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# ChangeLog for sci-biology/ncbi-tools
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.89 2013/03/01 14:52:31 jlec Exp $
*ncbi-tools-2.2.26-r2 (01 Mar 2013)
01 Mar 2013; Justin Lecher <jlec@gentoo.org> -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 <jlec@gentoo.org> +ncbi-tools-2.2.26-r1.ebuild:
Clean heuristic to fix build env, #459720 and #459726
18 Feb 2013; Justin Lecher <jlec@gentoo.org> 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 <ulm@gentoo.org> 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 <jlec@gentoo.org> +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 <jlec@gentoo.org> +ncbi-tools-2.2.26.ebuild:
Version BUmp, #416251; restructured large parts of the ebuild; move to EAPI=4
26 Apr 2012; Justin Lecher <jlec@gentoo.org> ncbi-tools-20080302.ebuild,
-ncbi-tools-20090809-r2.ebuild:
Dropped old
15 Nov 2010; Justin Lecher <jlec@gentoo.org> ncbi-tools-20080302.ebuild,
ncbi-tools-20090809-r2.ebuild, ncbi-tools-20100808.ebuild:
QA fixes from repoman
15 Nov 2010; Justin Lecher <jlec@gentoo.org>
ncbi-tools-20090809-r2.ebuild, ncbi-tools-20100808.ebuild:
Use system csh instead of shebang
10 Oct 2010; Ulrich Mueller <ulm@gentoo.org> 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 <weaver@gentoo.org>
-ncbi-tools-20090809-r1.ebuild, +ncbi-tools-20100808.ebuild:
Version bump
24 Jun 2010; Justin Lecher <jlec@gentoo.org> -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 <pacho@gentoo.org> ncbi-tools-20090809.ebuild:
amd64 stable, bug 298779
*ncbi-tools-20090809-r2 (07 Mar 2010)
07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+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) <jlec@gentoo.org>
+ncbi-tools-20090809-r1.ebuild:
Build spidey per bug 268042 and respect LDFLAGS
29 Dec 2009; Christian Faulhammer <fauli@gentoo.org>
ncbi-tools-20090809.ebuild:
stable x86, bug 298779
02 Oct 2009; Andrey Kislyuk <weaver@gentoo.org>
ncbi-tools-20090809.ebuild:
Update description
22 Sep 2009; Markus Meier <maekke@gentoo.org> ncbi-tools-20090301.ebuild:
x86 stable, bug #283678
06 Sep 2009; Jeremy Olexa <darkside@gentoo.org>
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 <weaver@gentoo.org> metadata.xml,
+ncbi-tools-20090809.ebuild:
Version bump, take maintainership
19 Apr 2009; Brent Baude <ranger@gentoo.org> ncbi-tools-20090301.ebuild:
Marking ncbi-tools-20090301 ~ppc64 for bug 266569
18 Apr 2009; Tobias Klausmann <klausman@gentoo.org>
ncbi-tools-20090301.ebuild:
Keyworded on alpha, bug #266569
*ncbi-tools-20090301 (17 Apr 2009)
17 Apr 2009; Andrey Kislyuk <weaver@gentoo.org>
+ncbi-tools-20090301.ebuild:
Version bump, minor cleanup
24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
Giving up maintainership of this package.
27 Jun 2008; Ulrich Mueller <ulm@gentoo.org> 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 <corsair@gentoo.org> ncbi-tools-20080302.ebuild:
Stable on ppc64
12 May 2008; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
Move pmake to DEPEND fixing bug #221441
22 Apr 2008; Olivier Fisette <ribosome@gentoo.org>
-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 <je_fro@gentoo.org> +ncbi-tools-20080302.ebuild:
Latest release from NCBI.
08 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>; Manifest:
Fix manifest, connection dropped mid-commit.
08 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>;
ncbi-tools-20070826.ebuild:
(#195251) Fix build with --as-needed by always linking against dynamic
libraries (Till Korten).
08 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>;
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 <je_fro@gentoo.org> ChangeLog:
fixing my email address
19 Oct 2007; Jeff Gardner <je_fro@gentoo.org> ncbi-tools-20070826.ebuild:
Commenting out any reference to USE=mpi, which is currently broken (bug
#196466).
14 Oct 2007; Jeff Gardner <je_fro@gentoo.org> ncbi-tools-20070826.ebuild:
Commented out a stray reference to mpi that I missed the first time.
13 Oct 2007; <je_fro@gentoo.org> ncbi-tools-20050605.ebuild,
+ncbi-tools-20070826.ebuild:
Added quotes to make repoman happy.
*ncbi-tools-20070826 (13 Oct 2007)
13 Oct 2007; <je_fro@gentoo.org> +ncbi-tools-20070826.ebuild:
New version - mpiblast compilation broken at present.
