw/atompaw-3.0.1.ebuild b/sci-physics/atompaw/atompaw-3.0.1.ebuild index 51a4d99f7..41a0bcf4f 100644 --- a/sci-physics/atompaw/atompaw-3.0.1.ebuild +++ b/sci-physics/atompaw/atompaw-3.0.1.ebuild @@ -1,21 +1,27 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 +# $Header: $ EAPI=3 -inherit eutils multilib toolchain-funcs +inherit eutils fortran-2 multilib toolchain-funcs DESCRIPTION="PAW atomic data generator" HOMEPAGE="http://www.wfu.edu/~natalie/papers/pwpaw/man.html" -IUSE="doc libxc" -SRC_URI="http://www.wfu.edu/~natalie/papers/pwpaw/${P}.tar.gz - doc? ( http://www.wfu.edu/~natalie/papers/pwpaw/atompaw.pdf +SRC_URI=" + http://www.wfu.edu/~natalie/papers/pwpaw/${P}.tar.gz + doc? ( + http://www.wfu.edu/~natalie/papers/pwpaw/atompaw.pdf http://www.wfu.edu/~natalie/papers/pwpaw/atompaw-usersguide.pdf http://www.wfu.edu/~natalie/papers/pwpaw/notes/atompaw/atompawEqns.pdf )" + LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -RDEPEND="virtual/lapack +IUSE="doc libxc" + +RDEPEND=" + virtual/lapack virtual/blas libxc? ( sci-libs/libxc[fortran] )" DEPEND="${RDEPEND} @@ -24,9 +30,9 @@ DEPEND="${RDEPEND} src_unpack() { unpack ${P}.tar.gz if use doc; then - cp ${DISTDIR}/atompaw.pdf ${S}/ - cp ${DISTDIR}/atompaw-usersguide.pdf ${S}/ - cp ${DISTDIR}/atompawEqns.pdf ${S}/ + cp "${DISTDIR}"/atompaw.pdf "${S}"/ + cp "${DISTDIR}"/atompaw-usersguide.pdf "${S}"/ + cp "${DISTDIR}"/atompawEqns.pdf "${S}"/ fi } diff --git a/sci-physics/atompaw/metadata.xml b/sci-physics/atompaw/metadata.xml new file mode 100644 index 000000000..a14e5e077 --- /dev/null +++ b/sci-physics/atompaw/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +<maintainer> + <email>sci@gentoo.org</email> +</maintainer> +<use><flag name='libxc'>Use libxc for something</flag></use> +</pkgmetadata> diff --git a/sci-physics/atompaw2abinit/ChangeLog b/sci-physics/atompaw2abinit/ChangeLog index 7b94567d3..b4c912c4d 100644 --- a/sci-physics/atompaw2abinit/ChangeLog +++ b/sci-physics/atompaw2abinit/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> atompaw2abinit-3.3.0.ebuild, + +metadata.xml: + Added fortran-2.eclass support + *atompaw2abinit-3.3.0 (25 Feb 2011) 25 Feb 2011; Honza Macháček <Hloupy.Honza@centrum.cz> diff --git a/sci-physics/atompaw2abinit/Manifest b/sci-physics/atompaw2abinit/Manifest index afd2990a6..5c2c47bf8 100644 --- a/sci-physics/atompaw2abinit/Manifest +++ b/sci-physics/atompaw2abinit/Manifest @@ -1,3 +1,14 @@ -DIST Atompaw2Abinit.tgz 53820 RMD160 691f537e13410ce12bf37b7088514d7ef65434e6 SHA1 4f4856668c7811d35180e8f881edd35eaaeab35b SHA256 001b7b7c71985a7824d670b2e59969d8abd941dc93f4456cd41edffa75d25e82 -EBUILD atompaw2abinit-3.3.0.ebuild 1264 RMD160 f2fc96afa05708d5dba167eb78b8bcb7567c146b SHA1 ea9c150700913ee5434fec1ead0be24f3540ec51 SHA256 448b9fab233fb89943c27901b8c662fb3b21e53720d89349c83da08167b9d8a5 -MISC ChangeLog 379 RMD160 957b76f9ab4f0fe7b39eceeda570d471e3a3d0ba SHA1 673db08b93fd1aea363da7ba879a7097f595a9c4 SHA256 4d15fd21192ed18600f082e3ef31eb3200fbeee4a22f453c347823ffedb05aee +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +DIST atompaw2abinit-3.3.0.tgz 53820 RMD160 691f537e13410ce12bf37b7088514d7ef65434e6 SHA1 4f4856668c7811d35180e8f881edd35eaaeab35b SHA256 001b7b7c71985a7824d670b2e59969d8abd941dc93f4456cd41edffa75d25e82 +EBUILD atompaw2abinit-3.3.0.ebuild 1273 RMD160 732d1625324c7462dfe70ea0784800fac528d995 SHA1 5c2b6d6716c1818626b5e072ca15db9c9376d34a SHA256 3d04137d078e3bb53d97cbf2bd779eb3f2166bcf46d234e6d635e9d442bdd4f8 +MISC ChangeLog 506 RMD160 4c429eede3dcd7aab729fcdb5069dd133cc8eed1 SHA1 8ae3fb227eaa805bc3328f3ffaa2dbdc5c8f83fb SHA256 9ada9a79b965cc6165b57e66e7558a6da3a12b6a9267267452cc8384f0385576 +MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Af/MACgkQgAnW8HDreRZX4ACfW5EkAe6p4xNCdNg1MZNPQvNj +tmcAn2rHgGUDWes1+F2oqtK2YYCnTDAD +=ytKi +-----END PGP SIGNATURE----- diff --git a/sci-physics/atompaw2abinit/atompaw2abinit-3.3.0.ebuild b/sci-physics/atompaw2abinit/atompaw2abinit-3.3.0.ebuild index 37c6dc648..eb93fa22e 100644 --- a/sci-physics/atompaw2abinit/atompaw2abinit-3.3.0.ebuild +++ b/sci-physics/atompaw2abinit/atompaw2abinit-3.3.0.ebuild @@ -1,18 +1,22 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 +# $Header: $ EAPI=3 -inherit eutils multilib toolchain-funcs +inherit eutils fortran-2 multilib toolchain-funcs DESCRIPTION="Abinit AtomPAW atomic data convertor" HOMEPAGE="http://www.abinit.org/downloads/PAW/AtomPAW2Abinit-Manual-html/AtomPAW2Abinit2.htm" -IUSE="" -SRC_URI="http://www.abinit.org/downloads/PAW/AtomPAW2Abinit-Manual-html/Atompaw2Abinit.tgz" +SRC_URI="http://www.abinit.org/downloads/PAW/AtomPAW2Abinit-Manual-html/Atompaw2Abinit.tgz -> ${P}.tgz" + LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -RDEPEND="virtual/lapack +IUSE="" + +RDEPEND=" + virtual/lapack virtual/blas sci-physics/atompaw" DEPEND="${RDEPEND} @@ -26,10 +30,6 @@ pkg_nofetch() { elog "is probably required." } -src_unpack() { - unpack ${A} -} - src_configure() { head -n 6 Makefile >Makefile.1 tail -n +6 Makefile >Makefile.2 @@ -49,4 +49,4 @@ src_compile() { src_install() { dobin atompaw2abinit -}
\ No newline at end of file +} diff --git a/sci-physics/atompaw2abinit/metadata.xml b/sci-physics/atompaw2abinit/metadata.xml new file mode 100644 index 000000000..efb490d78 --- /dev/null +++ b/sci-physics/atompaw2abinit/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +<maintainer> + <email>sci@gentoo.org</email> +</maintainer> +</pkgmetadata> diff --git a/sci-physics/espresso/ChangeLog b/sci-physics/espresso/ChangeLog index 75a907947..e5ea3c74d 100644 --- a/sci-physics/espresso/ChangeLog +++ b/sci-physics/espresso/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Christoph Junghans <ottxor@gentoo.org> espresso-9999.ebuild: + migrate to git-2 + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> espresso-9999.ebuild, + metadata.xml: + Cleaned ebuild + *espresso-3.0.0 (20 Apr 2011) 20 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -espresso-2.2.0b.ebuild, diff --git a/sci-physics/espresso/Manifest b/sci-physics/espresso/Manifest index 356bda77f..9f2366f3e 100644 --- a/sci-physics/espresso/Manifest +++ b/sci-physics/espresso/Manifest @@ -1,17 +1,3 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - -EBUILD espresso-9999.ebuild 2336 RMD160 3e4c6e21d50fbbf00f12f0095f7fd8e49ca6c3d2 SHA1 78262189c97d2c327eac014daad413a61dd75bee SHA256 ee1d62557c84b7c00410dcc0e2f673aa491fd54026e7dbca2f1e0edb0ebee179 -MISC ChangeLog 939 RMD160 1255798fb04df83c6490a3e8514bcecabf25fe88 SHA1 46de0580dcaacf413bcd8d2d930f5077ed1ddb66 SHA256 e0145ece907c91b819fa3b54a645c15a47b57c0a98ffc652dd5bb2bb78439844 -MISC metadata.xml 291 RMD160 5ae1471fd0e7b60d7de7027f8b807dcd005bd0b0 SHA1 10bcd36795a8dcc9ebf5b720fe79bd42a9518b7a SHA256 112c54edd1ef7cbe34d7132ba3fd95a0728b9298eea9b2e957fa5e40962842ea ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iQEcBAEBAgAGBQJNtze6AAoJEOeBhlrCAAWGqvQH/0ycS0Z1BpZZVEK1OKx0JAru -hVDwET5gkJ2iwGtwtDvJFwvL+70ZZem0UZcdwxcJl6BukBDOj2knEZ3q/cU//0qf -WA4vA7F6DByDAPtgAUGtJb1O5+2x5AtvtalB4E4wsxOvnMv6s0Sol/6iBW+HVPl6 -MUTwoW4SlT8nXAf8FbiYmgAilxWOZr1jWYPSvOY7RqPxAvhFTdygi+86PeOlqll1 -ZjQS+zBctYIv//IOsQ4wnQYBc3a5ke6zp3BdmpMQkZncAB/aTGlEDTzgTQEKaAWu -d49C5P2az3m0RLoLLRm2Fjv4HFAvo8gpxCMAh07t10/pkJ8ajoAiCZxCNluzTk0= -=WT8r ------END PGP SIGNATURE----- +EBUILD espresso-9999.ebuild 2340 RMD160 11de82a761ac701e9c47969f551e951352158820 SHA1 eaf870e110c9a917785cddd600e23bb0d491e64d SHA256 ee9568ddc8a254384cca94d1ae881865197ecc8b0c0488fca12211702d090fa3 +MISC ChangeLog 1138 RMD160 beb3e9fe6541b914e72c4722ca8593086a3f3e12 SHA1 da5e5c27cf2bea5b58ce256d0828c6b4df61b4af SHA256 96faaa2a8013c080c46a0795f38b892364793ee85c51dcc6af8cf2d6d3aca201 +MISC metadata.xml 291 RMD160 84daad3df42bb9c0c8df6209db215c4b1baf5ebf SHA1 e11cce7afa473f9e07767c735ddd77f103c6f350 SHA256 05ae7ea65ee894cccdd8feb7ee92963498fe13af6396bc0d99332fd5c0279791 diff --git a/sci-physics/espresso/espresso-9999.ebuild b/sci-physics/espresso/espresso-9999.ebuild index 55908dd46..9c2242542 100644 --- a/sci-physics/espresso/espresso-9999.ebuild +++ b/sci-physics/espresso/espresso-9999.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-physics/espresso/espresso-3.0.0.ebuild,v 1.1 2011/04/20 13:03:00 ottxor Exp $ -EAPI="4" +EAPI=4 inherit autotools-utils savedconfig @@ -12,7 +12,7 @@ HOMEPAGE="http://www.espressomd.org" if [ "${PV%9999}" != "${PV}" ]; then EGIT_REPO_URI="git://git.savannah.nongnu.org/espressomd.git" EGIT_BRANCH="master" - inherit git + inherit git-2 else SRC_URI="mirror://nongnu/${PN}md/${P}.tar.gz" fi @@ -25,14 +25,16 @@ REQUIRED_USE="tk? ( X )" RESTRICT="tk? ( test )" -RDEPEND="dev-lang/tcl - X? ( x11-libs/libX11 ) +RDEPEND=" + dev-lang/tcl fftw? ( sci-libs/fftw:3.0 ) mpi? ( virtual/mpi ) - tk? ( >=dev-lang/tk-8.4.18-r1 )" + tk? ( >=dev-lang/tk-8.4.18-r1 ) + X? ( x11-libs/libX11 )" DEPEND="${RDEPEND} - doc? ( app-doc/doxygen[-nodot] + doc? ( + app-doc/doxygen[-nodot] virtual/latex-base )" src_prepare() { diff --git a/sci-physics/espresso/metadata.xml b/sci-physics/espresso/metadata.xml index 03cc20a10..cb05f9bf1 100644 --- a/sci-physics/espresso/metadata.xml +++ b/sci-physics/espresso/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-physics</herd> <use> - <flag name='examples'>Installs the examples</flag> - <flag name='packages'>Installs extra subpackages</flag> + <flag name="examples">Installs the examples</flag> + <flag name="packages">Installs extra subpackages</flag> </use> </pkgmetadata> diff --git a/sci-physics/qcl/Manifest b/sci-physics/qcl/Manifest index e7c667e5b..9b1a2cf27 100644 --- a/sci-physics/qcl/Manifest +++ b/sci-physics/qcl/Manifest @@ -1,9 +1,19 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX qcl-0.6.3-gcc43.patch 231 RMD160 66080077bc6750739935ea999a98e3e5b419529b SHA1 1449b18d34638632619217f40d1990852e5c6682 SHA256 9cd24b2fbc7b2406849ce0c34d681b4396a74e39b79692a011acb3a2f0dc0cd1 AUX qcl-0.6.3-makefile.patch 757 RMD160 203ea8135ab22652d103bf40a9ebc1428e2a55f7 SHA1 401b11ddc4aa173c53f5abcb77ec58b832e462a1 SHA256 1f5d221ffa3d4efbc5444407d5541998725c37b436509eb16486b4376e6d28b9 DIST qcl-0.6.3.tgz 133786 RMD160 949a6d02224676cbd3f879801e22902347dc8296 SHA1 16ca54239d5f742a49ba400eeb766f6267a4f13a SHA256 c9f459b265ca181fdd4023cfb0d41a93a245eb5d47948a4002263384658d7cbb DIST qcldoc.pdf 435240 RMD160 6bbad4ec0c90f3bdd744014149699230a23f2b76 SHA1 97ba7d7f963ada3ea305f52ad4c61c0cba3f6df8 SHA256 a47f7e814b7848ba54d9e3749b66cc727376758dfdcb98c66531be01540f5886 DIST quprog.pdf 529617 RMD160 94f98069519b7154fe6210487fd0844645d9c6b4 SHA1 dbb8c4181ca89014299073adbecabb979201475a SHA256 d201296097d649b42da56fc713f7242b6786402ed936c28054eb530840d379ec DIST structquprog.pdf 662519 RMD160 6b1a3db3bcbeebbc0fc5e307f1208448598bb685 SHA1 06fab1a73be823b55d4902b421787ed833f99521 SHA256 0e5ea3f025c9c5eecb75ac1e408188ed1579aced1f4a45bbe7ff7b1b849d1c42 -EBUILD qcl-0.6.3-r1.ebuild 1013 RMD160 51529b61a39af766baf8024b361438eae661036e SHA1 258d1018fd901e1e7b7c3755a3a04b8d132bc169 SHA256 7f1103aa3cf5daa92019d708afd9045bac6ea9df6692c8d628eefd20211feeff +EBUILD qcl-0.6.3-r1.ebuild 1013 RMD160 2e0203e2598ea0634084d4a5af784b8357a8c009 SHA1 90688d53c0eb80a649a9dcbe8c93c1c39584a0d6 SHA256 3d2c5827435f1627a36ce0cc6778996c02f2f391967498f6a9134c5712cf8624 MISC ChangeLog 672 RMD160 06f37fbb83360f818ef28f1bab03277301f622d2 SHA1 64fe9e2990b5e8eef52f8fbdbdefe361d77627bc SHA256 c23353ee0a53980cc16dfe06fcc29b2a0a284d6df11ab9247203085430860c5e MISC metadata.xml 255 RMD160 3888d84eebc61a6fbe9ea73869ff58e096ff9377 SHA1 dc17c251c75cf6522bb086979083876d2f8b1620 SHA256 cbe073c7ed8462cb5b809f71393d81734ab4dec4f754022431070f1d7b58b2aa +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EsCoACgkQgAnW8HDreRZl6gCgjNnvdDT4MG2u3+ulqarjkIes +YCMAnjIiotNXmcbcQ2QJsrFgvD/FViaO +=fhCL +-----END PGP SIGNATURE----- diff --git a/sci-physics/qcl/qcl-0.6.3-r1.ebuild b/sci-physics/qcl/qcl-0.6.3-r1.ebuild index e101fae5a..4e74b2e0a 100644 --- a/sci-physics/qcl/qcl-0.6.3-r1.ebuild +++ b/sci-physics/qcl/qcl-0.6.3-r1.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI=2 -inherit flag-o-matic eutils +inherit eutils flag-o-matic DESCRIPTION="Quantum Computation Language with an emulator of a quantum computer" HOMEPAGE="http://tph.tuwien.ac.at/~oemer/qcl.html" diff --git a/sci-visualization/ferret-bin/Manifest b/sci-visualization/ferret-bin/Manifest index 8d47ba410..e9db31d89 100644 --- a/sci-visualization/ferret-bin/Manifest +++ b/sci-visualization/ferret-bin/Manifest @@ -1,9 +1,19 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX 99ferret 673 RMD160 4d3486b9c9612c0c2491c21744dae34d1a2d667c SHA1 0d93a2f271a7aed837fe79cd73504a266412e007 SHA256 23e1c54a4ee63f74ab44285d4362838a4cd49572aee9478c5b58a95458f81d6e DIST amd64fer_environment.v664.tar.gz 8079499 RMD160 dd0d4f84440fb78aebd42a8c2963935d261e82cc SHA1 864dace46d24ad8c9373b5a85066f6afbbd7e05a SHA256 de02d54e825e1f32d8fefc651027202941a8985425202f1872bab84119bed698 DIST amd64fer_executables.v664.tar.gz 5408420 RMD160 bb8eb43e9b835a51d66b33990c173e2a11fe5194 SHA1 395c0dd4498d0a0a2baf182bd70408f0bc8b5c6a SHA256 4212f24f079a599cbb5a15cd21f41b723ebe710208de4efc14b58222feb95c58 DIST fer_dsets.tar.gz 39991296 RMD160 dc3c8c67d86bcddad6bf1d984b524e1121ea5286 SHA1 4e0f514b7ae1441597e0f06fd06eda5797025ce6 SHA256 094645b275520321940002d286e792877a4867e2576832e246ab3d3f113425f3 DIST x86fer_environment.v664.tar.gz 7671499 RMD160 40912a10e921d1814a6a72a4c31f1230d4008804 SHA1 cc74b21df222236bae5e8038bedf4a6640ccc7fb SHA256 bf011446669aea636e3c3eff07c72792c6319ce12e3a589d8bd7b8ecd65503ec DIST x86fer_executables.v664.tar.gz 3813127 RMD160 1070576386af84e256da40f3bb21e76912f75a99 SHA1 5301cc8ae3e5611f34cc370fe1b0f9f49629ca42 SHA256 34416d6934dea3c938f51d18869b36fd78f2ca31d403e8303cd007f3c1a38e89 -EBUILD ferret-bin-6.6.4.ebuild 1576 RMD160 c533e5c40f9107acdb34561601c275d2316bb2a3 SHA1 352b82d8e7f63db2f95a13adb9d64f823ed082ad SHA256 a84387c478d1605407eae32b392dba9bd78019ffbf937fd809afd53df45a1084 +EBUILD ferret-bin-6.6.4.ebuild 1576 RMD160 1aa6e313f568fcb43d5b8a17e394031785d0e7da SHA1 3ca155cb3f3d2eea6fdf332e9f7a2f44ddbed11b SHA256 1d656e76757f08797c5e6d09912df5b212715d50723da663ec7356201c8f9b97 MISC ChangeLog 1709 RMD160 f83bc23549134197b4e1fe7213cca6233f1f1d4d SHA1 8068e562d08db44ab0b389beb41a112753145dc5 SHA256 59daaeb29bc423006aa8d881d27a82e60371c0761b0223d177651a3985bc93b4 MISC metadata.xml 362 RMD160 81d21aa9fb0e54a53c2db8ea0965a59a633417fa SHA1 8e0c5a42c19d225c6b0087173dfd3498fb6098ad SHA256 114c2d067f3f6e4e809739707c042f4a2959895fe4f8dfdd86f52857d6e4532a +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EsC0ACgkQgAnW8HDreRanyQCfXGCFAdvhehJthQ6g26q+/Mmt +TkcAn0gQH/a73+kewAlAG89jvaWPcie0 +=tzaD +-----END PGP SIGNATURE----- diff --git a/sci-visualization/ferret-bin/ferret-bin-6.6.4.ebuild b/sci-visualization/ferret-bin/ferret-bin-6.6.4.ebuild index fa19c3407..250a7498f 100644 --- a/sci-visualization/ferret-bin/ferret-bin-6.6.4.ebuild +++ b/sci-visualization/ferret-bin/ferret-bin-6.6.4.ebuild @@ -4,7 +4,7 @@ EAPI="2" -inherit versionator eutils +inherit eutils versionator MY_PV=$(delete_all_version_separators "${PV}" ) diff --git a/sci-visualization/gri/Manifest b/sci-visualization/gri/Manifest index f30799341..6471a8b3f 100644 --- a/sci-visualization/gri/Manifest +++ b/sci-visualization/gri/Manifest @@ -1,6 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX 50gri-gentoo.el 147 RMD160 2e69a5f9034ef82901a6c004a3f9e167e1e426e4 SHA1 530c8bf902635e5baa3215084b9fa454dcb1c31e SHA256 d3f04f7eb861ed663013e74d99981ea7c08ebf199de67c0ddd255eabc10ea09d AUX gri-2.12.18-postscript.patch 3997 RMD160 4b390be9c915573812ba2e3d2289b2d9037e85ad SHA1 c2993812fc3fbbbbb21bd0516c43e094d6a78090 SHA256 2d3c2d44f39507270581744de930fb92bdcab6c5e3d846653e08ccfec07375b9 DIST gri-2.12.22.tar.gz 1669555 RMD160 d1301823bb3510022f4146f23c42f059e0f4d2fc SHA1 e9778d9e01dd500dd13cc9c995691207cabd9a45 SHA256 01b5dfdb79125d87a17250c1e0aa0b1a894e5dc095473ae209f3a3fadebdba0e -EBUILD gri-2.12.22.ebuild 2002 RMD160 b5f7838f211c3c82bff4c55acc7b88576d360721 SHA1 9ef795559111b8e4308ff5a6b33e556dfd3ee86e SHA256 5eda809ce7d9b4bdf5645a0d4e9242bdec9c72689e0ee40937fb2dd8bea2140b +EBUILD gri-2.12.22.ebuild 2002 RMD160 e34e62cac74abee2e10014bd05f798be8a2f80fb SHA1 2a4df4436d80a131cb83d128af126200ed6ce60a SHA256 776b37070852aff7e0afbed71daf78f65c07fde11120814d84e2d7e5f90ea7d0 MISC ChangeLog 6769 RMD160 84bcfc795cc6c21cb98ab6811e29f83366c841d3 SHA1 f0153b5a4bc61de72a042f9e019aaec3de6afae4 SHA256 dd527c5a26d05787fa521815a4750b38812de75a48b5a08a31453652af9a101b MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EsDQACgkQgAnW8HDreRZaggCfZL0evOrTydXYTIYSrAgS9Rji +UdoAnjUtsyOmGa8HPkOmd2BVwNXOeang +=vV+k +-----END PGP SIGNATURE----- diff --git a/sci-visualization/gri/gri-2.12.22.ebuild b/sci-visualization/gri/gri-2.12.22.ebuild index 279b7fd0d..e05011e87 100644 --- a/sci-visualization/gri/gri-2.12.22.ebuild +++ b/sci-visualization/gri/gri-2.12.22.ebuild @@ -4,7 +4,7 @@ EAPI=2 -inherit eutils elisp-common +inherit elisp-common eutils DESCRIPTION="language for scientific graphics programming" HOMEPAGE="http://gri.sourceforge.net/" diff --git a/sci-visualization/paraview/Manifest b/sci-visualization/paraview/Manifest index ade2bc147..c319bc148 100644 --- a/sci-visualization/paraview/Manifest +++ b/sci-visualization/paraview/Manifest @@ -1,3 +1,6 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX paraview-3.8.0-h5part.patch 467 RMD160 bd34e8bf02a1855dcfeabdc77cac39bd78a41492 SHA1 8416ef8a782425624b04c28c379d383e8f924c44 SHA256 ea46a024d8cb398c93dabee22ac2bef66af3771477811551275bfa85a765cc3f AUX paraview-3.8.0-installpath.patch 1554 RMD160 c998ba929f32892191161a9ead0572e2afbef817 SHA1 41cc9dc5d83bc67290653997145fe9e1b45411c6 SHA256 b57a10a4a2e299385c581231173e4b2c67a0367cf7d8ce1ca618db4c370a9550 AUX paraview-3.8.0-pointsprite-example-install.patch 400 RMD160 e7e027393025767748844b13f32499134afd3ef1 SHA1 0a78a35d6f51cefe885b79438a94e655eab562f4 SHA256 217b1f02199fef668201ccc78d2db3fce50730123946b992567f1a925ef764dd @@ -8,7 +11,14 @@ AUX vtk-5.6.0-cg-path.patch 1106 RMD160 a6cb9f4855dfe417d83e7bba04a02da88af869a6 AUX vtk-5.6.0-libpng14.patch 734 RMD160 d54626d332130fe242b3a5b1300a650e45763d29 SHA1 e6480b68a14345d7dfa78f6d37ff7301366d99d8 SHA256 81565709c8cfb4df3c28d69df8094d15923d824345330ab5ba101a9780e6e9f9 DIST ParaView-3.10.1.tar.gz 40696006 RMD160 411087473102ee9d2daf7dd8b61390b4b120645e SHA1 2e56788c9d27f83b5400ffb3770024cf04fa0e4c SHA256 453deee23b6fa62ecb010d951adbc49e740dcb8875680725f93b8f76b9df5cfc DIST ParaView-3.8.1.tar.gz 33123181 RMD160 66dff2b84bb4d17b9d44142be79d08bc84c76fa0 SHA1 2cffb622f8b991a36df39bf260a1752de9036eb4 SHA256 37647172af0ac7fc3b677cc2d1e2e825cf364cb4915190da74f19992d84e263c -EBUILD paraview-3.10.1.ebuild 6901 RMD160 98caee44076c92f3378a1c83084faebdb4c2075b SHA1 5795fa99ac7739c039ce661ba9ddb1738b61d605 SHA256 6153a7027e9c273fcb5bfce0b3e94f661302c31aa1ab6aab607ee7b530badf77 -EBUILD paraview-3.8.1.ebuild 6586 RMD160 c8dbc56dcee166ebdf2b7a2ce7dd0956beae015c SHA1 79347f619c7123ef31314eba18f0d4b1d60351dc SHA256 7c24824fbfef3370f29fbfbf98b7f30518efcf018cc95b130c183d1f5fd80538 +EBUILD paraview-3.10.1.ebuild 6901 RMD160 6bb0af48a22901a61c23376deadab81c84a49fa0 SHA1 b0544ae5f6368dc78bb58e57bad0e0ad694ffdf7 SHA256 d1406c1871e26610cd49b82a71d95d52ce9247a268585e3082395e0bd887d47a +EBUILD paraview-3.8.1.ebuild 6586 RMD160 fae939107adbc9976502ca7cfd9bf5b049ae5839 SHA1 aec4247b1a4d55aafb4f3207f5208f63d1dbfa4e SHA256 a735f01a84a98096df3bf26ad7f2c66b1aa16391493222b565413e01403661c0 MISC ChangeLog 3244 RMD160 ef7f8ac239910f993306ef1ea9e135dd4bc33f06 SHA1 9dae3bd092a465d044caefc77a7acaa6ef6d6fe1 SHA256 3e08dbf16cb37fa5568091887b4fda85ca21e03fa91d2e0f1aaff1a49dd62cf9 MISC metadata.xml 948 RMD160 acd3fba24e9ce5a26d1e83eafd8ae2216ad5fdfa SHA1 f5dd4382e30821876edac2d40073dac7b7b1f51a SHA256 b76a387976f54894ee55f5dd310070810b5c7d7cc6b0aad3bd0e0d3e7265af90 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EsDoACgkQgAnW8HDreRanqQCgsyu4XyjmwghPYz6kcGrbePYo +5M4An17CRUJnoC1uua/JUUws3eOVZvH5 +=xLpZ +-----END PGP SIGNATURE----- diff --git a/sci-visualization/paraview/paraview-3.10.1.ebuild b/sci-visualization/paraview/paraview-3.10.1.ebuild index 923a8c50d..f17fcfced 100644 --- a/sci-visualization/paraview/paraview-3.10.1.ebuild +++ b/sci-visualization/paraview/paraview-3.10.1.ebuild @@ -6,7 +6,7 @@ EAPI=2 PYTHON_DEPEND="python? 