diff options
24 files changed, 303 insertions, 1482 deletions
diff --git a/licenses/vina_license b/licenses/vina_license new file mode 100644 index 000000000..3ccada273 --- /dev/null +++ b/licenses/vina_license @@ -0,0 +1,135 @@ +AUTODOCK VINA 1.0 SOFTWARE TRANSFER LICENSE AGREEMENT + +THIS SOFTWARE LICENSE AGREEMENT ("Agreement") is made by and between The +Scripps Research Institute ("TSRI"), having an address at 10550 N. Torrey Pines +Road, La Jolla, CA 92037 and yourself ("Recipient") + +RECITALS +A. TSRI is the owner of the Software (as defined below). +B. TSRI desires to grant to Recipient and Recipient desires to obtain from TSRI +a non-exclusive license to use the Software solely in accordance with the terms +and on the conditions set forth in this Agreement. + +NOW, THEREFORE, the parties hereto agree as follows: +1. DEFINITIONS. +1.1 "Software" shall mean the Vina computer program in binary executable form. + +2. GRANT OF RIGHTS. +The License granted for Software under this Agreement authorizes Recipient on a +nonexclusive basis to use one copy of the Software. Recipient may retain one +additional copy of the Software for archival purposes. Recipient agrees to use +the Software for internal non-commercial research purposes only, and shall not +distribute or transfer the Software to anyone not under the Recipient +Scientist's direct supervision or beyond the Recipient Scientist's +laboratory. + +3. DELIVERY. +3.1 Software. TSRI shall deliver to Recipient a master copy of the Software +licensed hereunder in binary executable form, suitable for reproduction, in +electronic files only. + +4. MODIFICATIONS. +4.1 Other Modifications. Recipient may, from time to time, request that TSRI +incorporate certain features, enhancements or modifications into the Software. +TSRI may, in its sole discretion, undertake to incorporate such changes, which +shall be the sole property of TSRI, and distribute the Software so modified to +all or any of TSRI's licensees. Any modifications or derivative works based on +the Software are considered part of the Software and ownership thereof is +retained by TSRI. + +5. COPIES AND RECORDS. Recipient agrees to maintain appropriate records of the +number and location of all copies of the Software. + +6. PROTECTION OF LICENSED SOFTWARE. +6.1 Proprietary Notices. Recipient agrees to respect and not to remove, +obliterate, or cancel from view any copyright, trademark, confidentiality or +other proprietary notice, mark, or legend appearing on any of the Software or +output generated by the Software, and to reproduce and include same on each +copy of the Software. + +6.2 Protection of Ownership. Recipient agrees to use its best efforts, +consistent with the practices and procedures Recipient takes to protect +Recipient's own most valuable proprietary information and materials, and will +take all reasonable steps to protect the Software and any pertinent +documentation and associated trade secrets against any unauthorized use, +reproduction, disclosure or distribution. + +7. CONFIDENTIALITY. +7.1 Acknowledgement. Recipient hereby acknowledges and agrees that the Software +constitutes and contains valuable proprietary products and trade secrets of +TSRI embodying substantial creative efforts and confidential information, +ideas, and expressions. Accordingly, Recipient agrees to treat (and take +precautions to ensure that its employees treat) the Software as confidential, +not to disclose or permit to any third party or entity access to the Software +or any portion thereof without the written permission of a duly authorized +representative of TSRI. + +7.2 Injunctive Relief. Recipient acknowledges that the unauthorized use, +transfer or disclosure of the Software or copies thereof will (i) substantially +diminish the value to TSRI of the trade secrets and other proprietary interests +that are the subject of this Agreement; (ii) render TSRI's remedy at law for +such unauthorized use, disclosure or transfer inadequate; and (iii) cause +irreparable injury in a short period of time. If Recipient breaches any of its +obligations with respect to the use or confidentiality of the +Software, TSRI shall be entitled to seek equitable relief to protect its +interests therein, including, but not limited to, preliminary and permanent +injunctive relief. + +7.3 Survival. Recipient's obligations under this Article 7 will survive the +termination of this Agreement or of any license granted under this Agreement +for whatever reason. + +8. WARRANTIES; SUPERIOR RIGHTS. +8.1 Government Rights. Recipient understands that the Software may have been +developed under a funding agreement with the Government of the United States of +America and, if so, that the Government may have certain rights relative +thereto. This Agreement is explicitly made subject to the Government's rights +under any such agreement and any applicable law or regulation, if any. To the +extent that there +is a conflict between any such agreement, applicable law or regulation and this +Agreement, the terms of such Government agreement, applicable law or regulation +shall prevail. + +8.2 Disclaimer of Warranties. ANY INFORMATION, MATERIALS OR SERVICES FURNISHED +BY TSRI PURSUANT TO THIS AGREEMENT ARE ON AN "AS IS" BASIS. TSRI DOES NOT +REPRESENT OR WARRANT THAT ALL ERRORS IN THE SOFTWARE WILL BE CORRECTED. THERE +ARE NO WARRANTIES RESPECTING THE SOFTWARE OR SERVICES PROVIDED HEREUNDER, +EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTY OF DESIGN, +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, EVEN IF TSRI HAS BEEN +INFORMED OF SUCH PURPOSE OR THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT, +COPYRIGHT, TRADEMARK, OR OTHER PROPRIETARY RIGHTS. NO AGENT OF TSRI IS +AUTHORIZED TO ALTER OR EXCEED THE WARRANTY OBLIGATIONS OF TSRI AS SET FORTH +HEREIN. + +9. INDEMNIFICATION. +Except to the extent prohibited by law, Recipient shall indemnify and hold +harmless, TSRI, its trustees, officers, agents and employees from and against +any claims, demands, or causes of action whatsoever, including without +limitation those arising on account of Recipient's modification or enhancement +of the Software or otherwise caused by, or arising out of, or resulting from, +the exercise or practice of the license granted hereunder by Recipient, its +sublicensees, if any, its subsidiaries or their officers, employees, agents or +representatives. + +10. NONASSIGNABILITY. Any and all assignments of this Agreement or any rights +granted hereunder by Recipient without the prior written consent of TSRI are +void except (i) to an affiliate of Recipient or (ii) as expressly permitted +hereunder. + +11. GOVERNING LAW; JURISDICTION AND VENUE. The validity, interpretation, +construction and performance of this Agreement shall be governed by the laws of +the State of California. + +12. SEVERABILITY. If any provision of this Agreement shall be held by a court +of competent jurisdiction to be illegal, invalid or unenforceable, the +remaining provisions shall remain in full force and effect. This Agreement and +its exhibits contain the entire understanding and agreement between the parties +respecting the subject matter hereof. This Agreement may not be supplemented, +modified, amended, released or discharged except by an instrument in writing +signed by each party's duly authorized representative. All captions and +headings in this Agreement are for purposes of convenience only and +shall not affect the construction or interpretation of any of its provisions. +Any waiver by either party of any default or breach hereunder shall not +constitute a waiver of any provision of this Agreement