* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2011-03-10 19:00 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2011-03-10 19:00 UTC (permalink / raw
To: gentoo-commits
commit: 895a849ade4a8dc6d5e0d49d6c8d8b5556eeca05
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 9 18:37:54 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Mar 9 18:37:54 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=895a849a
Emboss-6.3.1 imported from tree
---
sci-biology/emboss/ChangeLog | 299 +++++++++++
sci-biology/emboss/emboss-6.3.1_p4.ebuild | 116 +++++
sci-biology/emboss/files/6.3.1_p4.patch | 600 +++++++++++++++++++++++
sci-biology/emboss/files/emboss-README.Gentoo-2 | 34 ++
sci-biology/emboss/metadata.xml | 21 +
5 files changed, 1070 insertions(+), 0 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
new file mode 100644
index 0000000..5d6f872
--- /dev/null
+++ b/sci-biology/emboss/ChangeLog
@@ -0,0 +1,299 @@
+# ChangeLog for sci-biology/emboss
+# Copyright 1999-2011 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 $
+
+ 09 Mar 2011; Justin Lecher <jlec@gentoo.org> 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 <jlec@gentoo.org>
+ +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 <jlec@gentoo.org>
+ +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; <nixnut@gentoo.org> emboss-6.0.1.ebuild:
+ ppc stable #325457
+
+ 09 Jul 2010; Samuli Suominen <ssuominen@gentoo.org> emboss-6.0.1.ebuild:
+ ppc64 stable wrt #325457
+
+ 23 Jun 2010; Justin Lecher <jlec@gentoo.org> 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) <jlec@gentoo.org>
+ +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 <ribosome@gentoo.org> metadata.xml:
+ Giving up maintainership of this package.
+
+ 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.1.0.ebuild:
+ Remove documentation that conflicts with EMBASSY phylipnew.
+
+*emboss-6.1.0 (01 Sep 2009)
+
+ 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +emboss-6.1.0.ebuild:
+ New upstream version.
+
+ 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.0.1.ebuild:
+ Stabilised on x86 and amd64.
+
+ 31 Aug 2009; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild,
+ emboss-6.0.1.ebuild:
+ Q.A. fixes, including better dependency on ClustalW.
+
+ 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> -emboss-5.0.0.ebuild:
+ Pruning version that will never be stabilised.
+
+ 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> 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 <ribosome@gentoo.org> +emboss-6.0.1.ebuild:
+ New upstream version.
+
+ 25 Jan 2008; Markus Dittrich <markusle@gentoo.org>
+ +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 <dberkholz@gentoo.org>; emboss-4.0.0.ebuild:
+ Drop virtual/x11 references.
+
+ 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org>
+ +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 <ribosome@gentoo.org> +emboss-5.0.0.ebuild:
+ New upstream version.
+
+ 09 Apr 2007; Jeff Gardner <je_fro@gentoo.org> +files/22emboss,
+ -files/22emboss-r1, emboss-4.0.0.ebuild:
+ Fixed to use doenvd wrt bug #173884
+
+ 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org>
+ -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; <blubb@gentoo.org> emboss-4.0.0.ebuild:
+ stable on amd64
+
+ 15 Nov 2006; Markus Rothe <corsair@gentoo.org> emboss-4.0.0.ebuild:
+ Stable on ppc64; bug #153766
+
+ 03 Nov 2006; nixnut <nixnut@gentoo.org> emboss-4.0.0.ebuild:
+ Stable on ppc wrt bug 153766
+
+ 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> emboss-3.0.0-r1.ebuild:
+ Added ~sparc to emboss-3 for embassy-phylip-3.6b.
+
+ 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild:
+ Added to x86.
+
+ 18 Aug 2006; Jason Wever <weeve@gentoo.org> emboss-4.0.0.ebuild:
+ Added ~sparc keyword wrt bug #144241.
+
+*emboss-4.0.0 (21 Jul 2006)
+
+ 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +emboss-4.0.0.ebuild:
+ New upstream version. See change log:
+ "http://emboss.sourceforge.net/developers/changelog.html".
+
+ 20 Apr 2006; Olivier Fisette <ribosome@gentoo.org> -emboss-3.0.0.ebuild:
+ Removed old revision.
+
+ 08 Apr 2006; Simon Stelling <blubb@gentoo.org> emboss-3.0.0-r1.ebuild:
+ stable on amd64
+
+ 22 Feb 2006; Fabian Groffen <grobian@gentoo.org> ChangeLog:
+ Marked ppc-macos stable (bug #123332)
+
+ 22 Feb 2006; <nixnut@gentoo.org> emboss-3.0.0-r1.ebuild:
+ Stable on ppc. bug 123332
+
+ 21 Feb 2006; Markus Rothe <corsair@gentoo.org> emboss-3.0.0-r1.ebuild:
+ Stable on ppc64; bug #123332
+
+ 20 Feb 2006; Joshua Jackson <tsunam@gentoo.org> emboss-3.0.0-r1.ebuild:
+ Stable on x86; bug #123332
+
+ 19 Feb 2006; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0-r1.ebuild:
+ Block old versions of pscan to avoid file collisions (see bug #116236).
+
+ 23 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +files/README.Gentoo:
+ Added missing README file (fixes bug #120071).
+
+*emboss-3.0.0-r1 (21 Jan 2006)
+
+ 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org>
+ +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 <spyderous@gentoo.org>; emboss-3.0.0.ebuild:
+ Add modular X dependencies.
+
+ 19 Nov 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild:
+ stable on amd64
+
+ 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.10.0.ebuild:
+ Removed obsolete version.
+
+ 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild:
+ Stable on ppc-macos (with j4rg0n's permission, bug #102420).
+
+ 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-3.0.0.ebuild:
+ Stable on ppc.
+
+ 24 Sep 2005; Markus Rothe <corsair@gentoo.org> emboss-3.0.0.ebuild:
+ Stable on ppc64
+
+ 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild:
+ Added to x86.
+
+ 04 Sep 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild:
+ added ~amd64 keyword
+
+ 13 Aug 2005; Olivier Fisette <ribosome@gentoo.org> 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 <ribosome@gentoo.org> +emboss-3.0.0.ebuild:
+ New version.
+
+ 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.9.0.ebuild:
+ Removed old version.
+
+ 25 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.10.0.ebuild:
+ Stable ppc-macos
+
+ 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> emboss-2.10.0.ebuild:
+ Marked ppc stable for bug #96819.
+
+ 19 Jun 2005; Markus Rothe <corsair@gentoo.org> emboss-2.10.0.ebuild:
+ Stable on ppc64
+
+ 13 May 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.10.0.ebuild:
+ Added to x86.
+
+ 02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org> emboss-2.10.0.ebuild:
+ Added ~ppc64
+
+ 02 May 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-2.9.0.ebuild:
+ Stable on ppc.
+
+*emboss-2.10.0 (22 Mar 2005)
+
+ 22 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +emboss-2.10.0.ebuild:
+ New version.
+
+ 22 Feb 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild:
+ Added support for minimal build.
+
+ 09 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild:
+ Stable ppc-macos
+
+ 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild:
+ Ebuild cleanup.
+
+ 01 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild:
+ Unstable ppc-macos.
+
+*emboss-2.9.0 (23 Dec 2004)
+
+ 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+ +files/22emboss-r1, +emboss-2.9.0.ebuild:
+ Moved from app-sci/emboss to sci-biology/emboss.
+
+ 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> 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 <ribosome@gentoo.org>
+ emboss-2.8.0-r3.ebuild:
+ Added to x86.
+ emboss-2.8.0-r2.ebuild:
+ Removed obsolete ebuild.
+
+ 21 Jul 2004; David Holm <dholm@gentoo.org> emboss-2.9.0.ebuild:
+ Added to ~ppc.
+
+ 20 Jul 2004; Olivier Fisette <ribosome@gentoo.org>
+ emboss-2.8.0-r3.ebuild, emboss-2.9.0.ebuild:
+ Removed icc support since no patching is needed.
+
+ 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> 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 <ribosome@gentoo.org>
+ 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 <agriffis@gentoo.org> emboss-2.8.0-r1.ebuild,
+ emboss-2.8.0-r2.ebuild:
+ Fix use invocation
+
+ 12 May 2004; David Holm <dholm@gentoo.org> emboss-2.8.0-r2.ebuild:
+ Added to ~ppc.
+
+*emboss-2.8.0-r2 (11 May 2004)
+
+ 11 May 2004; Patrick Kursawe <phosphan@gentoo.org> 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 <sediener@gentoo.org> emboss-2.8.0-r1.ebuild:
+ Modified to use X and png properly for servers
+
+ 28 Jan 2004; Stephen Diener <sediener@gentoo.org> 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 <sediener@gentoo.org> emboss-2.7.1.ebuild,
+ emboss-2.8.0.ebuild:
+ Version bump...
+
+ 20 Oct 2003; George Shapovalov <george@gentoo.org> metdata.xml :
+ added metadata.xml, marked ebuild stable
+
+*emboss-2.7.1 (03 Sep 2003)
+
+ 03 Sep 2003; <sediener@gentoo.org> emboss-2.7.1.ebuild:
+ Initial ebuild
+
diff --git a/sci-biology/emboss/emboss-6.3.1_p4.ebuild b/sci-biology/emboss/emboss-6.3.1_p4.ebuild
new file mode 100644
index 0000000..e235c73
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.3.1_p4.ebuild
@@ -0,0 +1,116 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4.ebuild,v 1.2 2011/03/09 16:29:05 jlec Exp $
+
+EAPI="4"
+
+inherit autotools eutils
+
+MY_PATCH="4"
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+HOMEPAGE="http://emboss.sourceforge.net/"
+SRC_URI="
+ ftp://${PN}.open-bio.org/pub/EMBOSS/EMBOSS-${PV/_p${MY_PATCH}}.tar.gz
+ ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${MY_PATCH}.gz -> ${P}.patch.gz"
+
+LICENSE="GPL-2 LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc +largefile minimal mysql pdf png postgres static-libs X"
+
+DEPEND="
+ dev-libs/expat
+ dev-libs/libpcre:3
+ sci-libs/plplot
+ sys-libs/zlib
+ mysql? ( dev-db/mysql )
+ pdf? ( media-libs/libharu )
+ png? (
+ sys-libs/zlib
+ media-libs/libpng
+ media-libs/gd
+ )
+ postgres? ( dev-db/postgresql-base )
+ !minimal? (
+ sci-biology/primer3
+ sci-biology/clustalw
+ )
+ X? ( x11-libs/libXt )"
+RDEPEND="${DEPEND}
+ !sys-devel/cons"
+PDEPEND="
+ !minimal? (
+ sci-biology/aaindex
+ sci-biology/cutg
+ sci-biology/prints
+ sci-biology/prosite
+ sci-biology/rebase
+ sci-biology/transfac
+ )"
+
+S="${WORKDIR}/EMBOSS-${PV/_p${MY_PATCH}}"
+
+src_prepare() {
+ epatch "${WORKDIR}"/${P}.patch
+ epatch \
+ "${FILESDIR}"/${PV}-unbundle-libs.patch
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ $(use_with X x) \
+ $(use_with png pngdriver "${EPREFIX}/usr") \
+ $(use_with doc docroot "${EPREFIX}/usr") \
+ $(use_with pdf hpdf "${EPREFIX}/usr") \
+ $(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") \
+ $(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") \
+ $(use_enable amd64 64) \
+ $(use_enable largefile large) \
+ $(use_enable static-libs static) \
+ --without-java \
+ --enable-systemlibs \
+ --includedir="${ED}/usr/include/emboss"
+}
+
+src_install() {
+ einstall || die "Failed to install program files."
+
+ dodoc AUTHORS ChangeLog FAQ NEWS README THANKS
+ sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
+ dodoc README.Gentoo
+
+ # Install env file for setting libplplot and acd files path.
+ cat <<- EOF > 22emboss
+ # plplot libs dir
+ PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/"
+ # ACD files location
+ EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
+ EOF
+ doenvd 22emboss
+
+ # Symlink preinstalled docs to "/usr/share/doc".
+ dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals
+ dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs
+ dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials
+ dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html
+
+ # Clashes #330507
+ mv "${ED}"/usr/bin/{digest,pepdigest} || die
+
+ # Remove useless dummy files from the image.
+ find emboss/data -name dummyfile -delete || die "Failed to remove dummy files."
+
+ # Move the provided codon files to a different directory. This will avoid
+ # user confusion and file collisions on case-insensitive file systems (see
+ # bug #115446). This change is documented in "README.Gentoo".
+ mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
+ die "Failed to move CODON directory."
+
+ # Move the provided restriction enzyme prototypes file to a different name.
+ # This avoids file collisions with versions of rebase that install their
+ # own enzyme prototypes file (see bug #118832).
+ mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
+ die "Failed to move enzyme equivalence file."
+}
diff --git a/sci-biology/emboss/files/6.3.1_p4.patch b/sci-biology/emboss/files/6.3.1_p4.patch
new file mode 100644
index 0000000..5e46374
--- /dev/null
+++ b/sci-biology/emboss/files/6.3.1_p4.patch
@@ -0,0 +1,600 @@
+diff --git a/Makefile.am b/Makefile.am
+index 4fe2ed1..7f3a95f 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -5,12 +5,21 @@ ACLOCAL_AMFLAGS = -I m4
+
+ AUTOMAKE_OPTIONS = gnits
+
+-SUBDIRS = plplot ajax nucleus emboss test doc jemboss
++if !ESYSTEMLIBS
++EXTRA_DIRS = plplot
++endif
++
++if GJEMBOSS
++JEMBOSS_DIR = jemboss
++endif
++
++SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
++DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
+
+ # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
+
+ # files with nonstandard names in this directory
+-EXTRA_DIST = COMPAT LICENSE KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh
++EXTRA_DIST = COMPAT KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh
+
+ # tar to pick up the other directories
+ # then remove any CVS subdirectories
+diff --git a/README.fixes b/README.fixes
+new file mode 100644
+index 0000000..3c56d79
+--- /dev/null
++++ b/README.fixes
+@@ -0,0 +1,9 @@
++The files in this directory are bugfix replacements for files in
++the EMBOSS-6.3.1 distribution. Just drop the replacement files in
++the location shown and redo the 'make install.'
++
++Fix 1. EMBOSS-6.3.1/configure
++ EMBOSS-6.3.1/m4/mysql.m4
++
++21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of
++ hpdf support prevented inclusion of MySQL support.