2:2.6" -inherit eutils flag-o-matic toolchain-funcs versionator multilib python qt4-r2 cmake-utils +inherit cmake-utils eutils flag-o-matic multilib python qt4-r2 toolchain-funcs versionator MAIN_PV=$(get_major_version) MAJOR_PV=$(get_version_component_range 1-2) @@ -20,7 +20,7 @@ RESTRICT="mirror" LICENSE="paraview GPL-2" KEYWORDS="~x86 ~amd64" SLOT="0" -IUSE="mpi +python doc examples +gui plugins adaptive streaming cg mysql nvcontrol webkit -coprocessing" +IUSE="adaptive cg -coprocessing doc examples +gui mpi mysql nvcontrol plugins +python streaming webkit" RDEPEND=" sci-libs/hdf5[mpi=] diff --git a/sci-visualization/paraview/paraview-3.8.1.ebuild b/sci-visualization/paraview/paraview-3.8.1.ebuild index 1513fb188..5057b42e8 100644 --- a/sci-visualization/paraview/paraview-3.8.1.ebuild +++ b/sci-visualization/paraview/paraview-3.8.1.ebuild @@ -6,7 +6,7 @@ EAPI=2 PYTHON_DEPEND="python? 2:2.6" -inherit eutils flag-o-matic toolchain-funcs versionator multilib python qt4-r2 cmake-utils +inherit cmake-utils eutils flag-o-matic multilib python qt4-r2 toolchain-funcs versionator MAIN_PV=$(get_major_version) MAJOR_PV=$(get_version_component_range 1-2) @@ -20,7 +20,7 @@ RESTRICT="mirror" LICENSE="paraview GPL-2" KEYWORDS="~x86 ~amd64" SLOT="0" -IUSE="mpi +python doc examples +gui plugins adaptive streaming cg mysql -coprocessing" +IUSE="adaptive cg -coprocessing doc examples +gui mpi mysql plugins +python streaming" RDEPEND=" sci-libs/hdf5[mpi=] diff --git a/sci-visualization/v_sim/Manifest b/sci-visualization/v_sim/Manifest index 97aa559e8..84def6ffd 100644 --- a/sci-visualization/v_sim/Manifest +++ b/sci-visualization/v_sim/Manifest @@ -1,8 +1,18 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST v_sim-3.5.1.tar.bz2 2820832 RMD160 f97fa21f2fea92c759c7a595d1d55f4ea3831bee SHA1 b47b6e7611b891bc09799ca67167ce28040afc47 SHA256 8453adffdac1022cfe8e1aeee6117d5bb6a1e9e28f446c7ad6c0cdcc3e1884cd DIST v_sim-3.5.2.tar.bz2 2802637 RMD160 2f109591a0b6b424beb4391e4f3baaf54e56796d SHA1 d51aad9aa08f3ace4dc1a438ee4e45e90b767129 SHA256 22beab0f9f5e38d60cb13a8afa5f760ec7fd56cb9850c7b7d38a546448d62b15 DIST v_sim-3.6.0.tar.bz2 2953739 RMD160 09f57f5bb752934a3500b5d377b1694a35aefa0b SHA1 f502f3bff7b1c5d475950a126aaa7dbd222ffc55 SHA256 bd922961839367da935fc8b2ad5c9085c59dfb957e251ead36a06338a9045ad6 -EBUILD v_sim-3.5.1.ebuild 2567 RMD160 72b1cf63133219fc9b2bfbedd2d0afe5c06426e8 SHA1 f9862dbf19813c15506f2c9f9712192dad5209ea SHA256 50ced41fcdf92ac2b4c672a0ed6e383410ceccd57e10c5bef83a08bc86b8a7df -EBUILD v_sim-3.5.2.ebuild 2784 RMD160 f706c378007a13be9510c1d147a4039a5e781a90 SHA1 1607688481e7ca9459fad109caa5c9c1e7b78b60 SHA256 e855691b797279a4383ec8b8a6cf502891742e6b461feafcc506edd1d76d2d4e -EBUILD v_sim-3.6.0.ebuild 3025 RMD160 7ae4851c75e61b281fc9d4af4697ecf3e19d701f SHA1 ee451a035ba08abbfebc517bb8d93f527d3dc90b SHA256 0d8e30bb7fdb4b39d62cc977bb7bb2847e6fcf1a38aa75760037597da86f2e78 +EBUILD v_sim-3.5.1.ebuild 2567 RMD160 7522806f1343ffd6a7ece2a50a13c74b37484f7a SHA1 94218489289c2e4ff5c17dee8e1eb56da5a2d46c SHA256 9936a0715a435d437b96bc014b9aff4a26f4357b80b1a046de5064daaacb5262 +EBUILD v_sim-3.5.2.ebuild 2784 RMD160 6a954e02cac4e4fb2954a4f808a90137cc99cde5 SHA1 5fd80b9444302d77015bae75d4bc9f91485da055 SHA256 f84e6d07e3a903a207e54ecd41e9651fb621b53a956e5de9c15f9f10e965163b +EBUILD v_sim-3.6.0.ebuild 3025 RMD160 b27b18cc26f233905ab5b15c79abb727102c1e64 SHA1 079b2c46b3c6ecfc345616b052a6e1d89831df44 SHA256 87c33e4a9518d0139d65914e4be813b1fa9c3de384814bd1fb13157d5747de5d MISC ChangeLog 873 RMD160 873081050d16dd75458904d39db78925524be006 SHA1 41dcd3b7059a265c725d3b56715e856e5ce4b5a7 SHA256 069ad2f78571e44a663b75106f8e4f98f405f06557429c957009c328980f8f97 MISC metadata.xml 709 RMD160 34ba66e5ad93057127c7af73294471c1ac70b0c3 SHA1 531d4ff37cf95e79cb7ec7b4ff9ce12a279668ea SHA256 6e99ad5350e455a5134f9d6531593173428630f42aa772155583dd972b3f6b56 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EsEAACgkQgAnW8HDreRbb+gCfc/31lOgMeBJD1BRiaZBQVh34 +3UMAn31xanQVCAAzUEt3Z4dsglCUNkOk +=8abA +-----END PGP SIGNATURE----- diff --git a/sci-visualization/v_sim/v_sim-3.5.1.ebuild b/sci-visualization/v_sim/v_sim-3.5.1.ebuild index 1ce6e6e8f..ee8253a54 100644 --- a/sci-visualization/v_sim/v_sim-3.5.1.ebuild +++ b/sci-visualization/v_sim/v_sim-3.5.1.ebuild @@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~x86 ~alpha" # doc: Adds developer documentation (/usr/share/doc/${PF}/APIreference/) # Example files are copied even when USE='-doc' # debug: Adds console debug messages. This is really verbose. -IUSE="doc debug" +IUSE="debug doc" RDEPEND=" x11-libs/gtk+:2 diff --git a/sci-visualization/v_sim/v_sim-3.5.2.ebuild b/sci-visualization/v_sim/v_sim-3.5.2.ebuild index cbcd0c45c..478cacbfa 100644 --- a/sci-visualization/v_sim/v_sim-3.5.2.ebuild +++ b/sci-visualization/v_sim/v_sim-3.5.2.ebuild @@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~x86" # doc: Adds developer documentation (/usr/share/doc/${PF}/APIreference/) # Example files are copied even when USE='-doc' # debug: Adds console debug messages. This is really verbose. -IUSE="abinit blas doc debug netcdf openbabel" +IUSE="abinit blas debug doc netcdf openbabel" RDEPEND=" x11-libs/gtk+:2 diff --git a/sci-visualization/v_sim/v_sim-3.6.0.ebuild b/sci-visualization/v_sim/v_sim-3.6.0.ebuild index cf3db751a..23866174f 100644 --- a/sci-visualization/v_sim/v_sim-3.6.0.ebuild +++ b/sci-visualization/v_sim/v_sim-3.6.0.ebuild @@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~x86" # doc: Adds developer documentation (/usr/share/doc/${PF}/APIreference/) # Example files are copied even when USE='-doc' # debug: Adds console debug messages. This is really verbose. -IUSE="abinit blas doc cube debug netcdf openbabel xsf" +IUSE="abinit blas cube debug doc netcdf openbabel xsf" RDEPEND=" x11-libs/gtk+:2 diff --git a/sci-visualization/vtkPOFFReader/Manifest b/sci-visualization/vtkPOFFReader/Manifest index a5ad38348..aa452ac6c 100644 --- a/sci-visualization/vtkPOFFReader/Manifest +++ b/sci-visualization/vtkPOFFReader/Manifest @@ -1,3 +1,13 @@ -EBUILD vtkPOFFReader-300.ebuild 934 RMD160 a42f360f5175161a7b78503a4651f6e9783e039f SHA1 12f5dfebc161a6abe82bf17786b5737635da0679 SHA256 8c355f595add5d4f71f378728b8730e12d947eed37e6988b712c5654c5ad9f85 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +EBUILD vtkPOFFReader-300.ebuild 934 RMD160 f081c0c80479a15446631cb39720a43479be7dd2 SHA1 55328cc67cd1a301ee0b468993a027c8b5843af8 SHA256 ba6de9d4b3345ac3aa6ddb20847adfa1b186f27984f13037cd9d4c4ce7ef1e83 MISC ChangeLog 510 RMD160 a541bd98e23eb6bcf24a3d2aaa4822a6b0a926ba SHA1 2b2ab6cf878cad0a3f1f0c85816a9884f2588a23 SHA256 9ab9b6df3656aea62dd2f77bbf7fc0072a84303cdfe0ac14880067547e39ec4c MISC metadata.xml 172 RMD160 e1fc4210872c2891f78fbe54d0a63f6dfdd21992 SHA1 b04693e81308331acfa81c48171ea5222725597e SHA256 f7fe5da6e37a7833100ae83886ede9acb77d43c676cc69d2ccc1279259d8d11b +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EuKEACgkQgAnW8HDreRa9iACglgD/+CaDflgpLQMz1jtYzZsR +ft4An3CCXn5musq886pJ3y7JwhDFbWgs +=iXGd +-----END PGP SIGNATURE----- diff --git a/sci-visualization/vtkPOFFReader/vtkPOFFReader-300.ebuild b/sci-visualization/vtkPOFFReader/vtkPOFFReader-300.ebuild index aee2d7c2c..843418bb7 100644 --- a/sci-visualization/vtkPOFFReader/vtkPOFFReader-300.ebuild +++ b/sci-visualization/vtkPOFFReader/vtkPOFFReader-300.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit versionator multilib cmake-utils subversion +inherit cmake-utils multilib subversion versionator DESCRIPTION="Parallelized reader for OpenFOAM(R) file format for use with ParaView/VTK" HOMEPAGE="http://of-interfaces.sourceforge.net" diff --git a/sys-cluster/classads/ChangeLog b/sys-cluster/classads/ChangeLog index e3a1d4e7b..595747c83 100644 --- a/sys-cluster/classads/ChangeLog +++ b/sys-cluster/classads/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sys-cluster/classads -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + *classads-1.0.8 (14 Jun 2010) 14 Jun 2010; Sébastien Fabbro <bicatali@gentoo.org> diff --git a/sys-cluster/classads/Manifest b/sys-cluster/classads/Manifest index 0a5b6b031..8213f9321 100644 --- a/sys-cluster/classads/Manifest +++ b/sys-cluster/classads/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST classads-1.0.8.tar.gz 504575 RMD160 99e67e3016d4b37e19443703e3cc1afbcee45704 SHA1 f373d1b27f1c05a68822d9c8dd63a4678e280d3b SHA256 cdd48978bfc63db24f8c1496623230320a7b98c35a861893c433375786fadd4e EBUILD classads-1.0.8.ebuild 616 RMD160 f90a0eecbdc20e4bead260cd6bae0da2c485e5f7 SHA1 89022013b926d008bce624a5e7a2c92eca7df8d6 SHA256 ded68ff9317c5471a22afcb04ba7cbaa0cea5742c26db1178435bfdf16b5d5f1 -MISC ChangeLog 439 RMD160 c1697646e6a849f9f972f8f1a5df196f0ca27ed6 SHA1 59ba2c4e04a3dbd3d8512075c725c0162e245d70 SHA256 2cb1eaedc6e15d58072e79957a9f4eb3996da4545a3db9f5a739dd50dba1ac07 -MISC metadata.xml 606 RMD160 8fe159e007a7c369fbbae6e196c8a8859b0075dc SHA1 bcb1611db4fd205000278fdffc9d897a5789f288 SHA256 ea7b4eeeae4e0e3de862567b527a5a1ddfc0562abbeb7304d2b0538865a9c4b2 +MISC ChangeLog 536 RMD160 0390614ca5287c5f6b303a320e89ab341420029b SHA1 3ffcbb4b33754889eb6bd068229ca2cecab9e7db SHA256 a798f500dee48f60c575b5a60c6c8242fa08eeaafb14c130c8a7ddbd7ec0b54b +MISC metadata.xml 613 RMD160 b87cab4e8f36791796a36d3e00192f36fbc0e9fe SHA1 5b5cbb47222680ff92a04b2be6b2dfcc670a0284 SHA256 2d0042e4414ec845a617d83f35d5cc81d93cb31d741b23a10fe52db71c62c5f1 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4FkowACgkQgAnW8HDreRZouwCgndupruNiU4rBjb7qL4pciDdY +OLoAoLMYM3/kvupBl3GPpsGG4vneGc1p +=gCO3 +-----END PGP SIGNATURE----- diff --git a/sys-cluster/classads/metadata.xml b/sys-cluster/classads/metadata.xml index 21a1310c0..d3169273a 100644 --- a/sys-cluster/classads/metadata.xml +++ b/sys-cluster/classads/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>hp-cluster</herd> -<maintainer> - <email>bicatali@gentoo.org</email> -</maintainer> -<longdescription lang='en'> + <herd>cluster</herd> + <maintainer> + <email>bicatali@gentoo.org</email> + </maintainer> + <longdescription lang="en"> Classified Advertisements (classads) are the lingua franca of Condor. They are used for describing jobs, workstations, and other resources. They are exchanged by Condor processes to schedule diff --git a/sys-cluster/condor/Manifest b/sys-cluster/condor/Manifest index 795698cbb..bf9fdb695 100644 --- a/sys-cluster/condor/Manifest +++ b/sys-cluster/condor/Manifest @@ -1,9 +1,19 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX condor.confd 75 RMD160 a58d37af4bbbcf1df486dd1397209832114cb614 SHA1 fcc784f7af690943b215b97ebbc8f4a199f16fb4 SHA256 ee7d67f176996412d4de8b76b5720ef5c4da84eebe119ed1b4ad52ae8528eb30 AUX condor.initd 1783 RMD160 0af1b75734da761674693a768ef9a00fd3f1849c SHA1 2fa56c701351e15966754245893257e26defc642 SHA256 11d1ff517d1ca0ed53a69cdc444cf8020932b20970d1b73078c2b7223d57cf41 AUX condor_config.local 273 RMD160 5aa8e9b62d57059667aac9f2c583cf3f2490b603 SHA1 d53d14ce4fb79510ae267ad6070f0bf6e42e0db1 SHA256 849985bc53bb39c464c55e30a8ae5b7d33e90b2ccee8337452b17bf87edc0b1f DIST condor_src-7.5.2-all-all.tar.gz 21705891 RMD160 f9911e3a44b69bb22ef607964aec726b51ab9341 SHA1 7e85048545423b13f8173c6ba6d76d35b97f2dcc SHA256 1a4fc437541896aa9963f12ec9231495f6a5ab4cc5ca814b57755a38db407026 DIST condor_src-7.5.4-all-all.tar.gz 21870900 RMD160 7118a7a7ee32d5d7d9378ed5b94ad7a058ac1fca SHA1 877f748b53dd5e796592f812ae65d75f7b907812 SHA256 a0429b2525047b2eaca988ff4546ff177a5b4e55511354c793e4b3f01b032c08 -EBUILD condor-7.5.2.ebuild 4345 RMD160 912cb92deabde325068da49048edf483fb6b9f34 SHA1 73778f44eab0ab48d9466310b75bce1a54de2338 SHA256 37c88bdba428fb366ef8a220c492cbec73e6b84f3e5517b108c7869ce0aac237 -EBUILD condor-7.5.4.ebuild 4345 RMD160 c43f5b08d8d77cf07ca9b0d21c87e33eaf636b4e SHA1 0d25cdcc0c58506a8e9bcdfbaae2355dd5ab5998 SHA256 d0809dd9ec219939bba4788748a919a5950ed554f1b02c4d30794dc32b4df7f2 +EBUILD condor-7.5.2.ebuild 4345 RMD160 c69b1dd926e3224d764ca28a70bc6c4d86f06785 SHA1 ca7f528c61b756962482ee8dec036598406fa4df SHA256 107f4e40b5437df9f1206182fb57b89ca933cecd62d3dea8e81a0cd625b7b44d +EBUILD condor-7.5.4.ebuild 4345 RMD160 4ff75780a73c7d633bccdc485a337147d60254d9 SHA1 f399fa0250739c5e41c4b5370fc972b38634295d SHA256 eef6b189ab01d771b612091da0bccc08113e54d2e76ec6c290c5ac035707cdaa MISC ChangeLog 1583 RMD160 1d4525812580e576ad5b458172b791955f9040d3 SHA1 03a96168e04e92d8ed58dccd6b4a3ab023c9ec4d SHA256 90a334777278b4fdb6fdfca76bf3fa25f29c06541112c014caf4cabfe6673eb0 -MISC metadata.xml 1247 RMD160 bcc91575dc0a5cc4ac255d5c0c415d0ade7c96c4 SHA1 a9a3ca65688dc4f32a01df1a5c329065fc7b37bf SHA256 87fdc2d2b126339048785a67fa126a184ffdf08a6bf6e6e29e78c62581ca1f0f +MISC metadata.xml 1265 RMD160 acf5d07576492fda3e4f272ca6897bcb680e848b SHA1 f7ea88f45177584decd397fbdfd9acf2670c8ca1 SHA256 a1ecc03fb1396912c18edc729e9588706daff14937b281c9e6c2a6d162874c4b +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EuUcACgkQgAnW8HDreRYvAQCgmjQDDT6k0SMFCYlcBHfimplo +F1gAoIJxRyGUoIWDydAHV0z7kyWgYOkf +=KMi3 +-----END PGP SIGNATURE----- diff --git a/sys-cluster/condor/condor-7.5.2.ebuild b/sys-cluster/condor/condor-7.5.2.ebuild index ea978ca75..940d86040 100644 --- a/sys-cluster/condor/condor-7.5.2.ebuild +++ b/sys-cluster/condor/condor-7.5.2.ebuild @@ -4,7 +4,7 @@ EAPI=2 -inherit eutils flag-o-matic autotools +inherit autotools eutils flag-o-matic DESCRIPTION="Workload management system for compute-intensive jobs" HOMEPAGE="http://www.cs.wisc.edu/condor/" diff --git a/sys-cluster/condor/condor-7.5.4.ebuild b/sys-cluster/condor/condor-7.5.4.ebuild index daf9d0f73..fd28c19fb 100644 --- a/sys-cluster/condor/condor-7.5.4.ebuild +++ b/sys-cluster/condor/condor-7.5.4.ebuild @@ -4,7 +4,7 @@ EAPI=2 -inherit eutils flag-o-matic autotools +inherit autotools eutils flag-o-matic DESCRIPTION="Workload management system for compute-intensive jobs" HOMEPAGE="http://www.cs.wisc.edu/condor/" diff --git a/sys-cluster/condor/metadata.xml b/sys-cluster/condor/metadata.xml index e12acc536..bd197e13d 100644 --- a/sys-cluster/condor/metadata.xml +++ b/sys-cluster/condor/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>hp-cluster</herd> -<maintainer> - <email>bicatali@gentoo.org</email> -</maintainer> -<longdescription lang='en'> + <herd>cluster</herd> + <maintainer> + <email>bicatali@gentoo.org</email> + </maintainer> + <longdescription lang="en"> Condor is a open-source, specialized workload management system for compute-intensive jobs. Like other full-featured batch systems, Condor provides a job queueing mechanism, scheduling policy, priority scheme, @@ -16,11 +16,11 @@ also contains mechanisms to submit jobs to grid-sites and supports many different grid toolkits. </longdescription> -<use> - <flag name='classads'>Enable the Condor's classified advertisement language</flag> - <flag name='drmaa'>Enable the Distributed Resource Management + <use> + <flag name="classads">Enable the Condor's classified advertisement language</flag> + <flag name="drmaa">Enable the Distributed Resource Management Application API</flag> - <flag name='gcb'>Enable condor to communicate over firewall/NAT</flag> - <flag name='kbdd'>Enable the Condor Keyboard Daemon to monitor logged in X users for activity</flag> -</use> + <flag name="gcb">Enable condor to communicate over firewall/NAT</flag> + <flag name="kbdd">Enable the Condor Keyboard Daemon to monitor logged in X users for activity</flag> + </use> </pkgmetadata> diff --git a/sys-cluster/ganglia_jobmonarch/Manifest b/sys-cluster/ganglia_jobmonarch/Manifest new file mode 100644 index 000000000..443b56089 --- /dev/null +++ b/sys-cluster/ganglia_jobmonarch/Manifest @@ -0,0 +1,26 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX job_monarch_link.sh 2932 RMD160 eb65a06ae33306c62190b023b05a0e552156ac66 SHA1 90d21fbf79cbf6bca4b079066426eccb5eb84671 SHA256 0f7ed9181d7881f7c065f432ef62ed10c0860a89c18f29fe2db2194d14f7b83d +AUX jobarchived.initd 534 RMD160 f2a54dd08ef8c13ddc5a91aa6359980dabce7b1d SHA1 6d95bd5b32a94c520c780ca6d9f7839b066818d4 SHA256 b7f2a402db538db74c4ed85b85c372db1d15a564e0ffc9d38636996aef46d03f +AUX jobmond.initd 514 RMD160 4b05109aded899a3aa61dd4c39b3784bf1dc5d4b SHA1 7090273827ebe4064a7f766ab06046377346cfe9 SHA256 567c67b64c22a4fbb7991c574d2afe446afff9c5f676923f69b48c2f48459935 +DIST ganglia_jobmonarch-0.3.1.tar.bz2 113717 RMD160 9078550c4812dd5e55a4feae14a01e80a0b71d8a SHA1 cc40abe15d11dbe51c60ea23999614299813b77f SHA256 606911b14c367dd44ce2e180d88876b5fe6db006d4cec9d9ab9556c597e909c3 +EBUILD ganglia_jobmonarch-0.3.1.ebuild 1688 RMD160 5f3d2dd0ac107aa93170a011b1c3df71e75fc075 SHA1 daab3298df9a4f88f231ded93ef17c5e53880320 SHA256 72cf1381aca7d0c808b1aeeca7fff3d26ecff0648c8d1ab5c2af661305fab872 +MISC metadata.xml 162 RMD160 7800bf5ae6a087834e11dd1332107aa7ed5b0655 SHA1 dea0332aadbc22ba6bad0fc9cb993c6633e08d02 SHA256 ba8ac4b0fbb2acb09677330e980feed7de66b52d6ec4ee0ff9e44cccea58fa7c +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iQIcBAEBCAAGBQJOC2iiAAoJEOf+E+/4L5LmHMIP/3v+H+UuEsvuqTPiIrAKAWw+ +yh0GY+wPRc8T7Pmb8fSzCKFOZaPv9nG/J4Z/frBrr0Y0ME/0SAMCwk9xhzE8g292 +EiZ0xbkurx3ooQZqnDut4fvpVMLG0FG4KJcg6lntDlTkDX0nXDikk37yqWu1Z6Mk +beH71uXhp5SXXwbsR2GkizhqeuCNDdIAO2JY2LgIR5anvTn7zvQWBRoGIdpGWI2x +SYkxlYCHRg9HaVaf9hSKvTq8HajWR0MqUDLVIMk2wm9aTWQ/ftT343GfPrwzPkW6 +wkDijIXgGzmKRteeRUKeQ8v1+5k+OPB+7m9D4WdPd3pNmxQl6Npi++D7op6zKQtK +tRsxYqawe/OKPRi1b+l5Yl1xYY5lcPJj4LyfKn61GVLunlJIfdb8C6mKGoykf3ZR +SvCPxFZVL8yL8/Ymd+lE+lCV0teI6rw0Te2wwoVEmyp5JNLhp/hBmWLQgwQYJ4nd +XvsGpoTT6M/3Z4UXejdnqP+nS8ZfapdJj+dsWEQhaZ0tSNEH3pTbwqtxNfzz+hjV +GQErAn/rcyOUv86R4MCBumTnllKvvwQgTIVEJup3mhYuAerXIeyst+RAaWsp9dgX +7RSbtjWNIKm/zQQ40MMTjp2WG3/tFjqeNjnH9qdBKu8DsTFyVwG3gmeEl2rKjZNu +FSrlb4qk3fzxDp9oHEsw +=wyxf +-----END PGP SIGNATURE----- diff --git a/sys-cluster/ganglia_jobmonarch/files/job_monarch_link.sh b/sys-cluster/ganglia_jobmonarch/files/job_monarch_link.sh new file mode 100644 index 000000000..dfcbfea4f --- /dev/null +++ b/sys-cluster/ganglia_jobmonarch/files/job_monarch_link.sh @@ -0,0 +1,64 @@ +#!