or of any subsequent +default or breach of the same or a different kind. + diff --git a/sci-chemistry/autodock_vina/ChangeLog b/sci-chemistry/autodock_vina/ChangeLog new file mode 100644 index 000000000..8d4dac031 --- /dev/null +++ b/sci-chemistry/autodock_vina/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-chemistry/autodock_vina +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*autodock_vina-1.0.3 (04 Feb 2010) + + 04 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> + +autodock_vina-1.0.3.ebuild, +metadata.xml: + Initial import per bug #282682 + diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest new file mode 100644 index 000000000..ee486663c --- /dev/null +++ b/sci-chemistry/autodock_vina/Manifest @@ -0,0 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +DIST autodock_vina_1_0_3_linux_i386.tar.gz 807351 RMD160 463563f57a5c9892ffd6631b4fe19033997c52a5 SHA1 45419a5ab1e279ef8ce11b7201f0990d6e254898 SHA256 07b1f0b56d7d72c240f2b3bb89d2076e79a6f412d9d8207a7b2be0b5b3ce4aed +EBUILD autodock_vina-1.0.3.ebuild 783 RMD160 e64278ecf88de24efe12f4087da757dda0f94041 SHA1 4805d53f155da7e8c6b336617f9a9cad5167966b SHA256 c58031fdc69e90379d1aaa47b0cb016ecf5788b21a5802a1f1ca5ac37e723814 +MISC ChangeLog 295 RMD160 99a9c97f2a09c6f4847d6fa555ec27445e1dbadc SHA1 4fbf1f23badf3902886ea7ec63b2bf1779d5888f SHA256 a161eba92bb51b0e5bbefec09246a5f51adb0893cb56b1c8236d2ccb4e2c617b +MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.14 (GNU/Linux) + +iEYEARECAAYFAktqwjsACgkQ5BmOA85PVLga6gCgjeBVVn9vZwPRkXp3CbjBwRXm +xJkAn2jTa/gN/zCZnwBBFNULgifW4nHQ +=PJ5g +-----END PGP SIGNATURE----- diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.0.3.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.0.3.ebuild new file mode 100644 index 000000000..15672b80f --- /dev/null +++ b/sci-chemistry/autodock_vina/autodock_vina-1.0.3.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +DESCRIPTION="AutoDock Vina is a new program for drug discovery and molecular docking" +HOMEPAGE="http://vina.scripps.edu/" +MY_PN="${PN}_${PV//./_}_linux_i386" +SRC_URI="http://vina.scripps.edu/download/${MY_PN}.tar.gz" +MY_S="${PN}_${PV//./_}_linux_i386" + +LICENSE="vina_license" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="amd64? ( + app-emulation/emul-linux-x86-baselibs + app-emulation/emul-linux-x86-compat + )" + +src_unpack() { + unpack ${A} + cd "${MY_S}" + header=`grep --binary-files=text "header_length=" install.sh | cut -d "=" -f2` + tail -n+${header} install.sh | tar -xz +} + +src_install() { + dobin ${MY_S}/vina + dobin ${MY_S}/vina_split +} diff --git a/sci-chemistry/autodock_vina/metadata.xml b/sci-chemistry/autodock_vina/metadata.xml new file mode 100644 index 000000000..e42d0af60 --- /dev/null +++ b/sci-chemistry/autodock_vina/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>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog index 2cc27105f..87fbdd8df 100644 --- a/sci-chemistry/ccpn/ChangeLog +++ b/sci-chemistry/ccpn/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*ccpn-2.1.2.1_p100204 (04 Feb 2010) + + 04 Feb 2010; Justin Lecher (jlec) <jlec@j-schmitz.net> + +ccpn-2.1.2.1_p100204.ebuild: + 100204 python patches added + *ccpn-2.1.2.1_p100129 (29 Jan 2010) 29 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net> diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest index 2a48bba78..c842a746d 100644 --- a/sci-chemistry/ccpn/Manifest +++ b/sci-chemistry/ccpn/Manifest @@ -7,31 +7,15 @@ AUX dataShifter 313 RMD160 2f9d3ee79249a27c640f6bb19345f9f5dcb7e534 SHA1 783e377 AUX eci 298 RMD160 f0fe555b91bc2cf4c8f2672e23468098d1d82264 SHA1 7ccf78da2f9d5e726882fa3c2057b4e798acae0d SHA256 02e065abb5365661346d7b6b75313c1b50fc752a6853618bbe04f0231c147a23 AUX formatConverter 317 RMD160 a0f3424901c96bfffd01e8b8a667357b6a29f78a SHA1 cffb6eddcd15202bbda415938e0f9c75a4e98f56 SHA256 46e48c921b0d59b87bbd5dbda97065d35be7c8dd9f2234c9d97eefe5fa0d407d AUX pipe2azara 321 RMD160 c6ca09d178507af6dd2bff4bc8ad6765f4586b62 SHA1 96900b029b8bcdcc414b8e57877cac81d9aef95d SHA256 15fa8d6717e10e3e65d90d1bd89b81fb49a6b218923dc7d70234157c63286b0b -DIST analysis2.0.7.1.tar.gz 18142642 RMD160 b345c8c8a3cbee549f0ddffbe76d208aa0a93b42 SHA1 f1cade41ce9d488926873bbc6f83fa79af7d9623 SHA256 8d37aa12a3e18a875dcce8689751144c5a949e3431395d00fdef49fbbb0f4d69 -DIST analysis2.1.0.tar.gz 18962012 RMD160 3997fe7deafd50142f60d036e82f436519efe1d0 SHA1 df86d54a13fa1c955f47889f1310b62edfd9dc09 SHA256 132ab4a39fdeedde24385b0c976adea43efd512fefcff7dd973790e9faaf9d95 -DIST analysis2.1.1.tar.gz 18972580 RMD160 17e0fca7dc6b1c272ebbff68cb2589ab3bbff9c6 SHA1 62a28269e1215c458fbf8866c2323fbc690a7ea3 SHA256 1da964a61b98e29735dce1ba75f5f1fbf76dcded3bf93aaa05a4f1c05729972a DIST analysis2.1.2_1.tar.gz 19227793 RMD160 f633a8338e3fbb9d8ad77c9482d63191419b0885 SHA1 f711a424da22c84295610483a6cc481d2d2161e9 SHA256 e7eda0b50c357a2b62633c473da4621ccdc48c747c59d8ccb495d57e846308fa -DIST ccpn-update-100124.patch.bz2 21213 RMD160 51e4531acfbd57e795630e7dc6c260c2f92ce21d SHA1 8a065bb6cfa97ca88b15bac149c7af05c151fe27 SHA256 a075fa28527e1444b22340562cae4d6607d203a84cd163f404d0cc2854a66006 -DIST ccpn-update-100129.patch.bz2 23824 RMD160 845b61cdfacd59e42191303bd055c6a543970b12 SHA1 db5b66a29d86483142a7c57e46cc0b9f8539413d SHA256 357f6c2f4c912061f9b8ecbb2c857f8b37770037932829145fb4c5c38650f046 -DIST update-091012.patch.bz2 41959 RMD160 3ddb011d80935fea02fbf00fd06cadd32d86ecbc SHA1 467a41d1f634417739af09dc8a725f4b32238e5c SHA256 fe5051256f81d2f59a19b2463a7b6c5697680030b4b2823a6b6869eec85b8dbb -DIST update-091025.patch.bz2 17170 RMD160 5b2b440b742345a815158e63e356f82cfce933f6 SHA1 569e370e819c940e904696e1ab4eae7380e035d0 SHA256 5467ccd9bb437f1d0720a02e2629120319a61d77cc246cbdbaadc89deb884a51 -DIST update-091220.patch.bz2 16551 RMD160 6a4f12c88be5e0a5af3f4ec560d4e795006ea231 SHA1 f5b1c31f82f8ae930b11ba742ea09c09a9b45d24 SHA256 e355f42fd1e82fbf39377c56472f20346aea7c5aab97df4c36c508a31b6dacb5 -DIST update-100116.patch.bz2 18732 RMD160 859527394dd98ccf8040bbd79fe69e7b93eb022f SHA1 87f0829faa329180783c11754ab04bf95635eac6 SHA256 9bf976ddad8330ce313b61757708ba6cf65eb47870aa8aa168a04bb7f079ad8f -EBUILD ccpn-2.0.7.1-r2.ebuild 4550 RMD160 4adb7d8e25ae01b7c390475fa253e3408425e5fd SHA1 a177bc13e9f9da9f82e86acc6579ef3d11d227ff SHA256 e7f5ad42f1a095259c37ce9a6fe45a462fd105971b90719b3ad66cebe7e82865 -EBUILD ccpn-2.1.0-r4.ebuild 4167 RMD160 63f746dd33faa4a753d24ae0fc75c31bde3c3a61 SHA1 3624b2792b39a4db868006eb0711f180abb6dcd4 SHA256 3d82036ffcda14918e6924fd8eef89e56c85d1776f359071ad15d5620708f8e7 -EBUILD ccpn-2.1.1-r1.ebuild 4195 RMD160 7e67b7712b448f098c01fbe0c19d1f5eab7a8d64 SHA1 4580a861ce8fcafe6c82254117339d3a0fc36db2 SHA256 6a945186e8d349b3d53de852b8d651889cdc092f5b3123ec3c2c40b56b75c81c -EBUILD ccpn-2.1.2.1_p100124.ebuild 4292 RMD160 9cafce52f78af25c9e02b8770d56e466d3b67787 SHA1 632e3fc541b5b24893cea043eb00b618e931b7ba SHA256 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c28cee175f191dcbc4acf7841089fced91bd3724 SHA256 f32e2e5c77731c5aa9fb650342f938e4b1d20fee7e402d93e7107c5330e894c4 -MISC ChangeLog 6050 RMD160 9032cc151b9ba479d331748e9567bc40989e371d SHA1 e3a0580196e5fe6ee185e83402492966fc2aa3ef SHA256 bfb9643a04ad966f0c7219688b573920ed15484d4a8a257424a2cbd75a988eb9 +DIST ccpn-update-100204.patch.bz2 24401 RMD160 ec5f52845640706f87b7c04d83c6fb85140fd621 SHA1 f654efbaa66b26a596e77992ece2d8c9b2d41a27 SHA256 1888ad1857772a6adc79ec6d5e936e656cb2010532fa8b4ee7527a9938d5afb0 +EBUILD ccpn-2.1.2.1_p100204.ebuild 4292 RMD160 9cafce52f78af25c9e02b8770d56e466d3b67787 SHA1 632e3fc541b5b24893cea043eb00b618e931b7ba SHA256 26687db3db96cc44e15fd46d48d680b2d442b5f614824c819f5da4616e441fd8 +MISC ChangeLog 6207 RMD160 