+diff --git a/ajax/Makefile.am b/ajax/Makefile.am
+index 4a44f6f..cf27ff8 100644
+--- a/ajax/Makefile.am
++++ b/ajax/Makefile.am
+@@ -1,6 +1,6 @@
+ ## Process this file with automake to produce Makefile.in
+ if !ESYSTEMLIBS
+-EXTRA_DIRS = expat zlib
++EXTRA_DIRS = pcre expat zlib
+ endif
+
+-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
++SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
+diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
+index 02bcaa7..368ddfe 100644
+--- a/ajax/acd/Makefile.am
++++ b/ajax/acd/Makefile.am
+@@ -13,10 +13,13 @@ CYGWIN_LDACD = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \
+ endif
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
+ endif
+
+-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES = \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core \
+ -I$(top_srcdir)/ajax/graphics \
+@@ -38,3 +41,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libacd_la_LDFLAGS = $(LINKFLAGS)
++libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la
+diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
+index da57727..857ca5f 100644
+--- a/ajax/ajaxdb/Makefile.am
++++ b/ajax/ajaxdb/Makefile.am
+@@ -13,11 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \
+ endif
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+ endif
+
+
+-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES = \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl
+
+@@ -37,3 +38,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libajaxdb_la_LDFLAGS = $(LINKFLAGS)
++libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
+diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
+index af27cb0..8fa4a3a 100644
+--- a/ajax/core/Makefile.am
++++ b/ajax/core/Makefile.am
+@@ -12,13 +12,18 @@ CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \
+ endif
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_LIBS = -lexpat -lpcre
+ endif
+
++EXTRA_DIST = ajax-pcre-config.h.in
++DISTCLEAN = ajax-pcre-config.h
+
+ INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
+ -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
+--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
++$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS)
+
+ AJAXSRC = ajalign.c ajarr.c ajassert.c \
+ ajbase.c ajcall.c ajcod.c \
+@@ -44,7 +49,7 @@ ajindex.h ajjava.h ajlist.h \
+ ajmath.h ajmatrices.h ajmem.h ajmess.h \
+ ajnam.h ajnexus.h ajobo.h \
+ ajpat.h ajpdb.h ajpdbio.h ajphylo.h \
+-ajrange.h ajreg.h ajreport.h ajresource.h \
++ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \
+ ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h \
+ ajsort.h ajsql.h ajstr.h ajsys.h \
+ ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h
+@@ -61,3 +66,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libajax_la_LDFLAGS = $(LINKFLAGS)
++libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS)
+diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in
+new file mode 100644
+index 0000000..b09e4e6
+--- /dev/null
++++ b/ajax/core/ajax-pcre-config.h.in
+@@ -0,0 +1 @@
++@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE
+diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
+index 06793be..659f462 100644
+--- a/ajax/core/ajreg.h
++++ b/ajax/core/ajreg.h
+@@ -16,9 +16,14 @@ extern "C"
+ #define ajreg_h
+
+ #include "ajax.h"
++#include "ajax-pcre-config.h"
++#ifndef AJAX_USE_SYSTEM_PCRE
+ #include "pcre_config.h"
+ #include "pcre_internal.h"
+ #include "pcreposix.h"
++#else
++#include <pcre.h>
++#endif
+
+ #define AJREG_OVECSIZE 30
+
+@@ -41,7 +46,11 @@ extern "C"
+ ******************************************************************************/
+
+ typedef struct AjSRegexp {
++#ifndef AJAX_USE_SYSTEM_PCRE
+ real_pcre *pcre;
++#else
++ pcre *pcre;
++#endif
+ pcre_extra *extra;
+ int *ovector;
+ const char* orig;
+diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
+index ca33a84..87e51bd 100644
+--- a/ajax/ensembl/Makefile.am
++++ b/ajax/ensembl/Makefile.am
+@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo
+ endif
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+ endif
+
+
+-INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \
+--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core
++INCLUDES = $(EXTRA_INCLUDES) \
++-I$(top_srcdir)/ajax/core
+
+ ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \
+ ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \
+@@ -56,3 +57,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libensembl_la_LDFLAGS = $(LINKFLAGS)
++libensembl_la_LIBADD = ../core/libajax.la
+diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
+index ab45afc..f61c605 100644
+--- a/ajax/graphics/Makefile.am
++++ b/ajax/graphics/Makefile.am
+@@ -10,11 +10,15 @@ CYGWIN_LDAJAXG = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot
+ endif
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM
++EXTRA_LIBS = $(PLPLOT_LIBS)
+ endif
+
+
+-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES = \
+ $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
+
+ AJAXGSRC = ajgraph.c ajhist.c
+@@ -32,3 +36,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libajaxg_la_LDFLAGS = $(LINKFLAGS)
++libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
+diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c
+index 25e75e4..60f2743 100644
+--- a/ajax/graphics/ajgraph.c
++++ b/ajax/graphics/ajgraph.c
+@@ -34,10 +34,8 @@
+ #include <float.h>
+ #define AZ 28
+
+-
+ #include "plplotP.h"
+
+-
+ static void GraphArray(ajuint numofpoints,
+ float *x, float *y);
+ static void GraphArrayGaps(ajuint numofpoints,
+@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size)
+ ** @@
+ ******************************************************************************/
+
++#define _GNU_SOURCE
++#include <stdio.h>
++
+ static void GraphSetName(const AjPGraph thys,
+ const AjPStr txt, const char *ext)
+ {
+ if(!thys->ready)
+ {
++#ifdef USE_PLXSFNAM_SHIM
++ char *fullname;
++#endif
+ ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
++#ifdef USE_PLXSFNAM_SHIM
++ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext);
++ ajDebug("=g= plsfnam ('%S') instead\n", fullname);
++ plsfnam(fullname);
++ free(fullname);
++#else
+ plxsfnam(ajStrGetPtr(txt), ext);
++#endif
+ ajStrAssignS(&graphBasename, txt);
+ ajStrAssignC(&graphExtension, ext);
+ if(ajStrGetCharFirst(graphExtension) == '.')
+diff --git a/configure.in b/configure.in
+index ddb4f81..3f4fe5e 100644
+--- a/configure.in
++++ b/configure.in
+@@ -235,15 +235,6 @@ AC_PROG_INSTALL
+ AC_PROG_LN_S
+ AC_PROG_MAKE_SET
+
+-dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+-if test "${with_x}" != "no" ; then
+-if test "`uname -a | grep Darwin`"; then
+-OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
+-if test ${OSXX} '>' '10.4'; then
+-CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
+-fi
+-fi
+-fi
+
+ # Checks for header files.
+ #as# AC_PATH_X
+@@ -292,9 +283,6 @@ AC_CHECK_FUNCS(memmove)
+ #as# select socket sqrt strchr strcspn strdup strerror strpbrk \
+ #as# strrchr strspn strstr strtol])
+
+-if test "${with_x}" != "no" ; then
+-LF_EMBOSS_PATH_XLIB
+-fi
+
+ dnl Library checks
+ AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket")
+@@ -316,14 +304,16 @@ CHECK_PNGDRIVER
+ CHECK_AUTH
+ CHECK_AMD64
+
++AM_CONDITIONAL(GJEMBOSS, test "$JAVA_OK" = "yes")
++
+ AX_LIB_MYSQL
+ AX_LIB_POSTGRESQL
+
+ CFLAGS="$CFLAGS $MYSQL_CFLAGS"
+ LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
+
+-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
+-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
++CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
++LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
+
+
+ dnl Check for 'ant' for packaging Jemboss and export result
+@@ -443,13 +433,36 @@ fi
+
+ dnl Test if --enable-systemlibs given
+ have_systemlibs=no
++DEFINE_USE_SYSTEM_PCRE="#undef"
+ AC_ARG_ENABLE(systemlibs,
+ AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles]))
++AC_MSG_CHECKING(for systemlib usage)
+ if test "${enable_systemlibs}" = "yes" ; then
+ have_systemlibs=yes
++ DEFINE_USE_SYSTEM_PCRE="#define"
++ PKG_CHECK_MODULES([PLPLOT], [plplotd])
++ PKG_CHECK_MODULES([ZLIB], [zlib])
++else
++ dnl X11 is only used by plplot
++ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
++ if test "${with_x}" != "no" ; then
++ if test "`uname -a | grep Darwin`"; then
++ OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
++ if test ${OSXX} '>' '10.4'; then
++ CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
++ fi
++ fi
++ fi
++ if test "${with_x}" != "no" ; then
++ LF_EMBOSS_PATH_XLIB
++ fi
++ AC_MSG_NOTICE(USING bundled LIBS)
+ fi
+ AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
+ AC_SUBST(ESYSTEMLIBS)
++AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
++AC_SUBST(PLPLOT_CFLAGS)
++AC_SUBST(PLPLOT_LIBS)
+
+
+
+@@ -457,7 +470,6 @@ AC_SUBST(ESYSTEMLIBS)
+
+ dnl Test if purify exists and if --enable-purify given if so
+ dnl set "-g"
+-
+ AC_MSG_CHECKING(for purify)
+ dnl if(purify -version) < /dev/null > /dev/null 2>&1; then
+ AC_ARG_ENABLE(purify,
+@@ -683,6 +695,7 @@ CHECK_THREADS
+
+
+ AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile
++ajax/core/ajax-pcre-config.h
+ ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
+ ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
+ ajax/acd/Makefile
+diff --git a/emboss/Makefile.am b/emboss/Makefile.am
+index 0820517..a0257b2 100644
+--- a/emboss/Makefile.am
++++ b/emboss/Makefile.am
+@@ -79,14 +79,17 @@ wordcount wordfinder wordmatch wossname \
+ yank
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
+ endif
+
+-INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \
++INCLUDES = -I$(top_srcdir)/nucleus \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
+ -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
+- -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
++ -I$(top_srcdir)/ajax/acd
+
+
+ aaindexextract_SOURCES = aaindexextract.c
+@@ -319,7 +322,7 @@ testplot_SOURCES = testplot.c
+ treetypedisplay_SOURCES = treetypedisplay.c
+
+ if !ESYSTEMLIBS
+-EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
++EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../plplot/libeplplot.la ../ajax/pcre/libepcre.la
+ endif
+
+
+@@ -327,7 +330,6 @@ LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \
+ ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
+ ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
+ $(EXTRA_LDS) \
+- ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \
+ $(XLIB)
+
+ pkgdata_DATA = emboss.default.template
+diff --git a/m4/mysql.m4 b/m4/mysql.m4
+index fe413af..ebea25c 100644
+--- a/m4/mysql.m4
++++ b/m4/mysql.m4
+@@ -1,4 +1,6 @@
+-##### http://autoconf-archive.cryp.to/ax_lib_mysql.html
++# ===========================================================================
++# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html
++# ===========================================================================
+ #
+ # SYNOPSIS
+ #
+@@ -6,19 +8,18 @@
+ #
+ # DESCRIPTION
+ #
+-# This macro provides tests of availability of MySQL client library
+-# of particular version or newer.
++# This macro provides tests of availability of MySQL client library of
++# particular version or newer.
+ #
+-# AX_LIB_MYSQL macro takes only one argument which is optional. If
+-# there is no required version passed, then macro does not run
+-# version test.
++# AX_LIB_MYSQL macro takes only one argument which is optional. If there
++# is no required version passed, then macro does not run version test.
+ #
+ # The --with-mysql option takes one of three possible values:
+ #
+ # no - do not check for MySQL client library
+ #
+-# yes - do check for MySQL library in standard locations
+-# (mysql_config should be in the PATH)
++# yes - do check for MySQL library in standard locations (mysql_config
++# should be in the PATH)
+ #
+ # path - complete path to mysql_config utility, use this option if
+ # mysql_config can't be found in the PATH
+@@ -33,27 +34,23 @@
+ #
+ # HAVE_MYSQL
+ #
+-# LAST MODIFICATION
++# LICENSE
+ #
+-# 2006-07-16
+-# 2007-01-09 MS: mysql_config --cflags may set gcc -fomit-frame-pointers,
+-# which prevents gdb from displaying stack traces.
+-# Changed mysql_config --cflags to mysql_config --include
++# Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net>
+ #
+-# COPYLEFT
+-#
+-# Copyright (c) 2006 Mateusz Loskot <mateusz@loskot.net>
+-#
+-# Copying and distribution of this file, with or without
+-# modification, are permitted in any medium without royalty provided
+-# the copyright notice and this notice are preserved.
++# Copying and distribution of this file, with or without modification, are
++# permitted in any medium without royalty provided the copyright notice
++# and this notice are preserved. This file is offered as-is, without any
++# warranty.