/bin/sh + +install() { + cd /var/www/localhost/htdocs/$1 + mkdir addons; mkdir addons/job_monarch; cd addons/job_monarch + ln /var/www/localhost/htdocs/$2/addons/job_monarch/cal.gif + ln /var/www/localhost/htdocs/$2/addons/job_monarch/conf.php + ln /var/www/localhost/htdocs/$2/addons/job_monarch/document_archive.jpg + ln /var/www/localhost/htdocs/$2/addons/job_monarch/footer.php + ln /var/www/localhost/htdocs/$2/addons/job_monarch/graph.php + ln /var/www/localhost/htdocs/$2/addons/job_monarch/header.php + ln /var/www/localhost/htdocs/$2/addons/job_monarch/host_view.php + ln /var/www/localhost/htdocs/$2/addons/job_monarch/image.php + ln /var/www/localhost/htdocs/$2/addons/job_monarch/index.php + ln /var/www/localhost/htdocs/$2/addons/job_monarch/jobmonarch.gif + ln /var/www/localhost/htdocs/$2/addons/job_monarch/libtoga.js + ln /var/www/localhost/htdocs/$2/addons/job_monarch/libtoga.php + ln /var/www/localhost/htdocs/$2/addons/job_monarch/logo_ned.gif + ln /var/www/localhost/htdocs/$2/addons/job_monarch/next.gif + ln /var/www/localhost/htdocs/$2/addons/job_monarch/overview.php + ln /var/www/localhost/htdocs/$2/addons/job_monarch/prev.gif + ln /var/www/localhost/htdocs/$2/addons/job_monarch/redcross.jpg + ln /var/www/localhost/htdocs/$2/addons/job_monarch/search.php + ln /var/www/localhost/htdocs/$2/addons/job_monarch/styles.css + ln /var/www/localhost/htdocs/$2/addons/job_monarch/ts_picker.js + ln /var/www/localhost/htdocs/$2/addons/job_monarch/ts_validatetime.js + ln /var/www/localhost/htdocs/$2/addons/job_monarch/version.php + + mkdir clusterconf; cd clusterconf + ln /var/www/localhost/htdocs/$2/addons/job_monarch/clusterconf/example.php + cd .. + + mkdir templates; cd templates + ln /var/www/localhost/htdocs/$2/addons/job_monarch/templates/footer.tpl + ln /var/www/localhost/htdocs/$2/addons/job_monarch/templates/header.tpl + ln /var/www/localhost/htdocs/$2/addons/job_monarch/templates/host_view.tpl + ln /var/www/localhost/htdocs/$2/addons/job_monarch/templates/index.tpl + ln /var/www/localhost/htdocs/$2/addons/job_monarch/templates/overview.tpl + ln /var/www/localhost/htdocs/$2/addons/job_monarch/templates/search.tpl + ln -s ../../../templates/default/images + + cd /var/www/localhost/htdocs/$1 + mkdir templates/job_monarch; cd templates/job_monarch + ln /var/www/localhost/htdocs/$2/templates/job_monarch/cluster_extra.tpl + ln /var/www/localhost/htdocs/$2/templates/job_monarch/host_extra.tpl + ln -s ../default/images +} + +uninstall() { + rm -Rf /var/www/localhost/htdocs/$1/addons/job_monarch/* && rmdir /var/www/localhost/htdocs/$1/addons/job_monarch && rmdir /var/www/localhost/htdocs/$1/addons + rm -Rf /var/www/localhost/htdocs/$1/templates/job_monarch/* && rmdir /var/www/localhost/htdocs/$1/templates/job_monarch +} + +case "$1" in + install) + install $2 $3 + ;; + uninstall) + uninstall $2 + ;; + *) + echo -e "\033[34;1mUsage: job_monarch_link.sh [ install <ganglia_dir> <jobmonarch_dir> | uninstall <ganglia_dir> ]\033[0m" + ;; +esac diff --git a/sys-cluster/ganglia_jobmonarch/files/jobarchived.initd b/sys-cluster/ganglia_jobmonarch/files/jobarchived.initd new file mode 100644 index 000000000..e1de75d0b --- /dev/null +++ b/sys-cluster/ganglia_jobmonarch/files/jobarchived.initd @@ -0,0 +1,28 @@ +#!/sbin/runscript +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +PIDFILE=/var/run/jobarchived.pid + +depend() { + need gmond +} + +start() { + ebegin "Starting Jobarchived" + start-stop-daemon --start --exec /sbin/jobarchived.py -- -p ${PIDFILE} -c /etc/jobarchived.conf + eend 0 +} + +stop() { + ebegin "Stopping Jobarchived" + start-stop-daemon --stop --quiet --signal TERM -p ${PIDFILE} + eend $? +} + +restart() { + svc_stop + sleep 3 + svc_start +} +# vim:ts=4 diff --git a/sys-cluster/ganglia_jobmonarch/files/jobmond.initd b/sys-cluster/ganglia_jobmonarch/files/jobmond.initd new file mode 100644 index 000000000..619495c8b --- /dev/null +++ b/sys-cluster/ganglia_jobmonarch/files/jobmond.initd @@ -0,0 +1,28 @@ +#!/sbin/runscript +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +PIDFILE=/var/run/jobmond.pid + +depend() { + need gmond +} + +start() { + ebegin "Starting Jobmond" + start-stop-daemon --start --exec /sbin/jobmond.py -- -p ${PIDFILE} -c /etc/jobmond.conf + eend 0 +} + +stop() { + ebegin "Stopping Jobmond" + start-stop-daemon --stop --quiet --signal TERM -p ${PIDFILE} + eend $? +} + +restart() { + svc_stop + sleep 3 + svc_start +} +# vim:ts=4 diff --git a/sys-cluster/ganglia_jobmonarch/ganglia_jobmonarch-0.3.1.ebuild b/sys-cluster/ganglia_jobmonarch/ganglia_jobmonarch-0.3.1.ebuild new file mode 100644 index 000000000..b7e0e1d67 --- /dev/null +++ b/sys-cluster/ganglia_jobmonarch/ganglia_jobmonarch-0.3.1.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="4" + +WEBAPP_OPTIONAL="yes" +inherit eutils webapp depend.php + +DESCRIPTION="Ganglia addons for Torque" +HOMEPAGE="https://subtrac.sara.nl/oss/jobmonarch/" +SRC_URI="ftp://ftp.sara.nl/pub/outgoing/jobmonarch/latest/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="vhosts" +WEBAPP_MANUAL_SLOT="yes" + +GANGLIA="ganglia" +JOBMONARCH="ganglia_jobmonarch" + +DEPEND=" + sys-cluster/ganglia + dev-lang/php[gd,xml,ctype] + media-libs/gd + sys-cluster/pbs-python + dev-python/pypgsql + ${WEBAPP_DEPEND}" + +pkg_setup() { + webapp_pkg_setup +} + +src_compile() { + einfo "Nothing to do" +} + +src_install() { + insinto /etc + doins "${S}/jobmond/jobmond.conf" + doins "${S}/jobarchived/jobarchived.conf" + + insinto /usr/share/jobmonarch/ + doins "${S}/jobarchived/job_dbase.sql" + + dodir /var/lib/jobarchive + + insopts -m0755 + insinto /sbin + doins "${S}/jobmond/jobmond.py" + doins "${S}/jobarchived/jobarchived.py" + doins "${S}/jobarchived/pipe_jobarchived.py" + doins "${FILESDIR}/job_monarch_link.sh" + + newinitd "${FILESDIR}/jobmond.initd" jobmond + newinitd "${FILESDIR}/jobarchived.initd" jobarchived + + cd "${S}/web/templates/job_monarch/" + rm images/* + rmdir images + + cd "${S}" + webapp_src_preinst + insinto "${MY_HTDOCSDIR}" + doins -r web/* + + webapp_configfile "${MY_HTDOCSDIR}"/addons/job_monarch/conf.php + webapp_src_install + + ewarn + ewarn "You must Execute: job_monarch_link.sh install ${GANGLIA} ${JOBMONARCH} to have the JobMonArch installed under ganglia" + ewarn + ewarn "You must Execute: job_monarch_link.sh uninstall ${GANGLIA} to remove link from ganglia directories" + ewarn +} diff --git a/sys-cluster/ganglia_jobmonarch/metadata.xml b/sys-cluster/ganglia_jobmonarch/metadata.xml new file mode 100644 index 000000000..081af556e --- /dev/null +++ b/sys-cluster/ganglia_jobmonarch/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>cluster</herd> +</pkgmetadata> diff --git a/sys-cluster/mpe2/ChangeLog b/sys-cluster/mpe2/ChangeLog index 492e81894..9db3fa6c5 100644 --- a/sys-cluster/mpe2/ChangeLog +++ b/sys-cluster/mpe2/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sys-cluster/mpe2 -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> mpe2-1.0.6_p1.ebuild: + Added fortran-2.eclass support + 16 Dec 2010; Justin Lecher <jlec@gentoo.org> mpe2-1.0.6_p1.ebuild: Removal of fortran.eclass, #348851 diff --git a/sys-cluster/mpe2/Manifest b/sys-cluster/mpe2/Manifest index cc46a2530..cb7d2ee4d 100644 --- a/sys-cluster/mpe2/Manifest +++ b/sys-cluster/mpe2/Manifest @@ -4,13 +4,13 @@ Hash: SHA1 AUX slog2sdk-trace_rlog-makefile-fixes.patch 2734 RMD160 43e2aa5c7b83fce702e27d21c87dbbfbb00c7f4f SHA1 1077071d79b20bfec3a4ba7ab0be3724d2aa5ab8 SHA256 015ac2a9bed7d84a9e101c437b54c689e79f293c318e022a1d6884ed3571545e AUX slog2sdk-trace_sample-makefile-fixes.patch 2746 RMD160 a64dd4d6f574297b533d6631762ab9b022a74c26 SHA1 d370094c222b983d336c40302d4075735c268461 SHA256 e611b08f6c7a2cdccee7d37075ff1f8ab4bce84458b40bc859c87f541d54fd2a DIST mpe2-1.0.6p1.tar.gz 9313216 RMD160 1c52f379c3fff4bac5c68505ca657584d8092f7f SHA1 bc810c7a1f3ef5b9cf2563278053afadbc2029f2 SHA256 23cfef2b8a0a27408b5bdadeb216ba3adb3b02bf40d0fa6fc0a110cefd8c5863 -EBUILD mpe2-1.0.6_p1.ebuild 3571 RMD160 9fcad4bd252d32197b508266a16dc8758c004929 SHA1 67425b9290014d519c9674ddd6a430fb923a2830 SHA256 add09d9240fcd318a2af28f019d07734899928cf177a0d26f6edcdc8ec16d498 -MISC ChangeLog 460 RMD160 29139f15de615b4a6b99ba4f54a34ceaee89146d SHA1 ed8237c6f41c398d84b8403515ff7b377712b8ba SHA256 05623605f1317938b64f7cb8d73f176d2944e988cacc878a2aee75cd7e9e86d8 +EBUILD mpe2-1.0.6_p1.ebuild 3603 RMD160 f60c0c716d000da3207edafbdcbedde3ba5094c2 SHA1 5a048276e81079e5f1b6096f226a23adccc76cb9 SHA256 b2c822ab0c2d5ab231b0ef67eeec752f8ada2bd90f8b27db7b2b5613f8045112 +MISC ChangeLog 563 RMD160 b6b011305c4a3b38efcc2094f0a3680d50c8ef61 SHA1 65e6e529c1a5c3a04d9c9a0267ca506f85401ceb SHA256 0fd742b5c2a966b00b16d65ca76810e7f814c2315c4bff880c61fadaf60f8f0d MISC metadata.xml 259 RMD160 3288242cfd053d6b014e4d69d02f37eac4e8ca75 SHA1 15229a4dacc8a1d795b2e19612c45b61d64ad280 SHA256 51ab93c579e7aa6293a3478a36318bca710b3a79d6008a77643495fa2af1526b -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk0KOPgACgkQgAnW8HDreRaYXwCgncFZIvyyiC8xEj2uc4zZs9dH -L8EAoKKjDZ86wo/gz5r4Pc5q7DJJWMBh -=M1p1 +iEYEARECAAYFAk4EuUsACgkQgAnW8HDreRYADACeOgCX7YcGk7BrofXijOTbdQiT +nlsAnjse1A5fGbuN7UUbuYSEoEm6JqHM +=DNMF -----END PGP SIGNATURE----- diff --git a/sys-cluster/mpe2/mpe2-1.0.6_p1.ebuild b/sys-cluster/mpe2/mpe2-1.0.6_p1.ebuild index dfe639ded..73b088728 100644 --- a/sys-cluster/mpe2/mpe2-1.0.6_p1.ebuild +++ b/sys-cluster/mpe2/mpe2-1.0.6_p1.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ MPI_PKG_NEED_IMPS="openmpi mpich2" -inherit eutils java-utils-2 mpi + +inherit eutils fortran-2 java-utils-2 mpi MY_P=${P/_/} DESCRIPTION="MPI development tools" @@ -13,7 +14,7 @@ SRC_URI="ftp://ftp.mcs.anl.gov/pub/mpi/${PN%2}/${MY_P}.tar.gz" LICENSE="as-is" SLOT="0" KEYWORDS="~amd64" -IUSE="minimal fortran threads debug" +IUSE="debug fortran minimal threads" COMMON_DEPEND="$(mpi_pkg_deplist) !minimal? ( x11-libs/libXtst @@ -36,6 +37,7 @@ MPE_IMP="" # correctly in preperation. pkg_setup() { + fortran-2_pkg_setup local i MPE_IMP=$(mpi_pkg_base_imp) diff --git a/sys-cluster/mpich2/ChangeLog b/sys-cluster/mpich2/ChangeLog index dd19de233..a50bc0072 100644 --- a/sys-cluster/mpich2/ChangeLog +++ b/sys-cluster/mpich2/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> mpich2-1.2.1_p1-r2.ebuild, + mpich2-1.4_rc2-r1.ebuild: + Added fortran-2.eclass support + *mpich2-1.4_rc2-r1 (12 Jun 2011) 12 Jun 2011; Justin Bronder <jsbronder@gentoo.org> -mpich2-1.4_rc2.ebuild, diff --git a/sys-cluster/mpich2/Manifest b/sys-cluster/mpich2/Manifest index 3c4066f91..87286a1c1 100644 --- a/sys-cluster/mpich2/Manifest +++ b/sys-cluster/mpich2/Manifest @@ -15,14 +15,14 @@ AUX mpich2-1.2.1-fix-missing-libs.patch 1825 RMD160 aec1251aa66f0d63c5848920c633 AUX mpich2-1.3-libtvmpich2.so-respect-user-LDFLAGS.patch 1053 RMD160 e38a0c503bde8b66cd1d7efbeb674f14e0008a8d SHA1 f5691827c39a9bbf01c4c7e13d5fdf4aa1774558 SHA256 a0e79be986c29cc5aa1b0abb1bba27dc368a530d632a332e8701e9c02967224e DIST mpich2-1.2.1p1.tar.gz 18014859 RMD160 810cc486b65e4bcf977ac8d96ccbbcea87e0cbaa SHA1 26bd5620b45bc654aa3945755d11450be63d650c SHA256 a55d1682ee0b5ebbacc047f60620ed291e0a9b3ded3eaeb6a2c81a1598c4c964 DIST mpich2-1.4rc2.tar.gz 19764158 RMD160 2d5cbac33cd728ba0fb6b74d2fcd7f166f1bfc1e SHA1 53afd67e0527e0c1459330d70d7077a1da52fe0f SHA256 820fc929bd349a9b4e6ce4a2fa5e3b88b3abf6941a147f6921e3ab44f4a6015a -EBUILD mpich2-1.2.1_p1-r2.ebuild 4999 RMD160 e3003de505a38998e0163603fbedb6314ed2046d SHA1 eb17186e8ff543febad806e28acc8a6b358c14be SHA256 9a394130ebdc6c55ca6443fa66df14b5ee877b57eac1999db7760c4368542386 -EBUILD mpich2-1.4_rc2-r1.ebuild 3982 RMD160 658adbdb4c212b277457cc7e5f573189eee385f2 SHA1 e77c260c91ebaa474a325f075932ce42287c846e SHA256 8b499d5e5595fc5b64967d726bcdde797e9639c1829c3055bcfda20c42246e28 -MISC ChangeLog 5124 RMD160 451e7e19b4947d8af0544b85fe7479e3f596aa37 SHA1 040fbe058ad8ab3a3905b7d1aacfa856968cadae SHA256 2e883c71a9d65ebe5c2f973afc9b488e8336eb3015da1205ed812420a797e7fc +EBUILD mpich2-1.2.1_p1-r2.ebuild 5030 RMD160 b947f8a8fa374d4e49a407d212a61fdd20986e61 SHA1 264fa061d136685befd2637272510b2298f05ccb SHA256 48abd33f82ce7728c4fe2010c58fce7718e0e50ff0242f4d44d4781532a51a43 +EBUILD mpich2-1.4_rc2-r1.ebuild 4013 RMD160 2c50cdeeb7e33a3a4b305e55fd3a971ebac9a9de SHA1 f168cb1c108d2dbef6f8a8db02500bb19c81ddb0 SHA256 0951b54d17a90d7aa3101339e5569cb686a1a05f438ccc047d6654107e8aacac +MISC ChangeLog 5260 RMD160 dc912e3718b457ef68af2daf7f5cf659de4cc0b4 SHA1 b500f722ec2ae0a8358cb4b8bed5f650d98945a7 SHA256 921389a08b5464df754cc2c7e496e384a133262137d04c3238f3a2b40272864c MISC metadata.xml 534 RMD160 8d4fa7f5f4860a520e58b3866b2a2fdc04ab6d83 SHA1 60bc1b41a847e2f9fbf527b204fcafc054d04d33 SHA256 763dc9199c817bb987335dcdddcc65de5f419410aac2f027fc9a2208e91f5c0a -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk31Pi8ACgkQ4MrvBE1wQ8nhAwCeKEsSxR9Wwuys7DurVOqjvfAI -EX0An3EfkM7EbJaY1nIbycjEEINNxTpC -=5GLO +iEYEARECAAYFAk4EuVQACgkQgAnW8HDreRaDSgCeLxYb7V3dhFB+cItVF+HS5k+b +G9gAn1MgtgOkjcbdPs8Fj3oldbIGXTx+ +=o0CQ -----END PGP SIGNATURE----- diff --git a/sys-cluster/mpich2/mpich2-1.2.1_p1-r2.ebuild b/sys-cluster/mpich2/mpich2-1.2.1_p1-r2.ebuild index ae50b1128..eca3941fc 100644 --- a/sys-cluster/mpich2/mpich2-1.2.1_p1-r2.ebuild +++ b/sys-cluster/mpich2/mpich2-1.2.1_p1-r2.ebuild @@ -5,7 +5,7 @@ EAPI=2 PYTHON_DEPEND="2" -inherit eutils python mpi toolchain-funcs +inherit eutils fortran-2 mpi python toolchain-funcs MY_PV=${PV/_/} DESCRIPTION="MPICH2 - A portable MPI implementation" @@ -15,7 +15,7 @@ SRC_URI="http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/${MY LICENSE="as-is" SLOT="0" KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" -IUSE="+cxx debug doc fortran threads romio mpi-threads" +IUSE="+cxx debug doc fortran mpi-threads romio threads" MPI_UNCLASSED_DEP_STR="!media-sound/mpd" @@ -32,6 +32,7 @@ RDEPEND="${COMMON_DEPEND}" S="${WORKDIR}"/${PN}-${MY_PV} pkg_setup() { + fortran-2_pkg_setup python_set_active_version 2 python_pkg_setup diff --git a/sys-cluster/mpich2/mpich2-1.4_rc2-r1.ebuild b/sys-cluster/mpich2/mpich2-1.4_rc2-r1.ebuild index ddfe4b567..04ef15e41 100644 --- a/sys-cluster/mpich2/mpich2-1.4_rc2-r1.ebuild +++ b/sys-cluster/mpich2/mpich2-1.4_rc2-r1.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI=2 -inherit eutils mpi toolchain-funcs autotools +inherit autotools eutils fortran-2 mpi toolchain-funcs MY_PV=${PV/_/} DESCRIPTION="MPICH2 - A portable MPI implementation" @@ -13,7 +13,7 @@ SRC_URI="http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/${MY LICENSE="as-is" SLOT="0" KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~x86" -IUSE="+cxx debug doc fortran threads romio mpi-threads" +IUSE="+cxx debug doc fortran mpi-threads romio threads" COMMON_DEPEND="dev-libs/libaio >=sys-apps/hwloc-1.1.1 @@ -29,6 +29,7 @@ RDEPEND="${COMMON_DEPEND}" S="${WORKDIR}"/${PN}-${MY_PV} pkg_setup() { + fortran-2_pkg_setup MPI_ESELECT_FILE="eselect.mpi.mpich2" if use mpi-threads && ! use threads; then diff --git a/sys-cluster/nullmpi/ChangeLog b/sys-cluster/nullmpi/ChangeLog index 5f8d4df2b..f0f7252ce 100644 --- a/sys-cluster/nullmpi/ChangeLog +++ b/sys-cluster/nullmpi/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Christoph Junghans <ottxor@gentoo.org> nullmpi-9999.ebuild: + migrate to git-2 + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> nullmpi-0.7.ebuild, + nullmpi-9999.ebuild, metadata.xml: + migrate from 'git' to 'git-2' + *nullmpi-9999 (23 Jan 2011) 23 Jan 2011; Christoph Junghans <kleiner_otti@gmx.de> diff --git a/sys-cluster/nullmpi/Manifest b/sys-cluster/nullmpi/Manifest index 648615540..7e7de7f30 100644 --- a/sys-cluster/nullmpi/Manifest +++ b/sys-cluster/nullmpi/Manifest @@ -1,16 +1,6 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - AUX nullmpi-0.7-libtool.patch 1817 RMD160 5e5f928c71001c88f65306cc2db7bb98ad820038 SHA1 3bc54307cfac738862e8c8078e308831e601394a SHA256 dea202626599d20abf50c985a9b5b49620a145b32e5c90bf5e6562bd2f1be047 DIST nullmpi-0.7.tar.gz 148188 RMD160 feb30a64fdaf4555626e73ae3250d43e59abeffa SHA1 9a27e4b85d6675f763cc65ef70bdb6dff860ffb6 SHA256 88d6d09db717e22627fa7f225225f807d9315e611b903d2076ab0c83e74c8c96 -EBUILD nullmpi-0.7.ebuild 703 RMD160 f6588ba79159310680e602bb06ba8c1d8d44e346 SHA1 77d8c5954815bff347d2df288f11f5a0b30c5156 SHA256 786e895e0d95edbb95a72b46fa0c2b210c448b4aa60e21f063bdb890a26b393a -EBUILD nullmpi-9999.ebuild 701 RMD160 9fb6552f6330a2ecb2a4ae4899766cec4581dc6e SHA1 6ac1b4c7467dde0ffb02f6e263f669397519037f SHA256 c029abab19c73d3e8f57ae86c3f2f2ce39f51c0071b49981f4ef7f9116b3966e -MISC ChangeLog 535 RMD160 dc36db5fe35f340e5a87f3ffbc61f404efc19f4c SHA1 65c3f6b283fcb83abcb1173ace1a236431bd4941 SHA256 07a3710a4aa499a9692af30f46c639139ad6cd219c2f94a73fcf0fb8b3844551 -MISC metadata.xml 260 RMD160 53721e225895b3319360cd54759b0e5efb4b9d8a SHA1 8d26a53b300a15a73bc60b1e7da9e47cf042adaa SHA256 9f9291f05e38c47805dde0df950d68ce440730ad3976c651769dde186d846245 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) - -iEYEARECAAYFAk08XpEACgkQy0OE/ans1/kTVACcDDPzK9JjhvfbTTVoyrBhTuj8 -d0AAn0HSPouk8l3nfaaGnzfdgB5BJmah -=E0Nu ------END PGP SIGNATURE----- +EBUILD nullmpi-0.7.ebuild 675 RMD160 93cbe1d8def1a452c1e07f996a0acd2b43264e6f SHA1 9f54c6a1f14fe80fa62407c6b676a48767a4199f SHA256 06f99c5251ea44cbba63b716cf060724546eab5d24580f324d6f6de479421b4b +EBUILD nullmpi-9999.ebuild 601 RMD160 39e44491f49ef068484f073394a28638ac2af329 SHA1 1b32a573845455c3374c0aebb01731123ed50e1d SHA256 f42b902c2dc643c52b82340aef0ec39399bd121da694e0e4406595481af23c03 +MISC ChangeLog 767 RMD160 99a1cc41977a08a6c41f9e91c492070684fdf86b SHA1 4d409fa101d1198345d5f2fb2810fe4d8e62a5de SHA256 dbcd6f94cee959ad384dd4b9de8875ba21a87420421fc90a868c23ccbbaee2b8 +MISC metadata.xml 261 RMD160 803549c8dea5076513b626bd5f7bc30d98ae9aed SHA1 844661dd5d01619d641f6274718761c5ade3bbaf SHA256 efa4f30b31af6be6e8aafc0481c6144e5deebb4cded1d589ef8f644bc1043d16 diff --git a/sys-cluster/nullmpi/metadata.xml b/sys-cluster/nullmpi/metadata.xml index f46da0d09..e4c1734ee 100644 --- a/sys-cluster/nullmpi/metadata.xml +++ b/sys-cluster/nullmpi/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>cluster</herd> + <herd>cluster</herd> <maintainer> <email>kleiner_otti@gmx.de</email> <name>Christoph Junghans</name> diff --git a/sys-cluster/nullmpi/nullmpi-0.7.ebuild b/sys-cluster/nullmpi/nullmpi-0.7.ebuild index efd9147a4..bc15b1a13 100644 --- a/sys-cluster/nullmpi/nullmpi-0.7.ebuild +++ b/sys-cluster/nullmpi/nullmpi-0.7.