c6193ec5cbfa131ae44843610c302955a39d5e78 SHA1 ed89d6158e49224eab70aa19b764b659fdb16112 SHA256 459ab101fb5f1dc562eb345b369543f47b92dbf42e5de7b129913a5f9d0d2365 MISC metadata.xml 339 RMD160 2e62dd84c66f8229f9f75832b91b3921a23386c9 SHA1 3252b1e326b3ba201266861d6461bcc069ad770e SHA256 bbb58d377587da3e6a2d4a742829e24b2c840be26d8e8da2d3f6fbf26c0143ec -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.11 (GNU/Linux) +Version: GnuPG v2.0.14 (GNU/Linux) -iEYEARECAAYFAktjCpUACgkQgAnW8HDreRZ0YQCg0JVIf/ZA6jpXzirSvlzzRP1P -n9QAnRIIGMTlDON2ofIojvGolphvUX6V -=rNR8 +iEYEARECAAYFAktqkd0ACgkQgAnW8HDreRal4ACdF7r3eR07oakSS+EfnFW636i0 +K1EAoJ/UeZLVIFxdVqQ5jYOUWZcVk6lM +=iDOM -----END PGP SIGNATURE----- diff --git a/sci-chemistry/ccpn/ccpn-2.0.7.1-r2.ebuild b/sci-chemistry/ccpn/ccpn-2.0.7.1-r2.ebuild deleted file mode 100644 index 21d539e99..000000000 --- a/sci-chemistry/ccpn/ccpn-2.0.7.1-r2.ebuild +++ /dev/null @@ -1,190 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -NEED_PYTHON=2.4 -PYTHON_MODNAME="ccpn" -PYTHON_USE_WITH="ssl tk" -EAPI="2" - -inherit python toolchain-funcs portability distutils eutils - -MY_PN="${PN}mr" - -DESCRIPTION="The Collaborative Computing Project for NMR" -SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${PV}.tar.gz" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86" -IUSE="doc opengl" - -RDEPEND="virtual/glut - dev-python/elementtree - dev-tcltk/tix - dev-python/numpy" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN} - -pkg_setup() { - python_version -} - -src_prepare() { - distutils_src_prepare - echo "" > "${S}"/ccpnmr2.0/c/environment.txt || die "failed to kill environment.txt" -} - -src_compile() { - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - if has_version media-libs/freeglut; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - else - GLUT_NEED_INIT="" - fi - - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_FALSE" - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - GL_DIR="/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)" - - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - fi - - cd ccpnmr2.0/c - - emake \ - CC="$(tc-getCC)" \ - LDFLAGS="${LDFLAGGS}" \ - MALLOC_FLAG= \ - FPIC_FLAG="-fPIC" \ - SHARED_FLAGS="${LDFLAGS} -shared" \ - MATH_LIB="-lm" \ - X11_DIR="/usr" \ - X11_LIB="-lX11 -lXext" \ - X11_INCLUDE_FLAGS="-I\$(X11_DIR)/include" \ - X11_LIB_FLAGS="-L\$(X11_DIR)/lib" \ - TCL_DIR="/usr" \ - TCL_LIB="-ltcl${tk_ver}" \ - TCL_INCLUDE_FLAGS="-I\$(TCL_DIR)/include" \ - TCL_LIB_FLAGS="-L\$(TCL_DIR)/$(get_libdir)" \ - TK_DIR="/usr" \ - TK_LIB="-ltk${tk_ver}" \ - TK_INCLUDE_FLAGS="-I\$(TK_DIR)/include" \ - TK_LIB_FLAGS="-L\$(TK_DIR)/$(get_libdir)" \ - PYTHON_DIR="/usr" \ - PYTHON_INCLUDE_FLAGS="-I\$(PYTHON_DIR)/include/python${PYVER}" \ - CFLAGS="${CFLAGS} \$(MALLOC_FLAG) \$(FPIC_FLAG)" \ - GLUT_NEED_INIT="${GLUT_NEED_INIT}" \ - IGNORE_GL_FLAG="${IGNORE_GL_FLAG}" \ - GL_FLAG="${GL_FLAG}" \ - GLUT_NOT_IN_GL="${GLUT_NOT_IN_GL}" \ - GLUT_FLAG="${GLUT_FLAG}" \ - GL_DIR="${GL_DIR}" \ - GL_LIB="${GL_LIB}" \ - GL_INCLUDE_FLAGS="${GL_INCLUDE_FLAGS}" \ - GL_LIB_FLAGS="${GL_LIB_FLAGS}" \ - all links || \ - die "failed to compile" -} - -src_install() { - - local in_path - local gentoo_sitedir - local libdir - local files - local tkver - - in_path=$(python_get_sitedir)/${PN} - gentoo_sitedir=$(python_get_sitedir) - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - for wrapper in analysis dangle dataShifter formatConverter pipe2azara; do - sed -e "s:gentoo_sitedir:${gentoo_sitedir}:g" \ - -e "s:libdir:${libdir}:g" \ - -e "s:tkver:${tkver}:g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" - done - - use doc && treecopy $(find . -name doc) "${D}"usr/share/doc/${PF}/html/ - - ebegin "Removing unneeded docs" - find . -name doc -exec rm -rf '{}' \; 2> /dev/null - eend - - if [[ ${PYVER} > 2.4 ]]; then - for i in ccpnmr2.0/python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's:#from __future__:from __future__:g' \ - -i ${i} - done - fi - - insinto ${in_path} - - ebegin "Installing main files" - doins -r ccpnmr2.0/{data,model,python} || die "main files installation failed" - eend - - einfo "Adjusting permissions" - - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so - ccpnmr/c/ContourStyle.so - ccpnmr/c/PeakList.so - ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so - ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.so - ccpnmr/c/DistConstraint.so - ccpnmr/c/DistForce.so - ccpnmr/c/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.so - memops/c/BlockFile.so - memops/c/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so - memops/c/PdfHandler.so - memops/c/PsHandler.so - memops/c/ShapeFile.so - memops/c/StoreFile.so - memops/c/StoreHandler.so - memops/c/TkHandler.so" - - for FILE in ${files}; do - fperms 755 ${in_path}/python/${FILE} - done -} - -pkg_postrm() { - distutils_pkg_postrm - rm -rf $(python_get_sitedir)/${PN} -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.0-r4.ebuild b/sci-chemistry/ccpn/ccpn-2.1.0-r4.ebuild deleted file mode 100644 index cd2a25ad7..000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.0-r4.ebuild +++ /dev/null @@ -1,167 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -NEED_PYTHON=2.5 -PYTHON_MODNAME="${PN}" -PYTHON_USE_WITH="ssl tk" -PATCHSET="091012" -EAPI="2" - -inherit distutils portability python toolchain-funcs versionator - -MY_PN="${PN}mr" - -DESCRIPTION="The Collaborative Computing Project for NMR" -SRC_URI=" - http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${PV}.tar.gz - http://dev.gentooexperimental.org/~jlec/distfiles/update-${PATCHSET}.patch.bz2" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86" -IUSE="doc +opengl" - -RDEPEND=" - dev-lang/tk - dev-python/elementtree - dev-python/numpy - dev-tcltk/tix - virtual/glut" -DEPEND="${RDEPEND}" -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV}) - -pkg_setup() { - python_version -} - -src_prepare() { - epatch "${WORKDIR}"/update-${PATCHSET}.patch - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - if has_version media-libs/freeglut; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - else - GLUT_NEED_INIT="" - fi - - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_FALSE" - GL_DIR="/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)" - - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - sed \ - -e "s:^\(CC = \).*:\1$(tc-getCC):g" \ - -e "s:^\(OPT_FLAG = \).*:\1${CFLAGS}:g" \ - -e "s:^\(LINK_FLAGS =.*\):\1 ${LDFLAGS}:g" \ - -e "s:^\(IGNORE_GL_FLAG = \).*:\1${IGNORE_GL_FLAG}:g" \ - -e "s:^\(GL_FLAG = \).*:\1${GL_FLAG}:g" \ - -e "s:^\(GLUT_NEED_INIT = \).*:\1${GLUT_NEED_INIT}:g" \ - -e "s:^\(GLUT_NOT_IN_GL = \).*:\1:g" \ - -e "s:^\(X11_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \ - -e "s:^\(TCL_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \ - -e "s:^\(TK_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \ - -e "s:^\(PYTHON_INCLUDE_FLAGS = \).