++
++#serial 12
+
+ AC_DEFUN([AX_LIB_MYSQL],
+ [
+ AC_ARG_WITH([mysql],
+- [AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
++ AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
+ [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config]
+- )],
++ ),
+ [
+ if test "$withval" = "no"; then
+ want_mysql="no"
+@@ -66,19 +63,20 @@ AC_DEFUN([AX_LIB_MYSQL],
+ ],
+ [want_mysql="yes"]
+ )
++ AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program])
+
+ MYSQL_CFLAGS=""
+ MYSQL_LDFLAGS=""
+ MYSQL_VERSION=""
+
+ dnl
+- dnl Check MySQL libraries (libpq)
++ dnl Check MySQL libraries
+ dnl
+
+ if test "$want_mysql" = "yes"; then
+
+- if test -z "$MYSQL_CONFIG" -o test; then
+- AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no])
++ if test -z "$MYSQL_CONFIG" ; then
++ AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no])
+ fi
+
+ if test "$MYSQL_CONFIG" != "no"; then
+@@ -90,35 +88,8 @@ dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
+
+ MYSQL_VERSION=`$MYSQL_CONFIG --version`
+
+-dnl It isn't enough to just test for mysql_config as Fedora
+-dnl provides it in the mysql RPM even though mysql-devel may
+-dnl not be installed
+-
+- EMBCFLAGS=$CFLAGS
+- EMBLDFLAGS=$LDFLAGS
+- CFLAGS=$MYSQL_CFLAGS
+- LDFLAGS=$MYSQL_LDFLAGS
+-
+- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
+- #include "mysql.h"]],
+- [[mysql_info(NULL)]])],
+- [havemysql=yes],
+- [havemysql=no])
+-
+- CFLAGS=$EMBCFLAGS
+- LDFLAGS=$EMBLDFLAGS
+-
+- if test "$havemysql" = yes; then
+- AC_DEFINE([HAVE_MYSQL], [1],
+- [Define to 1 if MySQL libraries are available])
+- found_mysql="yes"
+- AC_MSG_RESULT([yes])
+- else
+- MYSQL_CFLAGS=""
+- MYSQL_LDFLAGS=""
+- found_mysql="no"
+- AC_MSG_RESULT([no])
+- fi
++ found_mysql="yes"
++ AC_MSG_RESULT([yes])
+ else
+ found_mysql="no"
+ AC_MSG_RESULT([no])
+@@ -170,6 +141,11 @@ dnl not be installed
+ fi
+ fi
+
++ if test "$found_mysql" = "yes" ; then
++ AC_DEFINE([HAVE_MYSQL], [1],
++ [Define to 1 if MySQL libraries are available])
++ fi
++
+ AC_SUBST([MYSQL_VERSION])
+ AC_SUBST([MYSQL_CFLAGS])
+ AC_SUBST([MYSQL_LDFLAGS])
+diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
+index c244786..ff301b9 100644
+--- a/nucleus/Makefile.am
++++ b/nucleus/Makefile.am
+@@ -19,13 +19,16 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre -L../ajax/expat -L../ajax/zlib \
+ -lezlib -leplplot
+ else
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
+ endif
+ endif
+
+
+-INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \
+- -I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \
++INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \
++ -I$(top_srcdir)/ajax \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
+ -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
+@@ -55,3 +58,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libnucleus_la_LDFLAGS = $(LINKFLAGS)
++libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la
diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-2 b/sci-biology/emboss/files/emboss-README.Gentoo-2
new file mode 100644
index 0000000..72fa366
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-README.Gentoo-2
@@ -0,0 +1,34 @@
+Administrating EMBOSS on Gentoo systems
+=======================================
+
+
+Codon data files location
+-------------------------
+
+The codon data files that are distributed with EMBOSS are installed in the
+``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
+``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
+these codon files and those installed with the CUTG database. The names of
+these files sometimes vary only by their case. Having both sets of files in
+the same directory is also impossible on systems such as MacOSX, where the
+root filesystem is case insensitive. If you do not have the CUTG database
+installed and want to use the codon files distributed with EMBOSS, you can
+symlink the ``CODONS.orig`` directory to ``CODONS``::
+
+ # cd EPREFIX/usr/share/EMBOSS/data
+ # ln -s CODONS.orig CODONS
+
+
+Restriction enzymes equivalence file location
+---------------------------------------------
+
+The restriction enzymes equivalence file distributed with EMBOSS is installed
+as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
+``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
+collision with the equivalence file provided by the Rebase database. If you do
+not have the Rebase database installed and want to use the equivalence file
+distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
+``embossre.equ``::
+
+ # cd EPREFIX/usr/share/EMBOSS/data
+ # ln -s embossre.equ.orig embossre.equ
diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml
new file mode 100644
index 0000000..747e4ab
--- /dev/null
+++ b/sci-biology/emboss/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ EMBOSS is "The European Molecular Biology Open Software Suite".
+ EMBOSS is a free Open Source software analysis package specially
+ developed for the needs of the molecular biology (e.g. EMBnet) user
+ community. The software automatically copes with data in a variety
+ of formats and even allows transparent retrieval of sequence data
+ from the web. Also, as extensive libraries are provided with the
+ package, it is a platform to allow other scientists to develop and
+ release software in true open source spirit. EMBOSS also integrates
+ a range of currently available packages and tools for sequence
+ analysis into a seamless whole. EMBOSS breaks the historical trend
+ towards commercial software packages.
+ </longdescription>
+<use>
+ <flag name='largefile'>Support for large files</flag>
+</use>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2011-03-10 19:00 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2011-03-10 19:00 UTC (permalink / raw
To: gentoo-commits
commit: 14f71c00e9f1d06a9f609e68a1cec296e10e9eb2
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 10 18:51:04 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 10 18:51:04 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=14f71c00
Correct naming of patch
(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 4 ++++
sci-biology/emboss/emboss-6.3.1_p4.ebuild | 1 +
.../{6.3.1_p4.patch => emboss-6.3.1_p4.patch} | 0
3 files changed, 5 insertions(+), 0 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 29ec8c8..4fd5745 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2011 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 $
+ 10 Mar 2011; Justin Lecher <jlec@gentoo.org> -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 <jlec@gentoo.org> metadata.xml:
Removed largefile from local USE description
diff --git a/sci-biology/emboss/emboss-6.3.1_p4.ebuild b/sci-biology/emboss/emboss-6.3.1_p4.ebuild
index c58dc29..64fbd39 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4.ebuild
@@ -4,6 +4,7 @@
EBO_PATCH="4"
EBOV="${PV/_p${EBO_PATCH}}"
+EBO_ECONF="--includedir=${EPREFIX}/usr/include/emboss"
inherit embassy-ng
diff --git a/sci-biology/emboss/files/6.3.1_p4.patch b/sci-biology/emboss/files/emboss-6.3.1_p4.patch
similarity index 100%
rename from sci-biology/emboss/files/6.3.1_p4.patch
rename to sci-biology/emboss/files/emboss-6.3.1_p4.patch
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2011-03-11 6:58 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2011-03-11 6:58 UTC (permalink / raw
To: gentoo-commits
commit: f04a733c00ec39e518fed64b4b5efde96fb24c60
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 11 06:58:44 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Mar 11 06:58:44 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f04a733c
Rev bump, to ahead of the tree ebuild
(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 7 +++++++
...s-6.3.1_p4.ebuild => emboss-6.3.1_p4-r1.ebuild} | 0
...oss-6.3.1_p4.patch => emboss-6.3.1_p4-r1.patch} | 0
3 files changed, 7 insertions(+), 0 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 4fd5745..6cb9905 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2011 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 $
+*emboss-6.3.1_p4-r1 (11 Mar 2011)
+
+ 11 Mar 2011; Justin Lecher <jlec@gentoo.org> -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 <jlec@gentoo.org> -files/6.3.1_p4.patch,
emboss-6.3.1_p4.ebuild, +files/emboss-6.3.1_p4.patch:
Correct naming of patch
diff --git a/sci-biology/emboss/emboss-6.3.1_p4.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
similarity index 100%
rename from sci-biology/emboss/emboss-6.3.1_p4.ebuild
rename to sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
similarity index 100%
rename from sci-biology/emboss/files/emboss-6.3.1_p4.patch
rename to sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2011-03-21 10:54 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2011-03-21 10:54 UTC (permalink / raw
To: gentoo-commits
commit: b07d85313116fbd69fa31dba1447bdd16894648a
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 21 10:53:59 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar 21 10:53:59 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b07d8531
Fixed for reviewed eclass
(Portage version: 2.2.0_alpha28/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 4 +
sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 39 ++-
sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch | 377 ++++++++++++++-------
3 files changed, 288 insertions(+), 132 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 84db2c6..959cce4 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2011 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 $
+ 21 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild,
+ files/emboss-6.3.1_p4-r1.patch:
+ Fixed for reviewed eclass
+
15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
Straighten ENV
diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
index d8e0747..83f1f31 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
@@ -2,17 +2,46 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4.ebuild,v 1.2 2011/03/09 16:29:05 jlec Exp $
-EBO_PATCH="4"
-EBO_ECONF="--includedir=${EPREFIX}/usr/include/emboss"
+EAPI="4"
inherit emboss
+EBO_PATCH="4"
+EBOV=${PV/_p*}
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz"
+[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}.patch.gz"
+
KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE+=" minimal"
+
+RDEPEND+=" !sys-devel/cons"
+PDEPEND+="
+ !minimal? (
+ sci-biology/aaindex
+ sci-biology/cutg
+ sci-biology/prints
+ sci-biology/prosite
+ sci-biology/rebase
+ sci-biology/transfac
+ )"
+
+S="${WORKDIR}"/EMBOSS-${EBOV}
+
+EBO_EXTRA_ECONF="--includedir=${EPREFIX}/usr/include/emboss"
+
+DOCS+=" FAQ THANKS"
+
+src_prepare() {
+ [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}.patch
+ emboss_src_prepare
+}
src_install() {
- emboss_src_install
+ default
- sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
+ sed -e "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
dodoc README.Gentoo
# Install env file for setting libplplot and acd files path.
@@ -23,7 +52,7 @@ src_install() {
EOF
doenvd 22emboss
- # Clashes #330507
+ # Clashes #330507, resolved upstream
mv "${ED}"/usr/bin/{digest,pepdigest} || die
# Remove useless dummy files from the image.
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
index 5e46374..fff158f 100644
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
+++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
@@ -276,7 +276,7 @@ index 25e75e4..60f2743 100644
ajStrAssignC(&graphExtension, ext);
if(ajStrGetCharFirst(graphExtension) == '.')
diff --git a/configure.in b/configure.in
-index ddb4f81..3f4fe5e 100644
+index ddb4f81..383b55f 100644
--- a/configure.in
+++ b/configure.in
@@ -235,15 +235,6 @@ AC_PROG_INSTALL
@@ -315,12 +315,13 @@ index ddb4f81..3f4fe5e 100644
AX_LIB_POSTGRESQL
CFLAGS="$CFLAGS $MYSQL_CFLAGS"
- LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
+-LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
++LIBS="${MYSQL_LIBS} ${LIBS}"
-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
+CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
-+LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
++LIBS="$POSTGRESQL_LIBS $LIBS"
dnl Check for 'ant' for packaging Jemboss and export result
@@ -377,6 +378,52 @@ index ddb4f81..3f4fe5e 100644
ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
ajax/acd/Makefile
+diff --git a/doc/manuals/Makefile.am b/doc/manuals/Makefile.am
+index 726add5..43a7bf2 100644
+--- a/doc/manuals/Makefile.am
++++ b/doc/manuals/Makefile.am
+@@ -2,5 +2,5 @@ pkgdata_DATA = admin.tex \
+ admin.aux admin.dvi admin.log admin.pdf admin.ps admin.toc \
+ adminguide.tar.gz domainatrix.doc program.ps.gz EMBOSS-FreeBSD-HOWTO.txt \
+ emboss_qg.pdf emboss_qg.ps emboss.sty fdl.txt
+-pkgdatadir=$(prefix)/share/$(PACKAGE)/doc/manuals
++pkgdatadir=$(docdir)/doc/manuals
+
+diff --git a/doc/programs/html/Makefile.am b/doc/programs/html/Makefile.am
+index 74bf4b1..141e7f1 100644
+--- a/doc/programs/html/Makefile.am
++++ b/doc/programs/html/Makefile.am
+@@ -112,5 +112,5 @@ pkgdata2_DATA = libscan.html lindna.html listor.html \
+ yank.html \
+ emboss_icon.jpg
+
+-pkgdatadir=$(prefix)/share/$(PACKAGE)/doc/programs/html
+-pkgdata2dir=$(prefix)/share/$(PACKAGE)/doc/programs/html
++pkgdatadir=$(docdir)/html
++pkgdata2dir=$(docdir)/html
+diff --git a/doc/programs/text/Makefile.am b/doc/programs/text/Makefile.am
+index 5b2486b..9d526c0 100644
+--- a/doc/programs/text/Makefile.am
++++ b/doc/programs/text/Makefile.am
+@@ -58,5 +58,5 @@ pkgdata2_DATA = lindna.txt listor.txt \
+ wordfinder.txt wordmatch.txt wossname.txt \
+ yank.txt
+
+-pkgdatadir=$(prefix)/share/$(PACKAGE)/doc/programs/text
+-pkgdata2dir=$(prefix)/share/$(PACKAGE)/doc/programs/text
++pkgdatadir=$(docdir)/programs/text
++pkgdata2dir=$(docdir)/programs/text
+diff --git a/doc/tutorials/Makefile.am b/doc/tutorials/Makefile.am
+index 97207c3..fc4ae48 100644
+--- a/doc/tutorials/Makefile.am
++++ b/doc/tutorials/Makefile.am
+@@ -2,5 +2,5 @@ pkgdata_DATA = emboss-gcg.ppt \
+ emboss-interfaces.ppt emboss-talk.ppt emboss_tut.tar.gz
+
+
+-pkgdatadir=$(prefix)/share/$(PACKAGE)/doc/tutorials
++pkgdatadir=$(prefix)/share/$(PACKAGE)/tutorials
+
diff --git a/emboss/Makefile.am b/emboss/Makefile.am
index 0820517..a0257b2 100644
--- a/emboss/Makefile.am
@@ -419,156 +466,232 @@ index 0820517..a0257b2 100644
$(XLIB)
pkgdata_DATA = emboss.default.template
-diff --git a/m4/mysql.m4 b/m4/mysql.m4
-index fe413af..ebea25c 100644
---- a/m4/mysql.m4
-+++ b/m4/mysql.m4
-@@ -1,4 +1,6 @@
--##### http://autoconf-archive.cryp.to/ax_lib_mysql.html
-+# ===========================================================================
-+# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html
-+# ===========================================================================
+diff --git a/m4/hpdf.m4 b/m4/hpdf.m4
+index a37940f..80b329c 100644
+--- a/m4/hpdf.m4
++++ b/m4/hpdf.m4
+@@ -33,8 +33,8 @@ ALT_HOME=/usr
#
- # SYNOPSIS
+ # Locate hpdf
#
-@@ -6,19 +8,18 @@
- #
- # DESCRIPTION
- #
--# This macro provides tests of availability of MySQL client library
--# of particular version or newer.
-+# This macro provides tests of availability of MySQL client library of
-+# particular version or newer.
+-if test -d "${ALT_HOME}"
+-then
++#if test -d "${ALT_HOME}"
++#then
+
#
--# AX_LIB_MYSQL macro takes only one argument which is optional. If
--# there is no required version passed, then macro does not run
--# version test.
-+# AX_LIB_MYSQL macro takes only one argument which is optional. If there
-+# is no required version passed, then macro does not run version test.
+ # Keep a copy if it fails
+@@ -45,13 +45,13 @@ then
#
- # The --with-mysql option takes one of three possible values:
+ # Set
#
- # no - do not check for MySQL client library
+- LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib"
+- CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include"
++# LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib"
++# CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include"
+
#
--# yes - do check for MySQL library in standard locations
--# (mysql_config should be in the PATH)
-+# yes - do check for MySQL library in standard locations (mysql_config
-+# should be in the PATH)
+ # Check for libharu in ALT_HOME
#
- # path - complete path to mysql_config utility, use this option if
- # mysql_config can't be found in the PATH
-@@ -33,27 +34,23 @@
+- AC_CHECK_LIB(hpdf, HPDF_New, CHECK=1, CHECK=0, -L${ALT_HOME}/lib)
++ AC_CHECK_LIB(hpdf, HPDF_New, CHECK=1, CHECK=0)
#
- # HAVE_MYSQL
#
--# LAST MODIFICATION
-+# LICENSE
+ # If everything found okay then proceed to include png driver in config.
+@@ -80,10 +80,4 @@ then
+ echo "No pdf support (libhpdf) found."