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 inherit autotools-utils @@ -15,8 +15,9 @@ SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="static-libs" -RDEPEND="!sys-cluster/mpich +RDEPEND=" !sys-cluster/lam-mpi + !sys-cluster/mpich !sys-cluster/mpich2 !sys-cluster/mpiexec" @@ -28,5 +29,5 @@ PATCHES=( "${FILESDIR}/${P}-libtool.patch" ) src_prepare() { autotools-utils_src_prepare - eautoreconf || die "eautoreconf failed" + eautoreconf } diff --git a/sys-cluster/nullmpi/nullmpi-9999.ebuild b/sys-cluster/nullmpi/nullmpi-9999.ebuild index 0df256372..1fb4fc4e3 100644 --- a/sys-cluster/nullmpi/nullmpi-9999.ebuild +++ b/sys-cluster/nullmpi/nullmpi-9999.ebuild @@ -2,12 +2,13 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 EGIT_REPO_URI="git://github.com/olenz/NullMPI.git" EGIT_BRANCH="master" +EGIT_BOOTSTRAP="eautoreconf" -inherit autotools-utils git +inherit autotools-utils git-2 DESCRIPTION="MPI substitute library" HOMEPAGE="http://wissrech.ins.uni-bonn.de/research/projects/nullmpi/" @@ -18,18 +19,12 @@ SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="static-libs" -RDEPEND="!sys-cluster/mpich +RDEPEND=" !sys-cluster/lam-mpi + !sys-cluster/mpich !sys-cluster/mpich2 !sys-cluster/mpiexec" DEPEND="${RDEPEND}" -DOCS=( AUTHORS ChangeLog README TODO ) - -S="${WORKDIR}/${EGIT_REPO_URI##*/}" - -src_prepare() { - autotools-utils_src_prepare - eautoreconf || die "eautoreconf failed" -} +DOCS=( AUTHORS NEWS README TODO ) diff --git a/sys-cluster/openmpi/ChangeLog b/sys-cluster/openmpi/ChangeLog index 1a5a8ff37..8224a9205 100644 --- a/sys-cluster/openmpi/ChangeLog +++ b/sys-cluster/openmpi/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> openmpi-1.5.3.ebuild: + Added fortran-2.eclass support + 28 Mar 2011; Justin Bronder <jsbronder@gentoo.org> -files/openmpi-1.4.1-r22513.patch, +files/openmpi-r24328.patch, openmpi-1.5.3.ebuild: diff --git a/sys-cluster/openmpi/Manifest b/sys-cluster/openmpi/Manifest index db5898e4e..2fa2d00aa 100644 --- a/sys-cluster/openmpi/Manifest +++ b/sys-cluster/openmpi/Manifest @@ -4,13 +4,13 @@ Hash: SHA1 AUX eselect.mpi.openmpi 225 RMD160 cf81165864aaad2833f7a8300c20376210a575dd SHA1 8b50b90346b52b831a59ec0abd8e3dbebad2b94e SHA256 df4d363e9fbab74c234b75f426b7f38ef83d16da2b099222c0dde4a2c3ece687 AUX openmpi-r24328.patch 1707 RMD160 4db5f60d692268e1e42ebbc5379cec245b14daa5 SHA1 25a3ac77307b4681e3f917e61ff88daa58dab508 SHA256 3149f47463057e3263a242b2df88b588074f07395d437b585c5ce37f84aadf83 DIST openmpi-1.5.3.tar.bz2 7589097 RMD160 c1d0950c9a5c53c8543838adadf6a7477abe3989 SHA1 669565c708deab82ad4069d82675b2020eb0e0c6 SHA256 70745806cdbe9b945d47d9fa058f99e072328e41e40c0ced6dd75220885c5263 -EBUILD openmpi-1.5.3.ebuild 3080 RMD160 4e482cbd034eb65427d2453cc1ae50afdd6ce0d5 SHA1 54cc5216c0094bffab4c1bbe849678e876a1d54d SHA256 67530c2d9172ba89ed5093783440af7c1d08b34429dda230710571043707dae7 -MISC ChangeLog 4117 RMD160 c8dca40ba9e0467cd56994e332dbb26f6b9923c2 SHA1 8b17d306d67417c83ca185447dafd9bcf30d9913 SHA256 ac3bf5229f83c6438730cfea55f2495b84fd95bd8606203fea201061fecda402 +EBUILD openmpi-1.5.3.ebuild 3085 RMD160 d009491b1fd14c6c02bbbcf8d511ba393e501ed9 SHA1 5c99d8a3ae9f3a53a40ea273445641c37c1dab81 SHA256 6b5451c54c26e829e54d6891f965cd328fceb25c4feaad1d5875066ee2ff32a3 +MISC ChangeLog 4220 RMD160 d0b11190f1952e8637c2b78f03ac3feb341ff8ca SHA1 cdcfcb71df57204a1d2389240185ee9dce61ba93 SHA256 c6feb34229728e5a1e6fbdbe0df315b299dd1177bceced4f988146871d0e476c MISC metadata.xml 656 RMD160 223aeb0c645345a35fc674e30cc9f17d936db762 SHA1 f0af00a84589ada70477d0fa12afe21c57a16071 SHA256 809b9f410e784da55e240612ca9542e718f25f65819acda4b3429b22114619e6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2Qvo4ACgkQ4MrvBE1wQ8kTFQCgj30m+GpKF3T58fbdbxthe2Hx -ANcAn2TlY1STINh+hjm5Px+mBGxljA83 -=dckP +iEYEARECAAYFAk4EucUACgkQgAnW8HDreRZfzgCgtNgpb3Hzg21shzmGCBv9c1J7 +2EAAn2iP3elThV2LJH3WTz1clij8Ctka +=a9w7 -----END PGP SIGNATURE----- diff --git a/sys-cluster/openmpi/openmpi-1.5.3.ebuild b/sys-cluster/openmpi/openmpi-1.5.3.ebuild index 16643c4c6..b69bc6b6d 100644 --- a/sys-cluster/openmpi/openmpi-1.5.3.ebuild +++ b/sys-cluster/openmpi/openmpi-1.5.3.ebuild @@ -3,7 +3,7 @@ # $Header: /var/cvsroot/gentoo-x86/sys-cluster/openmpi/openmpi-1.2.4.ebuild,v 1.2 2007/12/13 22:39:53 jsbronder Exp $ EAPI=3 -inherit eutils multilib flag-o-matic toolchain-funcs mpi +inherit eutils flag-o-matic fortran-2 mpi multilib toolchain-funcs MY_P=${P/-mpi} S=${WORKDIR}/${MY_P} @@ -13,8 +13,8 @@ HOMEPAGE="http://www.open-mpi.org" SRC_URI="http://www.open-mpi.org/software/ompi/v1.5/downloads/${MY_P}.tar.bz2" LICENSE="BSD" SLOT="0" -KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86" -IUSE="+cxx elibc_FreeBSD fortran heterogeneous ipv6 infiniband mpi-threads pbs romio threads vt" +KEYWORDS="~amd64 ~x86" +IUSE="+cxx elibc_FreeBSD fortran heterogeneous infiniband ipv6 mpi-threads pbs romio threads vt" MPI_UNCLASSED_DEP_STR=" vt? ( !dev-libs/libotf @@ -28,6 +28,7 @@ RDEPEND="pbs? ( sys-cluster/torque ) DEPEND="${RDEPEND}" pkg_setup() { + fortran-2_pkg_setup MPI_ESELECT_FILE="eselect.mpi.openmpi" if use mpi-threads; then diff --git a/sys-cluster/scalasca/ChangeLog b/sys-cluster/scalasca/ChangeLog index c842f1b11..b62632f47 100644 --- a/sys-cluster/scalasca/ChangeLog +++ b/sys-cluster/scalasca/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> scalasca-1.3.3.ebuild: + Added fortran-2.eclass support + *scalasca-1.3.3 (04 Apr 2011) 04 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -scalasca-1.3.2.ebuild, diff --git a/sys-cluster/scalasca/Manifest b/sys-cluster/scalasca/Manifest index 31fa69426..db9fe04bb 100644 --- a/sys-cluster/scalasca/Manifest +++ b/sys-cluster/scalasca/Manifest @@ -2,17 +2,13 @@ Hash: SHA1 DIST scalasca-1.3.3.tar.gz 5670414 RMD160 8b6c5a3974bb2447dba8577690ff163204468a7b SHA1 3cbe955bfe339bf383fe986b432732bb126f546a SHA256 a11a1fd2671035ec09c102ebb1029a3be14646ade2eb57a311b3e788e3f3472c -EBUILD scalasca-1.3.3.ebuild 2210 RMD160 3d6367f0fa4f466ab1f2a4c5a66de7d0ab58490b SHA1 e51470be91f2dc0d04f0bc6d7cf7d0e5c89413d1 SHA256 9942847b75b090cc95cac22d6940acce49e75721738b3d796b6f3f32f0828e28 -MISC ChangeLog 1730 RMD160 e68860bb0aad8a3c91b1c1aef5404de400b5be1b SHA1 e4229c459104631d178c8276556f0f4c234a463b SHA256 29c126eb14db0d14d30faa2836d1e7ad3613c457a05ac7f90e88f47ff7cf93ab +EBUILD scalasca-1.3.3.ebuild 2220 RMD160 fb903e0c9b5cc8855ac65c1af981a73210dc9a24 SHA1 90dab7670be2a8a84d803552783ddd8f9936732c SHA256 73337c65abea4484465ef6cbba3492f8467c2c4aa2f879e15ba07e7480f226f3 +MISC ChangeLog 1834 RMD160 d17be2797bf02f561f38b18393f28e1ac812fd9f SHA1 9a1dfc33fef6c5ed3e74f9505ed9d75b6093a7a7 SHA256 3157e1a8ddc67f9f7faca03b739115038827beb94ec5e53efd0884272817224a MISC metadata.xml 259 RMD160 c1c6c9a5b60a0af8d2472da02078ce98a1d445f6 SHA1 6d0e4e46ffdd6b697bd77ffa555ef612426408e4 SHA256 f515b404dda594fee3c71ca911656a7647c40538be1759103329ca935bae39d8 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iQEcBAEBAgAGBQJNquZ5AAoJEOeBhlrCAAWGkvUH/2Ooa0bcnpO/IXDlzVTz3+cH -ALHzThkWqsp4PGuL+Ox+692hf5y37hswie5gObxRsAXlFy5A2ALQdwUnxCvWQJW9 -qIhbddYc4dIz41pQox7lx7UcyfL9gKZHJrP/mvTATaXhe/Vf5jl49RE/5sThpx4e -9Cqj6GH3U/vnQuTI8bM6bHmyXxRt+T4YwMQ3NawlWIgGdfAxgXcEptpnZ90ZP2MO -sxLDHCNr9GdKVxZOtOxGBQGwKiU0KKkPG9srSyFnnQ4q3KBeoXxVXq0T3tE5OIT+ -kxYgsx3gf0yQICfgh+rIqH86yja3vB/m/CcvVe3TgLQLTO9sa0oawCfTU5Dh5I4= -=qTOe +iEYEARECAAYFAk4Afp4ACgkQgAnW8HDreRbdJwCdF2AnyDaTXlhdugzqMbDP+nSh +MiEAnRD1I/xGplxWdTeS/ykQjS49T20v +=+19R -----END PGP SIGNATURE----- diff --git a/sys-cluster/scalasca/scalasca-1.3.3.ebuild b/sys-cluster/scalasca/scalasca-1.3.3.ebuild index 8a6607563..75817c3f7 100644 --- a/sys-cluster/scalasca/scalasca-1.3.3.ebuild +++ b/sys-cluster/scalasca/scalasca-1.3.3.ebuild @@ -4,7 +4,7 @@ EAPI="4" -inherit eutils toolchain-funcs +inherit eutils fortran-2 toolchain-funcs DESCRIPTION="Scalable Performance Analysis of Large-Scale Applications" HOMEPAGE="http://www.scalasca.org" diff --git a/sys-devel/spl/Manifest b/sys-devel/spl/Manifest index e55a1eea3..8677759df 100644 --- a/sys-devel/spl/Manifest +++ b/sys-devel/spl/Manifest @@ -1,25 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA1 AUX spl-0.6.0-includedir.patch 1179 RMD160 cade3b696d6981b2583cc5ae8ecf614d38ef2efc SHA1 2c5ce007df75a7a8425e1a28308eefdcb29446c2 SHA256 8d05fc006348264e1633e14b73e022d482164d6cefc8d2425faffc50d2346150 DIST spl-0.6.0-rc4.tar.gz 428187 RMD160 13693caaff47dc5b852348b243ce519176580f2b SHA1 90c1d6d2fd621301f8aa87f7ee3e28c711db9b77 SHA256 2091ceb306e190c3bddb96df98fa9d165820f5f62ed3109e6b50e82ed002486a -EBUILD spl-0.6.0_rc4.ebuild 997 RMD160 bfd85e9c40654892fbd6f5bc32e961e6737a25c8 SHA1 70b42b028039f74654bdc641b2bcfd71ed3e44a9 SHA256 711bc2f9666d78a484adb2dbe621251a9fa86019dc6077f3dbaf6b46283fcbfc -EBUILD spl-9999.ebuild 959 RMD160 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WANT_AUTOMAKE="1.11" AT_M4DIR=./config # for aclocal called by eautoreconf -inherit linux-info eutils autotools +inherit autotools eutils linux-info DESCRIPTION="Solaris Porting Layer - a Linux kernel module providing some Solaris kernel APIs" HOMEPAGE="http://wiki.github.com/behlendorf/spl/" diff --git a/sys-devel/spl/spl-9999.ebuild b/sys-devel/spl/spl-9999.ebuild index 1d9ffaec3..bb3c60914 100644 --- a/sys-devel/spl/spl-9999.ebuild +++ b/sys-devel/spl/spl-9999.ebuild @@ -6,7 +6,7 @@ EAPI="2" WANT_AUTOMAKE="1.11" AT_M4DIR=./config # for aclocal called by eautoreconf -inherit git-2 linux-info eutils autotools +inherit autotools eutils git-2 linux-info DESCRIPTION="Solaris Porting Layer - a Linux kernel module providing some Solaris kernel APIs" HOMEPAGE="http://wiki.github.com/behlendorf/spl/" diff --git a/sys-devel/ucpp/Manifest b/sys-devel/ucpp/Manifest index e7a64de5d..f58fc295d 100644 --- a/sys-devel/ucpp/Manifest +++ b/sys-devel/ucpp/Manifest @@ -3,13 +3,13 @@ Hash: SHA1 AUX tune.h.patch 723 RMD160 411f358400f0c0a8f813e25f580f69b22bf759d3 SHA1 022f30c77266c9b4c0773e9bdf54296503570971 SHA256 27bdbc0e81ba1c60b4f069b6a05eedb44445d4768b2a5808e53117a7ed7e7871 DIST ucpp-1.3.tar.bz2 73958 RMD160 08f9ef1ada15c7451b7966733fb0a63bbe6b179a SHA1 12caf535986e3919d58c47ca35ae9ed4efaa1cf0 SHA256 d0a51c20040385b143f15fc08eefec6119773fb07232a14c08bbb49cb1c5f1fa -EBUILD ucpp-1.3.ebuild 679 RMD160 1146d76562b98f359c9bdc50576837bcb32a9384 SHA1 fdddc3af4efb91d3ae6d6c640606befcdd9e927f SHA256 af0b3757c2dd31da017cb3517c1c3e730399c5620c704182d02ccf4c9d634111 +EBUILD ucpp-1.3.ebuild 679 RMD160 532b7c5e391823e31fed386986ec226d597a432d SHA1 5d4ed0b064db619a2513175ff603bf7bde0d5ad1 SHA256 60bc54eb43a28f1ae834ba8c71f9a4266a18ee36c3099b5e09d82c2f2f2104a1 MISC ChangeLog 363 RMD160 eb1cf5a5381c54b50ff78ba4ebd6a3235d84a1cf SHA1 87b9ff7b57ce16e2d368306d007137bd135ff459 SHA256 58f1024b6da9925a18fd2c6421cd9190e4eec9bd65c085b2f4e24e9a56936bca MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk0nS0IACgkQgAnW8HDreRbOdgCg0Mxi6VxWxzB+lWPuB3h/koN1 -KewAoMweLB8JuYlVmGpiEOoBELeEfAtY -=yHs1 +iEYEARECAAYFAk4Euc4ACgkQgAnW8HDreRaqgACeK3Uyu4nfGXY95Lx+qGtHXZ1L +hecAoM0d7n6fOQ2uryyNfdHxEj76Dpv8 +=t9dK -----END PGP SIGNATURE----- diff --git a/sys-devel/ucpp/ucpp-1.3.ebuild b/sys-devel/ucpp/ucpp-1.3.ebuild index 1a62875c4..93085f9c4 100644 --- a/sys-devel/ucpp/ucpp-1.3.ebuild +++ b/sys-devel/ucpp/ucpp-1.3.ebuild @@ -4,7 +4,7 @@ EAPI="2" -inherit toolchain-funcs eutils +inherit eutils toolchain-funcs DESCRIPTION="A quick and light preprocessor, but anyway fully compliant to C99" HOMEPAGE="http://code.google.com/p/ucpp/" diff --git a/sys-fs/ocfs2-tools/ChangeLog b/sys-fs/ocfs2-tools/ChangeLog deleted file mode 100644 index 98dbc5038..000000000 --- a/sys-fs/ocfs2-tools/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sys-fs/ocfs2-tools -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 07 Mar 2011; Justin Lecher <jlec@gentoo.org> ocfs2-tools-1.4.4.ebuild, - +metadata.xml: - QA things - - 07 Mar 2011; Justin Lecher <jlec@gentoo.org> ocfs2-tools-1.4.4.ebuild: - Correct Slots for gtk 3 introduction to tree - diff --git a/sys-fs/ocfs2-tools/Manifest b/sys-fs/ocfs2-tools/Manifest index 1aee99ca3..69ed1b92e 100644 --- a/sys-fs/ocfs2-tools/Manifest +++ b/sys-fs/ocfs2-tools/Manifest @@ -1,18 +1,14 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 -AUX INSTALL.GENTOO 3672 RMD160 a817d6776be70f0ae773e24c224cecaf969b8993 SHA1 19e4bf7d2c0b246e1869f75cc0fb6a77b722033a SHA256 e1d415009a5cfbd021b24278c2c90485123c8159e68f88965acfbdaba75baedd -AUX gcc45-ftbfs.patch 807 RMD160 6e90024195735b7daa93a71f07ee80cd3e1677ed SHA1 fdbb4b1a9aeefd1151f926913d301fd178a6cb7f SHA256 416893dcab5d3aa92a1c9dc1b4c83201ef914c159533c1f1f0a37f35cf2c347d -AUX ocfs2.conf 917 RMD160 168922889cfb017e903634fb51116d1812e0a0f6 SHA1 a61a1a0247c340b09a7279b664e9a02f49ba7f5f SHA256 36f2d2b229773bffed94cb75029cd752e900e99762b95adbf3f11df9952e824b -AUX ocfs2.init 4214 RMD160 da27d35e471b712ca793f4d1ddfb96a036e6516b SHA1 6afef117ba3e0643fcd1855eaad215300f9040ba SHA256 32f725401ffd34fd015371fa7c50985c6a7a9251eac6cc47621b8ec5af2b59b8 -DIST ocfs2-tools-1.4.4.tar.gz 713145 RMD160 353733c6a7e17b1aba17d9d22546311eec4a02f6 SHA1 fd36df819a0677c5de8d7d59c804fb6cfa862d82 SHA256 fcfcce1057830c1975d57effc25cc78f3099be0c9e35ea92a9b9dbb185946530 -EBUILD ocfs2-tools-1.4.4.ebuild 1748 RMD160 5731c1383fed20666e3602e93bbdbdfdf506e152 SHA1 46502f8225af651cbfae49eec719d6e53f38b78f SHA256 27d66519332e357698fa3ea6ac1f13b97b20fb7ff94bf913cb30b991580342c0 -MISC ChangeLog 343 RMD160 bfeabe2b0e383fc842beffd703365a9186991147 SHA1 0684d438483ded06bc1eee5e72164d9fd604435d SHA256 a2338846f4381099e00ba0a174dab015d6b8d2d94d150fd0a94adac85c30ba44 -MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c +AUX ocfs2.init 4016 RMD160 3130241aee4014da821bf8b4b82a5004104697f4 SHA1 266895bb161daf3eca0d0f4b4fc3c9783a1bab8e SHA256 70be03610424926e4882a64f4530923f05ee882e7d9f6e242f8cde538665c275 +DIST ocfs2-tools-1.6.4.tar.gz 823914 RMD160 c8b65f4c26017e257c4190322d6df64e9ef7925b SHA1 1409a13f63b55457a474c5f5662260e420452ee9 SHA256 dda9db208312e3e5f4f55ee77e66e7b35b9cc10421bc02065a6c168e42b24755 +EBUILD ocfs2-tools-1.6.4.ebuild 1309 RMD160 99efb72953f654785dab35d650668006efc09bf0 SHA1 41e6c9332ec53cda148cf994d5851f82f77639eb SHA256 4e8f8063e924ee77aaf0c9a07277d802a4f7728ee9e404ac0e4348bb29605ae2 +MISC metadata.xml 282 RMD160 44cf28de660ee14ba14807a7c794e8527c49f435 SHA1 de84d24c38b1b661fb21d35bdd08702d1b522dc8 SHA256 616826b107b0ccaef8100ce70985e1d4f7c3f4d77bab9b83924da538df1002c9 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk10vOUACgkQgAnW8HDreRad1gCfTk6gz4bfcPuVLjztpivBzjyt -poAAoJZJb9y+UfoZkdAjiwkDM9Ob+LcZ -=ZWQC +iEYEARECAAYFAk4EudMACgkQgAnW8HDreRZ7pACfcrf4lN1NrX2yAEfN8yISWa5d +6ccAnj5aOhRvip6GGHVdYrlK+gqn+EZ+ +=Osd5 -----END PGP SIGNATURE----- diff --git a/sys-fs/ocfs2-tools/files/INSTALL.GENTOO b/sys-fs/ocfs2-tools/files/INSTALL.GENTOO deleted file mode 100644 index e05485c68..000000000 --- a/sys-fs/ocfs2-tools/files/INSTALL.GENTOO +++ /dev/null @@ -1,103 +0,0 @@ -Installing, configuring and running OCFS2 on Gentoo Linux - - -INSTALLING -========== -Step 1 - Inserting modules --------------------------- -Add 'ocfs2', 'configfs' to your /etc/modules.autoload.d/kernel-2.6 file: -# echo "ocfs2" >> /etc/modules.autoload.d/kernel-2.6 -# echo "configfs" >> /etc/modules.d/autoload.d/kernel-2.6 -# update-modules - -Step 2 - Mounting the pseudo-filesystems ----------------------------------------- -add mountpoints for configfs and dlmfs to /etc/fstab -# echo "none /sys/kernel/config configfs defaults 0 0" >> /etc/fstab -# echo "none /dlm ocfs2_dlmfs defaults 0 0" >> /etc/fstab - -Step 3 - Addding ocfs2 to default runlevel ------------------------------------------- -# rc-update add ocfs2 default - - -CONFIGURING -=========== -Step 1 - Edit your cluster.conf -------------------------------- -Edit /etc/ocfs2/cluster.conf and add your nodes. One node can be a member -of many cluster, so repeat the config for each node/cluster pair. In the case of -a multicluster node, "ip_port" must be different for every cluster. -You can also use ocfs2console for this task, if you compiled with USE=X. - -Step 2 - Copy config to other nodes ------------------------------------ -Make sure that every node in cluster(s) has an identical config file. - -Step 3 - Update /etc/conf.d/ocfs2 ---------------------------------- -Add names of cluster(s) in which this node belongs to the OCFS2_CLUSTERS list. - -Also, if you're running firewall on your nodes, make sure you've read -"Firewall restrictions" below. - -RUNNING -======= - -Notes about adding nodes while online -------------------------- -*DON'T* add nodes to /etc/ocfs2/cluster.conf while the cluster is online. -Use /sbin/o2cb_ctl instead, e.g.: - -# /sbin/o2cb_ctl -C -n <node_name> -t node -a number=<node_number> \ - -a ip_address=<ip_address> -a ip_port=<port> -a cluster=<clustername> - -If the complete cluster is down, you may add nodes to /etc/ocfs2/cluster.conf, -but make sure you end up with *SAME* cluster.conf on every node. - -For a complete reference, check files in this directory -as well as http://oss.oracle.com/projects/ocfs2 -You have been warned. - -Also, if you're running a firewall on your nodes, make sure you've read the -following section. - -Firewall restrictions ---------------------- -Logically, allow all nodes to connect to each other via specified port(s). -If you used 7777 as a port for communication, issue: - -# iptables -I INPUT 1 -m state --state ESTABLISHED,RELATED -j ACCEPT -# iptables -N OCFS2_NODES -# iptables -A OCFS2_NODES -s <node_ip_address> -j ACCEPT -(repeat former command for every node) -# iptables -A OCFS2_NODES -j DROP -# iptables -A INPUT -p tcp --dport 7777 -m state --state NEW -j OCFS2_NODES -# /etc/init.d/iptables save - -You should do this on every node. - -KNOWN BUGS -========== -1. Init script does not have all the funtionality of the o2cb script ----------------------------------------------------------------- -I know that, but o2cb script doesn't use "depend" and therefore its start -can't be controlled inside runlevels. I had to rewrite major portions of it -to make it Gentoo-friendly. o2cb is still available, and if you need -additional functionality from /etc/init.d/ocfs2, file a bug report (see -"Reporting Bugs" below). - -2. Booting off the ocfs2 cluster doesn't work ---------------------------------------------- -... or at least, isn't tested. If someone wants to play with it, I'd be -happy to incorporate any ideas or experiences. - -REPORTING BUGS -============== -Open a bug at http://bugs.gentoo.org and add laza@yu.net into the CC list. -If the problem is within my powers, I'll fix it, if not, I'll -escalate it to ocfs2 developers. - ---- -05. Aug 2005. -Lazar Obradovic diff --git a/sys-fs/ocfs2-tools/files/gcc45-ftbfs.patch b/sys-fs/ocfs2-tools/files/gcc45-ftbfs.patch deleted file mode 100644 index 0db24f49e..000000000 --- a/sys-fs/ocfs2-tools/files/gcc45-ftbfs.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -urN ocfs2-tools-1.4.3.orig//mount.ocfs2/mount.ocfs2.c ocfs2-tools-1.4.3/mount.ocfs2/mount.ocfs2.c ---- ocfs2-tools-1.4.3.orig//mount.ocfs2/mount.ocfs2.c 2009-04-14 00:10:40.000000000 +0200 -+++ ocfs2-tools-1.4.3/mount.ocfs2/mount.ocfs2.c 2010-03-24 07:23:45.000000000 +0100 -@@ -261,7 +261,7 @@ - char *extra = NULL; - int dev_ro = 0; - char *hbstr = NULL; -- char stackstr[strlen(OCFS2_CLUSTER_STACK_ARG) + OCFS2_STACK_LABEL_LEN + 1] = ""; -+ char stackstr[strlen(OCFS2_CLUSTER_STACK_ARG) + OCFS2_STACK_LABEL_LEN + 1]; - ocfs2_filesys *fs = NULL; - struct o2cb_cluster_desc cluster; - struct o2cb_region_desc desc; -@@ -269,6 +269,8 @@ - int hb_started = 0; - struct stat statbuf; - -+ stackstr[0] = '\0'; -+ - initialize_ocfs_error_table(); - initialize_o2dl_error_table(); - initialize_o2cb_error_table(); diff --git a/sys-fs/ocfs2-tools/files/ocfs2.conf b/sys-fs/ocfs2-tools/files/ocfs2.conf deleted file mode 100644 index 5217769a4..000000000 --- a/sys-fs/ocfs2-tools/files/ocfs2.conf +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 1999-2006 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sys-fs/ocfs2-tools/files/ocfs2.conf,v 1.1 2006/07/20 05:13:14 dberkholz Exp $ - -# Put your cluster names here, separated by space, ie. -# OCFS2_CLUSTER="cluster1 admincluster cluster2" -OCFS2_CLUSTER="ocfs2" - -# Some heartbeat tweaks to prevent self-fencing quite so much during heavy load. -# http://oss.oracle.com/projects/ocfs2/dist/documentation/ocfs2_faq.html - -# How long to wait before a node is considered dead from lack of network activity. -OCFS2_IDLE_TIMEOUT_MS="30000" -# How often we should attempt to send heartbeats. -OCFS2_KEEPALIVE_DELAY_MS="2000" -OCFS2_RECONNECT_DELAY_MS="2000" -# How often we should attempt to send heartbeats. -# How many interations before a node is considered dead from lack of IO activity. -# (dead_threshold - 1) * 2s -OCFS2_DEAD_THRESHOLD="31" diff --git a/sys-fs/ocfs2-tools/files/ocfs2.init b/sys-fs/ocfs2-tools/files/ocfs2.init index f454d4495..631c9bf91 100644 --- a/sys-fs/ocfs2-tools/files/ocfs2.init +++ b/sys-fs/ocfs2-tools/files/ocfs2.init @@ -1,7 +1,7 @@ #!/sbin/runscript -# Copyright 1999-2006 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sys-fs/ocfs2-tools/files/ocfs2.init,v 1.1 2006/07/20 05:13:14 dberkholz Exp $ +# $Header: $ depend() { need net localmount @@ -55,8 +55,7 @@ check_pseudofs() { ewarn "One or more pseudo-filesystes are not mounted." ewarn "Make sure you have following lines in your /etc/fstab:" ewarn "none /sys/kernel/config configfs defaults 0 0" - ewarn "none /dlm ocfs2_dlmfs defaults 0 0" - ewarn "For a (in)complete documentation, read /usr/share/doc/ocfs-<version>/INSTALL.GENTOO.bz2" + ewarn "none /sys/kernel/dlm ocfs2_dlmfs defaults 0 0" fi return ${retval} } diff --git a/sys-fs/ocfs2-tools/metadata.xml b/sys-fs/ocfs2-tools/metadata.xml index efb490d78..38074683a 100644 --- a/sys-fs/ocfs2-tools/metadata.xml +++ b/sys-fs/ocfs2-tools/metadata.xml @@ -5,4 +5,7 @@ <maintainer> <email>sci@gentoo.org</email> </maintainer> +<use> + <flag name='external'>Enable external locking</flag> +</use> </pkgmetadata> diff --git a/sys-fs/ocfs2-tools/ocfs2-tools-1.4.4.ebuild b/sys-fs/ocfs2-tools/ocfs2-tools-1.4.4.ebuild deleted file mode 100644 index 150093fa5..000000000 --- a/sys-fs/ocfs2-tools/ocfs2-tools-1.4.4.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="3" - -PYTHON_DEPEND="2" - -inherit eutils python - -PV_MAJOR="${PV%%.*}" -PV_MINOR="${PV#*.}" -PV_MINOR="${PV_MINOR%%.*}" - -DESCRIPTION="Support programs for the Oracle Cluster Filesystem 2" -HOMEPAGE="http://oss.oracle.com/projects/ocfs2-tools/" -SRC_URI="http://oss.oracle.com/projects/ocfs2-tools/dist/files/source/v${PV_MAJOR}.