# ChangeLog for sci-biology/emboss # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2011/03/09 16:29:05 jlec Exp $ 04 Jul 2014; Martin Mokrejs +files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch, emboss-6.3.1_p4-r2.ebuild: sci-biology/emboss-6.3.1_p4-r2: added a patch for 'undefined reference to c_plwid' bug #493724 24 Mar 2014; Martin Mokrejs emboss-6.3.1_p4-r2.ebuild: sci-biology/emboss-6.3.1_p4-r2: add plplot dependency, trying to get rid of a Makefile.patch using sed hackery 16 Sep 2013; Martin Mokrejs emboss-6.6.0.ebuild, +files/emboss-6.6.0_plcol.patch: emboss-6.6.0.ebuild files/emboss-6.6.0_plcol.patch Added the misisng patch, disabled searches for Gentoo-patches, fixed patch-related variable values in the 6.6.0 ebuild, BUT 1) the ebuild does not work, configure exits after looking for -lhpdf or later -lpng (that can be obeyed by omitting --with-hpdf --with-pngdriver) 2) if one relies on whatever configure detects compilation aborts while compiling embossversion.c or because -lexpat is not in LIBS. Well, expat is not in configure flags at all. Maybe something is caused by the --enable-systemlibs configure switch, I think it actually enables inclusion of these from their bundled copies in the EMBOSS tarball (and not use of the system-wide headers and libs). *emboss-6.3.1_p4-r2 (11 Sep 2013) *emboss-6.5.7 (11 Sep 2013) *emboss-6.6.0 (11 Sep 2013) 11 Sep 2013; Martin Mokrejs +emboss-6.3.1_p4-r2.ebuild, +emboss-6.5.7.ebuild, +emboss-6.6.0.ebuild, +files/ax_lib_mysql.m4, +files/emboss-6.3.1_p4-r2_Makefile.patch, +files/emboss-6.3.1_p4-r2_compilations-paths.patch, +files/emboss-6.3.1_p4-r2_libtool.patch, +files/emboss-6.3.1_p4-r2_plcol.patch, -emboss-6.3.1_p4-r1.ebuild, -files/emboss-6.3.1_p4-r1_plcol.patch: Partial success on removal of all crazy libraries and includes from CFLAGS and LDFLAGS used throught EMBOSS sources. While compile commandline are now clean still libtool is passed with LDFLAGS carrying over the many X11 and graphics libraries. Seems the source is ltmain.sh which uses on the linker lines but editing m4/libtool.m4 is not the right way to do it. Same applies to ltmain.sh in top-level directory. Any volunteers? Bug #394425 19 Jul 2012; Martin Mokrejs +files/emboss-6.3.1_p4-r1_plcol.patch, emboss-6.3.1_p4-r1.ebuild: added plcol patch with increased diff line count, bug #391669; same patch needs to go into offical emboss-6.3.1_p4 22 May 2012; Justin Lecher emboss-6.3.1_p4-r1.ebuild: Add missing eutils.eclass 24 Sep 2011; Justin Lecher emboss-6.3.1_p4-r1.ebuild: Use Fedora hosting because unpstream removed the patches 27 Mar 2011; Justin Lecher emboss-6.3.1_p4-r1.ebuild, -files/emboss-6.3.1_p4-r1.patch: Last fix for 64bitness 22 Mar 2011; Justin Lecher files/emboss-6.3.1_p4-r1.patch: Fix compile correctly against postgresql, #359959 21 Mar 2011; Justin Lecher files/emboss-6.3.1_p4-r1.patch: Implicit decs fix, thanks bicatali for help 21 Mar 2011; Justin Lecher emboss-6.3.1_p4-r1.ebuild, files/emboss-6.3.1_p4-r1.patch: Fixed for reviewed eclass 15 Mar 2011; Justin Lecher emboss-6.3.1_p4-r1.ebuild: