# ChangeLog for sci-biology/ncbi-tools # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.98 2015/03/11 13:17:35 jlec Exp $ 11 Mar 2015; Justin Lecher ncbi-tools-2.2.26-r2.ebuild: Add missing X deps, #542558 02 Mar 2015; Justin Lecher +files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch, +files/ncbi-tools-2.2.26-format-security.patch, ncbi-tools-2.2.26-r2.ebuild: Fix format-security and SLOT operators 12 Jun 2013; Justin Lecher ncbi-tools-2.2.26-r2.ebuild, files/ncbirc: Fix for prefix 11 Mar 2013; Justin Lecher metadata.xml: Drop Andrey as maintainer so that bugs get assigned to sci-biology directly 03 Mar 2013; Justin Lecher -ncbi-tools-0.20080302.ebuild, -ncbi-tools-0.20090809.ebuild, -ncbi-tools-2.2.26.ebuild: Drop old 03 Mar 2013; Agostino Sarubbo ncbi-tools-2.2.26-r2.ebuild: Stable for ppc64, wrt bug #458112 02 Mar 2013; Justin Lecher ncbi-tools-2.2.26-r2.ebuild, +files/ncbi-tools-2.2.26-bfr-overflow.patch: Fix typo in sed construct, #459920; add patch to fix buffer overflows 01 Mar 2013; Agostino Sarubbo ncbi-tools-2.2.26-r2.ebuild: Stable for x86, wrt bug #458112 01 Mar 2013; Agostino Sarubbo ncbi-tools-2.2.26-r2.ebuild: Stable for amd64, wrt bug #458112 *ncbi-tools-2.2.26-r2 (01 Mar 2013) 01 Mar 2013; Justin Lecher -ncbi-tools-2.2.26-r1.ebuild, +ncbi-tools-2.2.26-r2.ebuild: Fix all config files, #459720, #459726, #459878 *ncbi-tools-2.2.26-r1 (01 Mar 2013) 01 Mar 2013; Justin Lecher +ncbi-tools-2.2.26-r1.ebuild: Clean heuristic to fix build env, #459720 and #459726 18 Feb 2013; Justin Lecher ncbi-tools-0.20080302.ebuild, ncbi-tools-0.20090809.ebuild, ncbi-tools-2.2.26.ebuild, -ncbi-tools-20080302.ebuild, -ncbi-tools-20090809.ebuild, metadata.xml: Drop old; rename fmerge.1 to fmerg-ncbi.1 -> resolves collision with dev-util/fhist, #429560 24 Oct 2012; Ulrich Müller ncbi-tools-0.20080302.ebuild, ncbi-tools-0.20090809.ebuild, ncbi-tools-2.2.26.ebuild, ncbi-tools-20080302.ebuild, ncbi-tools-20090809.ebuild: Update dependency after package move from x11-libs/openmotif to x11-libs/motif. *ncbi-tools-0.20090809 (13 Jun 2012) *ncbi-tools-0.20080302 (13 Jun 2012) 13 Jun 2012; Justin Lecher +ncbi-tools-0.20080302.ebuild, +ncbi-tools-0.20090809.ebuild, -ncbi-tools-20100808.ebuild: Change Version numbers from x to 0.x in order to be able to follow upstream new versioning scheme; Drop old unstable *ncbi-tools-2.2.26 (22 May 2012) 22 May 2012; Justin Lecher +ncbi-tools-2.2.26.ebuild: Version BUmp, #416251; restructured large parts of the ebuild; move to EAPI=4 26 Apr 2012; Justin Lecher ncbi-tools-20080302.ebuild, -ncbi-tools-20090809-r2.ebuild: Dropped old 15 Nov 2010; Justin Lecher ncbi-tools-20080302.ebuild, ncbi-tools-20090809-r2.ebuild, ncbi-tools-20100808.ebuild: QA fixes from repoman 15 Nov 2010; Justin Lecher ncbi-tools-20090809-r2.ebuild, ncbi-tools-20100808.ebuild: Use system csh instead of shebang 10 Oct 2010; Ulrich Mueller ncbi-tools-20080302.ebuild, ncbi-tools-20090809.ebuild, ncbi-tools-20090809-r2.ebuild, ncbi-tools-20100808.ebuild: Fix openmotif dependency. *ncbi-tools-20100808 (30 Sep 2010) 30 Sep 2010; Andrey Kislyuk -ncbi-tools-20090809-r1.ebuild, +ncbi-tools-20100808.ebuild: Version bump 24 Jun 2010; Justin Lecher -ncbi-tools-20060507.ebuild, -ncbi-tools-20061015-r1.ebuild, -ncbi-tools-20070826.ebuild, -ncbi-tools-20090301.ebuild: Cleaned old version 29 Mar 2010; Pacho Ramos ncbi-tools-20090809.ebuild: amd64 stable, bug 298779 *ncbi-tools-20090809-r2 (07 Mar 2010) 07 Mar 2010; Justin Lecher (jlec) +ncbi-tools-20090809-r2.ebuild: Moved to EAPI=3 for PREFIX support, keyworded for *-linux, tested by me *ncbi-tools-20090809-r1 (13 Feb 2010) 13 Feb 2010; Justin Lecher (jlec) +ncbi-tools-20090809-r1.ebuild: Build spidey per bug 268042 and respect LDFLAGS 29 Dec 2009; Christian Faulhammer ncbi-tools-20090809.ebuild: stable x86, bug 298779 02 Oct 2009; Andrey Kislyuk ncbi-tools-20090809.ebuild: Update description 22 Sep 2009; Markus Meier ncbi-tools-20090301.ebuild: x86 stable, bug #283678 06 Sep 2009; Jeremy Olexa ncbi-tools-20090301.ebuild: amd64 stable, bug 283678. As requested, compile tested only due to complexity *ncbi-tools-20090809 (04 Sep 2009) 04 Sep 2009; Andrey Kislyuk metadata.xml, +ncbi-tools-20090809.ebuild: Version bump, take maintainership 19 Apr 2009; Brent Baude ncbi-tools-20090301.ebuild: Marking ncbi-tools-20090301 ~ppc64 for bug 266569 18 Apr 2009; Tobias Klausmann ncbi-tools-20090301.ebuild: Keyworded on alpha, bug #266569 *ncbi-tools-20090301 (17 Apr 2009) 17 Apr 2009; Andrey Kislyuk +ncbi-tools-20090301.ebuild: Version bump, minor cleanup 24 Mar 2009; Olivier Fisette metadata.xml: Giving up maintainership of this package. 27 Jun 2008; Ulrich Mueller ncbi-tools-20060507.ebuild, ncbi-tools-20061015-r1.ebuild, ncbi-tools-20070826.ebuild, ncbi-tools-20080302.ebuild: Change dependency from virtual/motif to x11-libs/openmotif, bug 224749. 12 May 2008; Markus Rothe ncbi-tools-20080302.ebuild: Stable on ppc64 12 May 2008; Jeff Gardner ChangeLog: Move pmake to DEPEND fixing bug #221441 22 Apr 2008; Olivier Fisette -ncbi-tools-20050605.ebuild, ncbi-tools-20080302.ebuild: Pruned old version. Added 20080302 to x86 and amd64 (fixes bug #218233). *ncbi-tools-20080302 (15 Apr 2008) 15 Apr 2008; Jeff Gardner +ncbi-tools-20080302.ebuild: Latest release from NCBI. 08 Apr 2008; Donnie Berkholz ; Manifest: Fix manifest, connection dropped mid-commit. 08 Apr 2008; Donnie Berkholz ; ncbi-tools-20070826.ebuild: (#195251) Fix build with --as-needed by always linking against dynamic libraries (Till Korten). 08 Apr 2008; Donnie Berkholz ; ncbi-tools-20070826.ebuild: Respect CFLAGS and compiler on 64-bit systems. Apparently I'm the only person on amd64 who actually watches it build. =) 31 Dec 2007; Jeff Gardner ChangeLog: fixing my email address 19 Oct 2007; Jeff Gardner ncbi-tools-20070826.ebuild: Commenting out any reference to USE=mpi, which is currently broken (bug #196466). 14 Oct 2007; Jeff Gardner ncbi-tools-20070826.ebuild: Commented out a stray reference to mpi that I missed the first time. 13 Oct 2007; ncbi-tools-20050605.ebuild, +ncbi-tools-20070826.ebuild: Added quotes to make repoman happy. *ncbi-tools-20070826 (13 Oct 2007) 13 Oct 2007; +ncbi-tools-20070826.ebuild: New version - mpiblast compilation broken at present. 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 .