*:\1-I\$(PYTHON_DIR)/include/python${PYVER}:g" \ - -e "s:^\(GL_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \ - c/environment_default.txt > c/environment.txt -} - -src_compile() { - emake \ - -C c \ - all links || \ - die "failed to compile" -} - -src_install() { - - local in_path - local gentoo_sitedir - local libdir - local files - local tkver - - in_path=$(python_get_sitedir)/${PN} - gentoo_sitedir=$(python_get_sitedir) - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do - sed -e "s:gentoo_sitedir:${gentoo_sitedir}:g" \ - -e "s:libdir:${libdir}:g" \ - -e "s:tkver:${tkver}:g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" - done - - use doc && treecopy $(find . -name doc) "${D}"usr/share/doc/${PF}/html/ - - ebegin "Removing unneeded docs" - find . -name doc -exec rm -rf '{}' \; 2> /dev/null - eend - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's:#from __future__:from __future__:g' \ - -i ${i} - done - - insinto ${in_path} - - ebegin "Installing main files" - doins -r data model python || die "main files installation failed" - eend - - einfo "Adjusting permissions" - - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so - ccpnmr/c/ContourStyle.so - ccpnmr/c/PeakList.so - ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so - ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.so - ccpnmr/c/DistConstraint.so - ccpnmr/c/DistForce.so - ccpnmr/c/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.so - memops/c/BlockFile.so - memops/c/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so - memops/c/PdfHandler.so - memops/c/PsHandler.so - memops/c/ShapeFile.so - memops/c/StoreFile.so - memops/c/StoreHandler.so - memops/c/TkHandler.so" - - for FILE in ${files}; do - fperms 755 ${in_path}/python/${FILE} - done -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.1-r1.ebuild b/sci-chemistry/ccpn/ccpn-2.1.1-r1.ebuild deleted file mode 100644 index 9116eaa5f..000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.1-r1.ebuild +++ /dev/null @@ -1,168 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -NEED_PYTHON=2.5 -PYTHON_MODNAME="${PN}" -PYTHON_USE_WITH="ssl tk" -PATCHSET="091025" -EAPI="2" - -inherit distutils portability python toolchain-funcs versionator - -MY_PN="${PN}mr" - -DESCRIPTION="The Collaborative Computing Project for NMR" -SRC_URI=" - http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${PV}.tar.gz - http://dev.gentooexperimental.org/~jlec/distfiles/update-${PATCHSET}.patch.bz2" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86" -IUSE="doc +opengl" - -RDEPEND=" - dev-lang/tk - dev-python/elementtree - dev-python/numpy - dev-tcltk/tix - virtual/glut" -DEPEND="${RDEPEND}" -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV}) - -pkg_setup() { - python_version -} - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - epatch "${WORKDIR}"/update-${PATCHSET}.patch - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - if has_version media-libs/freeglut; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - else - GLUT_NEED_INIT="" - fi - - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_FALSE" - GL_DIR="/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)" - - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - sed \ - -e "s:^\(CC = \).*:\1$(tc-getCC):g" \ - -e "s:^\(OPT_FLAG = \).*:\1${CFLAGS}:g" \ - -e "s:^\(LINK_FLAGS =.*\):\1 ${LDFLAGS}:g" \ - -e "s:^\(IGNORE_GL_FLAG = \).*:\1${IGNORE_GL_FLAG}:g" \ - -e "s:^\(GL_FLAG = \).*:\1${GL_FLAG}:g" \ - -e "s:^\(GLUT_NEED_INIT = \).*:\1${GLUT_NEED_INIT}:g" \ - -e "s:^\(GLUT_NOT_IN_GL = \).*:\1:g" \ - -e "s:^\(X11_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \ - -e "s:^\(TCL_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \ - -e "s:^\(TK_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \ - -e "s:^\(PYTHON_INCLUDE_FLAGS = \).*:\1-I\$(PYTHON_DIR)/include/python${PYVER}:g" \ - -e "s:^\(GL_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \ - c/environment_default.txt > c/environment.txt -} - -src_compile() { - emake \ - -C c \ - all links || \ - die "failed to compile" -} - -src_install() { - - local in_path - local gentoo_sitedir - local libdir - local files - local tkver - - in_path=$(python_get_sitedir)/${PN} - gentoo_sitedir=$(python_get_sitedir) - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do - sed -e "s:gentoo_sitedir:${gentoo_sitedir}:g" \ - -e "s:libdir:${libdir}:g" \ - -e "s:tkver:${tkver}:g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" - done - - use doc && treecopy $(find . -name doc) "${D}"usr/share/doc/${PF}/html/ - - ebegin "Removing unneeded docs" - find . -name doc -exec rm -rf '{}' \; 2> /dev/null - eend - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's:#from __future__:from __future__:g' \ - -i ${i} - done - - insinto ${in_path} - - ebegin "Installing main files" - doins -r data model python || die "main files installation failed" - eend - - einfo "Adjusting permissions" - - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so - ccpnmr/c/ContourStyle.so - ccpnmr/c/PeakList.so - ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so - ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.so - ccpnmr/c/DistConstraint.so - ccpnmr/c/DistForce.so - ccpnmr/c/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.so - memops/c/BlockFile.so - memops/c/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so - memops/c/PdfHandler.so - memops/c/PsHandler.so - memops/c/ShapeFile.so - memops/c/StoreFile.so - memops/c/StoreHandler.so - memops/c/TkHandler.so" - - for FILE in ${files}; do - fperms 755 ${in_path}/python/${FILE} - done -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.2.1_p100129.ebuild b/sci-chemistry/ccpn/ccpn-2.1.2.1_p100129.ebuild deleted file mode 100644 index d0387ed5e..000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.2.1_p100129.ebuild +++ /dev/null @@ -1,171 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -PYTHON_USE_WITH="ssl tk" - -inherit eutils portability python toolchain-funcs versionator - -PATCHSET="${PV##*_p}" -MY_PN="${PN}mr" -MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" - -DESCRIPTION="The Collaborative Computing Project for NMR" -SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz" - [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/distfiles/ccpn-update-${PATCHSET}.patch.bz2" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86" -IUSE="+opengl" - -RDEPEND=" - dev-lang/tk - dev-python/elementtree - dev-python/numpy - dev-tcltk/tix - opengl? ( virtual/glut )" -DEPEND="${RDEPEND}" -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV}) - -pkg_setup() { - python_version -} - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - epatch "${WORKDIR}"/ccpn-update-${PATCHSET}.patch - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_FALSE" - GL_DIR="/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)" - - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - sed \ - -e "s:^\(CC =\).*:\1 $(tc-getCC):g" \ - -e "s:^\(OPT_FLAG =\).*:\1 ${CFLAGS}:g" \ - -e "s:^\(LINK_FLAGS =.*\):\1 ${LDFLAGS}:g" \ - -e "s:^\(IGNORE_GL_FLAG =\).*:\1 ${IGNORE_GL_FLAG}:g" \ - -e "s:^\(GL_FLAG =\).*:\1 ${GL_FLAG}:g" \ - -e "s:^\(GLUT_NEED_INIT =\).*:\1 ${GLUT_NEED_INIT}:g" \ - -e "s:^\(GLUT_NOT_IN_GL =\).*:\1:g" \ - -e "s:^\(X11_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(TCL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(TK_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(PYTHON_INCLUDE_FLAGS =\).