+ fi
+
+-else
+- if test $withval != "no"; then
+- echo "Directory $ALT_HOME does not exist"
+- exit 0
+- fi
+-fi
+ ])
+diff --git a/m4/mysql.m4 b/m4/mysql.m4
+index fe413af..5cd8b90 100644
+--- a/m4/mysql.m4
++++ b/m4/mysql.m4
+@@ -26,7 +26,7 @@
+ # This macro calls:
#
--# 2006-07-16
--# 2007-01-09 MS: mysql_config --cflags may set gcc -fomit-frame-pointers,
--# which prevents gdb from displaying stack traces.
--# Changed mysql_config --cflags to mysql_config --include
-+# Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net>
+ # AC_SUBST(MYSQL_CFLAGS)
+-# AC_SUBST(MYSQL_LDFLAGS)
++# AC_SUBST(MYSQL_LIBS)
+ # AC_SUBST(MYSQL_VERSION)
#
--# COPYLEFT
--#
--# Copyright (c) 2006 Mateusz Loskot <mateusz@loskot.net>
--#
--# Copying and distribution of this file, with or without
--# modification, are permitted in any medium without royalty provided
--# the copyright notice and this notice are preserved.
-+# Copying and distribution of this file, with or without modification, are
-+# permitted in any medium without royalty provided the copyright notice
-+# and this notice are preserved. This file is offered as-is, without any
-+# warranty.
-+
-+#serial 12
-
- AC_DEFUN([AX_LIB_MYSQL],
- [
- AC_ARG_WITH([mysql],
-- [AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
-+ AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
- [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config]
-- )],
-+ ),
- [
- if test "$withval" = "no"; then
- want_mysql="no"
-@@ -66,19 +63,20 @@ AC_DEFUN([AX_LIB_MYSQL],
- ],
- [want_mysql="yes"]
+ # And sets:
+@@ -68,7 +68,7 @@ AC_DEFUN([AX_LIB_MYSQL],
)
-+ AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program])
MYSQL_CFLAGS=""
- MYSQL_LDFLAGS=""
+- MYSQL_LDFLAGS=""
++ MYSQL_LIBS=""
MYSQL_VERSION=""
dnl
-- dnl Check MySQL libraries (libpq)
-+ dnl Check MySQL libraries
- dnl
+@@ -86,7 +86,7 @@ AC_DEFUN([AX_LIB_MYSQL],
- if test "$want_mysql" = "yes"; then
-
-- if test -z "$MYSQL_CONFIG" -o test; then
-- AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no])
-+ if test -z "$MYSQL_CONFIG" ; then
-+ AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no])
- fi
-
- if test "$MYSQL_CONFIG" != "no"; then
-@@ -90,35 +88,8 @@ dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
+ dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
+ MYSQL_CFLAGS="`$MYSQL_CONFIG --include`"
+- MYSQL_LDFLAGS="`$MYSQL_CONFIG --libs`"
++ MYSQL_LIBS="`$MYSQL_CONFIG --libs`"
MYSQL_VERSION=`$MYSQL_CONFIG --version`
--dnl It isn't enough to just test for mysql_config as Fedora
--dnl provides it in the mysql RPM even though mysql-devel may
--dnl not be installed
--
-- EMBCFLAGS=$CFLAGS
-- EMBLDFLAGS=$LDFLAGS
+@@ -96,8 +96,8 @@ dnl not be installed
+
+ EMBCFLAGS=$CFLAGS
+ EMBLDFLAGS=$LDFLAGS
- CFLAGS=$MYSQL_CFLAGS
- LDFLAGS=$MYSQL_LDFLAGS
--
-- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
-- #include "mysql.h"]],
-- [[mysql_info(NULL)]])],
-- [havemysql=yes],
-- [havemysql=no])
--
-- CFLAGS=$EMBCFLAGS
-- LDFLAGS=$EMBLDFLAGS
--
-- if test "$havemysql" = yes; then
-- AC_DEFINE([HAVE_MYSQL], [1],
-- [Define to 1 if MySQL libraries are available])
-- found_mysql="yes"
-- AC_MSG_RESULT([yes])
-- else
-- MYSQL_CFLAGS=""
++ CFLAGS="$MYSQL_CFLAGS $EMBCFLAGS"
++ LIBS="${MYSQL_LIBS} ${LIBS}"
+
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
+ #include "mysql.h"]],
+@@ -115,7 +115,7 @@ dnl not be installed
+ AC_MSG_RESULT([yes])
+ else
+ MYSQL_CFLAGS=""
- MYSQL_LDFLAGS=""
-- found_mysql="no"
-- AC_MSG_RESULT([no])
-- fi
-+ found_mysql="yes"
-+ AC_MSG_RESULT([yes])
- else
- found_mysql="no"
- AC_MSG_RESULT([no])
-@@ -170,6 +141,11 @@ dnl not be installed
- fi
- fi
-
-+ if test "$found_mysql" = "yes" ; then
-+ AC_DEFINE([HAVE_MYSQL], [1],
-+ [Define to 1 if MySQL libraries are available])
-+ fi
-+
++ MYSQL_LIBS=""
+ found_mysql="no"
+ AC_MSG_RESULT([no])
+ fi
+@@ -172,5 +172,5 @@ dnl not be installed
+
AC_SUBST([MYSQL_VERSION])
AC_SUBST([MYSQL_CFLAGS])
- AC_SUBST([MYSQL_LDFLAGS])
+- AC_SUBST([MYSQL_LDFLAGS])
++ AC_SUBST([MYSQL_LIBS])
+ ])
+diff --git a/m4/pngdriver.m4 b/m4/pngdriver.m4
+index 5934321..de970ae 100644
+--- a/m4/pngdriver.m4
++++ b/m4/pngdriver.m4
+@@ -44,8 +44,8 @@ ALT_HOME=/usr
+ #
+ # Locate png/gd/zlib, if wanted
+ #
+-if test -d "${ALT_HOME}"
+-then
++#if test -d "${ALT_HOME}"
++#then
+
+ #
+ # Keep a copy if it fails
+@@ -69,20 +69,26 @@ then
+ fi
+
+
++PKG_CHECK_MODULES([PNG], [libpng])
++PKG_CHECK_MODULES([ZLIB], [zlib])
++AC_CHECK_PROG(GD_LIBS, [gdlib-config])
++GD_LIBS="`gdlib-config --libs` -lgd"
++GD_CFLAGS="`gdlib-config --cflags`"
++
+
+
+
+ #
+ # Check for zlib in ALT_HOME
+ #
+- AC_CHECK_LIB(z, inflateEnd, CHECK=1, CHECK=0, -L${ALT_HOME}/lib -lz)
++ AC_CHECK_LIB(z, inflateEnd, CHECK=1, CHECK=0, ${ZLIB_LIBS})
+ #
+
+ #
+ # Check for png
+ #
+ if test $CHECK = "1" ; then
+- AC_CHECK_LIB(png, png_destroy_read_struct, CHECK=1, CHECK=0 , -L${ALT_HOME}/lib -lz)
++ AC_CHECK_LIB(png, png_destroy_read_struct, CHECK=1, CHECK=0 , ${ZLIB_LIBS})
+ fi
+
+
+@@ -92,7 +98,7 @@ then
+ # Check for gd
+ #
+ if test $CHECK = "1"; then
+- AC_CHECK_LIB(gd, gdImageCreateFromPng, CHECK=1, CHECK=0 , -L${ALT_HOME}/lib -lgd -lpng -lz -lm)
++ AC_CHECK_LIB(gd, gdImageCreateFromPng, CHECK=1, CHECK=0 , ${PNG_LIBS} ${ZLIB_LIBS} ${GD_LIBS})
+ if test $CHECK = "0"; then
+ echo need to upgrade gd for png driver for plplot
+ fi
+@@ -101,7 +107,7 @@ then
+ # If everything found okay then proceed to include png driver in config.
+ #
+ if test $CHECK = "1" ; then
+- LIBS="$LIBS -lgd -lpng -lz -lm"
++ LIBS="$LIBS ${PNG_LIBS} ${ZLIB_LIBS} ${GD_LIBS}"
+
+ if test $ICCHECK = "1" ; then
+ LIBS="$LIBS -liconv"
+@@ -114,10 +120,11 @@ then
+ AC_DEFINE(PLD_png)
+ AM_CONDITIONAL(AMPNG, true)
+ echo PNG libraries found
+- if test $ALT_HOME = "/usr" ; then
++# if test $ALT_HOME = "/usr" ; then
+ LDFLAGS="$ALT_LDFLAGS"
+ CPPFLAGS="$ALT_CPPFLAGS"
+- fi
++ CFLAGS="${CFLAGS} ${PNG_CFLAGS} ${ZLIB_CFLAGS} ${GD_CFLAGS}"
++# fi
+ else
+ #
+ # If not okay then reset FLAGS.
+@@ -134,10 +141,4 @@ then
+ # echo CPPFLAGS = $CPPFLAGS
+
+
+-else
+- if test $withval != "no"; then
+- echo "Directory $ALT_HOME does not exist"
+- exit 0
+- fi
+-fi
+ ])
+diff --git a/m4/postgresql.m4 b/m4/postgresql.m4
+index e6a804d..ef4d49c 100644
+--- a/m4/postgresql.m4
++++ b/m4/postgresql.m4
+@@ -26,7 +26,7 @@
+ # This macro calls:
+ #
+ # AC_SUBST(POSTGRESQL_CFLAGS)
+-# AC_SUBST(POSTGRESQL_LDFLAGS)
++# AC_SUBST(POSTGRESQL_LIBS)
+ # AC_SUBST(POSTGRESQL_VERSION)
+ #
+ # And sets:
+@@ -65,7 +65,7 @@ AC_DEFUN([AX_LIB_POSTGRESQL],
+ )
+
+ POSTGRESQL_CFLAGS=""
+- POSTGRESQL_LDFLAGS=""
++ POSTGRESQL_LIBS=""
+ POSTGRESQL_POSTGRESQL=""
+
+ dnl
+@@ -82,7 +82,7 @@ AC_DEFUN([AX_LIB_POSTGRESQL],
+ AC_MSG_CHECKING([for PostgreSQL libraries])
+
+ POSTGRESQL_CFLAGS="-I`$PG_CONFIG --includedir`"
+- POSTGRESQL_LDFLAGS="-L`$PG_CONFIG --libdir` -lpq"
++ POSTGRESQL_LIBS="-L`$PG_CONFIG --libdir` `$PG_CONFIG --libs`"
+
+ POSTGRESQL_VERSION=`$PG_CONFIG --version | sed -e 's#PostgreSQL ##'`
+
+@@ -144,5 +144,5 @@ AC_DEFUN([AX_LIB_POSTGRESQL],
+
+ AC_SUBST([POSTGRESQL_VERSION])
+ AC_SUBST([POSTGRESQL_CFLAGS])
+- AC_SUBST([POSTGRESQL_LDFLAGS])
++ AC_SUBST([POSTGRESQL_LIBS])
+ ])
diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
index c244786..ff301b9 100644
--- a/nucleus/Makefile.am
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2011-03-22 6:58 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2011-03-22 6:58 UTC (permalink / raw
To: gentoo-commits
commit: c7348af7d96a099227cacb9ec168420a024bde03
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 21 20:03:41 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar 21 20:03:41 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c7348af7
Implicit decs fix, thanks bicatali for help
(Portage version: 2.2.0_alpha28/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 3 ++
sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch | 29 ++++++++++-----------
2 files changed, 17 insertions(+), 15 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 959cce4..002c99c 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2011 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 $
+ 21 Mar 2011; Justin Lecher <jlec@gentoo.org> files/emboss-6.3.1_p4-r1.patch:
+ Implicit decs fix, thanks bicatali for help
+
21 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild,
files/emboss-6.3.1_p4-r1.patch:
Fixed for reviewed eclass
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
index fff158f..6bc6351 100644
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
+++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
@@ -234,29 +234,28 @@ index ab45afc..f61c605 100644
libajaxg_la_LDFLAGS = $(LINKFLAGS)
+libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c
-index 25e75e4..60f2743 100644
+index 25e75e4..ce21a32 100644
--- a/ajax/graphics/ajgraph.c
+++ b/ajax/graphics/ajgraph.c
-@@ -34,10 +34,8 @@
+@@ -26,6 +26,9 @@
+
+ #define GRAPHMAIN 1
+
++#define _GNU_SOURCE
++#include <stdio.h>
++
+ #include "ajax.h"
+ #include "ajgraph.h"
+
+@@ -34,7 +37,6 @@
#include <float.h>
#define AZ 28
-
#include "plplotP.h"
--
- static void GraphArray(ajuint numofpoints,
- float *x, float *y);
- static void GraphArrayGaps(ajuint numofpoints,
-@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size)
- ** @@
- ******************************************************************************/
-+#define _GNU_SOURCE
-+#include <stdio.h>
-+
- static void GraphSetName(const AjPGraph thys,
- const AjPStr txt, const char *ext)
+@@ -1054,8 +1056,18 @@ static void GraphSetName(const AjPGraph thys,
{
if(!thys->ready)
{
@@ -265,7 +264,7 @@ index 25e75e4..60f2743 100644
+#endif
ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
+#ifdef USE_PLXSFNAM_SHIM
-+ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext);
++ asprintf(&fullname,"%s%s", ajStrGetPtr(txt), ext);
+ ajDebug("=g= plsfnam ('%S') instead\n", fullname);
+ plsfnam(fullname);
+ free(fullname);
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2011-03-22 19:23 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2011-03-22 19:23 UTC (permalink / raw
To: gentoo-commits
commit: dfccde9c75eeb9191772d8e03787ddeef89d905e
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 22 19:21:58 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 22 19:21:58 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dfccde9c
Fix compile correctly against postgresql, #359959
(Portage version: 2.2.0_alpha28/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 3 ++
sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch | 32 ++++++++++++++++++--
2 files changed, 31 insertions(+), 4 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 002c99c..8b56592 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2011 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 $
+ 22 Mar 2011; Justin Lecher <jlec@gentoo.org> files/emboss-6.3.1_p4-r1.patch:
+ Fix compile correctly against postgresql, #359959
+
21 Mar 2011; Justin Lecher <jlec@gentoo.org> files/emboss-6.3.1_p4-r1.patch:
Implicit decs fix, thanks bicatali for help
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
index 6bc6351..9bb97c1 100644
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
+++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
@@ -1,3 +1,27 @@
+ Makefile.am | 13 +++++++++-
+ README.fixes | 9 +++++++
+ ajax/Makefile.am | 4 +-
+ ajax/acd/Makefile.am | 8 +++++-
+ ajax/ajaxdb/Makefile.am | 6 +++-
+ ajax/core/Makefile.am | 12 +++++++--
+ ajax/core/ajax-pcre-config.h.in | 1 +
+ ajax/core/ajreg.h | 9 +++++++
+ ajax/ensembl/Makefile.am | 8 ++++--
+ ajax/graphics/Makefile.am | 9 ++++++-
+ ajax/graphics/ajgraph.c | 14 +++++++++++-
+ configure.in | 45 +++++++++++++++++++++++++-------------
+ doc/manuals/Makefile.am | 2 +-
+ doc/programs/html/Makefile.am | 4 +-
+ doc/programs/text/Makefile.am | 4 +-
+ doc/tutorials/Makefile.am | 2 +-
+ emboss/Makefile.am | 12 ++++++----
+ m4/hpdf.m4 | 16 ++++---------
+ m4/mysql.m4 | 14 ++++++------
+ m4/pngdriver.m4 | 29 +++++++++++++------------
+ m4/postgresql.m4 | 8 +++---
+ nucleus/Makefile.am | 10 ++++++--
+ 22 files changed, 156 insertions(+), 83 deletions(-)
+
diff --git a/Makefile.am b/Makefile.am
index 4fe2ed1..7f3a95f 100644
--- a/Makefile.am
@@ -104,7 +128,7 @@ index da57727..857ca5f 100644
libajaxdb_la_LDFLAGS = $(LINKFLAGS)
+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
-index af27cb0..8fa4a3a 100644