Straighten ENV 15 Mar 2011; Justin Lecher emboss-6.3.1_p4-r1.ebuild: New emboss_src_install used 15 Mar 2011; Justin Lecher emboss-6.3.1_p4-r1.ebuild: Naming of eclass changed 14 Mar 2011; Justin Lecher emboss-6.3.1_p4-r1.ebuild: Ebov not needed to be set anymore *emboss-6.3.1_p4-r1 (11 Mar 2011) 11 Mar 2011; Justin Lecher -emboss-6.3.1_p4.ebuild, +emboss-6.3.1_p4-r1.ebuild, +files/emboss-6.3.1_p4-r1.patch, -files/emboss-6.3.1_p4.patch: Rev bump, to ahead of the tree ebuild 10 Mar 2011; Justin Lecher -files/6.3.1_p4.patch, emboss-6.3.1_p4.ebuild, +files/emboss-6.3.1_p4.patch: Correct naming of patch 10 Mar 2011; Justin Lecher metadata.xml: Removed largefile from local USE description 10 Mar 2011; Justin Lecher emboss-6.3.1_p4.ebuild: Move to new embassy-ng.eclass 09 Mar 2011; Justin Lecher emboss-6.3.1_p4.ebuild: Move to new embassy-ng.eclass 09 Mar 2011; Justin Lecher emboss-6.3.1_p4.ebuild: EAPI=4 takes three arguments on use_with *emboss-6.3.1_p4 (09 Mar 2011) 09 Mar 2011; Justin Lecher +files/6.3.1_p4-unbundle-libs.patch, -files/6.3.1-unbundle-libs.patch, -emboss-6.3.1.ebuild, +emboss-6.3.1_p4.ebuild: Bump to latest upstream patches *emboss-6.3.1 (09 Mar 2011) 09 Mar 2011; Justin Lecher +files/6.3.1-unbundle-libs.patch, +files/emboss-README.Gentoo-2, emboss-4.0.0.ebuild, emboss-6.0.1.ebuild, emboss-6.1.0-r1.ebuild, +emboss-6.3.1.ebuild, metadata.xml: Version Bump #335603, Unbundled libs, removed old, fix clash with /usr/bin/digest, #330507 18 Jul 2010; emboss-6.0.1.ebuild: ppc stable #325457 09 Jul 2010; Samuli Suominen emboss-6.0.1.ebuild: ppc64 stable wrt #325457 23 Jun 2010; Justin Lecher emboss-4.0.0.ebuild, emboss-6.0.1.ebuild, emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild: Blocking sys-devel/cons, bug 248792 *emboss-6.1.0-r1 (07 Mar 2010) 07 Mar 2010; Justin Lecher (jlec) +emboss-6.1.0-r1.ebuild: Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, keyworded as in overlay 01 Sep 2009; Olivier Fisette metadata.xml: Giving up maintainership of this package. 01 Sep 2009; Olivier Fisette emboss-6.1.0.ebuild: Remove documentation that conflicts with EMBASSY phylipnew. *emboss-6.1.0 (01 Sep 2009) 01 Sep 2009; Olivier Fisette +emboss-6.1.0.ebuild: New upstream version. 01 Sep 2009; Olivier Fisette emboss-6.0.1.ebuild: Stabilised on x86 and amd64. 31 Aug 2009; Olivier Fisette emboss-4.0.0.ebuild, emboss-6.0.1.ebuild: Q.A. fixes, including better dependency on ClustalW. 27 Aug 2008; Olivier Fisette -emboss-5.0.0.ebuild: Pruning version that will never be stabilised. 27 Aug 2008; Olivier Fisette emboss-4.0.0.ebuild: Depend on ClustalW 1.83 since version 2.x will soon be added to Portage and is incompatible with EMBOSS wrapper programs. *emboss-6.0.1 (26 Aug 2008) 26 Aug 2008; Olivier Fisette +emboss-6.0.1.ebuild: New upstream version. 25 Jan 2008; Markus Dittrich +files/emboss-5.0.0-as-needed.patch, emboss-4.0.0.ebuild, emboss-5.0.0.ebuild: Fixed unresolved symbols with as-needed (see bug #207304). 22 Jul 2007; Donnie Berkholz ; emboss-4.0.0.ebuild: Drop virtual/x11 references. 