*:\1 -I\$(PYTHON_DIR)/include/python${PYVER}:g" \ - -e "s:^\(GL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - c/environment_default.txt > c/environment.txt -} - -src_compile() { - emake \ - -C c \ - all links || \ - die "failed to compile" -} - -src_install() { - - local in_path - local gentoo_sitedir - local libdir - local files - local tkver - - in_path=$(python_get_sitedir)/${PN} - gentoo_sitedir=$(python_get_sitedir) - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do - sed -e "s:gentoo_sitedir:${gentoo_sitedir}:g" \ - -e "s:libdir:${libdir}:g" \ - -e "s:tkver:${tkver}:g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" - done - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's:#from __future__:from __future__:g' \ - -i ${i} - done - - insinto ${in_path} - - dodir ${in_path}/c - - ebegin "Installing main files" - doins -r data model python || die "main files installation failed" - eend - - dohtml -r doc/* || die - dosym ../../../../share/doc/${PF}/html ${in_path}/doc || die - - einfo "Adjusting permissions" - - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so - ccpnmr/c/ContourStyle.so - ccpnmr/c/PeakList.so - ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so - ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.so - ccpnmr/c/DistConstraint.so - ccpnmr/c/DistForce.so - ccpnmr/c/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.so - memops/c/BlockFile.so - memops/c/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so - memops/c/PdfHandler.so - memops/c/PsHandler.so - memops/c/ShapeFile.so - memops/c/StoreFile.so - memops/c/StoreHandler.so - memops/c/TkHandler.so" - - for FILE in ${files}; do - fperms 755 ${in_path}/python/${FILE} - done -} - -pkg_postinst() { - python_need_rebuild - python_mod_optimize $(python_get_sitedir)/${PN} -} - -pkg_postrm() { - python_mod_cleanup $(python_get_sitedir)/${PN} -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.2.1_p100124.ebuild b/sci-chemistry/ccpn/ccpn-2.1.2.1_p100204.ebuild index d0387ed5e..d0387ed5e 100644 --- a/sci-chemistry/ccpn/ccpn-2.1.2.1_p100124.ebuild +++ b/sci-chemistry/ccpn/ccpn-2.1.2.1_p100204.ebuild diff --git a/sci-chemistry/ccpn/ccpn-2.1.2_p1-r3.ebuild b/sci-chemistry/ccpn/ccpn-2.1.2_p1-r3.ebuild deleted file mode 100644 index 2f1d0394c..000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.2_p1-r3.ebuild +++ /dev/null @@ -1,160 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -NEED_PYTHON=2.5 -PYTHON_MODNAME="${PN}" -PYTHON_USE_WITH="ssl tk" -PATCHSET="" -EAPI="2" - -inherit distutils portability python toolchain-funcs versionator - -MY_PN="${PN}mr" - -DESCRIPTION="The Collaborative Computing Project for NMR" -SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${PV/p/}.tar.gz" -[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/distfiles/update-${PATCHSET}.patch.bz2" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86" -IUSE="+opengl" - -RDEPEND=" - dev-lang/tk - dev-python/elementtree - dev-python/numpy - dev-tcltk/tix - opengl? ( virtual/glut )" -DEPEND="${RDEPEND}" -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV}) - -pkg_setup() { - python_version -} - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - epatch "${WORKDIR}"/update-${PATCHSET}.patch - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_FALSE" - GL_DIR="/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)" - - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - sed \ - -e "s:^\(CC =\).*:\1 $(tc-getCC):g" \ - -e "s:^\(OPT_FLAG =\).*:\1 ${CFLAGS}:g" \ - -e "s:^\(LINK_FLAGS =.*\):\1 ${LDFLAGS}:g" \ - -e "s:^\(IGNORE_GL_FLAG =\).*:\1 ${IGNORE_GL_FLAG}:g" \ - -e "s:^\(GL_FLAG =\).*:\1 ${GL_FLAG}:g" \ - -e "s:^\(GLUT_NEED_INIT =\).*:\1 ${GLUT_NEED_INIT}:g" \ - -e "s:^\(GLUT_NOT_IN_GL =\).*:\1:g" \ - -e "s:^\(X11_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(TCL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(TK_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(PYTHON_INCLUDE_FLAGS =\).*:\1 -I\$(PYTHON_DIR)/include/python${PYVER}:g" \ - -e "s:^\(GL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - c/environment_default.txt > c/environment.txt -} - -src_compile() { - emake \ - -C c \ - all links || \ - die "failed to compile" -} - -src_install() { - - local in_path - local gentoo_sitedir - local libdir - local files - local tkver - - in_path=$(python_get_sitedir)/${PN} - gentoo_sitedir=$(python_get_sitedir) - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do - sed -e "s:gentoo_sitedir:${gentoo_sitedir}:g" \ - -e "s:libdir:${libdir}:g" \ - -e "s:tkver:${tkver}:g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" - done - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's:#from __future__:from __future__:g' \ - -i ${i} - done - - insinto ${in_path} - - ebegin "Installing main files" - doins -r data model python || die "main files installation failed" - eend - - dohtml -r doc/* || die - dosym ../../../../share/doc/${PF}/html ${in_path}/doc || die - - einfo "Adjusting permissions" - - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so - ccpnmr/c/ContourStyle.so - ccpnmr/c/PeakList.so - ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so - ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.so - ccpnmr/c/DistConstraint.so - ccpnmr/c/DistForce.so - ccpnmr/c/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.so - memops/c/BlockFile.so - memops/c/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so - memops/c/PdfHandler.so - memops/c/PsHandler.so - memops/c/ShapeFile.so - memops/c/StoreFile.so - memops/c/StoreHandler.so - memops/c/TkHandler.so" - - for FILE in ${files}; do - fperms 755 ${in_path}/python/${FILE} - done -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.2_p1-r4.ebuild b/sci-chemistry/ccpn/ccpn-2.1.2_p1-r4.ebuild deleted file mode 100644 index eb6860ea8..000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.2_p1-r4.ebuild +++ /dev/null @@ -1,162 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -NEED_PYTHON=2.5 -PYTHON_MODNAME="${PN}" -PYTHON_USE_WITH="ssl tk" -PATCHSET="091220" -EAPI="2" - -inherit distutils portability python toolchain-funcs versionator - -MY_PN="${PN}mr" - -DESCRIPTION="The Collaborative Computing Project for NMR" -SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${PV/p/}.tar.gz" -[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/distfiles/update-${PATCHSET}.patch.bz2" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86" -IUSE="+opengl" - -RDEPEND=" - dev-lang/tk - dev-python/elementtree - dev-python/numpy - dev-tcltk/tix - opengl? ( virtual/glut )" -DEPEND="${RDEPEND}" -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV}) - -pkg_setup() { - python_version -} - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - epatch "${WORKDIR}"/update-${PATCHSET}.patch - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_FALSE" - GL_DIR="/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)" - - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - sed \ - -e "s:^\(CC =\).*:\1 $(tc-getCC):g" \ - -e "s:^\(OPT_FLAG =\).*:\1 ${CFLAGS}:g" \ - -e "s:^\(LINK_FLAGS =.*\):\1 ${LDFLAGS}:g" \ - -e "s:^\(IGNORE_GL_FLAG =\).*:\1 ${IGNORE_GL_FLAG}:g" \ - -e "s:^\(GL_FLAG =\).*:\1 ${GL_FLAG}:g" \ - -e "s:^\(GLUT_NEED_INIT =\).*:\1 ${GLUT_NEED_INIT}:g" \ - -e "s:^\(GLUT_NOT_IN_GL =\).*:\1:g" \ - -e "s:^\(X11_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(TCL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(TK_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(PYTHON_INCLUDE_FLAGS =\).*:\1 -I\$(PYTHON_DIR)/include/python${PYVER}:g" \ - -e "s:^\(GL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - c/environment_default.txt > c/environment.txt -} - -src_compile() { - emake \ - -C c \ - all links || \ - die "failed to compile" -} - -src_install() { - - local in_path - local gentoo_sitedir - local libdir - local files - local tkver - - in_path=$(python_get_sitedir)/${PN} - gentoo_sitedir=$(python_get_sitedir) - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do - sed -e "s:gentoo_sitedir:${gentoo_sitedir}:g" \ - -e "s:libdir:${libdir}:g" \ - -e "s:tkver:${tkver}:g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" - done - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's:#from __future__:from __future__:g' \ - -i ${i} - done - - insinto ${in_path} - - dodir ${in_path}/c - - ebegin "Installing main files" - doins -r data model python || die "main files installation failed" - eend - - dohtml -r doc/* || die - dosym ../../../../share/doc/${PF}/html ${in_path}/doc || die - - einfo "Adjusting permissions" - - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so - ccpnmr/c/ContourStyle.so - ccpnmr/c/PeakList.so - ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so - ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.so - ccpnmr/c/DistConstraint.so - ccpnmr/c/DistForce.so - ccpnmr/c/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.so - memops/c/BlockFile.so - memops/c/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so - memops/c/PdfHandler.so - memops/c/PsHandler.so - memops/c/ShapeFile.so - memops/c/StoreFile.so - memops/c/StoreHandler.so - memops/c/TkHandler.so" - - for FILE in ${files}; do - fperms 755 ${in_path}/python/${FILE} - done -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.2_p1-r5.ebuild b/sci-chemistry/ccpn/ccpn-2.1.2_p1-r5.ebuild deleted file mode 100644 index a4f45cd92..000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.2_p1-r5.ebuild +++ /dev/null @@ -1,170 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -PYTHON_USE_WITH="ssl tk" -PATCHSET="091220" - -inherit eutils portability python toolchain-funcs versionator - -MY_PN="${PN}mr" - -DESCRIPTION="The Collaborative Computing Project for NMR" -SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${PV/p/}.tar.gz" -[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/distfiles/update-${PATCHSET}.patch.bz2" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86" -IUSE="+opengl" - -RDEPEND=" - dev-lang/tk - dev-python/elementtree - dev-python/numpy - dev-tcltk/tix - opengl? ( virtual/glut )" -DEPEND="${RDEPEND}" -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV}) - -pkg_setup() { - python_version -} - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - epatch "${WORKDIR}"/update-${PATCHSET}.patch - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_FALSE" - GL_DIR="/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)" - - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - sed \ - -e "s:^\(CC =\).*:\1 $(tc-getCC):g" \ - -e "s:^\(OPT_FLAG =\).*:\1 ${CFLAGS}:g" \ - -e "s:^\(LINK_FLAGS =.*\):\1 ${LDFLAGS}:g" \ - -e "s:^\(IGNORE_GL_FLAG =\).*:\1 ${IGNORE_GL_FLAG}:g" \ - -e "s:^\(GL_FLAG =\).*:\1 ${GL_FLAG}:g" \ - -e "s:^\(GLUT_NEED_INIT =\).*:\1 ${GLUT_NEED_INIT}:g" \ - -e "s:^\(GLUT_NOT_IN_GL =\).*:\1:g" \ - -e "s:^\(X11_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(TCL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(TK_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(PYTHON_INCLUDE_FLAGS =\).*:\1 -I\$(PYTHON_DIR)/include/python${PYVER}:g" \ - -e "s:^\(GL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - c/environment_default.txt > c/environment.txt -} - -src_compile() { - emake \ - -C c \ - all links || \ - die "failed to compile" -} - -src_install() { - - local in_path - local gentoo_sitedir - local libdir - local files - local tkver - - in_path=$(python_get_sitedir)/${PN} - gentoo_sitedir=$(python_get_sitedir) - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do - sed -e "s:gentoo_sitedir:${gentoo_sitedir}:g" \ - -e "s:libdir:${libdir}:g" \ - -e "s:tkver:${tkver}:g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" - done - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's:#from __future__:from __future__:g' \ - -i ${i} - done - - insinto ${in_path} - - dodir ${in_path}/c - - ebegin "Installing main files" - doins -r data model python || die "main files installation failed" - eend - - dohtml -r doc/* || die - dosym ../../../../share/doc/${PF}/html ${in_path}/doc || die - - einfo "Adjusting permissions" - - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so - ccpnmr/c/ContourStyle.so - ccpnmr/c/PeakList.so - ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so - ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.so - ccpnmr/c/DistConstraint.so - ccpnmr/c/DistForce.so - ccpnmr/c/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.so - memops/c/BlockFile.so - memops/c/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so - memops/c/PdfHandler.so - memops/c/PsHandler.so - memops/c/ShapeFile.so - memops/c/StoreFile.so - memops/c/StoreHandler.so - memops/c/TkHandler.so" - - for FILE in ${files}; do - fperms 755 ${in_path}/python/${FILE} - done -} - -pkg_postinst() { - python_need_rebuild - python_mod_optimize $(python_get_sitedir)/${PN} -} - -pkg_postrm() { - python_mod_cleanup $(python_get_sitedir)/${PN} -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.2_p1-r6.ebuild b/sci-chemistry/ccpn/ccpn-2.1.2_p1-r6.ebuild deleted file mode 100644 index a08cac736..000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.2_p1-r6.ebuild +++ /dev/null @@ -1,170 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -PYTHON_USE_WITH="ssl tk" -PATCHSET="100116" - -inherit eutils portability python toolchain-funcs versionator - -MY_PN="${PN}mr" - -DESCRIPTION="The Collaborative Computing Project for NMR" -SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${PV/p/}.tar.gz" -[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/distfiles/update-${PATCHSET}.patch.bz2" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86" -IUSE="+opengl" - -RDEPEND=" - dev-lang/tk - dev-python/elementtree - dev-python/numpy - dev-tcltk/tix - opengl? ( virtual/glut )" -DEPEND="${RDEPEND}" -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV}) - -pkg_setup() { - python_version -} - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - epatch "${WORKDIR}"/update-${PATCHSET}.patch - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_FALSE" - GL_DIR="/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)" - - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - sed \ - -e "s:^\(CC =\).*:\1 $(tc-getCC):g" \ - -e "s:^\(OPT_FLAG =\).*:\1 ${CFLAGS}:g" \ - -e "s:^\(LINK_FLAGS =.*\):\1 ${LDFLAGS}:g" \ - -e "s:^\(IGNORE_GL_FLAG =\).*:\1 ${IGNORE_GL_FLAG}:g" \ - -e "s:^\(GL_FLAG =\).*:\1 ${GL_FLAG}:g" \ - -e "s:^\(GLUT_NEED_INIT =\).*:\1 ${GLUT_NEED_INIT}:g" \ - -e "s:^\(GLUT_NOT_IN_GL =\).*:\1:g" \ - -e "s:^\(X11_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(TCL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(TK_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - -e "s:^\(PYTHON_INCLUDE_FLAGS =\).*:\1 -I\$(PYTHON_DIR)/include/python${PYVER}:g" \ - -e "s:^\(GL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \ - c/environment_default.txt > c/environment.txt -} - -src_compile() { - emake \ - -C c \ - all links || \ - die "failed to compile" -} - -src_install() { - - local in_path - local gentoo_sitedir - local libdir - local files - local tkver - - in_path=$(python_get_sitedir)/${PN} - gentoo_sitedir=$(python_get_sitedir) - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do - sed -e "s:gentoo_sitedir:${gentoo_sitedir}:g" \ - -e "s:libdir:${libdir}:g" \ - -e "s:tkver:${tkver}:g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" - done - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's:#from __future__:from __future__:g' \ - -i ${i} - done - - insinto ${in_path} - - dodir ${in_path}/c - - ebegin "Installing main files" - doins -r data model python || die "main files installation failed" - eend - - dohtml -r doc/* || die - dosym ../../../../share/doc/${PF}/html ${in_path}/doc || die - - einfo "Adjusting permissions" - - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so - ccpnmr/c/ContourStyle.so - ccpnmr/c/PeakList.so - ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so - ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.so - ccpnmr/c/DistConstraint.so - ccpnmr/c/DistForce.so - ccpnmr/c/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.so - memops/c/BlockFile.so - memops/c/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so - memops/c/PdfHandler.so - memops/c/PsHandler.so - memops/c/ShapeFile.so - memops/c/StoreFile.so - memops/c/StoreHandler.so - memops/c/TkHandler.so" - - for FILE