+index af27cb0..fa57e93 100644
--- a/ajax/core/Makefile.am
+++ b/ajax/core/Makefile.am
@@ -12,13 +12,18 @@ CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \
@@ -141,7 +165,7 @@ index af27cb0..8fa4a3a 100644
endif
libajax_la_LDFLAGS = $(LINKFLAGS)
-+libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS)
++libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LIBS) $(MYSQL_LIBS)
diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in
new file mode 100644
index 0000000..b09e4e6
@@ -654,7 +678,7 @@ index 5934321..de970ae 100644
-fi
])
diff --git a/m4/postgresql.m4 b/m4/postgresql.m4
-index e6a804d..ef4d49c 100644
+index e6a804d..eb14d5c 100644
--- a/m4/postgresql.m4
+++ b/m4/postgresql.m4
@@ -26,7 +26,7 @@
@@ -680,7 +704,7 @@ index e6a804d..ef4d49c 100644
POSTGRESQL_CFLAGS="-I`$PG_CONFIG --includedir`"
- POSTGRESQL_LDFLAGS="-L`$PG_CONFIG --libdir` -lpq"
-+ POSTGRESQL_LIBS="-L`$PG_CONFIG --libdir` `$PG_CONFIG --libs`"
++ POSTGRESQL_LIBS="-L`$PG_CONFIG --libdir` `$PG_CONFIG --libs` -lpq"
POSTGRESQL_VERSION=`$PG_CONFIG --version | sed -e 's#PostgreSQL ##'`
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2011-03-27 15:50 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2011-03-27 15:50 UTC (permalink / raw
To: gentoo-commits
commit: 5ebb5e5f090a6a1729887e5e659435118eb8ef0f
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 27 15:50:46 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 27 15:50:46 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5ebb5e5f
Last fix for 64bitness
(Portage version: 2.2.0_alpha28/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 4 +
sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 9 +-
sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch | 746 ---------------------
3 files changed, 10 insertions(+), 749 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 8b56592..ba5fbee 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2011 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 $
+ 27 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild,
+ -files/emboss-6.3.1_p4-r1.patch:
+ Last fix for 64bitness
+
22 Mar 2011; Justin Lecher <jlec@gentoo.org> files/emboss-6.3.1_p4-r1.patch:
Fix compile correctly against postgresql, #359959
diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
index 83f1f31..15a4d2a 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
@@ -10,8 +10,10 @@ EBO_PATCH="4"
EBOV=${PV/_p*}
DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
-SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz"
-[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}.patch.gz"
+SRC_URI="
+ ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
+ http://dev.gentoo.org/~jlec/distfiles/${PF}.patch.bz2"
+[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
IUSE+=" minimal"
@@ -34,7 +36,8 @@ EBO_EXTRA_ECONF="--includedir=${EPREFIX}/usr/include/emboss"
DOCS+=" FAQ THANKS"
src_prepare() {
- [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}.patch
+ [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch
+ epatch "${WORKDIR}"/${PF}.patch
emboss_src_prepare
}
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
deleted file mode 100644
index 9bb97c1..0000000
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch
+++ /dev/null
@@ -1,746 +0,0 @@
- Makefile.am | 13 +++++++++-
- README.fixes | 9 +++++++
- ajax/Makefile.am | 4 +-
- ajax/acd/Makefile.am | 8 +++++-
- ajax/ajaxdb/Makefile.am | 6 +++-
- ajax/core/Makefile.am | 12 +++++++--
- ajax/core/ajax-pcre-config.h.in | 1 +
- ajax/core/ajreg.h | 9 +++++++
- ajax/ensembl/Makefile.am | 8 ++++--
- ajax/graphics/Makefile.am | 9 ++++++-
- ajax/graphics/ajgraph.c | 14 +++++++++++-
- configure.in | 45 +++++++++++++++++++++++++-------------
- doc/manuals/Makefile.am | 2 +-
- doc/programs/html/Makefile.am | 4 +-
- doc/programs/text/Makefile.am | 4 +-
- doc/tutorials/Makefile.am | 2 +-
- emboss/Makefile.am | 12 ++++++----
- m4/hpdf.m4 | 16 ++++---------
- m4/mysql.m4 | 14 ++++++------
- m4/pngdriver.m4 | 29 +++++++++++++------------
- m4/postgresql.m4 | 8 +++---
- nucleus/Makefile.am | 10 ++++++--
- 22 files changed, 156 insertions(+), 83 deletions(-)
-
-diff --git a/Makefile.am b/Makefile.am
-index 4fe2ed1..7f3a95f 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -5,12 +5,21 @@ ACLOCAL_AMFLAGS = -I m4
-
- AUTOMAKE_OPTIONS = gnits
-
--SUBDIRS = plplot ajax nucleus emboss test doc jemboss
-+if !ESYSTEMLIBS
-+EXTRA_DIRS = plplot
-+endif
-+
-+if GJEMBOSS
-+JEMBOSS_DIR = jemboss
-+endif
-+
-+SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
-+DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
-
- # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
-
- # files with nonstandard names in this directory
--EXTRA_DIST = COMPAT LICENSE KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh
-+EXTRA_DIST = COMPAT KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh
-
- # tar to pick up the other directories
- # then remove any CVS subdirectories
-diff --git a/README.fixes b/README.fixes
-new file mode 100644
-index 0000000..3c56d79
---- /dev/null
-+++ b/README.fixes
-@@ -0,0 +1,9 @@
-+The files in this directory are bugfix replacements for files in
-+the EMBOSS-6.3.1 distribution. Just drop the replacement files in
-+the location shown and redo the 'make install.'
-+
-+Fix 1. EMBOSS-6.3.1/configure
-+ EMBOSS-6.3.1/m4/mysql.m4
-+
-+21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of
-+ hpdf support prevented inclusion of MySQL support.
-diff --git a/ajax/Makefile.am b/ajax/Makefile.am
-index 4a44f6f..cf27ff8 100644
---- a/ajax/Makefile.am
-+++ b/ajax/Makefile.am
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- if !ESYSTEMLIBS
--EXTRA_DIRS = expat zlib
-+EXTRA_DIRS = pcre expat zlib
- endif
-
--SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
-+SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
-diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
-index 02bcaa7..368ddfe 100644
---- a/ajax/acd/Makefile.am
-+++ b/ajax/acd/Makefile.am
-@@ -13,10 +13,13 @@ CYGWIN_LDACD = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \
- endif
-
- if !ESYSTEMLIBS
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
-+else
-+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
- endif
-
--INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
-+INCLUDES = \
- $(EXTRA_INCLUDES) \
- -I$(top_srcdir)/ajax/core \
- -I$(top_srcdir)/ajax/graphics \
-@@ -38,3 +41,4 @@ LINKFLAGS = $(VERS_INF)
- endif
-
- libacd_la_LDFLAGS = $(LINKFLAGS)
-+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la
-diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
-index da57727..857ca5f 100644
---- a/ajax/ajaxdb/Makefile.am
-+++ b/ajax/ajaxdb/Makefile.am
-@@ -13,11 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \
- endif
-
- if !ESYSTEMLIBS
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
- endif
-
-
--INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
-+INCLUDES = \
- $(EXTRA_INCLUDES) \
- -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl
-
-@@ -37,3 +38,4 @@ LINKFLAGS = $(VERS_INF)
- endif
-
- libajaxdb_la_LDFLAGS = $(LINKFLAGS)
-+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
-diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
-index af27cb0..fa57e93 100644
---- a/ajax/core/Makefile.am
-+++ b/ajax/core/Makefile.am
-@@ -12,13 +12,18 @@ CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \
- endif
-
- if !ESYSTEMLIBS
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
-+else
-+EXTRA_LIBS = -lexpat -lpcre
- endif
-
-+EXTRA_DIST = ajax-pcre-config.h.in
-+DISTCLEAN = ajax-pcre-config.h
-
- INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
- -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
---I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
-+$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS)
-
- AJAXSRC = ajalign.c ajarr.c ajassert.c \
- ajbase.c ajcall.c ajcod.c \
-@@ -44,7 +49,7 @@ ajindex.h ajjava.h ajlist.h \
- ajmath.h ajmatrices.h ajmem.h ajmess.h \
- ajnam.h ajnexus.h ajobo.h \
- ajpat.h ajpdb.h ajpdbio.h ajphylo.h \
--ajrange.h ajreg.h ajreport.h ajresource.h \
-+ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \
- ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h \
- ajsort.h ajsql.h ajstr.h ajsys.h \
- ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h
-@@ -61,3 +66,4 @@ LINKFLAGS = $(VERS_INF)
- endif
-
- libajax_la_LDFLAGS = $(LINKFLAGS)
-+libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LIBS) $(MYSQL_LIBS)
-diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in
-new file mode 100644
-index 0000000..b09e4e6
---- /dev/null
-+++ b/ajax/core/ajax-pcre-config.h.in
-@@ -0,0 +1 @@
-+@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE
-diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
-index 06793be..659f462 100644
---- a/ajax/core/ajreg.h
-+++ b/ajax/core/ajreg.h
-@@ -16,9 +16,14 @@ extern "C"
- #define ajreg_h
-
- #include "ajax.h"
-+#include "ajax-pcre-config.h"
-+#ifndef AJAX_USE_SYSTEM_PCRE
- #include "pcre_config.h"
- #include "pcre_internal.h"
- #include "pcreposix.h"
-+#else
-+#include <pcre.h>
-+#endif
-
- #define AJREG_OVECSIZE 30
-
-@@ -41,7 +46,11 @@ extern "C"
- ******************************************************************************/
-
- typedef struct AjSRegexp {
-+#ifndef AJAX_USE_SYSTEM_PCRE
- real_pcre *pcre;
-+#else
-+ pcre *pcre;
-+#endif
- pcre_extra *extra;
- int *ovector;
- const char* orig;
-diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
-index ca33a84..87e51bd 100644
---- a/ajax/ensembl/Makefile.am
-+++ b/ajax/ensembl/Makefile.am
-@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo
- endif
-
- if !ESYSTEMLIBS
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
- endif
-
-
--INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \
---I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core
-+INCLUDES = $(EXTRA_INCLUDES) \
-+-I$(top_srcdir)/ajax/core
-
- ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \
- ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \
-@@ -56,3 +57,4 @@ LINKFLAGS = $(VERS_INF)
- endif
-
- libensembl_la_LDFLAGS = $(LINKFLAGS)
-+libensembl_la_LIBADD = ../core/libajax.la
-diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
-index ab45afc..f61c605 100644
---- a/ajax/graphics/Makefile.am
-+++ b/ajax/graphics/Makefile.am
-@@ -10,11 +10,15 @@ CYGWIN_LDAJAXG = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot
- endif
-
- if !ESYSTEMLIBS
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
-+else
-+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM
-+EXTRA_LIBS = $(PLPLOT_LIBS)
- endif
-
-
--INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
-+INCLUDES = \
- $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
-
- AJAXGSRC = ajgraph.c ajhist.c
-@@ -32,3 +36,4 @@ LINKFLAGS = $(VERS_INF)
- endif
-
- libajaxg_la_LDFLAGS = $(LINKFLAGS)
-+libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
-diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c
-index 25e75e4..ce21a32 100644
---- a/ajax/graphics/ajgraph.c
-+++ b/ajax/graphics/ajgraph.c
-@@ -26,6 +26,9 @@
-
- #define GRAPHMAIN 1
-
-+#define _GNU_SOURCE
-+#include <stdio.h>
-+
- #include "ajax.h"
- #include "ajgraph.h"
-
-@@ -34,7 +37,6 @@
- #include <float.h>
- #define AZ 28
-
--
- #include "plplotP.h"
-
-
-@@ -1054,8 +1056,18 @@ static void GraphSetName(const AjPGraph thys,
- {
- if(!thys->ready)
- {
-+#ifdef USE_PLXSFNAM_SHIM
-+ char *fullname;
-+#endif
- ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
-+#ifdef USE_PLXSFNAM_SHIM
-+ asprintf(&fullname,"%s%s", ajStrGetPtr(txt), ext);
-+ ajDebug("=g= plsfnam ('%S') instead\n", fullname);
-+ plsfnam(fullname);
-+ free(fullname);
-+#else
- plxsfnam(ajStrGetPtr(txt), ext);
-+#endif
- ajStrAssignS(&graphBasename, txt);
- ajStrAssignC(&graphExtension, ext);
- if(ajStrGetCharFirst(graphExtension) == '.')
-diff --git a/configure.in b/configure.in
-index ddb4f81..383b55f 100644
---- a/configure.in
-+++ b/configure.in
-@@ -235,15 +235,6 @@ AC_PROG_INSTALL
- AC_PROG_LN_S
- AC_PROG_MAKE_SET
-
--dnl Intel MacOSX 10.6 puts X11 in a non-standard place
--if test "${with_x}" != "no" ; then
--if test "`uname -a | grep Darwin`"; then
--OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
--if test ${OSXX} '>' '10.4'; then
--CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
--fi
--fi
--fi
-
- # Checks for header files.