${PV_MINOR}/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="X" - -# (#142216) build system's broke, always requires glib for debugfs utility -RDEPEND=" - dev-libs/glib:2 - sys-cluster/openais - sys-cluster/dlm-lib - sys-cluster/cman-lib - sys-fs/e2fsprogs - X? ( - x11-libs/gtk+:2 - dev-python/pygtk:2 - )" -DEPEND="${RDEPEND}" - -pkg_setup() { - python_set_active_version 2 -} - -src_prepare() { - epatch "${FILESDIR}/gcc45-ftbfs.patch" -} - -src_configure() { - #local myconf="--enable-dynamic-fsck --enable-dynamic-ctl" - - econf \ - $(use_enable X ocfs2console) \ - ${myconf} -} - -src_install() { - emake DESTDIR="${D}" install || die "Failed to install" - - dodoc \ - COPYING CREDITS MAINTAINERS README README.O2CB debugfs.ocfs2/README \ - documentation/users_guide.txt documentation/samples/cluster.conf \ - documentation/ocfs2_faq.txt "${FILESDIR}"/INSTALL.GENTOO \ - vendor/common/o2cb.init vendor/common/o2cb.sysconfig - - # Move programs not needed before /usr is mounted to /usr/sbin/ - newinitd "${FILESDIR}"/ocfs2.init ocfs2 - newconfd "${FILESDIR}"/ocfs2.conf ocfs2 - - insinto /etc/ocfs2 - newins "${S}"/documentation/samples/cluster.conf cluster.conf -} - -pkg_postinst() { - elog "Read ${ROOT}usr/share/doc/${P}/INSTALL.GENTOO* for instructions" - elog "about how to install, configure and run ocfs2." -} diff --git a/sys-fs/ocfs2-tools/ocfs2-tools-1.6.4.ebuild b/sys-fs/ocfs2-tools/ocfs2-tools-1.6.4.ebuild new file mode 100644 index 000000000..f8431e2cd --- /dev/null +++ b/sys-fs/ocfs2-tools/ocfs2-tools-1.6.4.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 +PYTHON_DEPEND="gtk? 2" +inherit base python versionator + +DESCRIPTION="Support programs for the Oracle Cluster Filesystem 2" +HOMEPAGE="http://oss.oracle.com/projects/ocfs2-tools/" +SRC_URI="http://oss.oracle.com/projects/${PN}/dist/files/source/v$(get_version_component_range 1-2)/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug external gtk" + +RDEPEND=" + sys-apps/util-linux + sys-cluster/cman-lib + external? ( + || ( sys-cluster/corosync sys-cluster/openais sys-cluster/dlm-lib ) + ) + sys-fs/e2fsprogs + sys-libs/ncurses + sys-libs/readline + sys-process/psmisc + gtk? ( + dev-python/pygtk + ) +" +# 99% of deps this thing has is automagic +# specialy cluster things corosync/pacemaker +DEPEND="${RDEPEND}" + +DOCS=( + "${S}/documentation/samples/cluster.conf" + "${S}/documentation/users_guide.txt" +) + +MAKEOPTS+=" -j1" + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_configure() { + econf \ + $(use_enable debug debug) \ + $(use_enable debug debugexe) \ + $(use_enable gtk ocfs2console) \ + --enable-dynamic-fsck \ + --enable-dynamic-ctl +} + +src_install() { + emake DESTDIR="${D}" install || die + newinitd "${FILESDIR}/ocfs2.init" ocfs2 || die +} diff --git a/sys-fs/zfs/Manifest b/sys-fs/zfs/Manifest index c379eb0ec..62c68a770 100644 --- a/sys-fs/zfs/Manifest +++ b/sys-fs/zfs/Manifest @@ -1,26 +1,16 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA1 AUX zfs-0.6.0-includedir.patch 586 RMD160 eb4cc6a9d66721e70c932b1dd640abd852d5470d SHA1 c673e057008b4cb7d4c45b936533e9bceff2443c SHA256 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c42c5cc57c32e698682eaf5cb9502011d770f34611d2933aab75fc7983da3998 MISC metadata.xml 160 RMD160 1233ca29861ca7c47f0b09d1d7a29def80f7df02 SHA1 1bfdc9d282a84c95e2bdcda19ace5b94e2e67349 SHA256 56717bdb03ad5d833acecfbc612a67f569256b328bf610fbc6cc33714186dae9 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBCAAGBQJNzsBFAAoJEOf+E+/4L5LmjPgP/1mBU0Pon1RnKbpZroMwiXi3 -lFht9q1mXvLUL2kZl/uijyd4YpI+jilrLrLEuSTPku0RTaw8yAXZ2l/qEYdWTC5l -EzBmU9D1HxPoeUCOc7o76LFsnsAhO8VUT4fv7J7VoFiFpW1GNcbPGti4lkqwZz5Y -bVrB2KfBbk47NYurXut5Pdpus/uaOag5jRAgI9DC2dl+hTsTEbbE4F6FYTfseizK -TRDo7fLAUXvCFM9PyfrCXSa04BdFZ8AbjpJhTB0e3oW9A/WLscy4Fa5dJJb4INTq -cAhdlDmeaqx0L/ldXBtYJ0IpZbS8hewOYHZJzmR8E/5mSqmjUfzTsiAEsj+ueIZ7 -eKDT7jz4aRnUZCDAhjHmZDYihw9QPDbruSqmhVL6UXSlCUG5FLI8tsrbe+jIvAaB -0w05fbNDHchbpmYaNofB2Z0GF+87KsQXgZo8ucyeYVhF8In2dxZbWQ7wiW7pExpJ -s17j0M31KPCFBiKuVj/s7IHMaL5+UcMcpHl0AT0grd9LGqYZmCJdPJ4heriDnxKT -EX9K5cOoFV0R+4lFvf1KFQexPpOhC/TMioD58YC4LVlJa8osmT3Djpntpx0q1uJB 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Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> libsdp-1.1.99.ebuild, + libsdp-1.1.99-r1.ebuild, metadata.xml: + Cleaned ebuild + *libsdp-1.1.99-r1 (20 Aug 2009) 20 Aug 2009; Alexey Shvetsov <alexxy@gentoo.org> +libsdp-1.1.99-r1.ebuild: diff --git a/sys-infiniband/libsdp/Manifest b/sys-infiniband/libsdp/Manifest index 3b761b83b..ee9b05620 100644 --- a/sys-infiniband/libsdp/Manifest +++ b/sys-infiniband/libsdp/Manifest @@ -1,6 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST OFED-1.4.1.tgz 65180617 RMD160 748e669a1a5aef90dd9cec3e8fce110d0051a3cd SHA1 e558bb16c414e0f40727ac046cbd80a3fc84c87f SHA256 5e73c9ead49f286ef68d1618a042b5101887cf0f8c66fbfea5a8a7648feee1e6 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee -EBUILD libsdp-1.1.99-r1.ebuild 442 RMD160 39597c3165ec00ed86145ce831f52e037283f244 SHA1 398f457490ab8d4d7e1e73c83c90bc754c228cb7 SHA256 674c7f2882cbd7a728a140ebb3f99566a0ee51328833f92f54ad9b186b527378 -EBUILD libsdp-1.1.99.ebuild 439 RMD160 240fc496d44d0d2cdc447ac42f3bc04dfa5298b7 SHA1 b5e5a967690b597731f3a18bddc872cc2eda1598 SHA256 a87f7fe695f516492ecdca88eb0777ce463991d30ee153689afee70090e8e1d7 -MISC ChangeLog 477 RMD160 d4d4a5421331327a8cf0a1443e0a7a738ee029a9 SHA1 fa5832bdee9307af281653eebccebdce07a1422d SHA256 22140d73e81d1be8c766c63288fbcc11f6e4d80fa9a06a5d843b8c7439b3b9d1 -MISC metadata.xml 394 RMD160 7b931750b94fec4eb68e8af81367a330572e65cc SHA1 99bba2f1b65d3bb0c9acb110b1f094910f3211b4 SHA256 ee18115d70440110f81c65f3220beaf2dc625049875515b2716a6e31093dbb12 +EBUILD libsdp-1.1.99-r1.ebuild 285 RMD160 c21af5bdeb51025648f129c5e182a7a4cf506aa7 SHA1 a67fd2860ff698776a3dbfe9454b38df5c659e5f SHA256 546d831d149d6756d5c020bf6a69e721b5fb964642587bd1b08ca34031d57403 +EBUILD libsdp-1.1.99.ebuild 281 RMD160 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@@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 OFED_VER="1.4.1" OFED_SUFFIX="1.ofed1.4.1" inherit openib -DESCRIPTION="OpenIB library that enables Socket Direct Protocol for unmodified applications" +DESCRIPTION="Socket Direct Protocol for unmodified applications" KEYWORDS="~amd64 ~x86" IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" - -src_install() { - make DESTDIR="${D}" install || die "install failed" - dodoc README ChangeLog -} diff --git a/sys-infiniband/libsdp/libsdp-1.1.99.ebuild b/sys-infiniband/libsdp/libsdp-1.1.99.ebuild index 69a2557b9..ead00d2d4 100644 --- a/sys-infiniband/libsdp/libsdp-1.1.99.ebuild +++ b/sys-infiniband/libsdp/libsdp-1.1.99.ebuild @@ -1,23 +1,14 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 OFED_VER="1.4" OFED_SUFFIX="1.ofed1.4" inherit openib -DESCRIPTION="OpenIB library that enables Socket Direct Protocol for unmodified applications" +DESCRIPTION="Socket Direct Protocol for unmodified applications" KEYWORDS="~amd64 ~x86" IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" - -src_install() { - make DESTDIR="${D}" install || die "install failed" - dodoc README ChangeLog -} - diff --git a/sys-infiniband/libsdp/metadata.xml b/sys-infiniband/libsdp/metadata.xml index ff86e9832..9590598de 100644 --- a/sys-infiniband/libsdp/metadata.xml +++ b/sys-infiniband/libsdp/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>cluster</herd> -<longdescription> + <herd>cluster</herd> + <longdescription> libsdp is a LD_PRELOAD-able library that can be used to migrate existing applications use InfiniBand Sockets Direct Protocol (SDP) instead of TCP sockets, transparently and without recompilations. diff --git a/sys-infiniband/openib-diags/ChangeLog b/sys-infiniband/openib-diags/ChangeLog index 16f97b91c..bf0242506 100644 --- a/sys-infiniband/openib-diags/ChangeLog +++ b/sys-infiniband/openib-diags/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sys-infiniband/openib-diags -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + openib-diags-1.4.4_p20081207.ebuild, openib-diags-1.4.4_p20090314.ebuild, + metadata.xml: + Cleaned ebuild + *openib-diags-1.4.4_p20090314 (20 Aug 2009) 20 Aug 2009; Alexey Shvetsov <alexxy@gentoo.org> diff --git a/sys-infiniband/openib-diags/Manifest b/sys-infiniband/openib-diags/Manifest index 3b91232ff..cf5f4542d 100644 --- a/sys-infiniband/openib-diags/Manifest +++ b/sys-infiniband/openib-diags/Manifest @@ -1,7 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + AUX openib-diags-1.4.4_p20081207-remove-osmv.patch 11381 RMD160 e84bae73e8866736c6ae50c354a7fde0ada8c9c0 SHA1 d7016beba804524b00cdceb0d5b5f03703186f7f SHA256 35d9b5fe53c003e51cf4942808f06364647622fee6030f22ece3f2115984621a DIST OFED-1.4.1.tgz 65180617 RMD160 748e669a1a5aef90dd9cec3e8fce110d0051a3cd SHA1 e558bb16c414e0f40727ac046cbd80a3fc84c87f SHA256 5e73c9ead49f286ef68d1618a042b5101887cf0f8c66fbfea5a8a7648feee1e6 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee -EBUILD openib-diags-1.4.4_p20081207.ebuild 637 RMD160 507b1b18bf2fcd6c611c5e7999b08756d65f95e5 SHA1 41c5eb16406c1d412b04e6421c1ce2efaa0dca1b SHA256 e44056acc67c38c2475daed69987ec1e433071528be3cbd3d23a78df6a01a81a -EBUILD openib-diags-1.4.4_p20090314.ebuild 590 RMD160 d10bf5dd21a21e9d35e4e3971c4a6022ba5f3f82 SHA1 d05d995e432be625a869b16df353af38a3c87a8a SHA256 87deea13d51567dee9454897adb67da179a946756dc916088d49decd09d28910 -MISC ChangeLog 1095 RMD160 377ff9c12dcd9572b157fbdff0a43d82bcb517b4 SHA1 134d01d3e28d75304746d87898ba985e8d3b282c SHA256 3cb52444d6ef605ecad473c56b6adbbb0fe908235487148ae4cfdcc554949abf -MISC metadata.xml 269 RMD160 313528b9b250be3cefa43fe1e6ae748c039d23ff SHA1 2b1efb89864ecc3dc8688cfff7c17cfe450a9c8b SHA256 84569c739f3fca7d8afe1d90bc7c700cd5435f3101ae16800e1a8af3a4711eee +EBUILD openib-diags-1.4.4_p20081207.ebuild 559 RMD160 11b85be15a2c5a877e2d9083bcaa67a4c0696465 SHA1 30e00a47883a6909a5a490735494f635746f63df SHA256 a7547bea86b9966372ce743caedf9a2f8f4a7ffeb5596ed07f01f7b4c25c0d97 +EBUILD openib-diags-1.4.4_p20090314.ebuild 514 RMD160 c4033599483322db5719ce9c65d63b6241c0aa2a SHA1 4a9f865d9acf05dd27a6fb538ce1932c03fc7f52 SHA256 6887c83322e91700421ee594ff93cbe972a61c206381382c3f34a2caef8013e8 +MISC ChangeLog 1252 RMD160 9d46dff647bc63ada76bf4dd80ba3bb2081ad0de SHA1 82c5ab13e4855b7db1ead8d1fff7bec9392529af SHA256 b221f0521a8bf164a872c2b14167480283e6b0ff31e47ba370fa115f59c90088 +MISC metadata.xml 271 RMD160 beb05a63fc99556443f6576c9abb6669b87940f8 SHA1 90e3621c3650c316fb6c80f2458686b19e7060fb SHA256 6cff21d05f51f76f9f7e0a2e17feafbba2bf9b7fea9053f517ac7873b7ed6594 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GFdwACgkQgAnW8HDreRasBACfWirEaozdDUS9pdHxpfww8FdE +QTgAoM04p42jshEEaw9JJsFLnpk2f8M/ +=XQLH +-----END PGP SIGNATURE----- diff --git a/sys-infiniband/openib-diags/metadata.xml b/sys-infiniband/openib-diags/metadata.xml index 95dca1aae..05102b86d 100644 --- a/sys-infiniband/openib-diags/metadata.xml +++ b/sys-infiniband/openib-diags/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>cluster</herd> -<longdescription> + <herd>cluster</herd> + <longdescription> OpenIB diagnostic programs and scripts needed to diagnose an IB subnet. </longdescription> </pkgmetadata> diff --git a/sys-infiniband/openib-diags/openib-diags-1.4.4_p20081207.ebuild b/sys-infiniband/openib-diags/openib-diags-1.4.4_p20081207.ebuild index 21eac5567..2347d7127 100644 --- a/sys-infiniband/openib-diags/openib-diags-1.4.4_p20081207.ebuild +++ b/sys-infiniband/openib-diags/openib-diags-1.4.4_p20081207.ebuild @@ -1,27 +1,23 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 OFED_VER="1.4" OFED_SUFFIX="1.ofed1.4" inherit openib -DESCRIPTION="OpenIB diagnostic programs and scripts needed to diagnose an IB subnet." +DESCRIPTION="OpenIB diagnostic programs and scripts needed to diagnose an IB subnet" KEYWORDS="~x86 ~amd64" IUSE="" -DEPEND=">=sys-infiniband/libibcommon-1.1.2_p20081020 - >=sys-infiniband/libibumad-1.2.3_p20081118 - >=sys-infiniband/libibmad-1.2.3_p20081118 - >=sys-infiniband/openib-osm-3.2.5_p20081207" +DEPEND=" + =sys-infiniband/libibcommon-1.1.2_p20081020 + >=sys-infiniband/libibumad-1.2.3_p20081118 + >=sys-infiniband/libibmad-1.2.3_p20081118 + >=sys-infiniband/openib-osm-3.2.5_p20081207" RDEPEND="${DEPEND}" PATCHES=( "${FILESDIR}/${P}-remove-osmv.patch" ) - -src_install() { - make DESTDIR="${D}" install || die "install failed" -} - diff --git a/sys-infiniband/openib-diags/openib-diags-1.4.4_p20090314.ebuild b/sys-infiniband/openib-diags/openib-diags-1.4.4_p20090314.ebuild index a94d4ef6e..acfe19df3 100644 --- a/sys-infiniband/openib-diags/openib-diags-1.4.4_p20090314.ebuild +++ b/sys-infiniband/openib-diags/openib-diags-1.4.4_p20090314.ebuild @@ -1,24 +1,21 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 OFED_VER="1.4.1" OFED_SUFFIX="1.ofed1.4.1" inherit openib -DESCRIPTION="OpenIB diagnostic programs and scripts needed to diagnose an IB subnet." +DESCRIPTION="OpenIB diagnostic programs and scripts needed to diagnose an IB subnet" KEYWORDS="~x86 ~amd64" IUSE="" -DEPEND=">=sys-infiniband/libibcommon-1.1.2_p20090314 - >=sys-infiniband/libibumad-1.2.3_p20090314 - >=sys-infiniband/libibmad-1.2.3_p20090314 - >=sys-infiniband/openib-osm-3.2.5_p20090314" +DEPEND=" + >=sys-infiniband/libibcommon-1.1.2_p20090314 + >=sys-infiniband/libibumad-1.2.3_p20090314 + >=sys-infiniband/libibmad-1.2.3_p20090314 + >=sys-infiniband/openib-osm-3.2.5_p20090314" RDEPEND="${DEPEND}" - -src_install() { - make DESTDIR="${D}" install || die "install failed" -} diff --git a/sys-infiniband/openib-drivers/Manifest b/sys-infiniband/openib-drivers/Manifest index abccdeba7..438454834 100644 --- a/sys-infiniband/openib-drivers/Manifest +++ b/sys-infiniband/openib-drivers/Manifest @@ -1,8 +1,18 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX openib 26019 RMD160 982d998e407973205b268311cf653650208338e6 SHA1 a0e88afc64cea2d33952783440bf65810527e265 SHA256 0dce134380e646be283ab406758ec07ee162a6d0504ef81373bb8f3a39ab6208 AUX openib.modprobe 350 RMD160 a40e8656ee1bdfc26a86b65aa3eaf5553a93b7b8 SHA1 623adbeccde3e88ce2c39d113a409c4d14091f0d SHA256 32054c7ee7caffc21ed320a9be5d0c2cd85e51295c0515521373d658f55ee68e DIST OFED-1.2.5.1.tgz 46256516 RMD160 b19f1917b32b7b15db75aace6ed433d57dc98fc5 SHA1 9a1ff30c97c94352f70e52d7cc31328013bea1b7 SHA256 41c6408135d8707d05bef8aa0a4ec548ae64ec010224e3b38746ab6f5c1e9b78 DIST OFED-1.2.5.5.tgz 46432282 RMD160 f5829858fca521d8675af1245d4764eeb87ff08d SHA1 faa027109b56583207eca9fd736164517acf7120 SHA256 ffb990b22d7b0f25026d9fe785aa97ca5920b5a0e620851deb057b9b83bbf907 -EBUILD openib-drivers-1.2.5.1.ebuild 6406 RMD160 b8459225d680696839a1150630c0d32b89473412 SHA1 ebecc32afc71bafdd0c7634e06814c7d49b19929 SHA256 82e5cfd66852e2f2a98673b6bf41587d29e616e746e51641b0f968d75af29080 -EBUILD openib-drivers-1.2.5.5.ebuild 3939 RMD160 522f4a4aa54041e0f2bd2d66f90e72ba8c41e1ae SHA1 ae7d218df3c765b08b76876ae7c20b289062318c SHA256 6ff86989c1230c6fc89d5aa649d0e3bce93c9f1fc76e26a1d8048be772ef7bb8 +EBUILD openib-drivers-1.2.5.1.ebuild 6406 RMD160 993261ee5cdf68e55fb91a4b08903a829239030e SHA1 ac9b3efa7f698da60c41faf4de45f6933a25da57 SHA256 e14bd98547359c99899e410d57703d7619a33065ba36ebf58677b8e098281ae8 +EBUILD openib-drivers-1.2.5.5.ebuild 3939 RMD160 386b8c0e89121fe3ec33d0eb01d627166d887608 SHA1 f2e5b09a1d4fbb1b6b1113db08b778184ac704c8 SHA256 36b582159684760c9d6f990bb729ae3e85c173f0f6ccdd9d02a5ae54cd34232c MISC ChangeLog 895 RMD160 6263ab0ef045e071ca9d22b36c056668b31d5b54 SHA1 a513ed90637419a9a51ffed37d25909430a17646 SHA256 1861f1f31364b459b68a2d62975861c0b87c234fdb8e419ab24d7174fc16c43e -MISC metadata.xml 220 RMD160 d33d570d49f634b36df8f6c179b8385e25562a56 SHA1 fffa23cb3edea7fe576a0d0e470df5750547f1cb SHA256 50078f776034343d365347ef90d5a0eb49faf851ed7f46e12cf9ce71e4cb5ea7 +MISC metadata.xml 1231 RMD160 4473f9d2a46305a1041a636b5ac79625796c878f SHA1 86189fe137f400954955e6b6b63130169755a206 SHA256 878c33613ae2619fb930ac5e83d747b56789895d585184196386da8ca708a86e +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EuvwACgkQgAnW8HDreRbO3gCgkN54yJedzZEYTwvIem7ZkMrq +mTUAoKWudMiqLc7xNW7sFuRftJ9/E5Ck +=4FlU +-----END PGP SIGNATURE----- diff --git a/sys-infiniband/openib-drivers/metadata.xml b/sys-infiniband/openib-drivers/metadata.xml index ec06e5682..53173c2cb 100644 --- a/sys-infiniband/openib-drivers/metadata.xml +++ b/sys-infiniband/openib-drivers/metadata.xml @@ -1,8 +1,23 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>cluster</herd> -<longdescription> + <herd>cluster</herd> + <longdescription> OpenIB kernel modules. </longdescription> + <use> + <flag name="cxgb3">Automatically generated description for cxgb3</flag> + <flag name="ehca">Automatically generated description for ehca</flag> + <flag name="hpage-patch">Automatically generated description for hpage-patch</flag> + <flag name="ipath">Automatically generated description for ipath</flag> + <flag name="iser">Automatically generated description for iser</flag> + <flag name="madeye">Automatically generated description for madeye</flag> + <flag name="memtrack">Automatically generated description for memtrack</flag> + <flag name="rds">Automatically generated description for rds</flag> + <flag name="srp">Automatically generated description for srp</flag> + <flag name="vnic">Automatically generated description for vnic</flag> + <flag name="cxgb3">Automatically generated description for cxgb3</flag> + <flag name="ehca">Automatically generated description for ehca</flag> + <flag name="mlx4">Automatically generated description for mlx4</flag> + </use> </pkgmetadata> diff --git a/sys-infiniband/openib-drivers/openib-drivers-1.2.5.1.ebuild b/sys-infiniband/openib-drivers/openib-drivers-1.2.5.1.ebuild index 88b3f0338..e639e72d9 100644 --- a/sys-infiniband/openib-drivers/openib-drivers-1.2.5.1.ebuild +++ b/sys-infiniband/openib-drivers/openib-drivers-1.2.5.1.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit rpm linux-mod +inherit linux-mod rpm DESCRIPTION="OpenIB kernel modules" HOMEPAGE="http://www.openfabrics.org/" @@ -15,7 +15,7 @@ LICENSE="|| ( GPL-2 BSD-2 )" SLOT="0" KEYWORDS="~x86 ~amd64" -IUSE="memtrack hpage-patch srp ipath iser ehca rds madeye vnic cxgb3 debug" +IUSE="cxgb3 debug ehca hpage-patch ipath iser madeye memtrack rds srp vnic" RDEPEND="" DEPEND="${RDEPEND} diff --git a/sys-infiniband/openib-drivers/openib-drivers-1.2.5.5.ebuild b/sys-infiniband/openib-drivers/openib-drivers-1.2.5.5.ebuild index 52d615744..cc14f8450 100644 --- a/sys-infiniband/openib-drivers/openib-drivers-1.2.5.5.ebuild +++ b/sys-infiniband/openib-drivers/openib-drivers-1.2.5.5.