in ${files}; do - fperms 755 ${in_path}/python/${FILE} - done -} - -pkg_postinst() { - python_need_rebuild - python_mod_optimize $(python_get_sitedir)/${PN} -} - -pkg_postrm() { - python_mod_cleanup $(python_get_sitedir)/${PN} -} diff --git a/sci-visualization/gnuplot/ChangeLog b/sci-visualization/gnuplot/ChangeLog index b8f2dec91..9f6715f2f 100644 --- a/sci-visualization/gnuplot/ChangeLog +++ b/sci-visualization/gnuplot/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Feb 2010; Christoph Junghans <kleiner_otti@gmx.de> + -files/gnuplot-4.2.5-colorbox_accounting.patch, gnuplot-4.5.9999.ebuild: + some bugfixes went upstream + 28 Jan 2010; Christoph Junghans <kleiner_otti@gmx.de> gnuplot-4.5.9999.ebuild: Added ~amd64 keyword diff --git a/sci-visualization/gnuplot/Manifest b/sci-visualization/gnuplot/Manifest index c9b7aa2f4..79211d0f9 100644 --- a/sci-visualization/gnuplot/Manifest +++ b/sci-visualization/gnuplot/Manifest @@ -4,7 +4,6 @@ Hash: SHA1 AUX gnuplot-4.2.2-disable_texi_generation.patch 763 RMD160 99368c05fe2907f445a49b4d0be782f0384f319e SHA1 17723d5e5a12eef274b6f9216c9a9cbbe05cba1e SHA256 87a3bed1e3be244a511f1cbeb9852484da59decdae75635ae900fbafe5db02f6 AUX gnuplot-4.2.3-app-defaults.patch 2097 RMD160 d0764b54424cfec60b22e498b8624801559e3526 SHA1 bac7dd281e679a6c638f7ba1b211e13443221486 SHA256 91cab9715e99c5e394ac6e08f17ef8063d3f0b574e0404fc5e6b643b26fddaf3 AUX gnuplot-4.2.3-disable-texhash.patch 677 RMD160 b299c7425e735ebad6afa1e2d154190fb2f3fdf8 SHA1 6e5f25a0283b2dd887738d8caee7c92d1905b1cc SHA256 af25fded8998eb48ea0b89f9ce0d5322721088c2b69a360ec7928a7f6115873e -AUX gnuplot-4.2.5-colorbox_accounting.patch 2925 RMD160 d34fd681bc9a17de6d612fe23df35f3963e3e1f3 SHA1 f2d16c98a733b801932c558481411101ca7a3c3b SHA256 6456dd2ff7baaa6c938ee33c7ebc62e00568049f76c219d3f4403d1c7ef3a38f AUX gnuplot-4.2.5-configure-pkgconfig.patch 484 RMD160 d1d8031382b8062c393fa430eb69f74f68d93c64 SHA1 e749dbd1cf8047a6274182cc0e2317d3f1b09a2e SHA256 58d0c0106337c5f48ad2f75671566556c055eb58ee016c4a125dbc6fd434d1b6 AUX gnuplot-4.4.0_rc1-app-defaults.patch 2651 RMD160 508e5f69923b6f5cee913cdc5bac6c7cda677869 SHA1 cda875c86a4faae596f0b7f243e659c8c03ac4e8 SHA256 4e207e71cb4b5c882d06857dc4f0482982ff3b822aa18bd57ef4d83901a807fc AUX gnuplot-4.4.0_rc1-disable-texhash.patch 1023 RMD160 088374701e4512d95050d7c3b46f8e5983bcbf86 SHA1 22ca8ab6ff12028c010dec3be501efa42686c042 SHA256 92bcd6c428c2686b48fc4b8dbca3ccd77d4e6c253c0160dcbc72ab8a18eb0612 @@ -17,13 +16,13 @@ DIST gnuplot-4.2.6.tar.gz 2936753 RMD160 3b1726e5327b17bb7b528198e62a12b9fe3e5a7 DIST gnuplot-4.4.0-rc1.tar.gz 3294054 RMD160 262cce576e6d64dd8a54edef0730f4576414456c SHA1 e9c2b99896a652a52d0160e8e2a6406ed861fda4 SHA256 d284ac5f75948e5a6716d26532adaf40e9ed8a205cbdeb75e76999dab07baf14 EBUILD gnuplot-4.2.6-r1.ebuild 6997 RMD160 ae586b402f58efb5e12f3eff39ce00db1a98f088 SHA1 0d705aa36ec4e162e12f13e486bdc0e4ab5fc665 SHA256 28f245975ef12746830103fdf5d4333dff288163a53c94a71c1da602b81f0afc EBUILD gnuplot-4.4.0_rc1.ebuild 6712 RMD160 62cbc04a43cee4212550168c2517ff01c2ed2710 SHA1 31fc52029dacdfbd792a1d9baae2c036e4e7ac4d SHA256 f164c5733a0e4ec29a1b1e35ac5a5f63468c5ea4aa9ba8b4b59c9861bb7e6594 -EBUILD gnuplot-4.5.9999.ebuild 6794 RMD160 6b71df384d528272af2307dd469e2f0a293f6192 SHA1 a3d89bee122821ec5e1ff63432bccfd215590e03 SHA256 a30a4e2ba3a9eb88db11759bf35c6f487c6f32c71eaf6bd09c8fd435b6da76f0 -MISC ChangeLog 1845 RMD160 62081dbf405e502aac38d594724032bd4dd7c9df SHA1 57ba44e48182638f37541144c341f851fa404a23 SHA256 d34ff970fe4d2a20e3a113ab7d69241f57d9841994820f97daf57390470ca832 +EBUILD gnuplot-4.5.9999.ebuild 6618 RMD160 c385d92f0e0a0bb1e651a32fd277c88e68b94c09 SHA1 98da6316139fdff3c8e8612695bd49231a9d99a4 SHA256 d3d849cd160f08750bcf808293fdd4116fb1a0480a85210aa439df92747b52fe +MISC ChangeLog 2007 RMD160 6c75f6211bb3c28edc7505d1d20f51187f3f5828 SHA1 7a7928dc90b33073b5e92f0c23cfb2601be53d3f SHA256 ea78740fb6b5423ae6ae6cc654d226f9441bacdb5f8f9d89937231cb49da3ef3 MISC metadata.xml 349 RMD160 87a767ce8e90a00d852a98474ba4613ec1311796 SHA1 d4de5b0b36dac3911669ae23a080982f0986d273 SHA256 70b5b4315995c437de4e5b0434d5f2034fbd35975be71ecc2782cffee5be16a2 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.11 (GNU/Linux) +Version: GnuPG v2.0.14 (GNU/Linux) -iEYEARECAAYFAkth/sgACgkQy0OE/ans1/kINACeJuEvrtTnHhFTF6ExcYXDOH2i -xeMAnjZUijT+vBEgBlKuPvhIXiw9UbZs -=s/mv +iEYEARECAAYFAktqcOIACgkQy0OE/ans1/mcagCfSn/Jjpit1c3pRghdsUO2qIMJ +AgIAnj74JUXGw195W6PFpUsAYXzNG2BW +=YYdj -----END PGP SIGNATURE----- diff --git a/sci-visualization/gnuplot/files/gnuplot-4.2.5-colorbox_accounting.patch b/sci-visualization/gnuplot/files/gnuplot-4.2.5-colorbox_accounting.patch deleted file mode 100644 index 126d80b5a..000000000 --- a/sci-visualization/gnuplot/files/gnuplot-4.2.5-colorbox_accounting.patch +++ /dev/null @@ -1,81 +0,0 @@ -http://bugs.gentoo.org/274693 -Solves: "cb axis range undefined or overflow" error after fit -Fix from upstream: https://sourceforge.net/tracker/?func=detail&atid=102055&aid=2808641&group_id=2055 - ---- gnuplot42/src/pm3d.c 2009-03-24 09:04:10.000000000 -0700 -+++ test42/src/pm3d.c 2009-06-18 16:45:36.000000000 -0700 -@@ -65,7 +65,6 @@ static quadrangle* quadrangles = (quadra - - /* Internal prototypes for this module */ - static TBOOLEAN plot_has_palette; --static TBOOLEAN plot_wants_colorbox; - static double geomean4 __PROTO((double, double, double, double)); - static double median4 __PROTO((double, double, double, double)); - static void pm3d_plot __PROTO((struct surface_points *, int)); -@@ -1020,10 +1019,8 @@ set_plot_with_palette(int plot_num, int - struct curve_points *this_2dplot = first_plot; - int surface = 0; - struct text_label *this_label = first_label; -- TBOOLEAN want_palette_but_not_colorbox = FALSE; - - plot_has_palette = TRUE; -- plot_wants_colorbox = TRUE; - /* Is pm3d switched on globally? */ - if (pm3d.implicit == PM3D_IMPLICIT) - return; -@@ -1035,18 +1032,12 @@ set_plot_with_palette(int plot_num, int - if (this_2dplot->plot_style == IMAGE) - return; - #endif -- if (this_2dplot->lp_properties.use_palette) { -- if (this_2dplot->lp_properties.pm3d_color.type <= TC_RGB) -- want_palette_but_not_colorbox = TRUE; -- /* don't return yet -- decide later whether showing color box is desirable */ -- else -- return; -- } --#ifdef EAM_DATASTRINGS -- if (this_2dplot->labels && -- this_2dplot->labels->textcolor.type >= TC_CB) -+ if (this_2dplot->lp_properties.use_palette -+ && this_2dplot->lp_properties.pm3d_color.type > TC_RGB) -+ return; -+ if (this_2dplot->labels -+ && this_2dplot->labels->textcolor.type >= TC_CB) - return; --#endif - this_2dplot = this_2dplot->next; - } - } -@@ -1064,8 +1055,8 @@ set_plot_with_palette(int plot_num, int - if (this_3dplot->lp_properties.use_palette) { - int type = this_3dplot->lp_properties.pm3d_color.type; - if (type == TC_LT || type == TC_LINESTYLE || type == TC_RGB) -- want_palette_but_not_colorbox = TRUE; -- /* don't return yet -- decide later whether showing color box is desirable */ -+ /* don't return yet */ -+ ; - else - /* TC_DEFAULT: splot x with line|lp|dot palette */ - return; -@@ -1097,9 +1088,7 @@ set_plot_with_palette(int plot_num, int - #undef TC_USES_PALETTE - - /* Palette with continuous colors is not used. */ -- if (want_palette_but_not_colorbox == FALSE) -- plot_has_palette = FALSE; /* otherwise it stays TRUE */ -- plot_wants_colorbox = FALSE; -+ plot_has_palette = FALSE; /* otherwise it stays TRUE */ - } - - TBOOLEAN -@@ -1111,6 +1100,6 @@ is_plot_with_palette() - TBOOLEAN - is_plot_with_colorbox() - { -- return plot_wants_colorbox; -+ return plot_has_palette && (color_box.where != SMCOLOR_BOX_NO); - } - - - diff --git a/sci-visualization/gnuplot/gnuplot-4.5.9999.ebuild b/sci-visualization/gnuplot/gnuplot-4.5.9999.ebuild index 858aae871..077f3c4ee 100644 --- a/sci-visualization/gnuplot/gnuplot-4.5.9999.ebuild +++ b/sci-visualization/gnuplot/gnuplot-4.5.9999.ebuild @@ -69,7 +69,6 @@ src_prepare() { local dir epatch "${FILESDIR}"/${PN}-4.2.2-disable_texi_generation.patch #194216 epatch "${FILESDIR}"/${PF}-app-defaults.patch #219323 - epatch "${FILESDIR}"/${PN}-4.4.0_rc1-disable-texhash.patch #201871 # Add Gentoo version identification since the licence requires it epatch "${FILESDIR}"/${PF}-gentoo-version.patch @@ -81,12 +80,6 @@ src_prepare() { } src_configure() { - # See bug #156427. - if use latex ; then - sed -i -e "s:\`kpsexpand.