18 Jul 2007; Olivier Fisette +files/emboss-README.Gentoo-1: Added updated Gentoo README file in reStructuredText format. *emboss-5.0.0 (18 Jul 2007) 18 Jul 2007; Olivier Fisette +emboss-5.0.0.ebuild: New upstream version. 09 Apr 2007; Jeff Gardner +files/22emboss, -files/22emboss-r1, emboss-4.0.0.ebuild: Fixed to use doenvd wrt bug #173884 10 Dec 2006; Olivier Fisette -emboss-3.0.0-r1.ebuild, emboss-4.0.0.ebuild: Pruned old version. Removed ppc-macos keyword, as grobian said the package and its dependencies were fully moved into "prefix". 20 Nov 2006; emboss-4.0.0.ebuild: stable on amd64 15 Nov 2006; Markus Rothe emboss-4.0.0.ebuild: Stable on ppc64; bug #153766 03 Nov 2006; nixnut emboss-4.0.0.ebuild: Stable on ppc wrt bug 153766 03 Nov 2006; Jeff Gardner emboss-3.0.0-r1.ebuild: Added ~sparc to emboss-3 for embassy-phylip-3.6b. 02 Nov 2006; Olivier Fisette emboss-4.0.0.ebuild: Added to x86. 18 Aug 2006; Jason Wever emboss-4.0.0.ebuild: Added ~sparc keyword wrt bug #144241. *emboss-4.0.0 (21 Jul 2006) 21 Jul 2006; Olivier Fisette +emboss-4.0.0.ebuild: New upstream version. See change log: "http://emboss.sourceforge.net/developers/changelog.html". 20 Apr 2006; Olivier Fisette -emboss-3.0.0.ebuild: Removed old revision. 08 Apr 2006; Simon Stelling emboss-3.0.0-r1.ebuild: stable on amd64 22 Feb 2006; Fabian Groffen ChangeLog: Marked ppc-macos stable (bug #123332) 22 Feb 2006; emboss-3.0.0-r1.ebuild: Stable on ppc. bug 123332 21 Feb 2006; Markus Rothe emboss-3.0.0-r1.ebuild: Stable on ppc64; bug #123332 20 Feb 2006; Joshua Jackson emboss-3.0.0-r1.ebuild: Stable on x86; bug #123332 19 Feb 2006; Olivier Fisette emboss-3.0.0-r1.ebuild: Block old versions of pscan to avoid file collisions (see bug #116236). 23 Jan 2006; Olivier Fisette +files/README.Gentoo: Added missing README file (fixes bug #120071). *emboss-3.0.0-r1 (21 Jan 2006) 21 Jan 2006; Olivier Fisette +emboss-3.0.0-r1.ebuild: Install codons and restriction enzyme equivalence files in alternative directories. This avoids file collisions on case insensitive filesystems (see bug #115446), allows the installation of an updated enzyme prototypes file that will give more consistent results (see bug #118832). 14 Dec 2005; Donnie Berkholz ; emboss-3.0.0.ebuild: Add modular X dependencies. 19 Nov 2005; Simon Stelling emboss-3.0.0.ebuild: stable on amd64 04 Oct 2005; Olivier Fisette -emboss-2.10.0.ebuild: Removed obsolete version. 03 Oct 2005; Olivier Fisette emboss-3.0.0.ebuild: Stable on ppc-macos (with j4rg0n's permission, bug #102420). 02 Oct 2005; Michael Hanselmann emboss-3.0.0.ebuild: Stable on ppc. 24 Sep 2005; Markus Rothe emboss-3.0.0.ebuild: Stable on ppc64 21 Sep 2005; Olivier Fisette emboss-3.0.0.ebuild: Added to x86. 04 Sep 2005; Simon Stelling emboss-3.0.0.ebuild: added ~amd64 keyword 13 Aug 2005; Olivier Fisette emboss-3.0.0.ebuild, emboss-2.10.0.ebuild: Fixed Prosite dependency. *emboss-3.0.0 (06 Aug 2005) 06 Aug 2005; Olivier Fisette +emboss-3.0.0.ebuild: New version. 28 Jul 2005; Olivier Fisette -emboss-2.9.0.ebuild: Removed old version. 