- #as# AC_PATH_X
-@@ -292,9 +283,6 @@ AC_CHECK_FUNCS(memmove)
- #as# select socket sqrt strchr strcspn strdup strerror strpbrk \
- #as# strrchr strspn strstr strtol])
-
--if test "${with_x}" != "no" ; then
--LF_EMBOSS_PATH_XLIB
--fi
-
- dnl Library checks
- AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket")
-@@ -316,14 +304,16 @@ CHECK_PNGDRIVER
- CHECK_AUTH
- CHECK_AMD64
-
-+AM_CONDITIONAL(GJEMBOSS, test "$JAVA_OK" = "yes")
-+
- AX_LIB_MYSQL
- AX_LIB_POSTGRESQL
-
- CFLAGS="$CFLAGS $MYSQL_CFLAGS"
--LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
-+LIBS="${MYSQL_LIBS} ${LIBS}"
-
--CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
--LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
-+CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
-+LIBS="$POSTGRESQL_LIBS $LIBS"
-
-
- dnl Check for 'ant' for packaging Jemboss and export result
-@@ -443,13 +433,36 @@ fi
-
- dnl Test if --enable-systemlibs given
- have_systemlibs=no
-+DEFINE_USE_SYSTEM_PCRE="#undef"
- AC_ARG_ENABLE(systemlibs,
- AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles]))
-+AC_MSG_CHECKING(for systemlib usage)
- if test "${enable_systemlibs}" = "yes" ; then
- have_systemlibs=yes
-+ DEFINE_USE_SYSTEM_PCRE="#define"
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd])
-+ PKG_CHECK_MODULES([ZLIB], [zlib])
-+else
-+ dnl X11 is only used by plplot
-+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
-+ if test "${with_x}" != "no" ; then
-+ if test "`uname -a | grep Darwin`"; then
-+ OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
-+ if test ${OSXX} '>' '10.4'; then
-+ CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
-+ fi
-+ fi
-+ fi
-+ if test "${with_x}" != "no" ; then
-+ LF_EMBOSS_PATH_XLIB
-+ fi
-+ AC_MSG_NOTICE(USING bundled LIBS)
- fi
- AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
- AC_SUBST(ESYSTEMLIBS)
-+AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
-+AC_SUBST(PLPLOT_CFLAGS)
-+AC_SUBST(PLPLOT_LIBS)
-
-
-
-@@ -457,7 +470,6 @@ AC_SUBST(ESYSTEMLIBS)
-
- dnl Test if purify exists and if --enable-purify given if so
- dnl set "-g"
--
- AC_MSG_CHECKING(for purify)
- dnl if(purify -version) < /dev/null > /dev/null 2>&1; then
- AC_ARG_ENABLE(purify,
-@@ -683,6 +695,7 @@ CHECK_THREADS
-
-
- AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile
-+ajax/core/ajax-pcre-config.h
- ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
- ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
- ajax/acd/Makefile
-diff --git a/doc/manuals/Makefile.am b/doc/manuals/Makefile.am
-index 726add5..43a7bf2 100644
---- a/doc/manuals/Makefile.am
-+++ b/doc/manuals/Makefile.am
-@@ -2,5 +2,5 @@ pkgdata_DATA = admin.tex \
- admin.aux admin.dvi admin.log admin.pdf admin.ps admin.toc \
- adminguide.tar.gz domainatrix.doc program.ps.gz EMBOSS-FreeBSD-HOWTO.txt \
- emboss_qg.pdf emboss_qg.ps emboss.sty fdl.txt
--pkgdatadir=$(prefix)/share/$(PACKAGE)/doc/manuals
-+pkgdatadir=$(docdir)/doc/manuals
-
-diff --git a/doc/programs/html/Makefile.am b/doc/programs/html/Makefile.am
-index 74bf4b1..141e7f1 100644
---- a/doc/programs/html/Makefile.am
-+++ b/doc/programs/html/Makefile.am
-@@ -112,5 +112,5 @@ pkgdata2_DATA = libscan.html lindna.html listor.html \
- yank.html \
- emboss_icon.jpg
-
--pkgdatadir=$(prefix)/share/$(PACKAGE)/doc/programs/html
--pkgdata2dir=$(prefix)/share/$(PACKAGE)/doc/programs/html
-+pkgdatadir=$(docdir)/html
-+pkgdata2dir=$(docdir)/html
-diff --git a/doc/programs/text/Makefile.am b/doc/programs/text/Makefile.am
-index 5b2486b..9d526c0 100644
---- a/doc/programs/text/Makefile.am
-+++ b/doc/programs/text/Makefile.am
-@@ -58,5 +58,5 @@ pkgdata2_DATA = lindna.txt listor.txt \
- wordfinder.txt wordmatch.txt wossname.txt \
- yank.txt
-
--pkgdatadir=$(prefix)/share/$(PACKAGE)/doc/programs/text
--pkgdata2dir=$(prefix)/share/$(PACKAGE)/doc/programs/text
-+pkgdatadir=$(docdir)/programs/text
-+pkgdata2dir=$(docdir)/programs/text
-diff --git a/doc/tutorials/Makefile.am b/doc/tutorials/Makefile.am
-index 97207c3..fc4ae48 100644
---- a/doc/tutorials/Makefile.am
-+++ b/doc/tutorials/Makefile.am
-@@ -2,5 +2,5 @@ pkgdata_DATA = emboss-gcg.ppt \
- emboss-interfaces.ppt emboss-talk.ppt emboss_tut.tar.gz
-
-
--pkgdatadir=$(prefix)/share/$(PACKAGE)/doc/tutorials
-+pkgdatadir=$(prefix)/share/$(PACKAGE)/tutorials
-
-diff --git a/emboss/Makefile.am b/emboss/Makefile.am
-index 0820517..a0257b2 100644
---- a/emboss/Makefile.am
-+++ b/emboss/Makefile.am
-@@ -79,14 +79,17 @@ wordcount wordfinder wordmatch wossname \
- yank
-
- if !ESYSTEMLIBS
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
-+else
-+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
- endif
-
--INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \
-+INCLUDES = -I$(top_srcdir)/nucleus \
- $(EXTRA_INCLUDES) \
- -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
- -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
-- -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
-+ -I$(top_srcdir)/ajax/acd
-
-
- aaindexextract_SOURCES = aaindexextract.c
-@@ -319,7 +322,7 @@ testplot_SOURCES = testplot.c
- treetypedisplay_SOURCES = treetypedisplay.c
-
- if !ESYSTEMLIBS
--EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
-+EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../plplot/libeplplot.la ../ajax/pcre/libepcre.la
- endif
-
-
-@@ -327,7 +330,6 @@ LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \
- ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
- ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
- $(EXTRA_LDS) \
-- ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \
- $(XLIB)
-
- pkgdata_DATA = emboss.default.template
-diff --git a/m4/hpdf.m4 b/m4/hpdf.m4
-index a37940f..80b329c 100644
---- a/m4/hpdf.m4
-+++ b/m4/hpdf.m4
-@@ -33,8 +33,8 @@ ALT_HOME=/usr
- #
- # Locate hpdf
- #
--if test -d "${ALT_HOME}"
--then
-+#if test -d "${ALT_HOME}"
-+#then
-
- #
- # Keep a copy if it fails
-@@ -45,13 +45,13 @@ then
- #
- # Set
- #
-- LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib"
-- CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include"
-+# LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib"
-+# CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include"
-
- #
- # Check for libharu in ALT_HOME
- #
-- AC_CHECK_LIB(hpdf, HPDF_New, CHECK=1, CHECK=0, -L${ALT_HOME}/lib)
-+ AC_CHECK_LIB(hpdf, HPDF_New, CHECK=1, CHECK=0)
- #
- #
- # If everything found okay then proceed to include png driver in config.
-@@ -80,10 +80,4 @@ then
- echo "No pdf support (libhpdf) found."
- fi
-
--else
-- if test $withval != "no"; then
-- echo "Directory $ALT_HOME does not exist"
-- exit 0
-- fi
--fi
- ])
-diff --git a/m4/mysql.m4 b/m4/mysql.m4
-index fe413af..5cd8b90 100644
---- a/m4/mysql.m4
-+++ b/m4/mysql.m4
-@@ -26,7 +26,7 @@
- # This macro calls:
- #
- # AC_SUBST(MYSQL_CFLAGS)
--# AC_SUBST(MYSQL_LDFLAGS)
-+# AC_SUBST(MYSQL_LIBS)
- # AC_SUBST(MYSQL_VERSION)
- #
- # And sets:
-@@ -68,7 +68,7 @@ AC_DEFUN([AX_LIB_MYSQL],
- )
-
- MYSQL_CFLAGS=""
-- MYSQL_LDFLAGS=""
-+ MYSQL_LIBS=""
- MYSQL_VERSION=""
-
- dnl
-@@ -86,7 +86,7 @@ AC_DEFUN([AX_LIB_MYSQL],
-
- dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
- MYSQL_CFLAGS="`$MYSQL_CONFIG --include`"
-- MYSQL_LDFLAGS="`$MYSQL_CONFIG --libs`"
-+ MYSQL_LIBS="`$MYSQL_CONFIG --libs`"
-
- MYSQL_VERSION=`$MYSQL_CONFIG --version`
-
-@@ -96,8 +96,8 @@ dnl not be installed
-
- EMBCFLAGS=$CFLAGS
- EMBLDFLAGS=$LDFLAGS
-- CFLAGS=$MYSQL_CFLAGS
-- LDFLAGS=$MYSQL_LDFLAGS
-+ CFLAGS="$MYSQL_CFLAGS $EMBCFLAGS"
-+ LIBS="${MYSQL_LIBS} ${LIBS}"
-
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
- #include "mysql.h"]],
-@@ -115,7 +115,7 @@ dnl not be installed
- AC_MSG_RESULT([yes])
- else
- MYSQL_CFLAGS=""
-- MYSQL_LDFLAGS=""
-+ MYSQL_LIBS=""
- found_mysql="no"
- AC_MSG_RESULT([no])
- fi
-@@ -172,5 +172,5 @@ dnl not be installed
-
- AC_SUBST([MYSQL_VERSION])
- AC_SUBST([MYSQL_CFLAGS])
-- AC_SUBST([MYSQL_LDFLAGS])
-+ AC_SUBST([MYSQL_LIBS])
- ])
-diff --git a/m4/pngdriver.m4 b/m4/pngdriver.m4
-index 5934321..de970ae 100644
---- a/m4/pngdriver.m4
-+++ b/m4/pngdriver.m4
-@@ -44,8 +44,8 @@ ALT_HOME=/usr
- #
- # Locate png/gd/zlib, if wanted
- #
--if test -d "${ALT_HOME}"
--then
-+#if test -d "${ALT_HOME}"
-+#then
-
- #
- # Keep a copy if it fails
-@@ -69,20 +69,26 @@ then
- fi
-
-
-+PKG_CHECK_MODULES([PNG], [libpng])
-+PKG_CHECK_MODULES([ZLIB], [zlib])
-+AC_CHECK_PROG(GD_LIBS, [gdlib-config])
-+GD_LIBS="`gdlib-config --libs` -lgd"
-+GD_CFLAGS="`gdlib-config --cflags`"
-+
-
-
-
- #
- # Check for zlib in ALT_HOME
- #
-- AC_CHECK_LIB(z, inflateEnd, CHECK=1, CHECK=0, -L${ALT_HOME}/lib -lz)
-+ AC_CHECK_LIB(z, inflateEnd, CHECK=1, CHECK=0, ${ZLIB_LIBS})
- #
-
- #
- # Check for png
- #
- if test $CHECK = "1" ; then
-- AC_CHECK_LIB(png, png_destroy_read_struct, CHECK=1, CHECK=0 , -L${ALT_HOME}/lib -lz)
-+ AC_CHECK_LIB(png, png_destroy_read_struct, CHECK=1, CHECK=0 , ${ZLIB_LIBS})
- fi
-
-
-@@ -92,7 +98,7 @@ then
- # Check for gd
- #
- if test $CHECK = "1"; then
-- AC_CHECK_LIB(gd, gdImageCreateFromPng, CHECK=1, CHECK=0 , -L${ALT_HOME}/lib -lgd -lpng -lz -lm)
-+ AC_CHECK_LIB(gd, gdImageCreateFromPng, CHECK=1, CHECK=0 , ${PNG_LIBS} ${ZLIB_LIBS} ${GD_LIBS})
- if test $CHECK = "0"; then
- echo need to upgrade gd for png driver for plplot
- fi
-@@ -101,7 +107,7 @@ then
- # If everything found okay then proceed to include png driver in config.
- #
- if test $CHECK = "1" ; then
-- LIBS="$LIBS -lgd -lpng -lz -lm"
-+ LIBS="$LIBS ${PNG_LIBS} ${ZLIB_LIBS} ${GD_LIBS}"
-
- if test $ICCHECK = "1" ; then
- LIBS="$LIBS -liconv"
-@@ -114,10 +120,11 @@ then
- AC_DEFINE(PLD_png)
- AM_CONDITIONAL(AMPNG, true)
- echo PNG libraries found
-- if test $ALT_HOME = "/usr" ; then
-+# if test $ALT_HOME = "/usr" ; then
- LDFLAGS="$ALT_LDFLAGS"
- CPPFLAGS="$ALT_CPPFLAGS"
-- fi
-+ CFLAGS="${CFLAGS} ${PNG_CFLAGS} ${ZLIB_CFLAGS} ${GD_CFLAGS}"
-+# fi
- else
- #
- # If not okay then reset FLAGS.