05 Jun 2007; Raúl Porcel <armin76@gentoo.org> ncbi-tools-20060507.ebuild:
alpha stable wrt #152292
10 Mar 2007; Olivier Fisette <ribosome@gentoo.org>
+files/ncbi-tools-extra_vib.patch:
Added missing patch. Thanks to Walter Meinl <wuno@lsvw.de> for reporting
(bug #170202).
*ncbi-tools-20061015-r1 (09 Mar 2007)
09 Mar 2007; Olivier Fisette <ribosome@gentoo.org>
-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
<jmfernandez@cnio.es> for his work (see bug #169822). Pruned old version.
03 Nov 2006; Olivier Fisette <ribosome@gentoo.org>
-ncbi-tools-20050605-r2.ebuild:
Pruned old version.
*ncbi-tools-20061015 (03 Nov 2006)
03 Nov 2006; Olivier Fisette <ribosome@gentoo.org>
+ncbi-tools-20061015.ebuild:
New upstream version.
30 Oct 2006; Christian Faulhammer <opfer@gentoo.org>
ncbi-tools-20060507.ebuild:
stable x86 as requested in bug #152292
25 Oct 2006; Lars Weiler <pylon@gentoo.org> ncbi-tools-20060507.ebuild:
Stable on ppc; bug #152292.
25 Oct 2006; Fabian Groffen <grobian@gentoo.org>
ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild:
Dropped ppc-macos, see you in prefix.
24 Oct 2006; Fabian Groffen <grobian@gentoo.org>
ncbi-tools-20060507.ebuild:
Dropped ppc-macos, we don't have pmake
24 Oct 2006; Jeff Gardner <je_fro@gentoo.org> ncbi-tools-20060507.ebuild:
Stable on amd64.
23 Oct 2006; Markus Rothe <corsair@gentoo.org> ncbi-tools-20060507.ebuild:
Stable on ppc64; bug #152292
23 Oct 2006; Jeff Gardner <je_fro@gentoo.org> ncbi-tools-20060507.ebuild:
Stable on sparc - bug #152292
27 Jun 2006; Brent Baude <ranger@gentoo.org> ncbi-tools-20060507.ebuild:
Keywording ncbi-tools-20060507 ~ppc64 for bug #138082
27 Jun 2006; Olivier Fisette <ribosome@gentoo.org>
-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 <ribosome@gentoo.org>
+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 <spyderous@gentoo.org>;
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 <ribosome@gentoo.org>
-ncbi-tools-20050605-r1.ebuild:
Removed buggy version.
*ncbi-tools-20050605-r2 (14 Dec 2005)
14 Dec 2005; Olivier Fisette <ribosome@gentoo.org>
+ncbi-tools-20050605-r2.ebuild:
Fixed file collisions with "dev-libs/libpcre" (bug #115463).
16 Nov 2005; Olivier Fisette <ribosome@gentoo.org>
ncbi-tools-20050605-r1.ebuild:
Readded ~sparc (closes bug #111807).
15 Nov 2005; Fernando J. Pereda <ferdy@gentoo.org>
ncbi-tools-20050605-r1.ebuild:
re-add ~alpha wrt bug #111807
*ncbi-tools-20050605-r1 (15 Nov 2005)
15 Nov 2005; Olivier Fisette <ribosome@gentoo.org>
+ncbi-tools-20050605-r1.ebuild:
Added MPI support for the BLAST family of programs. Thanks to Brady
Catherman <bradyc@uidaho.edu> for his work (fixes bug #111807).
09 Nov 2005; Jason Wever <weeve@gentoo.org> ncbi-tools-20050605.ebuild:
Stable on SPARC wrt bug #108334.
22 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -files/21ncbi,
-ncbi-tools-20041020-r1.ebuild, -ncbi-tools-20050429.ebuild:
Pruning old versions.
22 Oct 2005; Fabian Groffen <grobian@gentoo.org>
ncbi-tools-20050605.ebuild:
Marked ppc-macos per bug #108334
18 Oct 2005; Aron Griffis <agriffis@gentoo.org>
ncbi-tools-20050605.ebuild:
Mark 20050605 stable on alpha
12 Oct 2005; Michael Hanselmann <hansmi@gentoo.org>
ncbi-tools-20050605.ebuild:
Stable on ppc.
11 Oct 2005; Luis Medinas <metalgod@gentoo.org>
ncbi-tools-20050605.ebuild:
Marked Stable on amd64
09 Oct 2005; Mark Loeser <halcy0n@gentoo.org> ncbi-tools-20050605.ebuild:
Stable on x86
07 Oct 2005; Brent Baude <ranger@gentoo.org> ncbi-tools-20050605.ebuild:
Marking ncbi-tools-200506 ppc64 stable for bug 108334
19 Sep 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
Maintainer changed from Stephen Diener (MIA) to Olivier Fisette.
