From 59f1a67714e374b84b9909c583c9fc4953ad97ce Mon Sep 17 00:00:00 2001 From: Jeffrey Gardner Date: Sun, 14 Oct 2007 00:04:56 +0000 Subject: Added to tree svn path=/; revision=88 --- sci-biology/ncbi-tools/ChangeLog | 334 --------------------- sci-biology/ncbi-tools/Manifest | 38 --- sci-biology/ncbi-tools/files/21ncbi-r1 | 6 - .../ncbi-tools/files/digest-ncbi-tools-20061015-r1 | 8 - .../ncbi-tools/files/digest-ncbi-tools-20070826 | 8 - .../ncbi-tools/files/ncbi-tools-asn2all.patch | 27 -- .../ncbi-tools/files/ncbi-tools-extra_vib.patch | 37 --- sci-biology/ncbi-tools/files/ncbi-tools-lop.patch | 15 - sci-biology/ncbi-tools/files/ncbirc | 2 - sci-biology/ncbi-tools/metadata.xml | 9 - sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild | 200 ------------ 11 files changed, 684 deletions(-) delete mode 100644 sci-biology/ncbi-tools/ChangeLog delete mode 100644 sci-biology/ncbi-tools/Manifest delete mode 100644 sci-biology/ncbi-tools/files/21ncbi-r1 delete mode 100644 sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1 delete mode 100644 sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 delete mode 100644 sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch delete mode 100644 sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch delete mode 100644 sci-biology/ncbi-tools/files/ncbi-tools-lop.patch delete mode 100644 sci-biology/ncbi-tools/files/ncbirc delete mode 100644 sci-biology/ncbi-tools/metadata.xml delete mode 100644 sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild (limited to 'sci-biology') diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog deleted file mode 100644 index ed0294c..0000000 --- a/sci-biology/ncbi-tools/ChangeLog +++ /dev/null @@ -1,334 +0,0 @@ -# ChangeLog for sci-biology/ncbi-tools -# Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.53 2007/06/05 11:00:49 armin76 Exp $ - - 05 Jun 2007; Raúl Porcel ncbi-tools-20060507.ebuild: - alpha stable wrt #152292 - - 10 Mar 2007; Olivier Fisette - +files/ncbi-tools-extra_vib.patch: - Added missing patch. Thanks to Walter Meinl for reporting - (bug #170202). - -*ncbi-tools-20061015-r1 (09 Mar 2007) - - 09 Mar 2007; Olivier Fisette - -ncbi-tools-20061015.ebuild, +ncbi-tools-20061015-r1.ebuild: - Install ans2all utility. Added support for compiling/installing arbitrary - NCBI utilities. Thanks to José María Fernández González - for his work (see bug #169822). Pruned old version. - - 03 Nov 2006; Olivier Fisette - -ncbi-tools-20050605-r2.ebuild: - Pruned old version. - -*ncbi-tools-20061015 (03 Nov 2006) - - 03 Nov 2006; Olivier Fisette - +ncbi-tools-20061015.ebuild: - New upstream version. - - 30 Oct 2006; Christian Faulhammer - ncbi-tools-20060507.ebuild: - stable x86 as requested in bug #152292 - - 25 Oct 2006; Lars Weiler ncbi-tools-20060507.ebuild: - Stable on ppc; bug #152292. - - 25 Oct 2006; Fabian Groffen - ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild: - Dropped ppc-macos, see you in prefix. - - 24 Oct 2006; Fabian Groffen - ncbi-tools-20060507.ebuild: - Dropped ppc-macos, we don't have pmake - - 24 Oct 2006; Jeff Gardner ncbi-tools-20060507.ebuild: - Stable on amd64. - - 23 Oct 2006; Markus Rothe ncbi-tools-20060507.ebuild: - Stable on ppc64; bug #152292 - - 23 Oct 