-@@ -134,10 +141,4 @@ then
- # echo CPPFLAGS = $CPPFLAGS
-
-
--else
-- if test $withval != "no"; then
-- echo "Directory $ALT_HOME does not exist"
-- exit 0
-- fi
--fi
- ])
-diff --git a/m4/postgresql.m4 b/m4/postgresql.m4
-index e6a804d..eb14d5c 100644
---- a/m4/postgresql.m4
-+++ b/m4/postgresql.m4
-@@ -26,7 +26,7 @@
- # This macro calls:
- #
- # AC_SUBST(POSTGRESQL_CFLAGS)
--# AC_SUBST(POSTGRESQL_LDFLAGS)
-+# AC_SUBST(POSTGRESQL_LIBS)
- # AC_SUBST(POSTGRESQL_VERSION)
- #
- # And sets:
-@@ -65,7 +65,7 @@ AC_DEFUN([AX_LIB_POSTGRESQL],
- )
-
- POSTGRESQL_CFLAGS=""
-- POSTGRESQL_LDFLAGS=""
-+ POSTGRESQL_LIBS=""
- POSTGRESQL_POSTGRESQL=""
-
- dnl
-@@ -82,7 +82,7 @@ AC_DEFUN([AX_LIB_POSTGRESQL],
- AC_MSG_CHECKING([for PostgreSQL libraries])
-
- POSTGRESQL_CFLAGS="-I`$PG_CONFIG --includedir`"
-- POSTGRESQL_LDFLAGS="-L`$PG_CONFIG --libdir` -lpq"
-+ POSTGRESQL_LIBS="-L`$PG_CONFIG --libdir` `$PG_CONFIG --libs` -lpq"
-
- POSTGRESQL_VERSION=`$PG_CONFIG --version | sed -e 's#PostgreSQL ##'`
-
-@@ -144,5 +144,5 @@ AC_DEFUN([AX_LIB_POSTGRESQL],
-
- AC_SUBST([POSTGRESQL_VERSION])
- AC_SUBST([POSTGRESQL_CFLAGS])
-- AC_SUBST([POSTGRESQL_LDFLAGS])
-+ AC_SUBST([POSTGRESQL_LIBS])
- ])
-diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
-index c244786..ff301b9 100644
---- a/nucleus/Makefile.am
-+++ b/nucleus/Makefile.am
-@@ -19,13 +19,16 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre -L../ajax/expat -L../ajax/zlib \
- -lezlib -leplplot
- else
- if !ESYSTEMLIBS
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
-+else
-+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
- endif
- endif
-
-
--INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \
-- -I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \
-+INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \
-+ -I$(top_srcdir)/ajax \
- $(EXTRA_INCLUDES) \
- -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
- -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
-@@ -55,3 +58,4 @@ LINKFLAGS = $(VERS_INF)
- endif
-
- libnucleus_la_LDFLAGS = $(LINKFLAGS)
-+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2012-07-19 20:51 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2012-07-19 20:51 UTC (permalink / raw
To: gentoo-commits
commit: f8535528b56268c093926eb0715c7d16cb6680c4
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jul 19 20:51:31 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jul 19 20:51:31 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f8535528
added plcol patch with increased diff line count, bug #391669; same patch needs to go into offical emboss-6.3.1_p4
(Portage version: 2.1.11.7/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/emboss/ChangeLog | 6 +-
sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 1 +
.../emboss/files/emboss-6.3.1_p4-r1_plcol.patch | 112 ++++++++++++++++++++
3 files changed, 118 insertions(+), 1 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index ef98d4f..ebe4896 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2012 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 $
+ 19 Jul 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +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 <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
Add missing eutils.eclass
@@ -348,4 +353,3 @@
03 Sep 2003; <sediener@gentoo.org> emboss-2.7.1.ebuild:
Initial ebuild
-
diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
index af8b56f..5f02bb9 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
@@ -39,6 +39,7 @@ DOCS+=" FAQ THANKS"
src_prepare() {
[[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch
epatch "${WORKDIR}"/${PF}.patch
+ epatch "${FILESDIR}/${PF}_plcol.patch"
emboss_src_prepare
}
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch
new file mode 100644
index 0000000..0f5e592
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch
@@ -0,0 +1,112 @@
+--- EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2012-07-19 23:29:05.000000000 +0200
++++ /tmp/ajgraph.c 2012-07-19 23:25:00.000000000 +0200
+@@ -1645,14 +1645,14 @@
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+ static void GraphSetPen(ajint colour)
+ {
+- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]);
+- plcol((PLINT)colour);
++ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]);
++ plcol0((PLINT)colour);
+
+ return;
+ }
+
+
+
+--- EMBOSS-6.3.1/plplot/plcore.c 2007-10-24 15:14:43.000000000 +0200
++++ /tmp/plcore.c 2012-07-19 23:25:00.000000000 +0200
+@@ -1709,13 +1709,13 @@
+ if (plsc->zdigmax == 0)
+ plsc->zdigmax = 3;
+
+ /* Switch to graphics mode and set color and arrow style*/
+
+ plgra();
+- plcol(1);
++ plcol0(1);
+
+ plstyl(0, &mk, &sp);
+ plpat(1, &inc, &del);
+
+ plsvect(def_arrow_x, def_arrow_y, 6, 0);
+
+--- EMBOSS-6.3.1/plplot/plstripc.c 2007-05-08 11:09:37.000000000 +0200
++++ /tmp/plstripc.c 2012-07-19 23:25:00.000000000 +0200
+@@ -153,17 +153,17 @@
+
+ plgchr(&sc, &dy);
+ sc = dy = dy/100;
+ plwind(-0.01, 1.01, -0.01, 1.01);
+ for (i=0; i<PEN; i++) {
+ if (mystripc->npts[i] || first) {
+- plcol(mystripc->colline[i]);
++ plcol0(mystripc->colline[i]);
+ pllsty(mystripc->styline[i]);
+ pljoin(mystripc->xlpos, mystripc->ylpos - sc,
+ mystripc->xlpos + 0.1, mystripc->ylpos - sc);
+- plcol(mystripc->collab);
++ plcol0(mystripc->collab);
+ plptex(mystripc->xlpos + 0.11, mystripc->ylpos - sc,
+ 0., 0., 0, mystripc->legline[i]);
+ sc += dy;
+ }
+ }
+ plwind(mystripc->xmin, mystripc->xmax, mystripc->ymin, mystripc->ymax);
+@@ -184,34 +184,34 @@
+ PLFLT x[]={0.,1.,1.,0.}, y[]={0.,0.,1.,1.};
+
+ /* Set up window */
+
+ plvpor(0,1,0,1);
+ plwind(0,1,0,1);
+- plcol(0);plpsty(0);
++ plcol0(0);plpsty(0);
+ plfill(4, &x[0], &y[0]);
+ plvsta();
+
+ /* Draw box and same window dimensions */
+ mystrip->wxmin=mystrip->xmin;
+ mystrip->wxmax=mystrip->xmax;
+ mystrip->wymin=mystrip->ymin;
+ mystrip->wymax=mystrip->ymax; /* FIXME - can exist some redundancy here */
+
+ plwind(mystrip->xmin, mystrip->xmax, mystrip->ymin, mystrip->ymax);
+
+ pllsty(1);
+- plcol(mystrip->colbox);
++ plcol0(mystrip->colbox);
+ plbox(mystrip->xspec, 0.0, 0, mystrip->yspec, 0.0, 0);
+
+- plcol(mystrip->collab);
++ plcol0(mystrip->collab);
+ pllab(mystrip->labx, mystrip->laby, mystrip->labtop);
+
+ for (i=0; i<PEN; i++) {
+ if (mystrip->npts[i] > 0) {
+- plcol(mystrip->colline[i]);pllsty(mystrip->styline[i]);
++ plcol0(mystrip->colline[i]);pllsty(mystrip->styline[i]);
+ plline(mystrip->npts[i], mystrip->x[i], mystrip->y[i]);
+ }
+ }
+
+ plstrip_legend(mystrip,0);
+ }
+@@ -269,13 +269,13 @@
+ if (stripc->xmax - stripc->xmin < stripc->xlen) {
+ if( yasc == 0) {
+
+ /* If user has changed subwindow, make shure we have the correct one */
+ plvsta();
+ plwind(stripc->wxmin, stripc->wxmax, stripc->wymin, stripc->wymax); /* FIXME - can exist some redundancy here */
+- plcol(stripc->colline[p]); pllsty(stripc->styline[p]);
++ plcol0(stripc->colline[p]); pllsty(stripc->styline[p]);
+ if ((stripc->npts[p]-2) < 0)
+ plP_movwor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
+ else
+ plP_movwor(stripc->x[p][stripc->npts[p]-2], stripc->y[p][stripc->npts[p]-2]);
+ plP_drawor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
+ plflush();
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2013-09-11 20:30 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2013-09-11 20:30 UTC (permalink / raw
To: gentoo-commits
commit: 3362e038f385b2bc8fb9feb38fd317a0031d6045
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Sep 11 20:29:58 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Sep 11 20:29:58 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3362e038
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
Package-Manager: portage-2.1.12.2
---
sci-biology/emboss/ChangeLog | 20 +-
....3.1_p4-r1.ebuild => emboss-6.3.1_p4-r2.ebuild} | 15 +-
...boss-6.3.1_p4-r1.ebuild => emboss-6.5.7.ebuild} | 10 +-
...boss-6.3.1_p4-r1.ebuild => emboss-6.6.0.ebuild} | 10 +-
sci-biology/emboss/files/ax_lib_mysql.m4 | 147 ++++++++++
.../emboss/files/emboss-6.3.1_p4-r2_Makefile.patch | 47 +++
.../emboss-6.3.1_p4-r2_compilations-paths.patch | 315 +++++++++++++++++++++
.../emboss/files/emboss-6.3.1_p4-r2_libtool.patch | 18 ++
..._plcol.patch => emboss-6.3.1_p4-r2_plcol.patch} | 0
9 files changed, 571 insertions(+), 11 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index ebe4896..76a5b35 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,7 +1,25 @@
# ChangeLog for sci-biology/emboss
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 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 $
+*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 <mmokrejs@fold.natur.cuni.cz>
+ +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 <mmokrejs@fold.natur.cuni.cz>
+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
diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
similarity index 84%
copy from sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
copy to sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
index 5f02bb9..dd7737a 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4.ebuild,v 1.2 2011/03/09 16:29:05 jlec Exp $
@@ -39,8 +39,16 @@ DOCS+=" FAQ THANKS"
src_prepare() {
[[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch
epatch "${WORKDIR}"/${PF}.patch
- epatch "${FILESDIR}/${PF}_plcol.patch"
+ epatch "${FILESDIR}/${PF}"_plcol.patch
+ epatch "${FILESDIR}/${PF}"_compilations-paths.patch
+ # cp "${FILESDIR}"/ax_lib_mysql.m4 "${S}"/m4/mysql.m4
emboss_src_prepare
+ autoreconf -vfi
+ epatch "${FILESDIR}/${PF}"_libtool.patch
+}
+
+src_compile() {
+ epatch "${FILESDIR}/${PF}"_Makefile.patch
}
src_install() {
@@ -74,4 +82,7 @@ src_install() {
# own enzyme prototypes file (see bug #118832).
mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
die "Failed to move enzyme equivalence file."
+
+ # fix /usr/share/doc/emboss-6.3.1_p4-r1/html to point to /usr/share/doc/emboss-6.3.1_p4-r1/programs/html
+ # instead of /usr/share/EMBOSS/doc/html (which does not exist)
}
diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.5.7.ebuild
similarity index 84%
copy from sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
copy to sci-biology/emboss/emboss-6.5.7.ebuild
index 5f02bb9..48be3bf 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.5.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4.ebuild,v 1.2 2011/03/09 16:29:05 jlec Exp $
@@ -11,10 +11,12 @@ EBOV=${PV/_p*}
DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
SRC_URI="
- ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
- http://dev.gentoo.org/~jlec/distfiles/${PF}.patch.bz2"
+ ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-${EBOV}.tar.gz"
+# ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz
+# ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-6.5.7.tar.gz
+
##[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
-[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
+#[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
IUSE+=" minimal"
diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
similarity index 84%
rename from sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
rename to sci-biology/emboss/emboss-6.6.0.ebuild
index 5f02bb9..4ab7353 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4.ebuild,v 1.2 2011/03/09 16:29:05 jlec Exp $
@@ -11,10 +11,12 @@ EBOV=${PV/_p*}
DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
SRC_URI="
- ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
- http://dev.gentoo.org/~jlec/distfiles/${PF}.patch.bz2"
+ ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
+# ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz
+# ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-6.5.7.tar.gz
+
##[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
-[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
+#[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
IUSE+=" minimal"
diff --git a/sci-biology/emboss/files/ax_lib_mysql.m4 b/sci-biology/emboss/files/ax_lib_mysql.m4
new file mode 100644
index 0000000..e27d755
--- /dev/null
+++ b/sci-biology/emboss/files/ax_lib_mysql.m4
@@ -0,0 +1,147 @@
+# ===========================================================================
+# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+# AX_LIB_MYSQL([MINIMUM-VERSION])
+#
+# DESCRIPTION
+#
+# This macro provides tests of availability of MySQL client library of
+# particular version or newer.
+#
+# AX_LIB_MYSQL macro takes only one argument which is optional. If there
+# is no required version passed, then macro does not run version test.
+#
+# The --with-mysql option takes one of three possible values:
+#
+# no - do not check for MySQL client library
+#
+# yes - do check for MySQL library in standard locations (mysql_config
+# should be in the PATH)
+#
+# path - complete path to mysql_config utility, use this option if
+# mysql_config can't be found in the PATH
+#
+# This macro calls:
+#
+# AC_SUBST(MYSQL_CFLAGS)
+# AC_SUBST(MYSQL_LDFLAGS)
+# AC_SUBST(MYSQL_VERSION)
+#
+# And sets:
+#
+# HAVE_MYSQL
+#
+# LICENSE
+#
+# Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net>
+#
+# Copying and distribution of this file, with or without modification, are
+# permitted in any medium without royalty provided the copyright notice
+# and this notice are preserved. This file is offered as-is, without any
+# warranty.