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit rpm linux-mod +inherit linux-mod rpm DESCRIPTION="OpenIB kernel modules" HOMEPAGE="http://www.openfabrics.org/" @@ -15,7 +15,7 @@ LICENSE="|| ( GPL-2 BSD-2 )" SLOT="0" KEYWORDS="~x86 ~amd64" -IUSE="memtrack hpage-patch srp ipath iser ehca mlx4 rds madeye vnic cxgb3 debug" +IUSE="cxgb3 debug ehca hpage-patch ipath iser madeye memtrack mlx4 rds srp vnic" RDEPEND="" PDEPEND="=sys-infiniband/openib-files-${PV}" diff --git a/sys-infiniband/openib-files/Manifest b/sys-infiniband/openib-files/Manifest index dc74e81e7..4d7556267 100644 --- a/sys-infiniband/openib-files/Manifest +++ b/sys-infiniband/openib-files/Manifest @@ -10,15 +10,15 @@ AUX openib.modprobe.1.2.5.5 378 RMD160 9f1e3ac9e64dd8f6e06c5897f89adda6938ae32a DIST OFED-1.2.5.5.tgz 46432282 RMD160 f5829858fca521d8675af1245d4764eeb87ff08d SHA1 faa027109b56583207eca9fd736164517acf7120 SHA256 ffb990b22d7b0f25026d9fe785aa97ca5920b5a0e620851deb057b9b83bbf907 DIST OFED-1.4.1.tgz 65180617 RMD160 748e669a1a5aef90dd9cec3e8fce110d0051a3cd SHA1 e558bb16c414e0f40727ac046cbd80a3fc84c87f SHA256 5e73c9ead49f286ef68d1618a042b5101887cf0f8c66fbfea5a8a7648feee1e6 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee -EBUILD openib-files-1.2.5.5.ebuild 4373 RMD160 cd8e4cf2fb7ef3326ce8ac11c2f4ce90459ca646 SHA1 c6e345bec229844c545c4154ef5024a71b7edb55 SHA256 40da3fde8b732e1b93f0b235005be40d618e0e9089dbbcc44db90467089134bf -EBUILD openib-files-1.4.1.ebuild 4100 RMD160 d718d2199a3962e3761ba4ed3dee26234526a5b3 SHA1 1a02cb43cda13ab8c77606ebda8e6b415912ffd3 SHA256 e8db24266a686c10c4a16067d48dcb6eb6fe68236cd6468e155bb981b7d91e55 -EBUILD openib-files-1.4.ebuild 4096 RMD160 2e2f1c407fca258ddfb2f117c7334cfd8c95f9bf SHA1 6be4e56f05211d5c62395a791949a7f6e9ab65ac SHA256 a9aae3d0a021aeb45c33796b267b5de3f998322b865314797b50014cfa28c5b4 +EBUILD openib-files-1.2.5.5.ebuild 4373 RMD160 53614e50c11f0c84e7b2f5d28b809d49179caae6 SHA1 d1c11c822e8774e010e017a6f20b8de1295b924f SHA256 d874a7c53dc5ace005d0d7e0367f7b1ef211acc6dc671bcea80d3d6df04afa6f +EBUILD openib-files-1.4.1.ebuild 4100 RMD160 cbc50f047903cf06f4d3c7f1bac2231de1c0d6c9 SHA1 02eb1be62587a8b49d3a285ea90efb8d1b8a8cd5 SHA256 bdac35395b4c2562cc991726f25ff318a600eaa26b4084404f500e898ef168e3 +EBUILD openib-files-1.4.ebuild 4096 RMD160 9a4e27467d12b389bd5e7aa2e7a3d600fd4eb48b SHA1 a1ec543d1e04cd2e0e2b3299c0dc87d15a5806c3 SHA256 113788c761b7a8bffdb07f05e433c33f2ee884eb77745618b8b423a42f890722 MISC ChangeLog 846 RMD160 34827369060857414925d5227a45231a46794298 SHA1 d78bddbb5f09d239462d0a8314496d65f3f6ef60 SHA256 45f09c8c1c8ea292e586636ca59dbdcbf01d4a165c0ef5cdeb4550223df5bf40 -MISC metadata.xml 231 RMD160 064e6234f88fbb875c0c8fcc15c6b94dac933543 SHA1 cf668e559ad68beff6f02f857375242b7dd31754 SHA256 c41922d8d18696ec022ac5d34af8583bbb4b6eff6698ae5f0aa9c87631d112d7 +MISC metadata.xml 768 RMD160 f6ee09bfb00901e428ff9aa5eb30d039cca1d205 SHA1 827e5343a8e735a7e65b442af452cf2286a67faf SHA256 cd6e4455c6d58d7be09f28c1bb7fbab102f39484a1e68eb8bf0e3dfd710d4648 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.13 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAksJq/QACgkQ5BmOA85PVLj2VQCfZIn7ZluqAxfTgyKenayhvM+J -mssAnAwWK9SkVp0CJDIpajbytX2//0vE -=f82H +iEUEARECAAYFAk4EuwEACgkQgAnW8HDreRbA1ACfd335KOagslEhWyKv3gg2vryH +PFwAmOHuvQPp5+aRipiAk2AyzTA+U+c= +=Qmhz -----END PGP SIGNATURE----- diff --git a/sys-infiniband/openib-files/metadata.xml b/sys-infiniband/openib-files/metadata.xml index 32075071c..f1ef0107e 100644 --- a/sys-infiniband/openib-files/metadata.xml +++ b/sys-infiniband/openib-files/metadata.xml @@ -1,8 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>cluster</herd> -<longdescription> + <herd>cluster</herd> + <longdescription> OpenIB system files and examples. </longdescription> + <use> + <flag name="ehca">Automatically generated description for ehca</flag> + <flag name="ipath">Automatically generated description for ipath</flag> + <flag name="iser">Automatically generated description for iser</flag> + <flag name="srp">Automatically generated description for srp</flag> + <flag name="vnic">Automatically generated description for vnic</flag> + <flag name="mlx4">Automatically generated description for mlx4</flag> + <flag name="rds">Automatically generated description for rds</flag> + </use> </pkgmetadata> diff --git a/sys-infiniband/openib-files/openib-files-1.2.5.5.ebuild b/sys-infiniband/openib-files/openib-files-1.2.5.5.ebuild index 48cabf027..872bf29fa 100644 --- a/sys-infiniband/openib-files/openib-files-1.2.5.5.ebuild +++ b/sys-infiniband/openib-files/openib-files-1.2.5.5.ebuild @@ -16,7 +16,7 @@ LICENSE="|| ( GPL-2 BSD-2 )" SLOT="0" KEYWORDS="~x86 ~amd64" -IUSE="srp ipath iser ehca mlx4 rds vnic" +IUSE="ehca ipath iser mlx4 rds srp vnic" RDEPEND="" DEPEND="${RDEPEND}" diff --git a/sys-infiniband/openib-files/openib-files-1.4.1.ebuild b/sys-infiniband/openib-files/openib-files-1.4.1.ebuild index 8b65653f5..1878890c1 100644 --- a/sys-infiniband/openib-files/openib-files-1.4.1.ebuild +++ b/sys-infiniband/openib-files/openib-files-1.4.1.ebuild @@ -12,7 +12,7 @@ inherit openib DESCRIPTION="OpenIB system files" SCRIPTDIR="${S}/ofed_scripts" KEYWORDS="~x86 ~amd64" -IUSE="srp ipath iser ehca mlx4 rds vnic" +IUSE="ehca ipath iser mlx4 rds srp vnic" DEPEND="" RDEPEND="${DEPEND}" diff --git a/sys-infiniband/openib-files/openib-files-1.4.ebuild b/sys-infiniband/openib-files/openib-files-1.4.ebuild index 335378fe0..59108532d 100644 --- a/sys-infiniband/openib-files/openib-files-1.4.ebuild +++ b/sys-infiniband/openib-files/openib-files-1.4.ebuild @@ -12,7 +12,7 @@ inherit openib DESCRIPTION="OpenIB system files" SCRIPTDIR="${S}/ofed_scripts" KEYWORDS="~x86 ~amd64" -IUSE="srp ipath iser ehca mlx4 rds vnic" +IUSE="ehca ipath iser mlx4 rds srp vnic" DEPEND="" RDEPEND="${DEPEND}" diff --git a/sys-infiniband/openib-mvapich2/ChangeLog b/sys-infiniband/openib-mvapich2/ChangeLog index c6c92d2c0..993841b39 100644 --- a/sys-infiniband/openib-mvapich2/ChangeLog +++ b/sys-infiniband/openib-mvapich2/ChangeLog @@ -1,7 +1,17 @@ # ChangeLog for sys-infiniband/openib-mvapich2 -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> openib-mvapich2-0.9.5.ebuild, + openib-mvapich2-0.9.6.ebuild, openib-mvapich2-1.0.ebuild, + openib-mvapich2-1.0.1.ebuild, openib-mvapich2-1.0.1-r1.ebuild: + Fix repoman warnings + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> openib-mvapich2-0.9.5.ebuild, + openib-mvapich2-0.9.6.ebuild, openib-mvapich2-1.0.ebuild, + openib-mvapich2-1.0.1.ebuild, openib-mvapich2-1.0.1-r1.ebuild: + Added fortran-2.eclass support + 16 Dec 2010; Justin Lecher <jlec@gentoo.org> openib-mvapich2-1.0.1-r1.ebuild: Removal of fortran.eclass, #348851 diff --git a/sys-infiniband/openib-mvapich2/Manifest b/sys-infiniband/openib-mvapich2/Manifest index 37af7acb4..0eda6cfa3 100644 --- a/sys-infiniband/openib-mvapich2/Manifest +++ b/sys-infiniband/openib-mvapich2/Manifest @@ -6,17 +6,17 @@ DIST mvapich2-0.9.5.tar.gz 13873 RMD160 56e146c80be3cd7b5f1e1469f20e2c17549b15d7 DIST mvapich2-0.9.6.tar.gz 13873 RMD160 56e146c80be3cd7b5f1e1469f20e2c17549b15d7 SHA1 4026f5d3b32fc279a1480842599f0dd1a04b4621 SHA256 1dcd75956f8d947c5cbdeed39d7d39440d9cb0132aa3607042452514ca922d8f DIST mvapich2-1.0.1.tar.gz 14062480 RMD160 da9e4dd07998d82ead0276e8b264a487c4d4fe79 SHA1 3edc9720251f8060e0f9c8cc58800a45a66cc7ae SHA256 a20fb87ed674bec3b2de87c47cc3965c33248e00b37f7eb08ba40d0bab07ca5e DIST mvapich2-1.0.tar.gz 14061056 RMD160 ba57d0d51bbdd3956dce446575d2ecbed4fe5b2f SHA1 b2f6ecf3e3b06c63b443bbcc55c2043f6d683f67 SHA256 30c0849dc7e8d4581cfee16a824f5e384e8198b60b7f54f880f4e25da7d1c143 -EBUILD openib-mvapich2-0.9.5.ebuild 3239 RMD160 f7a4069ba76fb382c2ee6e86d5ff2d9f8df16b9c SHA1 fbdba2a2e3263ae2905b9faf4f389bfbdca4870d SHA256 36f2eaab54101f737dc0778e551855502da293e4f567fea8012ca3731b78d232 -EBUILD openib-mvapich2-0.9.6.ebuild 3234 RMD160 bb96cb6dab553cd1cf65b49c0a6c2133365c7253 SHA1 6301eef31380d259a07f8a2347f6f0621b006bfc SHA256 5ae2d8c34fa2cec57ebb6a5e4229ac86f3d109ab7d817bd31f896942e198817f -EBUILD openib-mvapich2-1.0.1-r1.ebuild 4279 RMD160 0c60ae549611876a56a723df73aa763e4b9e7e8f SHA1 6ce518df99ef8692b83ddc9460a730695a387b1b SHA256 b61eaa1c4a0738eb9530023167233f1d101554c35b5fcfe152841266e1b78217 -EBUILD openib-mvapich2-1.0.1.ebuild 3139 RMD160 94391f18ea842c2284ddc5f3a2fbf726a32552b1 SHA1 912eca3e1bb59995b84a7d988c58d5f8323c7542 SHA256 8db00d2a93794610cbfaabb7338e655b547f2e800a831b64572be357bb2be177 -EBUILD openib-mvapich2-1.0.ebuild 3139 RMD160 94391f18ea842c2284ddc5f3a2fbf726a32552b1 SHA1 912eca3e1bb59995b84a7d988c58d5f8323c7542 SHA256 8db00d2a93794610cbfaabb7338e655b547f2e800a831b64572be357bb2be177 -MISC ChangeLog 949 RMD160 fab4c52da596c3339c375ef6624353aeb7c1fb13 SHA1 e7d5b7f077817d2bdfb30f34c53e384b8c35a930 SHA256 497a4184fa7f08b2fa3296c977a7dec60eb665d3fbb792dd0a696c8c8de6f42b -MISC metadata.xml 262 RMD160 2e8cfe97bd1a25814de0657adb7f9ab7f2861895 SHA1 e8a4f573ce01738445befdd0a3e597a79385c0cb SHA256 c54bb4a2708874d3875753c62b071b05f08f6947f71767ac26a4063ad3e4871a +EBUILD openib-mvapich2-0.9.5.ebuild 3270 RMD160 b8ba92963ade597d941a652232792d299fec4739 SHA1 237a36ee157063c7525b6e20a66b41666d2c57ae SHA256 7c995e26f8b9799fde81d03a27d92b108f5f6896aaf92d94e8e61b8260a14989 +EBUILD openib-mvapich2-0.9.6.ebuild 3270 RMD160 b8ba92963ade597d941a652232792d299fec4739 SHA1 237a36ee157063c7525b6e20a66b41666d2c57ae SHA256 7c995e26f8b9799fde81d03a27d92b108f5f6896aaf92d94e8e61b8260a14989 +EBUILD openib-mvapich2-1.0.1-r1.ebuild 4289 RMD160 423fab6e5db1c7706515d390757f7cef0a3e8bb5 SHA1 f89c43373166e57c00f67002251eee07b9897f24 SHA256 49008a0ffadfe9d27a1c9f65e3da0c277c8cf15f8710a8bdad7cd2a2b1e32cc1 +EBUILD openib-mvapich2-1.0.1.ebuild 3163 RMD160 1161e420d046662c1e4af9f77282d074751eae10 SHA1 430efc70090d8b3d1ebf1608fab5d651766f025f SHA256 e0c348edd235ea1fa272a6be857b76ba4e56f9eee8d8a3399203b4c8412f08b8 +EBUILD openib-mvapich2-1.0.ebuild 3163 RMD160 1161e420d046662c1e4af9f77282d074751eae10 SHA1 430efc70090d8b3d1ebf1608fab5d651766f025f SHA256 e0c348edd235ea1fa272a6be857b76ba4e56f9eee8d8a3399203b4c8412f08b8 +MISC ChangeLog 1411 RMD160 a0de1966435ce62c050b1df6b685bcf0fefb799a SHA1 ff6d178e2f97c5cccc29506be178779f550f5c6c SHA256 60255e43ebec78343472ec5b2b06b366b23463199a565da9c244decfe64887ed +MISC metadata.xml 619 RMD160 d5e91eed039a36ad9bba07f8e105b88d6a1d0474 SHA1 3fb8063b009c9ea3c821229411cedf1f93a9909d SHA256 16fa6109f915534a90483380520a27b4233b080a1b5c16b0392275b3bed7837c -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk0LrSQACgkQgAnW8HDreRbIzACfQwwGm7Qm91B4Rh69EVzfe1t6 -FPIAn0VZa10M9Kx+E7RDrbVW57mrSLJO -=2RTG +iEYEARECAAYFAk4EvyEACgkQgAnW8HDreRZclQCgyBeBEjNkPi4HloU9iOEIWZZl +q8YAnRlB6XNMtrQjbOccn+v4pWAJGEYw +=avAa -----END PGP SIGNATURE----- diff --git a/sys-infiniband/openib-mvapich2/metadata.xml b/sys-infiniband/openib-mvapich2/metadata.xml index 537c22a0e..a5a004383 100644 --- a/sys-infiniband/openib-mvapich2/metadata.xml +++ b/sys-infiniband/openib-mvapich2/metadata.xml @@ -1,8 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>cluster</herd> -<longdescription> + <herd>cluster</herd> + <longdescription> MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB. </longdescription> + <use> + <flag name="large-cluster">Automatically generated description for large-cluster</flag> + <flag name="medium-cluster">Automatically generated description for medium-cluster</flag> + <flag name="rdma">Automatically generated description for rdma</flag> + <flag name="romio">Automatically generated description for romio</flag> + </use> </pkgmetadata> diff --git a/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.5.ebuild b/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.5.ebuild index 0dd97ab0d..436fa5019 100644 --- a/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.5.ebuild +++ b/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.5.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -6,28 +6,30 @@ # the type of HCA to configure for. This needs to be fixed to take out the # interactivity. -SLOT="0" -LICENSE="BSD" - -KEYWORDS="~x86 ~amd64" - -DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB." +inherit fortran-2 +DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB" HOMEPAGE="http://nowlab.cse.ohio-state.edu/projects/mpi-iba/" SRC_URI="http://nowlab.cse.ohio-state.edu/projects/mpi-iba/download-mvapich2/mvapich2-$PV.tar.gz" -S="${WORKDIR}/mvapich2-$PV" - -IUSE="threads debug medium-cluster large-cluster" +SLOT="0" +LICENSE="BSD" +IUSE="debug large-cluster medium-cluster threads" +KEYWORDS="~x86 ~amd64" DEPEND=" - || ( sys-infiniband/libibverbs - sys-infiniband/openib-userspace ) - || ( sys-infiniband/librdmacm - sys-infiniband/openib-userspace )" + || ( + sys-infiniband/libibverbs + sys-infiniband/openib-userspace ) + || ( + sys-infiniband/librdmacm + sys-infiniband/openib-userspace )" RDEPEND="${DEPEND}" +S="${WORKDIR}/mvapich2-$PV" + pkg_setup() { + fortran-2_pkg_setup ARCH= VCLUSTER=_SMALL_CLUSTER HAVE_MPD_RING="-DUSE_MPD_RING" @@ -112,4 +114,3 @@ pkg_postinst() { einfo "echo 512000000 > /proc/sys/kernel/shmmax" einfo "echo -e '* soft memlock 500000\n* hard memlock 500000' > /etc/security/limits.conf" } - diff --git a/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.6.ebuild b/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.6.ebuild index c3f7d2285..436fa5019 100644 --- a/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.6.ebuild +++ b/sys-infiniband/openib-mvapich2/openib-mvapich2-0.9.6.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -6,28 +6,30 @@ # the type of HCA to configure for. This needs to be fixed to take out the # interactivity. -SLOT="0" -LICENSE="BSD" - -KEYWORDS="-amd64" - -DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB." +inherit fortran-2 +DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB" HOMEPAGE="http://nowlab.cse.ohio-state.edu/projects/mpi-iba/" SRC_URI="http://nowlab.cse.ohio-state.edu/projects/mpi-iba/download-mvapich2/mvapich2-$PV.tar.gz" -S="${WORKDIR}/mvapich2-$PV" - -IUSE="threads debug medium-cluster large-cluster" +SLOT="0" +LICENSE="BSD" +IUSE="debug large-cluster medium-cluster threads" +KEYWORDS="~x86 ~amd64" DEPEND=" - || ( sys-infiniband/libibverbs - sys-infiniband/openib-userspace ) - || ( sys-infiniband/librdmacm - sys-infiniband/openib-userspace )" + || ( + sys-infiniband/libibverbs + sys-infiniband/openib-userspace ) + || ( + sys-infiniband/librdmacm + sys-infiniband/openib-userspace )" RDEPEND="${DEPEND}" +S="${WORKDIR}/mvapich2-$PV" + pkg_setup() { + fortran-2_pkg_setup ARCH= VCLUSTER=_SMALL_CLUSTER HAVE_MPD_RING="-DUSE_MPD_RING" @@ -112,4 +114,3 @@ pkg_postinst() { einfo "echo 512000000 > /proc/sys/kernel/shmmax" einfo "echo -e '* soft memlock 500000\n* hard memlock 500000' > /etc/security/limits.conf" } - diff --git a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1-r1.ebuild b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1-r1.ebuild index 988b97116..083493bf7 100644 --- a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1-r1.ebuild +++ b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1-r1.ebuild @@ -1,33 +1,32 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit mpi - -SLOT="0" -LICENSE="BSD" - -KEYWORDS="~x86 ~amd64" - -DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB." +inherit fortran-2 mpi +DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB" HOMEPAGE="http://mvapich.cse.ohio-state.edu/" SRC_URI="${HOMEPAGE}/download/mvapich2/mvapich2-${PV/_/-}.tar.gz" -S="${WORKDIR}/mvapich2-${PV/_/-}" - -IUSE="debug medium-cluster large-cluster rdma romio threads fortran" +SLOT="0" +LICENSE="BSD" +KEYWORDS="~x86 ~amd64" +IUSE="debug fortran large-cluster medium-cluster rdma romio threads" RDEPEND=" - || ( ( sys-infiniband/libibverbs + || ( + ( + sys-infiniband/libibverbs sys-infiniband/libibumad sys-infiniband/libibmad rdma? ( sys-infiniband/librdmacm ) ) - sys-infiniband/openib-userspace ) - $(mpi_imp_deplist)" + sys-infiniband/openib-userspace )" DEPEND="${RDEPEND}" +S="${WORKDIR}/mvapich2-${PV/_/-}" + pkg_setup() { + fortran-2_pkg_setup MPI_ESELECT_FILE="eselect.mpi.mvapich2" if [ -z "${MVAPICH_HCA_TYPE}" ]; then @@ -154,4 +153,3 @@ pkg_postinst() { einfo "echo 512000000 > /proc/sys/kernel/shmmax" einfo "echo -e '* soft memlock 500000\n* hard memlock 500000' > /etc/security/limits.conf" } - diff --git a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1.ebuild b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1.ebuild index d738fff21..734d8b8e3 100644 --- a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1.ebuild +++ b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.1.ebuild @@ -1,34 +1,36 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ +inherit fortran-2 + # WARNING: this script is interactive - it requires user-input once to verify # the type of HCA to configure for. This needs to be fixed to take out the # interactivity. -SLOT="0" -LICENSE="BSD" - -KEYWORDS="~amd64" - -DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB." - +DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB" HOMEPAGE="http://mvapich.cse.ohio-state.edu/" SRC_URI="${HOMEPAGE}/download/mvapich2/mvapich2-${PV/_/-}.tar.gz" -S="${WORKDIR}/mvapich2-${PV/_/-}" - -IUSE="threads debug medium-cluster large-cluster rdma" +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64" +IUSE="debug large-cluster medium-cluster rdma threads" RDEPEND=" - || ( ( sys-infiniband/libibverbs - sys-infiniband/libibumad - sys-infiniband/libibmad - rdma? ( sys-infiniband/librdmacm ) ) - sys-infiniband/openib-userspace )" + || ( + ( + sys-infiniband/libibverbs + sys-infiniband/libibumad + sys-infiniband/libibmad + rdma? ( sys-infiniband/librdmacm ) ) + sys-infiniband/openib-userspace )" DEPEND="${RDEPEND}" +S="${WORKDIR}/mvapich2-${PV/_/-}" + pkg_setup() { + fortran-2_pkg_setup ARCH= VCLUSTER=_SMALL_CLUSTER HAVE_MPD_RING="-DUSE_MPD_RING" @@ -109,4 +111,3 @@ pkg_postinst() { einfo "echo 512000000 > /proc/sys/kernel/shmmax" einfo "echo -e '* soft memlock 500000\n* hard memlock 500000' > /etc/security/limits.conf" } - diff --git a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.ebuild b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.ebuild index d738fff21..734d8b8e3 100644 --- a/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.ebuild +++ b/sys-infiniband/openib-mvapich2/openib-mvapich2-1.0.ebuild @@ -1,34 +1,36 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ +inherit fortran-2 + # WARNING: this script is interactive - it requires user-input once to verify # the type of HCA to configure for. This needs to be fixed to take out the # interactivity. -SLOT="0" -LICENSE="BSD" - -KEYWORDS="~amd64" - -DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB." - +DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB" HOMEPAGE="http://mvapich.cse.ohio-state.edu/" SRC_URI="${HOMEPAGE}/download/mvapich2/mvapich2-${PV/_/-}.tar.gz" -S="${WORKDIR}/mvapich2-${PV/_/-}" - -IUSE="threads debug medium-cluster large-cluster rdma" +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64" +IUSE="debug large-cluster medium-cluster rdma threads" RDEPEND=" - || ( ( sys-infiniband/libibverbs - sys-infiniband/libibumad - sys-infiniband/libibmad - rdma? ( sys-infiniband/librdmacm ) ) - sys-infiniband/openib-userspace )" + || ( + ( + sys-infiniband/libibverbs + sys-infiniband/libibumad + sys-infiniband/libibmad + rdma? ( sys-infiniband/librdmacm ) ) + sys-infiniband/openib-userspace )" DEPEND="${RDEPEND}" +S="${WORKDIR}/mvapich2-${PV/_/-}" + pkg_setup() { + fortran-2_pkg_setup ARCH= VCLUSTER=_SMALL_CLUSTER HAVE_MPD_RING="-DUSE_MPD_RING" @@ -109,4 +111,3 @@ pkg_postinst() { einfo "echo 512000000 > /proc/sys/kernel/shmmax" einfo "echo -e '* soft memlock 500000\n* hard memlock 500000' > /etc/security/limits.conf" } - diff --git a/sys-infiniband/openib-osm/ChangeLog b/sys-infiniband/openib-osm/ChangeLog index 02bc30e18..33cd8f929 100644 --- a/sys-infiniband/openib-osm/ChangeLog +++ b/sys-infiniband/openib-osm/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sys-infiniband/openib-osm -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + openib-osm-3.2.5_p20081207.ebuild, openib-osm-3.2.6_p20090317.ebuild, + metadata.xml: + Cleaned ebuild + *openib-osm-3.2.6_p20090317 (20 Aug 2009) 20 Aug 2009; Alexey Shvetsov <alexxy@gentoo.org> diff --git a/sys-infiniband/openib-osm/Manifest b/sys-infiniband/openib-osm/Manifest index 78fdead16..e1b252637 100644 --- a/sys-infiniband/openib-osm/Manifest +++ b/sys-infiniband/openib-osm/Manifest @@ -1,8 +1,18 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + AUX openib-osm-3.2.6_p20090317-fix.patch 371 RMD160 dab18a2acd6225ba56f3661d87f81845cfbbcc86 SHA1 cd36ed2e5c3c1105f1a9daf7b4ae566b4c741479 SHA256 81ce28317f31c3e88d63c448f85f45ae8e81f9eb240446a6f1ab5083a20b354a AUX opensm.init.d 711 RMD160 2d2679a8bd09eabdcd4207e77f4dc8cebaa33c1c SHA1 91cefc35cadb03e68ef7c740eac5f417b20cf818 SHA256 e7a32165d81c6065fe0caf1c2fe2709610ac8a24e8e5a0ed342a066a6feb8f94 DIST OFED-1.4.1.tgz 65180617 RMD160 748e669a1a5aef90dd9cec3e8fce110d0051a3cd SHA1 e558bb16c414e0f40727ac046cbd80a3fc84c87f SHA256 5e73c9ead49f286ef68d1618a042b5101887cf0f8c66fbfea5a8a7648feee1e6 DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee -EBUILD openib-osm-3.2.5_p20081207.ebuild 1167 RMD160 46247f24be8d10db11d20d3a1357d50d4c374e51 SHA1 3d01788973abe09dea75ecbc0269be307afe3635 SHA256 53a75d47712db1b51719e3617a52fb5d43ca8f28b4132df01964cf9117ee1079 -EBUILD openib-osm-3.2.6_p20090317.ebuild 1226 RMD160 0d2569bd869e3fc07aac0390c709549f118b463a SHA1 8f3caa4d30ad5568a406d27d3d885aef057cd8be SHA256 cb6a8fda5ce95817e2738fb78b09b273f5f03f9406b9e0bda755ac97023f6a27 -MISC ChangeLog 1007 RMD160 538ae44b536de813409fcfabc52774a576352b98 SHA1 2bec9f3c24c5b63253d05890d188873d259fd2fd SHA256 055f7cdbea978139bd5addb1ee925818dc503334f0fb4447a610c0c241d8609b -MISC metadata.xml 419 RMD160 f9b6f7b72f595559b5fdbf3c2bf6cad3490b5900 SHA1 be8a65515c13b833f49766db58e9486961c65078 SHA256 e33518d9908c9e6ee2629959038228160a7215b5b7e04cab593a9734c40df34b +EBUILD openib-osm-3.2.5_p20081207.ebuild 1082 RMD160 6025b9ef74f43c95d04e2685a6dd92dfe39a5e05 SHA1 4cfcf9624e39322a4abeb9f3f0f2e5c878f03663 SHA256 e74924e6cd22012d90e58b0c41edaeee692d32e9c1f72751726727f24ec15792 +EBUILD openib-osm-3.2.6_p20090317.ebuild 1142 RMD160 e6979d234487d82b093d37127b0203463f681b27 SHA1 a70176c5de12ed25619e976a82b56389127b7e76 SHA256 b7b0d7320aae44d548e076994578760572bcbfa54bc83c3198bed45bedf2a6e9 +MISC ChangeLog 1160 RMD160 da15f7d2ba444ec3a7440105cfb8389883977120 SHA1 35e4dfc27012e223e1092d9de1f19f9f0ffdb574 SHA256 a54aed610ca7da609787c92ba6e4b234a43f5aea77a52d06a007ec61a9478afd +MISC metadata.xml 421 RMD160 b9ff53511dc2fcd9c5b3ac94f5028d018440dada SHA1 97f82cbaddd3275d7f906cac68018c5d2433e975 SHA256 78b506cf13aff9269660e6e54f6c27e82e8359c52746036c43841feb140907f8 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4GFoAACgkQgAnW8HDreRY8zQCfSp0HPq3O2378LrP7HUiBuUwh +Q5gAn3BqbEziRZohyjnt0CRzf8OGl96X +=knse +-----END PGP SIGNATURE----- diff --git a/sys-infiniband/openib-osm/metadata.xml b/sys-infiniband/openib-osm/metadata.xml index aa628f31d..82f7df3d4 100644 --- a/sys-infiniband/openib-osm/metadata.xml +++ b/sys-infiniband/openib-osm/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>cluster</herd> -<longdescription> + <herd>cluster</herd> + <longdescription> OpenSM provides an implementation for an InfiniBand Subnet Manager and Administrator. Such a software entity is required to run for in order to initialize the InfiniBand hardware (at least one per each InfiniBand subnet). diff --git a/sys-infiniband/openib-osm/openib-osm-3.2.5_p20081207.ebuild b/sys-infiniband/openib-osm/openib-osm-3.2.5_p20081207.ebuild index 788f75017..71ea15192 100644 --- a/sys-infiniband/openib-osm/openib-osm-3.2.5_p20081207.ebuild +++ b/sys-infiniband/openib-osm/openib-osm-3.2.5_p20081207.