2006; Jeff Gardner ncbi-tools-20060507.ebuild: - Stable on sparc - bug #152292 - - 27 Jun 2006; Brent Baude ncbi-tools-20060507.ebuild: - Keywording ncbi-tools-20060507 ~ppc64 for bug #138082 - - 27 Jun 2006; Olivier Fisette - -files/ncbi-tools-20050605-lop.patch, +files/ncbi-tools-lop.patch, - ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild, - ncbi-tools-20060507.ebuild: - Fixed ppc64 lop patch (my mistake). - -*ncbi-tools-20060507 (26 Jun 2006) - - 26 Jun 2006; Olivier Fisette - +files/ncbi-tools-asn2all.patch, +ncbi-tools-20060507.ebuild: - New upstream version. Switched from GNU make to pmake as GNU make 3.81 is - confused by some Makefiles (fixes bug #136904, thanks to Greg Wilson for - reporting). Compile and install asn2all (fixes bug #136206, thanks to José - María Fernández González for the suggestion). Minor bugfixes and ebuild - clean-up. ppc64 keyword dropped as pmake is not available for that arch. - - 01 Feb 2006; Donnie Berkholz ; - ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild: - (#121066) Port to modular X. Add some die messages to -r2 so the die's - aren't completely unhelpful. Fix the path expansion for html docs so it - doesn't break the installation -- not sure how it got committed as is: - {*.html *.gif} is missing a comma. - - 21 Jan 2006; Olivier Fisette - -ncbi-tools-20050605-r1.ebuild: - Removed buggy version. - -*ncbi-tools-20050605-r2 (14 Dec 2005) - - 14 Dec 2005; Olivier Fisette - +ncbi-tools-20050605-r2.ebuild: - Fixed file collisions with "dev-libs/libpcre" (bug #115463). - - 16 Nov 2005; Olivier Fisette - ncbi-tools-20050605-r1.ebuild: - Readded ~sparc (closes bug #111807). - - 15 Nov 2005; Fernando J. Pereda - ncbi-tools-20050605-r1.ebuild: - re-add ~alpha wrt bug #111807 - -*ncbi-tools-20050605-r1 (15 Nov 2005) - - 15 Nov 2005; Olivier Fisette - +ncbi-tools-20050605-r1.ebuild: - Added MPI support for the BLAST family of programs. Thanks to Brady - Catherman for his work (fixes bug #111807). - - 09 Nov 2005; Jason Wever ncbi-tools-20050605.ebuild: - Stable on SPARC wrt bug #108334. - - 22 Oct 2005; Olivier Fisette -files/21ncbi, - -ncbi-tools-20041020-r1.ebuild, -ncbi-tools-20050429.ebuild: - Pruning old versions. - - 22 Oct 2005; Fabian Groffen - ncbi-tools-20050605.ebuild: - Marked ppc-macos per bug #108334 - - 18 Oct 2005; Aron Griffis - ncbi-tools-20050605.ebuild: - Mark 20050605 stable on alpha - - 12 Oct 2005; Michael Hanselmann - ncbi-tools-20050605.ebuild: - Stable on ppc. - - 11 Oct 2005; Luis Medinas - ncbi-tools-20050605.ebuild: - Marked Stable on amd64 - - 09 Oct 2005; Mark Loeser ncbi-tools-20050605.ebuild: - Stable on x86 - - 07 Oct 2005; Brent Baude ncbi-tools-20050605.ebuild: - Marking ncbi-tools-200506 ppc64 stable for bug 108334 - - 19 Sep 2005; Olivier Fisette metadata.xml: - Maintainer changed from Stephen Diener (MIA) to Olivier Fisette. - - 16 Sep 2005; Aron Griffis - ncbi-tools-20050429.ebuild: - Mark 20050429 stable on alpha - - 19 Aug 2005; Michael Hanselmann - ncbi-tools-20050429.ebuild: - Removed from ppc (xlc not available). - - 09 Aug 2005; Brent Baude - +files/ncbi-tools-20050605-lop.patch, - -files/ncbi-tools-20050605-lop.patch.gz, ncbi-tools-20050605.ebuild: - For the ebuild ncbi-tools-20050605, I was asked