25 Jun 2005; Lina Pezzella emboss-2.10.0.ebuild: Stable ppc-macos 24 Jun 2005; Joseph Jezak emboss-2.10.0.ebuild: Marked ppc stable for bug #96819. 19 Jun 2005; Markus Rothe emboss-2.10.0.ebuild: Stable on ppc64 13 May 2005; Olivier Fisette emboss-2.10.0.ebuild: Added to x86. 02 May 2005; Omkhar Arasaratnam emboss-2.10.0.ebuild: Added ~ppc64 02 May 2005; Michael Hanselmann emboss-2.9.0.ebuild: Stable on ppc. *emboss-2.10.0 (22 Mar 2005) 22 Mar 2005; Olivier Fisette +emboss-2.10.0.ebuild: New version. 22 Feb 2005; Olivier Fisette emboss-2.9.0.ebuild: Added support for minimal build. 09 Feb 2005; Lina Pezzella emboss-2.9.0.ebuild: Stable ppc-macos 30 Jan 2005; Olivier Fisette emboss-2.9.0.ebuild: Ebuild cleanup. 01 Jan 2005; Lina Pezzella emboss-2.9.0.ebuild: Unstable ppc-macos. *emboss-2.9.0 (23 Dec 2004) 23 Dec 2004; Olivier Fisette +metadata.xml, +files/22emboss-r1, +emboss-2.9.0.ebuild: Moved from app-sci/emboss to sci-biology/emboss. 31 Oct 2004; Olivier Fisette emboss-2.9.0.ebuild, -emboss-2.8.0-r3.ebuild: Removed old version. Added 2.9.0 to x86. 10 Aug 2004; Olivier Fisette emboss-2.8.0-r3.ebuild: Added to x86. emboss-2.8.0-r2.ebuild: Removed obsolete ebuild. 21 Jul 2004; David Holm emboss-2.9.0.ebuild: Added to ~ppc. 20 Jul 2004; Olivier Fisette emboss-2.8.0-r3.ebuild, emboss-2.9.0.ebuild: Removed icc support since no patching is needed. 19 Jul 2004; Olivier Fisette emboss-2.9.0.ebuild: Version bump. Changed the configuration and install steps a bit to reflect the fact that header files are now installed automatically. 14 Jul 2004; Olivier Fisette emboss-2.8.0-r3.ebuild: Modified configuration step to make the X and png USE flags independent; Added support for icc; Added primer3 and clustalw to the dependencies since some EMBOSS programs won't work without them; Added support for the biological databases aaindex, cutg, prints, prosite, rebase and transfac, which are needed for many EMBOSS programs (the databases are PDEPENDencies since they all must be indexed with an EMBOSS program before use) (this database support is optional); Added header files installation for EMBOSS development. emboss-2.8.0-r2.ebuild: Added to x86. emboss-2.8.0-r1.ebuild, emboss-2.8.0.ebuild, emboss-2.7.1.ebuild: Removed files. metadata.xml: Added long description; Set myself as maintainer. 02 Jun 2004; Aron Griffis emboss-2.8.0-r1.ebuild, emboss-2.8.0-r2.ebuild: Fix use invocation 12 May 2004; David Holm emboss-2.8.0-r2.ebuild: Added to ~ppc. *emboss-2.8.0-r2 (11 May 2004) 11 May 2004; Patrick Kursawe emboss-2.8.0-r2.ebuild, files/22emboss-r1: Adjusted value of PLPLOT_LIB, see bug #50176 *emboss-2.8.0-r1 (30 Jan 2004) 30 Jan 2004; Stephen Diener emboss-2.8.0-r1.ebuild: Modified to use X and png properly for servers 28 Jan 2004; Stephen Diener emboss-2.8.0.ebuild: Modified 2.8.0 ebuild to require X not just USE it. *emboss-2.8.0 (13 Dec 2003) 13 Dec 2003; Stephen Diener emboss-2.7.1.ebuild, emboss-2.8.0.ebuild: Version bump... 20 Oct 2003; George Shapovalov metdata.xml : added metadata.xml, marked ebuild stable *emboss-2.7.1 (03 Sep 2003) 03 Sep 2003; emboss-2.7.1.ebuild: Initial ebuild