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 OFED_VER="1.4" OFED_SUFFIX="1.ofed1.4" @@ -13,11 +13,12 @@ DESCRIPTION="OpenSM - InfiniBand Subnet Manager and Administration for OpenIB" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND=">=sys-infiniband/libibmad-1.2.3_p20081118 - >=sys-infiniband/libibumad-1.2.3_p20081118" +DEPEND=" + >=sys-infiniband/libibmad-1.2.3_p20081118 + >=sys-infiniband/libibumad-1.2.3_p20081118" RDEPEND="$DEPEND - sys-infiniband/openib-files - net-misc/iputils" + sys-infiniband/openib-files + net-misc/iputils" src_configure() { econf \ @@ -27,8 +28,7 @@ src_configure() { } src_install() { - make DESTDIR="${D}" install || die "install failed" - dodoc AUTHORS README NEWS ChangeLog + default newconfd "${S}/scripts/opensm.sysconfig" opensm newinitd "${FILESDIR}/opensm.init.d" opensm insinto /etc/logrotate.d @@ -42,4 +42,3 @@ pkg_postinst() { einfo "edit /etc/opensm.conf and add opensm to your start-up scripts:" einfo "\`rc-update add opensm default\`" } - diff --git a/sys-infiniband/openib-osm/openib-osm-3.2.6_p20090317.ebuild b/sys-infiniband/openib-osm/openib-osm-3.2.6_p20090317.ebuild index 0f5e7687c..2aa061616 100644 --- a/sys-infiniband/openib-osm/openib-osm-3.2.6_p20090317.ebuild +++ b/sys-infiniband/openib-osm/openib-osm-3.2.6_p20090317.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=4 OFED_VER="1.4.1" OFED_SUFFIX="1.ofed1.4.1" @@ -13,11 +13,12 @@ DESCRIPTION="OpenSM - InfiniBand Subnet Manager and Administration for OpenIB" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND=">=sys-infiniband/libibmad-1.2.3_p20090314 - >=sys-infiniband/libibumad-1.2.3_p20090314" +DEPEND=" + >=sys-infiniband/libibmad-1.2.3_p20090314 + >=sys-infiniband/libibumad-1.2.3_p20090314" RDEPEND="$DEPEND - sys-infiniband/openib-files - net-misc/iputils" + sys-infiniband/openib-files + net-misc/iputils" src_prepare() { epatch "${FILESDIR}/${P}-fix.patch" @@ -31,8 +32,7 @@ src_configure() { } src_install() { - make DESTDIR="${D}" install || die "install failed" - dodoc AUTHORS README NEWS ChangeLog + default newconfd "${S}/scripts/opensm.sysconfig" opensm newinitd "${FILESDIR}/opensm.init.d" opensm insinto /etc/logrotate.d diff --git a/sys-infiniband/openib-perf/ChangeLog b/sys-infiniband/openib-perf/ChangeLog index 23518041c..a46004e39 100644 --- a/sys-infiniband/openib-perf/ChangeLog +++ b/sys-infiniband/openib-perf/ChangeLog @@ -1,7 +1,11 @@ -# ChangeLog for sys-cluster/openib-perf -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# ChangeLog for sys-infiniband/openib-perf +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> openib-perf-1.2.ebuild, + metadata.xml: + RDEPEND is not explicitly assigned -> fixed + *openib-perf-1.2 (21 Jan 2009) 21 Jan 2009; Alexey Shvetsov <alexxy@gentoo.org> -openib-perf-1.1.ebuild, diff --git a/sys-infiniband/openib-perf/Manifest b/sys-infiniband/openib-perf/Manifest index fe723d3e2..dfd74f5ef 100644 --- a/sys-infiniband/openib-perf/Manifest +++ b/sys-infiniband/openib-perf/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST OFED-1.4.tgz 61398547 RMD160 55fdf86f788a1ac86f0de842ffda545967f25431 SHA1 4d0c61409e0d41dc65906b93b592b9c331399392 SHA256 da1adc3d413b3a5731c9c46443c42fcfb88c1ad6bb9d77175a315a26a07ecaee -EBUILD openib-perf-1.2.ebuild 450 RMD160 da8b2de1cee5903a6433e24d4677925382102f76 SHA1 8c3702d164a6fd703aa61cb77cbfdd17b7c67337 SHA256 54f24cba1a1fe1f8fac4e9abe350533cc061405cd841bc5d780762beed1a2838 -MISC ChangeLog 388 RMD160 2326a7c7c41bfee76bc48ec1c6d21a9f63be0be5 SHA1 7cd2c531e3c3f5ed037a21c4ddc80787dea6d6cd SHA256 349876c40e3be8ff57d617e6835508c13f4f2024fb757e4effdb913d593dfc01 -MISC metadata.xml 229 RMD160 e1401ca7c2210ebd7f7951139300cb05b871720c SHA1 847c1c0aca9c9a309fc80aa1345fa6b9df91c5c1 SHA256 30506429bac849161d32a0e3960a93cfacd4e931f8b6cb986965e3a4239ac8c0 +EBUILD openib-perf-1.2.ebuild 421 RMD160 cd1afc23293a017e858980f854a71b0844dc95da SHA1 588e11654661f5ee377c9453ca248e5cdd3b73da SHA256 ef1d0886c8b0743670a852f4938d8f8a76f8eab403f22016a02633f4cf121b89 +MISC ChangeLog 525 RMD160 4930664b8813d779fc2b246178bb7522ee835b68 SHA1 9365880b18a63759c79931cdcabe09fac59a1064 SHA256 de5f6d5349313f62fa109963c135eeda1b243ceaf0ae8d1eb9eb8504e1bdb632 +MISC metadata.xml 231 RMD160 63d19745f140ecfd3d8d08eaa29516c7fc3bf9e4 SHA1 d0b96186aa67812efcab2d708a2d260d7d001117 SHA256 dc980d7e9f97b8ab1fb350c7985d591e521468c5c4824cab1624845e86ae2173 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F570ACgkQgAnW8HDreRZyOwCgpR4cnmM263tYc1TPNEuWlI0N +LEcAoLELvTwu57M7VUjLLuQnS0olSEAO +=WZCb +-----END PGP SIGNATURE----- diff --git a/sys-infiniband/openib-perf/metadata.xml b/sys-infiniband/openib-perf/metadata.xml index 32ace613a..8fb8c1c2e 100644 --- a/sys-infiniband/openib-perf/metadata.xml +++ b/sys-infiniband/openib-perf/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>cluster</herd> -<longdescription> + <herd>cluster</herd> + <longdescription> OpenIB uverbs micro-benchmarks. </longdescription> </pkgmetadata> diff --git a/sys-infiniband/openib-perf/openib-perf-1.2.ebuild b/sys-infiniband/openib-perf/openib-perf-1.2.ebuild index 1ca0caf9c..d251c368e 100644 --- a/sys-infiniband/openib-perf/openib-perf-1.2.ebuild +++ b/sys-infiniband/openib-perf/openib-perf-1.2.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=3 OFED_VER="1.4" OFED_SUFFIX="1.ofed1.4" @@ -10,18 +10,16 @@ OFED_SUFFIX="1.ofed1.4" inherit openib DESCRIPTION="OpenIB uverbs micro-benchmarks" + KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND=">=sys-infiniband/libibverbs-1.1.2 - >=sys-infiniband/librdmacm-1.0.8" - -src_compile() { - emake || die "emake failed" -} +DEPEND=" + >=sys-infiniband/libibverbs-1.1.2 + >=sys-infiniband/librdmacm-1.0.8" +RDEPEND="${DEPEND}" src_install() { dodoc README Copying runme dobin ib_* } - diff --git a/sys-infiniband/openib-srptools/ChangeLog b/sys-infiniband/openib-srptools/ChangeLog index ed9c29773..eef35149b 100644 --- a/sys-infiniband/openib-srptools/ChangeLog +++ b/sys-infiniband/openib-srptools/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sys-infiniband/openib-srptools -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> openib-srptools-1.1.ebuild, + metadata.xml: + Cleaned ebuild + 10 Jul 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> openib-srptools-1.1.ebuild: Silenced repoman. diff --git a/sys-infiniband/openib-srptools/Manifest b/sys-infiniband/openib-srptools/Manifest index e13492656..e05e6d49f 100644 --- a/sys-infiniband/openib-srptools/Manifest +++ b/sys-infiniband/openib-srptools/Manifest @@ -1,24 +1,14 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 DIST openib-userspace-1.1.tgz 12361548 RMD160 53f69c5b66ac1a9bd7c22ebda39439453802204f SHA1 8993b2724d798f27ed560cf3ce4e8c1b9e6fffb1 SHA256 2e8430443a40eed95f1492c1e11aa515f8b4f20ab431b0cf588032fc6a01d04a -EBUILD openib-srptools-1.1.ebuild 734 RMD160 c249ad2cd59de0b68d644addce133f70fbfc9af5 SHA1 dcf828f5973cbdc4ed5640188e6437e8153bae7d SHA256 df9717ec9cc2c4e29d063dea7d120c4f87b68a41cd05f6de57c3715b52c7c954 -MISC ChangeLog 365 RMD160 00dbcb2251203f3bb7721fdf2dee72fd6f493673 SHA1 7007d949e5ef302539dd923f5c79a5b711a6f8e6 SHA256 44512455ca6d95c84e9267b9f821dae6b220d6cd1a23e5fee039b2d0152c1e3d -MISC metadata.xml 429 RMD160 3b6d065ac43345b5e65c5a181afd399664a11f20 SHA1 215bb27b90f91a8f1ea7c64443f18b1bdc2bb2f4 SHA256 0eb38e83ed8571c48d07c71e2fabf00b3c3bca279342c6796a41b9c24437a1a6 +EBUILD openib-srptools-1.1.ebuild 528 RMD160 a9a822ed04e38afa4dbfe5d68c1bfcc116388950 SHA1 72b83e590749059937d8e1c9e183e447ed889c11 SHA256 a93c3d9a26d4b84d6c9856e9f19a76775984bf150fc23eeb7a8b2ce0653cd452 +MISC ChangeLog 474 RMD160 9d7efbdca028088a7640881f83c8a051e91af6f1 SHA1 db2a3ae6a6c617dbf8d8be98bc7aa58c4b53f38c SHA256 011f1ae3212ef4ffd7c728345f1769f6ee18277a309d0ac65659285528312c35 +MISC metadata.xml 431 RMD160 1f63a84d34521f76e23ee627196d782d6e37690e SHA1 acc7f29668f9e490fdefa1c2e3f11a825637fc49 SHA256 cf32380ef10f4d25441d325b0de187897e4934f450de53ceae3db3ff301f8b2b -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMOO9eAAoJENwGBM22xffeFNsQAJfxYXbLVqOs6ndH1Jw0wT8A -A5dove/XwWYEz7hMCUridRrQ7xncRuvMCHrtqKE7LvcSQlDKQkJfcNiDW55cTOeQ -6DUTAC/0NBErthwBJc7WGzkr+y47I/G8spgOCkWckmQj2aAcgD9O47Ljkr8XeSv0 -7MZ/tdlplgTsbDgDM+5hB+dlULkSXkDejFbKszEaYilcEp5QUpVFCnxG6LobW7ZT -AcaFoi6SUWcBa8A8LvrmU1HNgmdX9FrEiKWsnQKUDGy4hrGLoTWSt3lPM43HVHKw -9JNUCkBCAaBj9nxRXhP3EXUQYslchO024cHnzny0lai2KGtSe6T6HAkaTdC4lv+L -EXIPVJzcs4GbtHoO7Ca+q5DXeFTQpFhbzNGBFfGmA1udgdVb657tTnMl70nXPOmg -IbLn31mjcbCL1EdN5J4aeTVM1miQY9u0WEeJhoZ5zOmoBxIzmunXnqOCXS7qRP6v -sDZsJWvkeV5D9xWYSs3ytjNE2x/DsstrOe0/foxiGiLN1t7862XanjIM7ofaOFbo -ep6sJ3X/NEhZaezw6mNgEmi3JpNOONAg/C/GOL3ZpcUHU59+lyzsgwb6j062Ccpw -n/ZhssU8RwYzTIQeF2HE7cpVp8gA/B5MswjvGEZKFwZCRwuWzraYW8KcKnU/fKQJ -NfAmu8MGQS/aSeMR7N9N -=L9VU +iEYEAREIAAYFAk4GFhMACgkQgAnW8HDreRYZCgCfSidBxTnSlzRWmpRbBSRYOr0i +2x4AoMX2nmWRoxP8jthu9bmgwEgngD/u +=/pcM -----END PGP SIGNATURE----- diff --git a/sys-infiniband/openib-srptools/metadata.xml b/sys-infiniband/openib-srptools/metadata.xml index 27d6ce8d1..68d6e02a6 100644 --- a/sys-infiniband/openib-srptools/metadata.xml +++ b/sys-infiniband/openib-srptools/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>cluster</herd> -<longdescription> + <herd>cluster</herd> + <longdescription> srptools is a package of tools for discovering and connecting to SRP SCSI targets on InfiniBand fabrics. These targets can be accessed with the InfiniBand SRP initiator module, "ib_srp," included in Linux diff --git a/sys-infiniband/openib-srptools/openib-srptools-1.1.ebuild b/sys-infiniband/openib-srptools/openib-srptools-1.1.ebuild index 687db1c38..2ef2575c5 100644 --- a/sys-infiniband/openib-srptools/openib-srptools-1.1.ebuild +++ b/sys-infiniband/openib-srptools/openib-srptools-1.1.ebuild @@ -1,29 +1,17 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -SLOT="0" -LICENSE="|| ( GPL-2 BSD-2 )" - -KEYWORDS="~amd64" - -DESCRIPTION="OpenIB tools for discovering and connecting to SRP CSI targets on InfiniBand fabrics." +EAPI=4 +DESCRIPTION="Tools for discovering and connecting to SRP CSI targets on InfiniBand fabrics" HOMEPAGE="http://www.openfabrics.org/" #SRC_URI="http://www.openfabrics.org/downloads/openib-userspace-${PV}.tgz" SRC_URI="http://mirror.gentooscience.org/openib-userspace-${PV}.tgz" -S="${WORKDIR}/openib-userspace-${PV}/src/userspace/${PN}" +SLOT="0" +LICENSE="|| ( GPL-2 BSD-2 )" +KEYWORDS="~amd64" IUSE="" -DEPEND="" - -src_compile() { - econf || die "could not configure" - emake || die "emake failed" -} - -src_install() { - make DESTDIR="${D}" install || die "install failed" - dodoc README Copying Changelog NEWS -} +S="${WORKDIR}/openib-userspace-${PV}/src/userspace/${PN}" diff --git a/sys-infiniband/openib-userspace/Manifest b/sys-infiniband/openib-userspace/Manifest index 09abbc4ce..a27faa627 100644 --- a/sys-infiniband/openib-userspace/Manifest +++ b/sys-infiniband/openib-userspace/Manifest @@ -1,10 +1,20 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX opensm.conf.d 69 RMD160 b828bbee03a1ce5155719d1f2ecf4eed5125fd4e SHA1 ca2c9ff5da8775fcd9be6bf9a5b2e2904edf813d SHA256 3852877c73799b7b5524006dca058564f555947ccbdabb0c9909af5b1ac51425 AUX opensm.init.d 835 RMD160 645d929c491f26d5615c536e40cf5b54b8b7369a SHA1 d7520f02564f1f4cfa280dd0fb8872cd2346bb56 SHA256 71c5ec02ea9e17b61ed94a6938c8a390e027c11469d52a0baa933ae5d32eb591 DIST OFED-1.2.5.1.tgz 46256516 RMD160 b19f1917b32b7b15db75aace6ed433d57dc98fc5 SHA1 9a1ff30c97c94352f70e52d7cc31328013bea1b7 SHA256 41c6408135d8707d05bef8aa0a4ec548ae64ec010224e3b38746ab6f5c1e9b78 DIST OFED-1.2.5.5.tgz 46432282 RMD160 f5829858fca521d8675af1245d4764eeb87ff08d SHA1 faa027109b56583207eca9fd736164517acf7120 SHA256 ffb990b22d7b0f25026d9fe785aa97ca5920b5a0e620851deb057b9b83bbf907 DIST OFED-1.2.tgz 45785235 RMD160 22abc8ea493c01f18a5ca93f24645c0b3de81f49 SHA1 e179640b8f700b6dff9cc747910d786bba986175 SHA256 05ac6c3a96902388b40b05c6af0f0ce80059fc51980a039d53bfc94874166144 -EBUILD openib-userspace-1.2.5.1-r1.ebuild 3027 RMD160 64ea2851a66eeabaacf5d6425d0c09d6f60b3c5c SHA1 2135c63c540d38afd271c00ce003692a9e329354 SHA256 71fe087dbfa3495aa3ecc911c33634f1aa01e8c0d6de1ef3545bad917401f51b -EBUILD openib-userspace-1.2.5.5.ebuild 2826 RMD160 08f330716c0789aaff76069b49b3996f065f3679 SHA1 633bcc0cf3ce199fa958e82ca823ac41efa3d14b SHA256 926f1084f242f483e50b2bf1cdf7f541c63ddc7dfe835a8682c1d5e371b23589 -EBUILD openib-userspace-1.2.ebuild 2675 RMD160 6f0b0cf57ac739e8cedebbb8b86355c79328cca8 SHA1 40e5a13c968de73d83bf669cd3784d02c5974d34 SHA256 f39b51fc4d9e49c127fccc10accbed0accc5dcf6bdc49bdd046b7f68935762cc +EBUILD openib-userspace-1.2.5.1-r1.ebuild 2727 RMD160 c101f0687d063794300f6de8bbfc48823a2e250f SHA1 6cab3508d499b7572d745f92d9e34b043c8aeebc SHA256 a301dcc9d21d62c62d697a2d24931789727aabe7627568f71c59057c667c6466 +EBUILD openib-userspace-1.2.5.5.ebuild 2704 RMD160 67e11523d2683ad5786d92ba313cb1375556eba7 SHA1 7a1d16e43a637d8a5494475affb87be96a10b553 SHA256 3dafe1df02e3a51739ffb1670cf7935db88187f9108929af61ddd68a1c3b857e +EBUILD openib-userspace-1.2.ebuild 2373 RMD160 96db80604255fc4447b55a0657be042f9f09127b SHA1 2c88c633400b541bab796b46c501c6209eca199a SHA256 0a0fa50730db588900fa05156e076de352329b6f521232470f2abd179b21f1d6 MISC ChangeLog 930 RMD160 7f896de7f67d0e05d717429577f217a39f4ca8b6 SHA1 bc46a4100c7b63d0b29c12338dc32d63f7ead9ee SHA256 2e3f89049910bc854b1174a4c38b59e78d9bab9f07e38ac2d615e3a8f4570c94 -MISC metadata.xml 290 RMD160 8deacc2efb676788b32b4961d7f30b1b968e057c SHA1 3a6a067aef6960a9d8ddc5f26d12a5d7653cb19d SHA256 86cfc299f76b8bdda514e8817c8ef3a4d49de1938ccc79bdcb98a73dcbc4d6a3 +MISC metadata.xml 1021 RMD160 67fe0fbffca3d3359c162803d984cdcc14e7c50a SHA1 66d882a536442dc00ce965314d95363eace3e833 SHA256 c0f89e4a4ade066b4611e801face9d2110978f70d7f0e9d560ebc307a2c3013a +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Evf8ACgkQgAnW8HDreRa+2wCeIBZcesbai+3PdA5YOMBMezXT +35oAn3GSeiQr0IwjMGcqJ0HsQhMZ9YzQ +=F9oJ +-----END PGP SIGNATURE----- diff --git a/sys-infiniband/openib-userspace/metadata.xml b/sys-infiniband/openib-userspace/metadata.xml index d79dcfd92..d6772dac2 100644 --- a/sys-infiniband/openib-userspace/metadata.xml +++ b/sys-infiniband/openib-userspace/metadata.xml @@ -1,9 +1,20 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>cluster</herd> -<longdescription> + <herd>cluster</herd> + <longdescription> OpenFabrics Userspace libraries and tools. Infiniband for Linux. See 'www.openfabrics.org'. </longdescription> + <use> + <flag name="cxgb3">Automatically generated description for cxgb3</flag> + <flag name="dapl">Automatically generated description for dapl</flag> + <flag name="ehca">Automatically generated description for ehca</flag> + <flag name="ipath">Automatically generated description for ipath</flag> + <flag name="mstflint">Automatically generated description for mstflint</flag> + <flag name="opensm">Automatically generated description for opensm</flag> + <flag name="qlvnictools">Automatically generated description for qlvnictools</flag> + <flag name="srptools">Automatically generated description for srptools</flag> + <flag name="tvflash">Automatically generated description for tvflash</flag> + </use> </pkgmetadata> diff --git a/sys-infiniband/openib-userspace/openib-userspace-1.2.5.1-r1.ebuild b/sys-infiniband/openib-userspace/openib-userspace-1.2.5.1-r1.ebuild index 31221cd5d..0c984382d 100644 --- a/sys-infiniband/openib-userspace/openib-userspace-1.2.5.1-r1.ebuild +++ b/sys-infiniband/openib-userspace/openib-userspace-1.2.5.1-r1.ebuild @@ -1,46 +1,44 @@ # Copyright 1999-2008 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /CVS/groups/vistech/bgreen-overlay/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild,v 1.1.1.1 2007/10/12 20:18:26 bgreen Exp $ +# $Header: $ inherit rpm -LICENSE="|| ( GPL-2 BSD-2 )" -SLOT="0" - -KEYWORDS="~x86 ~amd64" - -DESCRIPTION="OpenFabrics userspace libraries and utilities. This ebuild is an -all-inclusive alternative to the openib metapackage and dependencies" - -HOMEPAGE="http://www.openfabrics.org/" SHORT_PV=${PV%\.[^.]} -SRC_URI="http://www.openfabrics.org/builds/ofed-${SHORT_PV}/release/OFED-${PV}.tgz" MY_P="OFED-${PV}" -S="${WORKDIR}/ofa_user-${PV}" OSM="${S}/src/userspace/management/osm" -IUSE="ehca ipath cxgb3 opensm dapl srptools qlvnictools tvflash mstflint" +DESCRIPTION="OpenFabrics userspace libraries and utilities" +HOMEPAGE="http://www.openfabrics.org/" +SRC_URI="http://www.openfabrics.org/builds/ofed-${SHORT_PV}/release/OFED-${PV}.tgz" + +SLOT="0" +LICENSE="|| ( GPL-2 BSD-2 )" +KEYWORDS="~x86 ~amd64" +IUSE="cxgb3 dapl ehca ipath mstflint opensm qlvnictools srptools tvflash" DEPEND="" RDEPEND="${DEPEND} - !<=sys-infiniband/openib-drivers-1.2 - !sys-infiniband/libibverbs - !sys-infiniband/libmthca - !sys-infiniband/libipathverbs - !sys-infiniband/librdmacm - !sys-infiniband/libsdp - !sys-infiniband/dapl - !sys-infiniband/libehca - !sys-infiniband/libibcm - !sys-infiniband/libibcommon - !sys-infiniband/libibmad - !sys-infiniband/libibumad - !sys-infiniband/openib-diags - !sys-infiniband/openib-files - !sys-infiniband/openib-osm - !sys-infiniband/openib-perf - !sys-infiniband/openib-srptools - !sys-infiniband/openib" + !