to remove the gz patch and - submit it as plain text. This commit will remove the gz patch and replace it - with a plain text one. The patch name change is also reflected in the - ebuild. - - 08 Aug 2005; Brent Baude - +files/ncbi-tools-20050605-lop.patch.gz, ncbi-tools-20050605.ebuild: - Added patch for 20050506 which when ppc64, will patch the makefile to use - gcc instead of the default xlc (IBM compiler) which doesnt exist on gentoo. - - 08 Aug 2005; Brent Baude ncbi-tools-20050429.ebuild: - ncbi-tools-20050429.ebuild does not compile on ppc64; will fix later ebuild - -*ncbi-tools-20050605 (06 Aug 2005) - - 06 Aug 2005; Olivier Fisette - -ncbi-tools-20040616.ebuild, ncbi-tools-20050429.ebuild, - +ncbi-tools-20050605.ebuild: - New version. Added 20050429 to x86. Removed old version. - - 09 Jun 2005; Markus Rothe - ncbi-tools-20041020-r1.ebuild: - Stable on ppc64 - - 02 Jun 2005; Olivier Fisette ChangeLog: - Use "virtual/motif" instead of "x11-libs/openmotif". - - 16 May 2005; Olivier Fisette - ncbi-tools-20050429.ebuild: - Fixed CFLAGS not being applied properly (bug #92564). - -*ncbi-tools-20050429 (13 May 2005) - - 13 May 2005; Olivier Fisette - +ncbi-tools-20050429.ebuild: - New version. - - 29 Apr 2005; Markus Rothe - ncbi-tools-20041020-r1.ebuild: - Added ~ppc64 to KEYWORDS - - 24 Apr 2005; Michael Hanselmann - ncbi-tools-20041020-r1.ebuild: - Stable on ppc. - -*ncbi-tools-20041020-r1 (06 Mar 2005) - - 06 Mar 2005; Olivier Fisette +files/21ncbi-r1, - +ncbi-tools-20041020-r1.ebuild, -ncbi-tools-20041020.ebuild: - Added the "BLASTMAT" environment variable to the env.d file. - - 02 Mar 2005; Lina Pezzella ncbi-tools-20041020.ebuild: - Stable ppc-macos - - 01 Mar 2005; Olivier Fisette - ncbi-tools-20041020.ebuild: - Added to x86. - - 02 Feb 2005; Lina Pezzella ncbi-tools-20040616.ebuild: - Stable ppc-macos - - 30 Jan 2005; Olivier Fisette - ncbi-tools-20041020.ebuild: - Ebuild cleanup. - -*ncbi-tools-20041020 (18 Jan 2005) - - 18 Jan 2005; Olivier Fisette - +ncbi-tools-20041020.ebuild: - New version. - - 02 Jan 2005; Olivier Fisette : - Added to x86. Use toolchain-funcs rather than gcc eclass. - - 29 Dec 2004; Ciaran McCreesh : - Change encoding to UTF-8 for GLEP 31 compliance - -*ncbi-tools-20040616 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette +metadata.xml, - +files/21ncbi, +files/ncbirc, +ncbi-tools-20040616.ebuild: - Moved from app-sci/ncbi-tools to sci-biology/ncbi-tools. - - 30 Nov 2004; ncbi-tools-20040616.ebuild: - Keyworded ~ppc-macos. - - 22 Nov 2004; Karol Wojtaszek - ncbi-tools-20040616.ebuild: - Added to ~amd64 - - 14 Oct 2004; Olivier Fisette - ncbi-tools-20040616.ebuild: - Use gcc-getCC from gcc.eclass rather than ${CC}. - - 04 Oct 2004; Olivier Fisette - ncbi-tools-20040616.ebuild: - Fixed potential bug in "SRC_URI". - -*ncbi-tools-20040616 (03 Oct 2004) - - 03 Oct 2004; Olivier Fisette files/21ncbi, - -files/dot-ncbirc, +files/ncbirc, -ncbi-tools-20031103.ebuild, - -ncbi-tools-20040202-r1.ebuild, +ncbi-tools-20040616.ebuild: - Updated version and new ebuild. This fixes bug #65941. - - 02 Jun 2004; Aron Griffis ncbi-tools-20031103.ebuild, - ncbi-tools-20040202-r1.ebuild: - Fix use invocation - - 05 May 2004; Bryan Østergaard - ncbi-tools-20040202-r1.ebuild: - Stable on alpha. - - 19 Apr 2004; Patrick Kursawe - ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild, - ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild, - ncbi-tools-20040202.ebuild: - Cleanup, removing S=... with no effect - - 30 Mar 2004; Donnie Berkholz ; - ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild, - ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild, - ncbi-tools-20040202.ebuild: - Change x11-base/xfree dependency to virtual/x11. - - 21 Mar 2004; Martin Holzer - ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild, - ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild, - ncbi-tools-20040202.ebuild: - adding categorie. see 45110 for details - -*ncbi-tools-20040202-r1 (06 Feb 2004) - - 06 Feb 2004; Stephen Diener - ncbi-tools-20040202-r1.ebuild: - Replaced buggy tarball with new one. Bumped revision to propogate. - -*ncbi-tools-20040202 (05 Feb 2004) - - 05 Feb 2004; Stephen Diener - ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003.ebuild, - ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild, - ncbi-tools-20040202.ebuild: - Bumped 20031103 to x86, removed old ebuilds, added new release 20040202 - -*ncbi-tools-20040202 (04 Feb 2004) - - 04 Feb 2004; Stephen Diener - ncbi-tools-20031103.ebuild, ncbi-tools-20040202.ebuild: - Version bump. Changes -O3 -> -O2 so X11 apps will work. - - 11 Jan 2004; Heinrich Wendel - ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003-r2.ebuild, - ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild: - fixed motif dep - -*ncbi-tools-20031103 (13 Dec 2003) - - 13 Dec 2003; Stephen Diener - ncbi-tools-20031103.ebuild: - Added november release of ncbi-tools (blast-2.2.6 included); - Added support for -X - -*ncbi-tools-20030422 (11 Nov 2003) - - 11 Nov 2003; ncbi-tools-20030422.ebuild: - added bl2seq to list of installed binaries; changed date format from 04222003 - to 20030422; renamed files to have date appended to not collide and changed - SRC_URI to mirror://gentoo/ - -*ncbi-tools-04222003-r2 (08 Oct 2003) - - 08 Oct 2003; Robin H. Johnson - ncbi-tools-04222003-r2.ebuild: - modified patch from #30656, corrected two pathes in the postinst message - -*ncbi-tools-04222003-r1 (05 May 2003) - - 05 May 2003; Jon Portnoy ncbi-tools-04222003-r1.ebuild : - A few enhancements from Gontran Zepeda . - -*ncbi-tools-04222003 (03 May 2003) - - 03 May 2003; Jon Portnoy ncbi-tools-04222003 : - Initial important. Ebuild submitted by Steve Diener - . diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest deleted file mode 100644 index 58ff038..0000000 --- a/sci-biology/ncbi-tools/Manifest +++ /dev/null @@ -1,38 +0,0 @@ -AUX 21ncbi-r1 232 RMD160 ba65fe937c9a29f4cc185d99db18522343bbb28b SHA1 5674f379f7a70e71394bca272fedd72a1622a7da SHA256 55d5d53c177200d4a9369102d3e2d8ef232f09dd8559aab6c6e4d2173e8bb411 -MD5 a5f54430f6f7422d75320e91068cae0b files/21ncbi-r1 232 -RMD160 ba65fe937c9a29f4cc185d99db18522343bbb28b files/21ncbi-r1 232 -SHA256 55d5d53c177200d4a9369102d3e2d8ef232f09dd8559aab6c6e4d2173e8bb411 files/21ncbi-r1 232 -AUX ncbi-tools-asn2all.patch 1190 RMD160 3aaccc677bd8b9bad6c6424f5080c71cdac553d7 SHA1 ae22c77cfcd7d416a89ea3fe1e0331264473669d SHA256 e2fd71fdaa07b9e1c9cf646b2d3aa02c2ec822d41dcd45cadfced4164f458bed -MD5 b89cb833887b3e3efda83d074b4b8edb files/ncbi-tools-asn2all.patch 1190 -RMD160 3aaccc677bd8b9bad6c6424f5080c71cdac553d7 files/ncbi-tools-asn2all.patch 1190 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-# Location of the ".ncbi.rc" file which sets the default path for shared data. -NCBI=/etc/ncbi diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1 deleted file mode 100644 index a80231e..0000000 --- a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1 +++ /dev/null @@ -1,8 +0,0 @@ -MD5 14ee6d612d0d86e0dee7eb5f0c38839f mpiblast-20060625.tar.gz 165096 -RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 mpiblast-20060625.tar.gz 165096 -SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097 mpiblast-20060625.tar.gz 165096 -MD5 8eca84753fd7a1d39bab256a4944f65e ncbi-tools-20061015.tar.gz 15772715 -RMD160 034124b92d4320be31b2bacbb0966270cbfa63b3 ncbi-tools-20061015.tar.gz 15772715 -SHA256 0833f4b4f0389f75cdc0754329b3b8c1420c5b9abd7f3d8e352b4c134b3446de ncbi-tools-20061015.tar.gz 15772715 -RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b ncbi-tools-sdk-doc.tar.bz2 263568 -SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 ncbi-tools-sdk-doc.tar.bz2 263568 diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 deleted file mode 100644 index 3c82f07..0000000 --- a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 +++ /dev/null @@ -1,8 +0,0 @@ -MD5 14ee6d612d0d86e0dee7eb5f0c38839f mpiblast-20060625.tar.gz 165096 -RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 mpiblast-20060625.tar.gz 165096 -SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097 mpiblast-20060625.tar.gz 165096 -MD5 c17f7b08c12823e4320661894110dcb1 ncbi-tools-20070826.tar.gz 17076175 -RMD160 00daadd503bf729c15ada0008e305492a076fe15 ncbi-tools-20070826.tar.gz 17076175 -SHA256 58be3bb76c4a112217c414fd5d05de58a893cfd6ace3856629616a97a61ee4c8 ncbi-tools-20070826.tar.gz 17076175 -RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b ncbi-tools-sdk-doc.tar.bz2 263568 -SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 ncbi-tools-sdk-doc.tar.bz2 263568 diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch deleted file mode 100644 index 1cd7976..0000000 --- a/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch +++ /dev/null @@ -1,27 +0,0 @@ ---- ncbi-20050605/make/makedis.csh 2005-05-13 05:42:12.000000000 +0200 -+++ ncbi/make/makedis.csh 2005-09-20 22:02:38.000000000 +0200 -@@ -472,6 +472,24 @@ - - set net_stat = $status - -+if ("$?NCBI_MT_OTHERLIBS" == "1") then -+ set CMD='make $MFLG -f makenet.unx \ -+ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ -+ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ -+ THREAD_OBJ=$NCBI_THREAD_OBJ \ -+ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \ -+ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all' -+else -+ set CMD='make $MFLG -f makenet.unx \ -+ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ -+ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ -+ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all' -+endif -+eval echo $CMD -+eval echo $CMD | sh -+ - if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then - echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat - cat <