*\`:${TEXMF}/tex/latex/${PN}/${GP_VERSION}:" \ - share/LaTeX/Makefile.in || die "sed kpsexpand removed failed" - fi - local myconf="--enable-thin-splines" myconf="${myconf} $(use_with latex)" @@ -100,6 +93,8 @@ src_configure() { myconf="${myconf} $(use_with doc tutorial)" myconf="${myconf} $(use_enable qt4 qt)" + use latex && myconf="${myconf} --with-texdir=${TEXMF}/${PN}/${GP_VERSION}" + use ggi \ && myconf="${myconf} --with-ggi=/usr/$(get_libdir) --with-xmi=/usr/$(get_libdir)" \ diff --git a/sys-cluster/openmpi/ChangeLog b/sys-cluster/openmpi/ChangeLog index 498678662..1394cdb3d 100644 --- a/sys-cluster/openmpi/ChangeLog +++ b/sys-cluster/openmpi/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 03 Feb 2010; Justin Bronder <jsbronder@gentoo.org> openmpi-1.4.1.ebuild, + +files/openmpi-1.4.1-r22513.patch: + Add upstream fix for wrapper flag ordering + 19 Jan 2010; Justin Bronder <jsbronder@gentoo.org> openmpi-1.4.1.ebuild: Move include files into a subdirectory diff --git a/sys-cluster/openmpi/Manifest b/sys-cluster/openmpi/Manifest index 20dc5d91d..71a0aa277 100644 --- a/sys-cluster/openmpi/Manifest +++ b/sys-cluster/openmpi/Manifest @@ -1,9 +1,10 @@ AUX eselect.mpi.openmpi 225 RMD160 cf81165864aaad2833f7a8300c20376210a575dd SHA1 8b50b90346b52b831a59ec0abd8e3dbebad2b94e SHA256 df4d363e9fbab74c234b75f426b7f38ef83d16da2b099222c0dde4a2c3ece687 +AUX openmpi-1.4.1-r22513.patch 2460 RMD160 94c6ca7c7d869039e73f1dbd5402ccd0d5949f11 SHA1 a924c63a94546f25a25beb15328ff2ee18c388e8 SHA256 083528f3ccdda8e1654accd5a6d3c79231d7d727cbd1f05293d7850a32503379 DIST openmpi-1.3.3.tar.bz2 6695647 RMD160 209972fdbf52787ea0482d9b89fad2c1f59e6e87 SHA1 f668feb22ff0a4c4d9b438e4e69a97b08aa73234 SHA256 e1425853282da9237f5b41330207e54da1dc803a2e19a93dacc3eca1d083e422 DIST openmpi-1.4.1.tar.bz2 6571835 RMD160 c6fd5f0871eb5f963fe58270f5340a2629f5fd68 SHA1 c5107c03a9fc738dfb4f309b470d052becfdde19 SHA256 d4d71d7c670d710d2d283ea60af50d6c315318a4c35ec576bedfd0f3b7b8c218 DIST openmpi-1.4.tar.bz2 6699638 RMD160 61f7665c69ea019d347b983062a1eee0ae807c9b SHA1 8e98ceae223f52f147d5151779ed1a43f2865a7f SHA256 fa55edef1bd8af256e459d4d9782516c6998b9d4698eda097d5df33ae499858e EBUILD openmpi-1.3.3.ebuild 2907 RMD160 28f671b67cb8423c923377d1b1c4596798ecf878 SHA1 a9ab364c1104bd769f50a42186491b6358f88364 SHA256 c2bab10c70f85bdd1b1f029a9a708f360a558fbc58c1fd1858a05a7c3365d68d -EBUILD openmpi-1.4.1.ebuild 3097 RMD160 0034dfe11daa891f9e70534c261e8f4d8c419ede SHA1 30ac5116957d0d20e95dc57e29590c9b8f158b9c SHA256 8deee3c5d71373253d2c00014f85be08e03d920b3293cae8aecad7261c90db1f +EBUILD openmpi-1.4.1.ebuild 2996 RMD160 e2d9027c25d614035c894175124542340bdf3671 SHA1 b77bc16233bf970aacbbefe56f2e43aa5282ab37 SHA256 b9db925aca0601039dd2ec6b8071b3dae33409b62d05480942e426932b2360d1 EBUILD openmpi-1.4.ebuild 2905 RMD160 bca7ff76c9ab92db2a9f475b5b995d25faeac3e6 SHA1 76022fd4c572a52665495ce9850645b65ba8ff19 SHA256 0e9b38ac5f98549468ad981fc70d22506f7112eaa267655c65c91b1a282d3c5a -MISC ChangeLog 2212 RMD160 550be7f77e8969be87c1d8a218a18264a001f1f2 SHA1 60b879cc3203cd0f2912e77b4870c7770aa508ad SHA256 619a34eaf5c69935b280fa3a5e56337d67d562cc83ac725c87596a424beffc54 +MISC ChangeLog 2370 RMD160 2294304b7354670a871a61012efd4b14aafe9b57 SHA1 b21e406f0b629e01d2b3eb1bec71b80dae37da98 SHA256 d63d268041169c3533983cfc4c7ab3d083d21bbcdd419f98342e459db72c96a5 MISC metadata.xml 706 RMD160 d497cb759e382f2b07d5233f99f391e5c6f667d3 SHA1 870215f9b18002f5dc24fa742b0e740a8d730e4f SHA256 11a597b8ce26a8293a4b7ad9f0373c0c57ad99425ede80e8136747fab504807e diff --git a/sys-cluster/openmpi/files/openmpi-1.4.1-r22513.patch b/sys-cluster/openmpi/files/openmpi-1.4.1-r22513.patch new file mode 100644 index 000000000..128443be5 --- /dev/null +++ b/sys-cluster/openmpi/files/openmpi-1.4.1-r22513.patch @@ -0,0 +1,72 @@ +From 9657a0fc671dd0987b6954932a08b680c35f480f Mon Sep 17 00:00:00 2001 +From: Justin Bronder <jsbronder@gmail.com> +Date: Wed, 3 Feb 2010 17:13:13 -0500 +Subject: [PATCH] Backport r22513 + +Per #2201, move the user arguments up to be the first set of argv +after the compiler argv tokens. + +Not closing #2201 yet; there's still discussion on that ticket about +whether we want to do more or not. + +Refs #2201 +cmr:v1.4.2 +cmr:v1.5 + +Author: jsquyres +--- + ompi/tools/wrappers/ompi_wrapper_script.in | 4 +++- + opal/tools/wrappers/opal_wrapper.c | 9 +++++---- + 2 files changed, 8 insertions(+), 5 deletions(-) + +diff --git a/ompi/tools/wrappers/ompi_wrapper_script.in b/ompi/tools/wrappers/ompi_wrapper_script.in +index 24726ad..87fd8a5 100644 +--- a/ompi/tools/wrappers/ompi_wrapper_script.in ++++ b/ompi/tools/wrappers/ompi_wrapper_script.in +@@ -140,13 +140,15 @@ my @exec_argv = (); + + # assemble command + push(@exec_argv, split(' ', $comp)); ++# Per https://svn.open-mpi.org/trac/ompi/ticket/2201, add all the user ++# arguments before anything else. ++push(@exec_argv, @appargs); + if ($want_preproc == 1) { + push(@exec_argv, split(' ', $preproc_flags)); + } + if ($want_compile == 1) { + push(@exec_argv, split(' ', $comp_flags)); + } +-push(@exec_argv, @appargs); + if ($want_link == 1) { + push(@exec_argv, split(' ', $linker_flags)); + push(@exec_argv, split(' ', $libs)); +diff --git a/opal/tools/wrappers/opal_wrapper.c b/opal/tools/wrappers/opal_wrapper.c +index 86ece5b..1b80f53 100644 +--- a/opal/tools/wrappers/opal_wrapper.c ++++ b/opal/tools/wrappers/opal_wrapper.c +@@ -712,6 +712,11 @@ main(int argc, char *argv[]) + exec_argc = 0; + } + ++ /* Per https://svn.open-mpi.org/trac/ompi/ticket/2201, add all the ++ user arguments before anything else. */ ++ opal_argv_insert(&exec_argv, exec_argc, user_argv); ++ exec_argc = opal_argv_count(exec_argv); ++ + /* preproc flags */ + if (flags & COMP_WANT_PREPROC) { + opal_argv_insert(&exec_argv, exec_argc, options_data[user_data_idx].preproc_flags); +@@ -732,10 +737,6 @@ main(int argc, char *argv[]) + exec_argc = opal_argv_count(exec_argv); + } + +- /* add all the user arguments */ +- opal_argv_insert(&exec_argv, exec_argc, user_argv); +- exec_argc = opal_argv_count(exec_argv); +- + /* link flags and libs */ + if (flags & COMP_WANT_LINK) { + opal_argv_insert(&exec_argv, exec_argc, options_data[user_data_idx].link_flags); +-- +1.6.4.4 + diff --git a/sys-cluster/openmpi/openmpi-1.4.1.ebuild b/sys-cluster/openmpi/openmpi-1.4.1.ebuild index 58d88461c..18f3d6903 100644 --- a/sys-cluster/openmpi/openmpi-1.4.1.ebuild +++ b/sys-cluster/openmpi/openmpi-1.4.1.ebuild @@ -60,6 +60,9 @@ src_prepare() { echo 'oob_tcp_listen_mode = listen_thread' \ >> opal/etc/openmpi-mca-params.conf fi + + # https://svn.open-mpi.org/trac/ompi/ticket/2201 + epatch "${FILESDIR}"/${P}-r22513.patch } src_configure() { @@ -69,10 +72,6 @@ src_configure() { --enable-orterun-prefix-by-default --without-slurm" - # Workaround for #288147 which also caused packages like hdf5 to fail. - # http://www.open-mpi.org/community/lists/users/2009/12/11419.php - c="${c} --includedir=$(mpi_root)usr/include/${PN}" - if use mpi-threads; then c="${c} --enable-mpi-threads |