16 Sep 2005; Aron Griffis <agriffis@gentoo.org>
ncbi-tools-20050429.ebuild:
Mark 20050429 stable on alpha
19 Aug 2005; Michael Hanselmann <hansmi@gentoo.org>
ncbi-tools-20050429.ebuild:
Removed from ppc (xlc not available).
09 Aug 2005; Brent Baude <ranger@gentoo.org>
+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 <ranger@gentoo.org>
+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 <ranger@gentoo.org> 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 <ribosome@gentoo.org>
-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 <corsair@gentoo.org>
ncbi-tools-20041020-r1.ebuild:
Stable on ppc64
02 Jun 2005; Olivier Fisette <ribosome@gentoo.org> ChangeLog:
Use "virtual/motif" instead of "x11-libs/openmotif".
16 May 2005; Olivier Fisette <ribosome@gentoo.org>
ncbi-tools-20050429.ebuild:
Fixed CFLAGS not being applied properly (bug #92564).
*ncbi-tools-20050429 (13 May 2005)
13 May 2005; Olivier Fisette <ribosome@gentoo.org>
+ncbi-tools-20050429.ebuild:
New version.
29 Apr 2005; Markus Rothe <corsair@gentoo.org>
ncbi-tools-20041020-r1.ebuild:
Added ~ppc64 to KEYWORDS
24 Apr 2005; Michael Hanselmann <hansmi@gentoo.org>
ncbi-tools-20041020-r1.ebuild:
Stable on ppc.
*ncbi-tools-20041020-r1 (06 Mar 2005)
06 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +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 <j4rg0n@gentoo.org> ncbi-tools-20041020.ebuild:
Stable ppc-macos
01 Mar 2005; Olivier Fisette <ribosome@gentoo.org>
ncbi-tools-20041020.ebuild:
Added to x86.
02 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> ncbi-tools-20040616.ebuild:
Stable ppc-macos
30 Jan 2005; Olivier Fisette <ribosome@gentoo.org>
ncbi-tools-20041020.ebuild:
Ebuild cleanup.
*ncbi-tools-20041020 (18 Jan 2005)
18 Jan 2005; Olivier Fisette <ribosome@gentoo.org>
+ncbi-tools-20041020.ebuild:
New version.
02 Jan 2005; Olivier Fisette <ribosome@gentoo.org> :
Added to x86. Use toolchain-funcs rather than gcc eclass.
29 Dec 2004; Ciaran McCreesh <ciaranm@gentoo.org> :
Change encoding to UTF-8 for GLEP 31 compliance
*ncbi-tools-20040616 (23 Dec 2004)
23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+files/21ncbi, +files/ncbirc, +ncbi-tools-20040616.ebuild:
Moved from app-sci/ncbi-tools to sci-biology/ncbi-tools.
30 Nov 2004; <j4rg0n@gentoo.org> ncbi-tools-20040616.ebuild:
Keyworded ~ppc-macos.
22 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org>
ncbi-tools-20040616.ebuild:
Added to ~amd64
14 Oct 2004; Olivier Fisette <ribosome@gentoo.org>
ncbi-tools-20040616.ebuild:
Use gcc-getCC from gcc.eclass rather than ${CC}.
04 Oct 2004; Olivier Fisette <ribosome@gentoo.org>
ncbi-tools-20040616.ebuild:
Fixed potential bug in "SRC_URI".
*ncbi-tools-20040616 (03 Oct 2004)
03 Oct 2004; Olivier Fisette <ribosome@gentoo.org> 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 <agriffis@gentoo.org> ncbi-tools-20031103.ebuild,
ncbi-tools-20040202-r1.ebuild:
Fix use invocation
05 May 2004; Bryan Østergaard <kloeri@gentoo.org>
ncbi-tools-20040202-r1.ebuild:
Stable on alpha.
19 Apr 2004; Patrick Kursawe <phosphan@gentoo.org>
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 <spyderous@gentoo.org>;
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 <mholzer@gentoo.org>
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 <sediener@gentoo.org>
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 <sediener@gentoo.org>
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 <sediener@gentoo.org>
ncbi-tools-20031103.ebuild, ncbi-tools-20040202.ebuild:
Version bump. Changes -O3 -> -O2 so X11 apps will work.
11 Jan 2004; Heinrich Wendel <lanius@gentoo.org>
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 <sediener@gentoo.org>
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; <sediener@gentoo.org> 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 <robbat2@gentoo.org>
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 <avenj@gentoo.org> ncbi-tools-04222003-r1.ebuild :
A few enhancements from Gontran Zepeda <gontran@gontran.net>.
*ncbi-tools-04222003 (03 May 2003)
03 May 2003; Jon Portnoy <avenj@gentoo.org> ncbi-tools-04222003 :
Initial important. Ebuild submitted by Steve Diener
<sediener@unity.ncsu.edu>.
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