<=sys-infiniband/openib-drivers-1.2 + !sys-infiniband/libibverbs + !sys-infiniband/libmthca + !sys-infiniband/libipathverbs + !sys-infiniband/librdmacm + !sys-infiniband/libsdp + !sys-infiniband/dapl + !sys-infiniband/libehca + !sys-infiniband/libibcm + !sys-infiniband/libibcommon + !sys-infiniband/libibmad + !sys-infiniband/libibumad + !sys-infiniband/openib-diags + !sys-infiniband/openib-files + !sys-infiniband/openib-osm + !sys-infiniband/openib-perf + !sys-infiniband/openib-srptools + !sys-infiniband/openib" + +S="${WORKDIR}/ofa_user-${PV}" src_unpack() { unpack ${A} || die "unpack failed" @@ -49,15 +47,15 @@ src_unpack() { } src_compile() { + use ipath && myconf="$myconf --with-libipathverbs" + use ehca && myconf="$myconf --with-libehca" + use cxgb3 && myconf="$myconf --with-libcxgb3" + use opensm && myconf="$myconf --with-management-libs" myconf="--with-libibverbs --with-libmthca" - if use ipath ; then myconf="$myconf --with-libipathverbs"; fi - if use ehca ; then myconf="$myconf --with-libehca"; fi - if use cxgb3 ; then myconf="$myconf --with-libcxgb3"; fi myconf="$myconf --with-libibcm" myconf="$myconf --with-libsdp" myconf="$myconf --with-librdmacm" myconf="$myconf $(use_with dapl)" - if use opensm ; then myconf="$myconf --with-management-libs"; fi myconf="$myconf $(use_with opensm)" myconf="$myconf --with-openib-diags" myconf="$myconf --with-perftest" @@ -71,7 +69,7 @@ src_compile() { ./configure --prefix=/usr --mandir=/usr/share/man \ --sysconfdir=/etc \ ${myconf} ${EXTRA_ECONF} || die "configure failed" - emake -j1 + emake -j1 || die } src_install() { @@ -92,4 +90,3 @@ pkg_postinst() { einfo "edit /etc/opensm.conf and add opensm to your start-up scripts:" einfo "\`rc-update add opensm default\`" } - diff --git a/sys-infiniband/openib-userspace/openib-userspace-1.2.5.5.ebuild b/sys-infiniband/openib-userspace/openib-userspace-1.2.5.5.ebuild index d8bbe3b30..95faf6144 100644 --- a/sys-infiniband/openib-userspace/openib-userspace-1.2.5.5.ebuild +++ b/sys-infiniband/openib-userspace/openib-userspace-1.2.5.5.ebuild @@ -1,45 +1,43 @@ # Copyright 1999-2008 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header$ +# $Header: $ inherit rpm -LICENSE="|| ( GPL-2 BSD-2 )" -SLOT="0" - -KEYWORDS="~x86 ~amd64" - -DESCRIPTION="OpenFabrics userspace distribution. An all-inclusive ebuild -alternative to the openib meta-ebuild" - -HOMEPAGE="http://www.openfabrics.org/" SHORT_PV=${PV%\.[^.]} -SRC_URI="http://www.openfabrics.org/builds/ofed-${SHORT_PV}/release/OFED-${PV}.tgz" MY_P="OFED-${PV}" -S="${WORKDIR}/ofa_user-${PV}" OSM="${S}/src/userspace/management/osm" -IUSE="ehca ipath cxgb3 opensm dapl srptools qlvnictools tvflash mstflint" +DESCRIPTION="OpenFabrics userspace libraries and utilities" +HOMEPAGE="http://www.openfabrics.org/" +SRC_URI="http://www.openfabrics.org/builds/ofed-${SHORT_PV}/release/OFED-${PV}.tgz" + +SLOT="0" +LICENSE="|| ( GPL-2 BSD-2 )" +KEYWORDS="~x86 ~amd64" +IUSE="cxgb3 dapl ehca ipath mstflint opensm qlvnictools srptools tvflash" DEPEND="" PDEPEND="=sys-infiniband/openib-files-${PV}" RDEPEND="${DEPEND} - !sys-infiniband/libibverbs - !sys-infiniband/libmthca - !sys-infiniband/libipathverbs - !sys-infiniband/librdmacm - !sys-infiniband/libsdp - !sys-infiniband/dapl - !sys-infiniband/libehca - !sys-infiniband/libibcm - !sys-infiniband/libibcommon - !sys-infiniband/libibmad - !sys-infiniband/libibumad - !sys-infiniband/openib-diags - !sys-infiniband/openib-osm - !sys-infiniband/openib-perf - !sys-infiniband/openib-srptools - !sys-infiniband/openib" + !sys-infiniband/libibverbs + !sys-infiniband/libmthca + !sys-infiniband/libipathverbs + !sys-infiniband/librdmacm + !sys-infiniband/libsdp + !sys-infiniband/dapl + !sys-infiniband/libehca + !sys-infiniband/libibcm + !sys-infiniband/libibcommon + !sys-infiniband/libibmad + !sys-infiniband/libibumad + !sys-infiniband/openib-diags + !sys-infiniband/openib-osm + !sys-infiniband/openib-perf + !sys-infiniband/openib-srptools + !sys-infiniband/openib" + +S="${WORKDIR}/ofa_user-${PV}" src_unpack() { unpack ${A} || die "unpack failed" @@ -48,15 +46,15 @@ src_unpack() { } src_compile() { + use ipath && myconf="$myconf --with-libipathverbs" + use ehca && myconf="$myconf --with-libehca" + use cxgb3 && myconf="$myconf --with-libcxgb3" + use opensm && myconf="$myconf --with-management-libs" myconf="--with-libibverbs --with-libmthca" - if use ipath ; then myconf="$myconf --with-libipathverbs"; fi - if use ehca ; then myconf="$myconf --with-libehca"; fi - if use cxgb3 ; then myconf="$myconf --with-libcxgb3"; fi myconf="$myconf --with-libibcm" myconf="$myconf --with-libsdp" myconf="$myconf --with-librdmacm" myconf="$myconf $(use_with dapl)" - if use opensm ; then myconf="$myconf --with-management-libs"; fi myconf="$myconf $(use_with opensm)" myconf="$myconf --with-openib-diags" myconf="$myconf --with-perftest" @@ -70,7 +68,7 @@ src_compile() { ./configure --prefix=/usr --mandir=/usr/share/man \ --sysconfdir=/etc \ ${myconf} ${EXTRA_ECONF} || die "configure failed" - emake -j1 + emake -j1 || die } src_install() { @@ -91,4 +89,3 @@ pkg_postinst() { einfo "edit /etc/opensm.conf and add opensm to your start-up scripts:" einfo "\`rc-update add opensm default\`" } - diff --git a/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild b/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild index 02d1ee458..c1088f106 100644 --- a/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild +++ b/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild @@ -1,45 +1,43 @@ # Copyright 1999-2008 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /CVS/groups/vistech/bgreen-overlay/sys-infiniband/openib-userspace/openib-userspace-1.2.ebuild,v 1.1.1.1 2007/10/12 20:18:26 bgreen Exp $ +# $Header: $ inherit rpm -LICENSE="|| ( GPL-2 BSD-2 )" -SLOT="0" - -KEYWORDS="~x86 ~amd64" - -DESCRIPTION="OpenFabrics userspace libraries and utilities. This ebuild is an -all-inclusive alternative to the openib metapackage and dependencies" +MY_P="OFED-${PV}" +DESCRIPTION="OpenFabrics userspace libraries and utilities" HOMEPAGE="http://www.openfabrics.org/" SRC_URI="http://www.openfabrics.org/builds/ofed-${PV}/OFED-${PV}.tgz" -MY_P="OFED-${PV}" -S="${WORKDIR}/ofa_user-${PV}" -IUSE="ehca ipath cxgb3 opensm dapl srptools qlvnictools tvflash mstflint" +SLOT="0" +LICENSE="|| ( GPL-2 BSD-2 )" +KEYWORDS="~x86 ~amd64" +IUSE="cxgb3 dapl ehca ipath mstflint opensm qlvnictools srptools tvflash" DEPEND="" RDEPEND="${DEPEND} - >=sys-infiniband/openib-drivers-1.2 - !sys-infiniband/libibverbs - !sys-infiniband/libmthca - !sys-infiniband/libipathverbs - !sys-infiniband/librdmacm - !sys-infiniband/libsdp - !sys-infiniband/dapl - !sys-infiniband/libehca - !sys-infiniband/libibcm - !sys-infiniband/libibcommon - !sys-infiniband/libibmad - !sys-infiniband/libibumad - !sys-infiniband/openib-diags - !sys-infiniband/openib-files - !sys-infiniband/openib-mvapich2 - !sys-infiniband/openib-osm - !sys-infiniband/openib-perf - !sys-infiniband/openib-srptools - !sys-infiniband/openib" + >=sys-infiniband/openib-drivers-1.2 + !sys-infiniband/libibverbs + !sys-infiniband/libmthca + !sys-infiniband/libipathverbs + !sys-infiniband/librdmacm + !sys-infiniband/libsdp + !sys-infiniband/dapl + !sys-infiniband/libehca + !sys-infiniband/libibcm + !sys-infiniband/libibcommon + !sys-infiniband/libibmad + !sys-infiniband/libibumad + !sys-infiniband/openib-diags + !sys-infiniband/openib-files + !sys-infiniband/openib-mvapich2 + !sys-infiniband/openib-osm + !sys-infiniband/openib-perf + !sys-infiniband/openib-srptools + !sys-infiniband/openib" + +S="${WORKDIR}/ofa_user-${PV}" src_unpack() { unpack ${A} || die "unpack failed" @@ -48,15 +46,15 @@ src_unpack() { } src_compile() { + use ipath && myconf="$myconf --with-libipathverbs" + use ehca && myconf="$myconf --with-libehca" + use cxgb3 && myconf="$myconf --with-libcxgb3" + use opensm && myconf="$myconf --with-management-libs" myconf="--with-libibverbs --with-libmthca" - if use ipath ; then myconf="$myconf --with-libipathverbs"; fi - if use ehca ; then myconf="$myconf --with-libehca"; fi - if use cxgb3 ; then myconf="$myconf --with-libcxgb3"; fi myconf="$myconf --with-libibcm" myconf="$myconf --with-libsdp" myconf="$myconf --with-librdmacm" myconf="$myconf $(use_with dapl)" - if use opensm ; then myconf="$myconf --with-management-libs"; fi myconf="$myconf $(use_with opensm)" myconf="$myconf --with-openib-diags" myconf="$myconf --with-perftest" @@ -70,7 +68,7 @@ src_compile() { ./configure --prefix=/usr --mandir=/usr/share/man \ --sysconfdir=/etc \ ${myconf} ${EXTRA_ECONF} || die "configure failed" - emake + emake || die } src_install() { @@ -82,4 +80,3 @@ src_install() { newinitd "${FILESDIR}/opensm.init.d" opensm fi } - diff --git a/sys-infiniband/openib/Manifest b/sys-infiniband/openib/Manifest index df9d53904..650dabda0 100644 --- a/sys-infiniband/openib/Manifest +++ b/sys-infiniband/openib/Manifest @@ -1,4 +1,14 @@ -EBUILD openib-1.4.1.ebuild 991 RMD160 23d9c3ffc78bbf16eea53f1503ebfc77878a3091 SHA1 ca3cc19cfe9fdb7bccaa7c1d6db631e866614786 SHA256 89a366b8f83736a8e1be6309fae9e53df229ca4823d4e8ebcd28e75cf2348c72 -EBUILD openib-1.4.ebuild 991 RMD160 23d9c3ffc78bbf16eea53f1503ebfc77878a3091 SHA1 ca3cc19cfe9fdb7bccaa7c1d6db631e866614786 SHA256 89a366b8f83736a8e1be6309fae9e53df229ca4823d4e8ebcd28e75cf2348c72 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +EBUILD openib-1.4.1.ebuild 991 RMD160 333b2a72f53c434ada3f9d511d51e3189f4a7647 SHA1 36945fc4c6920838ed851041c91d732e206b90fd SHA256 0affaf0b72fef9f3bcd9a8ed8c0cceffe546addfd2b1175b31ca607824e18ca2 +EBUILD openib-1.4.ebuild 991 RMD160 333b2a72f53c434ada3f9d511d51e3189f4a7647 SHA1 36945fc4c6920838ed851041c91d732e206b90fd SHA256 0affaf0b72fef9f3bcd9a8ed8c0cceffe546addfd2b1175b31ca607824e18ca2 MISC ChangeLog 711 RMD160 82de0290b4307933e0b181a5a36511c4dcda0837 SHA1 7d10ddbf126212718a0951967f103e42aadb97f3 SHA256 bcf0743c4e5bbbed593876476d2fac956eaff4787359bd8d514db09276109825 -MISC metadata.xml 273 RMD160 19db7de67d8f6f506a22dd8adc8cd2e2a562b6bb SHA1 e9d1b4bb8fb0323553f656b2d11cc1cf2a900196 SHA256 8c90385fd9c444052c28524c0d9a29397513de5e72444efabcdf196e76f1e50d +MISC metadata.xml 894 RMD160 5907d918dc57337abf7c4f19a74d3b42f0c3c792 SHA1 37a1544f7c9fd66717c64d8f24242d9e2df6c5dc SHA256 559dbcfa2f5d1da63813b08548f01b5b343204b048c1895caa683179ad10ae88 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EvgQACgkQgAnW8HDreRYw+gCfeF9czO6QPMhZaX305X7MEkgV +dOMAoKceWaEnvRJrAAsasSdXPXnczddy +=j/Df +-----END PGP SIGNATURE----- diff --git a/sys-infiniband/openib/metadata.xml b/sys-infiniband/openib/metadata.xml index d904018fd..df7ed29c5 100644 --- a/sys-infiniband/openib/metadata.xml +++ b/sys-infiniband/openib/metadata.xml @@ -1,8 +1,18 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>cluster</herd> -<longdescription> + <herd>cluster</herd> + <longdescription> Meta package for OpenIB. Infiniband for Linux. See 'www.openfabrics.org'. </longdescription> + <use> + <flag name="dapl">Automatically generated description for dapl</flag> + <flag name="diags">Automatically generated description for diags</flag> + <flag name="ehca">Automatically generated description for ehca</flag> + <flag name="ipath">Automatically generated description for ipath</flag> + <flag name="mlx4">Automatically generated description for mlx4</flag> + <flag name="mthca">Automatically generated description for mthca</flag> + <flag name="nes">Automatically generated description for nes</flag> + <flag name="opensm">Automatically generated description for opensm</flag> + </use> </pkgmetadata> diff --git a/sys-infiniband/openib/openib-1.4.1.ebuild b/sys-infiniband/openib/openib-1.4.1.ebuild index 4356196d0..5bce57cc8 100644 --- a/sys-infiniband/openib/openib-1.4.1.ebuild +++ b/sys-infiniband/openib/openib-1.4.1.ebuild @@ -2,17 +2,19 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=3 HOMEPAGE="http://www.openfabrics.org/" DESCRIPTION="Meta package OFED" SRC_URI="" + SLOT="0" LICENSE="|| ( GPL-2 BSD-2 )" KEYWORDS="~amd64 ~x86" IUSE="+dapl diags ehca ipath mlx4 mthca nes +opensm" -DEPEND=">=sys-infiniband/libibcm-1.0.4 +DEPEND=" + >=sys-infiniband/libibcm-1.0.4 >=sys-infiniband/libibcommon-1.1.2_p20081020 >=sys-infiniband/libibmad-1.2.3_p20081118 >=sys-infiniband/libibumad-1.2.3_p20081118 @@ -28,4 +30,3 @@ DEPEND=">=sys-infiniband/libibcm-1.0.4 nes? ( >=sys-infiniband/libnes-0.5 ) opensm? ( >=sys-infiniband/openib-osm-3.2.5_p20081207 )" RDEPEND="${DEPEND}" - diff --git a/sys-infiniband/openib/openib-1.4.ebuild b/sys-infiniband/openib/openib-1.4.ebuild index 4356196d0..5bce57cc8 100644 --- a/sys-infiniband/openib/openib-1.4.ebuild +++ b/sys-infiniband/openib/openib-1.4.ebuild @@ -2,17 +2,19 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=3 HOMEPAGE="http://www.openfabrics.org/" DESCRIPTION="Meta package OFED" SRC_URI="" + SLOT="0" LICENSE="|| ( GPL-2 BSD-2 )" KEYWORDS="~amd64 ~x86" IUSE="+dapl diags ehca ipath mlx4 mthca nes +opensm" -DEPEND=">=sys-infiniband/libibcm-1.0.4 +DEPEND=" + >=sys-infiniband/libibcm-1.0.4 >=sys-infiniband/libibcommon-1.1.2_p20081020 >=sys-infiniband/libibmad-1.2.3_p20081118 >=sys-infiniband/libibumad-1.2.3_p20081118 @@ -28,4 +30,3 @@ DEPEND=">=sys-infiniband/libibcm-1.0.4 nes? ( >=sys-infiniband/libnes-0.5 ) opensm? ( >=sys-infiniband/openib-osm-3.2.5_p20081207 )" RDEPEND="${DEPEND}" - diff --git a/sys-kernel/cluster-sources/ChangeLog b/sys-kernel/cluster-sources/ChangeLog new file mode 100644 index 000000000..087e3232f --- /dev/null +++ b/sys-kernel/cluster-sources/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sys-kernel/cluster-sources +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + diff --git a/sys-kernel/cluster-sources/Manifest b/sys-kernel/cluster-sources/Manifest new file mode 100644 index 000000000..2bd874718 --- /dev/null +++ b/sys-kernel/cluster-sources/Manifest @@ -0,0 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +DIST clusterpathches-2.6.39-2.tar.bz2 23913 RMD160 72073d57382a7dac648be3ab73487e4812476293 SHA1 343de96de7405129e2c5c868cd0d043eb021d994 SHA256 92fa832384c988c075128a1f30c1befd698fec9859c1926720c7ae23c6b777a3 +DIST genpatches-2.6.39-2.base.tar.bz2 57467 RMD160 c20f1d07ea619bbd1d9edab6418507127f8ae4c5 SHA1 d32a62dc405c0fbc002b7d1946959a036c5a2217 SHA256 0cc7c4b536be7eaba3a3f1875132570d5ccc0ea1317ff9891544c492330350e6 +DIST genpatches-2.6.39-2.extras.tar.bz2 15672 RMD160 e94ef6536034ccb5e8cf7d5b0282c2274f33cc0d SHA1 68edf710278d5c0454f361b140663d9eb4ea6998 SHA256 8cd7268fc0329278e0fd00fdde9e928c353e591c5147fb4eed50a80fefbf87fa +DIST linux-2.6.39.tar.bz2 76096559 RMD160 feddc516bc15e78f12f611ff184d38baa4eac4ee SHA1 68518112821e55f4ac1df64f2e0e809cedfcc5ef SHA256 584d17f2a3ee18a9501d7ff36907639e538cfdba4529978b8550c461d45c61f6 +EBUILD cluster-sources-2.6.39.ebuild 1011 RMD160 c670c8b465c1cd43b4abdecce00b0fe97a1cec0e SHA1 f324d4980fda6d96e5aac32578767cbc6504a7af SHA256 3ffe7c1da5669c15ea19dce3cd865216ea35d0004d7ed6d47b326b2ca3384378 +MISC ChangeLog 224 RMD160 ff4aa0a28e1d45c57f66007e3b7797838f256186 SHA1 6135eda91b602423fd3af553e7fbb6ae6e4d2d03 SHA256 d7dcc5f5faf81cd00fde16d5ef110df318fe3e0c01cc3bcf50a64b400b61e43c +MISC metadata.xml 263 RMD160 e82d25514ec790cf4184509b1be7ee226dcc20ab SHA1 1aa6ac017f9d83f5e58ef71827371b28b0e1b93f SHA256 c823c9de88cec66a61b8a6111630efe0435fa05142df06a24fe243d6570f0ac3 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Fkl8ACgkQgAnW8HDreRY/MwCfdKMSYXr0TQiNrY7LW2X2utYF +BK0An1OlCM4DMZHJEVxbjVcutcAoEgwM +=A6E4 +-----END PGP SIGNATURE----- diff --git a/sys-kernel/cluster-sources/cluster-sources-2.6.39.ebuild b/sys-kernel/cluster-sources/cluster-sources-2.6.39.ebuild new file mode 100644 index 000000000..21e573652 --- /dev/null +++ b/sys-kernel/cluster-sources/cluster-sources-2.6.39.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sys-kernel/tuxonice-sources/tuxonice-sources-2.6.38-r1.ebuild,v 1.1 2011/05/24 14:11:20 nelchael Exp $ + +ETYPE="sources" +K_WANT_GENPATCHES="base extras" +K_GENPATCHES_VER="2" + +inherit kernel-2 +detect_version +detect_arch + +DESCRIPTION="Gentoo patchset + some additional cluster related patches" +HOMEPAGE="http://dev.gentoo.org/~mpagano/genpatches/ http://dev.gentoo.org/~alexxy/cluster/" +IUSE="" + +CLUSTER_VERSION="2" + +CLUSTER_SRC="clusterpathches-${PV}-${CLUSTER_VERSION}.tar.bz2" + +CLUSTER_URI="http://dev.gentoo.org/~alexxy/cluster/${CLUSTER_SRC}" + +UNIPATCH_LIST="${DISTDIR}/${CLUSTER_SRC}" +UNIPATCH_STRICTORDER="yes" +SRC_URI="${KERNEL_URI} ${GENPATCHES_URI} ${ARCH_URI} ${CLUSTER_URI}" + +KEYWORDS="~amd64" + +K_SECURITY_UNSUPPORTED="1" + +pkg_postinst() { + kernel-2_pkg_postinst + einfo "For more info on this patchset, and how to report problems, see:" + einfo "${HOMEPAGE}" +} diff --git a/sys-kernel/cluster-sources/metadata.xml b/sys-kernel/cluster-sources/metadata.xml new file mode 100644 index 000000000..528cfaa46 --- /dev/null +++ b/sys-kernel/cluster-sources/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>cluster</herd> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> +</pkgmetadata> diff --git a/x11-libs/xview/ChangeLog b/x11-libs/xview/ChangeLog index 84009e26e..c281a436f 100644 --- a/x11-libs/xview/ChangeLog +++ b/x11-libs/xview/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for x11-libs/xview -# Copyright 2000-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + 03 Feb 2009; justin Lecher (jlec) <jlec@j-schmitz.net> xview-3.2-r6.ebuild, -xview-3.2-r7.ebuild, xview-3.2-r8.ebuild: included fix from bug 245409 Thanks to pva diff --git a/x11-libs/xview/Manifest b/x11-libs/xview/Manifest index 0ba7c7ac1..78a164100 100644 --- a/x11-libs/xview/Manifest +++ b/x11-libs/xview/Manifest @@ -7,12 +7,12 @@ AUX lseek2.diff 815 RMD160 008b5a039b5014b581d0699a3241142d2a019c1c SHA1 a1b6899 DIST xview-3.2-gcc-4.1-v0.1.patch.bz2 8018 RMD160 0387c073d7f4c8303467f3065ba2a573fdb6710e SHA1 f06eb2412e4d61dffaee7db436527d7933a50931 SHA256 2b26f10122535eff43a4f87fc97ffb54eac88c312a3688b05bce806ce9a273ba DIST xview-3.2p1.4-19c.tar.gz 3350088 RMD160 6e0e90a737df7de8d30dbbd647527d599f13e8dd SHA1 1a2023945edef33ea4251fcb3b9e69bcf35a531c SHA256 ce05762918ccaa0bd86819e1347b57b6d0e5d515b148f9f740d3ffd1fa9eea83 EBUILD xview-3.2-r6.ebuild 3630 RMD160 354aba1eefb98be96218800e60861a92a31e87d6 SHA1 b147c1fba7ab2d318af0fa574f968e944f774f3a SHA256 cd2b1eb82c556997fdbdd92baebef56118393b5ad6274434b2553e25cfe7493b -MISC ChangeLog 5022 RMD160 3fbdbd059b25f0eae2cebd5a9bedccec6d5a12ec SHA1 a157b30526742c77d9605399d65c01a910c489ea SHA256 e9123b0ae8a53056c7e862e1945c047d83e68a0ecb506414c679c4f7ebcd27f7 -MISC metadata.xml 263 RMD160 6a7463bafc4f1e7df75d12fc57c693ad582d58fa SHA1 e38c1eecffc0f52395d69359a9e3dd1114bcf550 SHA256 31cd25872ef5bc46e50dd04eb523bd093d07797f39b072177df59690a4fc07a3 +MISC ChangeLog 5119 RMD160 3f6c89da5f2a9e937413df0488d9eae765591892 SHA1 f070a4eb5d89832e4d71558627e3d560732ab2bd SHA256 bc43a074deb589f024bd720341dce223bbfb0a6df318329541919930ffb80754 +MISC metadata.xml 255 RMD160 a86d48ddbccb0fabe237d68dcc9989b53cb0550b SHA1 91fd2c69d256979c92ac85401420c2760fb80c44 SHA256 d39da63d4038ef783fada0c4970d172c9620ae6727b88cd8406ee2d6afc9770a -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAkwgXbkACgkQgAnW8HDreRaq1gCeNlxEsp29pcQmQV6dg10LMFAU -oxsAn3KAn2oA90/n/oOUFeYuM73PUzU0 -=zjOn +iEYEARECAAYFAk4FkrgACgkQgAnW8HDreRbhrwCgrdbBMgdCTw1TYQkNBipcPPyg +/8IAoIoGyRhSMBhLolU0FCf9b/VrxwZt +=3JTl -----END PGP SIGNATURE----- diff --git a/x11-libs/xview/metadata.xml b/x11-libs/xview/metadata.xml index 27e626a3f..59d99c304 100644 --- a/x11-libs/xview/metadata.xml +++ b/x11-libs/xview/metadata.xml @@ -1,10 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>maintainer-wanted</herd> - <maintainer> - <email>jlec@gentoo.org</email> - <name>Justin Lecher</name> - </maintainer> + <herd>sci</herd> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher</name> + </maintainer> </pkgmetadata> - |