+
+#serial 12
+
+AC_DEFUN([AX_LIB_MYSQL],
+[
+ AC_ARG_WITH([mysql],
+ AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
+ [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config]
+ ),
+ [
+ if test "$withval" = "no"; then
+ want_mysql="no"
+ elif test "$withval" = "yes"; then
+ want_mysql="yes"
+ else
+ want_mysql="yes"
+ MYSQL_CONFIG="$withval"
+ fi
+ ],
+ [want_mysql="yes"]
+ )
+ AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program])
+
+ MYSQL_CFLAGS=""
+ MYSQL_LDFLAGS=""
+ MYSQL_VERSION=""
+
+ dnl
+ dnl Check MySQL libraries
+ dnl
+
+ if test "$want_mysql" = "yes"; then
+
+ if test -z "$MYSQL_CONFIG" ; then
+ AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no])
+ fi
+
+ if test "$MYSQL_CONFIG" != "no"; then
+ MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
+ MYSQL_LDFLAGS="`$MYSQL_CONFIG --libs`"
+
+ MYSQL_VERSION=`$MYSQL_CONFIG --version`
+
+ found_mysql="yes"
+ else
+ found_mysql="no"
+ fi
+ fi
+
+ dnl
+ dnl Check if required version of MySQL is available
+ dnl
+
+
+ mysql_version_req=ifelse([$1], [], [], [$1])
+
+ if test "$found_mysql" = "yes" -a -n "$mysql_version_req"; then
+
+ AC_MSG_CHECKING([if MySQL version is >= $mysql_version_req])
+
+ dnl Decompose required version string of MySQL
+ dnl and calculate its number representation
+ mysql_version_req_major=`expr $mysql_version_req : '\([[0-9]]*\)'`
+ mysql_version_req_minor=`expr $mysql_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
+ mysql_version_req_micro=`expr $mysql_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
+ if test "x$mysql_version_req_micro" = "x"; then
+ mysql_version_req_micro="0"
+ fi
+
+ mysql_version_req_number=`expr $mysql_version_req_major \* 1000000 \
+ \+ $mysql_version_req_minor \* 1000 \
+ \+ $mysql_version_req_micro`
+
+ dnl Decompose version string of installed MySQL
+ dnl and calculate its number representation
+ mysql_version_major=`expr $MYSQL_VERSION : '\([[0-9]]*\)'`
+ mysql_version_minor=`expr $MYSQL_VERSION : '[[0-9]]*\.\([[0-9]]*\)'`
+ mysql_version_micro=`expr $MYSQL_VERSION : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
+ if test "x$mysql_version_micro" = "x"; then
+ mysql_version_micro="0"
+ fi
+
+ mysql_version_number=`expr $mysql_version_major \* 1000000 \
+ \+ $mysql_version_minor \* 1000 \
+ \+ $mysql_version_micro`
+
+ mysql_version_check=`expr $mysql_version_number \>\= $mysql_version_req_number`
+ if test "$mysql_version_check" = "1"; then
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ fi
+ fi
+
+ if test "$found_mysql" = "yes" ; then
+ AC_DEFINE([HAVE_MYSQL], [1],
+ [Define to 1 if MySQL libraries are available])
+ fi
+
+ AC_SUBST([MYSQL_VERSION])
+ AC_SUBST([MYSQL_CFLAGS])
+ AC_SUBST([MYSQL_LDFLAGS])
+])
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch
new file mode 100644
index 0000000..419369e
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch
@@ -0,0 +1,47 @@
+--- EMBOSS-6.3.1/nucleus/Makefile 2013-09-11 14:50:25.140219756 +0200
++++ nucleus/Makefile 2013-09-11 14:52:00.920220006 +0200
+@@ -165,7 +165,7 @@
+ ESYSTEMLIBS =
+ EXEEXT =
+ FGREP = /bin/grep -F
+-GD_LIBS = -ljpeg -lfontconfig -lfreetype -lz -lm -lgd
++GD_LIBS =
+ GREP = /bin/grep
+ HAVE_MEMMOVE =
+ HAVE_STRERROR =
+@@ -180,7 +180,7 @@
+ LD = /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
+ LDFLAGS = -Wl,--as-needed
+ LIBOBJS =
+-LIBS = -L/usr/lib64/mysql -lmysqlclient -lpthread -lz -lm -lrt -lssl -lcrypto -ldl -lm -lhpdf -lpng16 -L/usr/lib64 -lz -ljpeg -lfontconfig -lfreetype -lz -lm -lgd
++LIBS =
+ LIBTOOL = $(SHELL) $(top_builddir)/libtool
+ LIPO =
+ LN_S = ln -s
+@@ -219,7 +219,7 @@
+ # zap the crap
+ PLPLOT_CFLAGS =
+ PLPLOT_CPPFLAGS =
+-PLPLOT_LIBS = -lplplotd -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lSM -lICE -lX11 -lXext -lgd -lpng -lz -ljpeg -lfreetype -lSM -lICE -lX11 -lXext -lpthread -lLASi -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfreetype -lfontconfig -lhpdf -lm -lcsirocsa -lnistcd -lqsastime -lfreetype
++PLPLOT_LIBS =
+ PNG_CFLAGS = -I/usr/include/libpng16
+ PNG_LIBS = -lpng16
+ POSIX_MALLOC_THRESHOLD = -DPOSIX_MALLOC_THRESHOLD=10
+@@ -336,7 +336,7 @@
+ VERS_INF = -version-info 6:3:0
+ LINKFLAGS = $(VERS_INF)
+ #LINKFLAGS = $(VERS_INF) $(CYGWIN_LDFLAGS) $(CYGWIN_LIBS)
+-libnucleus_la_LDFLAGS = $(LINKFLAGS)
++libnucleus_la_LDFLAGS = $(LDFLAGS)
+ libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd
+ all: all-am
+
+@@ -407,7 +407,7 @@
+ rm -f $${locs}; \
+ }
+ libnucleus.la: $(libnucleus_la_OBJECTS) $(libnucleus_la_DEPENDENCIES) $(EXTRA_libnucleus_la_DEPENDENCIES)
+- $(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(libnucleus_la_LIBADD) $(LIBS)
++ $(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(LIBS)
+
+ mostlyclean-compile:
+ -rm -f *.$(OBJEXT)
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch
new file mode 100644
index 0000000..8f87ef9
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch
@@ -0,0 +1,315 @@
+--- EMBOSS-6.3.1/configure.in 2013-09-11 03:55:15.510117066 +0200
++++ configure.in 2013-09-11 03:48:10.410115955 +0200
+@@ -449,7 +447,8 @@
+ if test "`uname -a | grep Darwin`"; then
+ OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
+ if test ${OSXX} '>' '10.4'; then
+- CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
++ CPPFLAGS="$CPPFLAGS -I/usr/X11/include"
++ LDFLAGS="$LDFLAGS -L/usr/X11/lib"
+ fi
+ fi
+ fi
+@@ -461,7 +460,7 @@
+ AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
+ AC_SUBST(ESYSTEMLIBS)
+ AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
+-AC_SUBST(PLPLOT_CFLAGS)
++AC_SUBST(PLPLOT_CPPFLAGS)
+ AC_SUBST(PLPLOT_LIBS)
+
+
+--- EMBOSS-6.3.1/ajax/graphics/Makefile.am 2013-09-11 03:27:30.110112715 +0200
++++ ajax/graphics/Makefile.am 2013-09-11 03:58:50.860117628 +0200
+@@ -19,7 +19,7 @@
+
+
+ INCLUDES = \
+-$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
++$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core -I$(top_srcdir)/plplot
+
+ AJAXGSRC = ajgraph.c ajhist.c
+
+--- EMBOSS-6.3.1/ajax/acd/Makefile.am 2013-09-11 03:27:30.110112715 +0200
++++ ajax/acd/Makefile.am 2013-09-11 03:59:10.310117679 +0200
+@@ -24,7 +24,8 @@
+ -I$(top_srcdir)/ajax/core \
+ -I$(top_srcdir)/ajax/graphics \
+ -I$(top_srcdir)/ajax/ensembl \
+--I$(top_srcdir)/ajax/ajaxdb
++-I$(top_srcdir)/ajax/ajaxdb \
++-I$(top_srcdir)/plplot
+
+ ACDSRC = ajacd.c
+
+--- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 03:27:30.110112715 +0200
++++ nucleus/Makefile.am 2013-09-11 03:59:28.630117727 +0200
+@@ -32,7 +32,7 @@
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
+ -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
+- -I$(top_srcdir)/ajax/acd
++ -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
+
+ NUCLSRC = embaln.c embcom.c embcons.c embdata.c embdbi.c embdmx.c \
+ embdomain.c embest.c embexit.c embgroup.c embiep.c embindex.c \
+--- EMBOSS-6.3.1/emboss/Makefile.am 2013-09-11 03:27:30.110112715 +0200
++++ emboss/Makefile.am 2013-09-11 03:59:46.340117773 +0200
+@@ -89,7 +89,7 @@
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
+ -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
+- -I$(top_srcdir)/ajax/acd
++ -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
+
+
+ aaindexextract_SOURCES = aaindexextract.c
+--- EMBOSS-6.3.1/Makefile.am 2013-09-11 04:19:01.770120791 +0200
++++ Makefile.am 2013-09-11 04:19:18.460120835 +0200
+@@ -13,8 +13,8 @@
+ JEMBOSS_DIR = jemboss
+ endif
+
+-SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
+-DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
++SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR)
++DIST_SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR)
+
+ # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
+
+--- EMBOSS-6.3.1/plplot/Makefile.am 2013-09-11 09:34:44.620170277 +0200
++++ plplot/Makefile.am 2013-09-11 09:35:35.820170411 +0200
+@@ -10,26 +10,27 @@
+ if AMPNG
+
+ if AMPDF
+-TESTPDF_CFLAGS = -Wl,-G -lhpdf
++TESTPDF_LIBS = -Wl,-G -lhpdf
+ else
+-TESTPDF_CFLAGS = -Wl,-G
++TESTPDF_LIBS = -Wl,-G
+ endif
+
+-TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lgd -lpng -lz -lX11 -lm
++TESTPNG_LIBS = $(TESTPDF_LIBS) -lgd -lpng -lz -lX11 -lm
+ else
+-TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lX11
++TESTPNG_LIBS = $(TESTPDF_LIBS) -lX11
+ endif
+ endif
+ endif
+
+-AM_CFLAGS = $(TESTPNG_CFLAGS)
++AM_LIBS = $(TESTPNG_LIBS)
+
+ if ISCYGWIN
+ CYGWIN_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import
+ CYGWIN_LIBS = -lX11 -lgd -lpng -lz
+ endif
+
+-INCLUDES = $(X_CFLAGS) -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\"
++INCLUDES = -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\"
++LIBS = $(AM_LIBS)
+
+ PLPLOTSRC = pdfutils.c plargs.c plbox.c plcont.c plcore.c \
+ plctrl.c plcvt.c pldtik.c plfill.c plhist.c plline.c plmap.c \
+--- EMBOSS-6.3.1/m4/pngdriver.m4 2013-09-11 10:39:07.680180369 +0200
++++ m4/pngdriver.m4 2013-09-11 10:44:16.000181174 +0200
+@@ -63,7 +63,8 @@
+ if test "`uname`" = "SunOS"; then
+ AC_CHECK_LIB(iconv, libiconv_close, ICCHECK=1, ICCHECK=0, -L${ALT_HOME}/lib -liconv)
+ if test $ICCHECK = "1" ; then
+- LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib -liconv"
++ LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib"
++ LIBS="${LIBS} -liconv"
+ fi
+ LDFLAGS="$LDFLAGS -R$ALT_HOME/lib"
+ fi
+--- EMBOSS-6.3.1/m4/java.m4 2013-09-11 10:39:03.490180358 +0200
++++ m4/java.m4 2013-09-11 10:46:08.240181467 +0200
+@@ -180,7 +180,7 @@
+
+ if test "$withval" = "yes" ; then
+ CFLAGS="$CFLAGS -D_REENTRANT"
+- LDFLAGS="$LDFLAGS -lpthread"
++ LDFLAGS="$LDFLAGS"
+ LIBS="$LIBS -lpthread"
+ fi
+
+@@ -192,38 +192,38 @@
+
+ if test "$withval" = "linux" ; then
+ CFLAGS="$CFLAGS -D_REENTRANT"
+- LDFLAGS="$LDFLAGS -lpthread"
++ LDFLAGS="$LDFLAGS"
+ LIBS="$LIBS -lpthread"
+ fi
+
+ if test "$withval" = "solaris" ; then
+ CFLAGS="$CFLAGS -D_POSIX_C_SOURCE=199506L"
+- LDFLAGS="$LDFLAGS -lpthread"
++ LDFLAGS="$LDFLAGS"
+ LIBS="$LIBS -lpthread"
+ fi
+ if test "$withval" = "macos" ; then
+ CFLAGS="$CFLAGS"
+- LDFLAGS="$LDFLAGS -lpthread"
++ LDFLAGS="$LDFLAGS"
+ LIBS="$LIBS -lpthread"
+ fi
+ if test "$withval" = "hpux" ; then
+ CFLAGS="$CFLAGS -Ae +z -DNATIVE -D_POSIX_C_SOURCE=199506L"
+- LDFLAGS="$LDFLAGS -lpthread"
++ LDFLAGS="$LDFLAGS"
+ LIBS="$LIBS -lpthread"
+ fi
+ if test "$withval" = "irix" ; then
+ CFLAGS="$CFLAGS"
+- LDFLAGS="$LDFLAGS -lpthread"
++ LDFLAGS="$LDFLAGS"
+ LIBS="$LIBS -lpthread"
+ fi
+ if test "$withval" = "aix" ; then
+ CFLAGS="$CFLAGS -D_REENTRANT"
+- LDFLAGS="$LDFLAGS -lpthread"
++ LDFLAGS="$LDFLAGS"
+ LIBS="$LIBS -lpthread"
+ fi
+ if test "$withval" = "osf" ; then
+ CFLAGS="$CFLAGS -D_REENTRANT -D_OSF_SOURCE"
+- LDFLAGS="$LDFLAGS -lpthread"
++ LDFLAGS="$LDFLAGS"
+ LIBS="$LIBS -lpthread"
+ fi
+ else
+--- EMBOSS-6.3.1/m4/mysql.m4 2013-09-11 11:03:07.160184129 +0200
++++ m4/mysql.m4 2013-09-11 11:04:39.440184370 +0200
+@@ -85,7 +85,6 @@
+ AC_MSG_CHECKING([for MySQL libraries])
+
+ dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
+- MYSQL_CFLAGS="`$MYSQL_CONFIG --include`"
+ MYSQL_LIBS="`$MYSQL_CONFIG --libs`"
+
+ MYSQL_VERSION=`$MYSQL_CONFIG --version`
+--- EMBOSS-6.3.1/m4/mysql.m4 2013-09-11 11:38:09.330189621 +0200
++++ m4/mysql.m4 2013-09-11 11:41:02.170190072 +0200
+@@ -170,6 +170,4 @@
+ fi
+
+ AC_SUBST([MYSQL_VERSION])
+- AC_SUBST([MYSQL_CFLAGS])
+- AC_SUBST([MYSQL_LIBS])
+ ])
+--- EMBOSS-6.3.1/configure.in 2013-09-11 12:23:17.330196695 +0200
++++ configure.in 2013-09-11 12:23:21.480196706 +0200
+@@ -8,6 +8,8 @@
+ AC_INIT(ajax/core/ajmath.c)
+ AM_INIT_AUTOMAKE([EMBOSS],[6.3.1])
+
++AC_CONFIG_MACRO_DIR([m4])
++
+ # Make sure CFLAGS is defined to stop LT_INIT adding -g
+ CFLAGS="$CFLAGS "
+
+--- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 12:33:14.260198254 +0200
++++ nucleus/Makefile.am 2013-09-11 12:33:16.650198260 +0200
+@@ -58,4 +58,4 @@
+ endif
+
+ libnucleus_la_LDFLAGS = $(LINKFLAGS)
+-libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la
++libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd
+--- EMBOSS-6.3.1/ajax/ensembl/Makefile.am 2013-09-11 12:41:06.340199487 +0200
++++ ajax/ensembl/Makefile.am 2013-09-11 12:41:40.460199577 +0200
+@@ -56,5 +56,5 @@
+ LINKFLAGS = $(VERS_INF)
+ endif
+
+-libensembl_la_LDFLAGS = $(LINKFLAGS)
+-libensembl_la_LIBADD = ../core/libajax.la
++libensembl_la_LDFLAGS = $(LINKFLAGS) -L../core
++libensembl_la_LIBADD = -lajax
+--- EMBOSS-6.3.1/ajax/graphics/Makefile.am 2013-09-11 12:42:17.730199674 +0200
++++ ajax/graphics/Makefile.am 2013-09-11 12:42:47.000199750 +0200
+@@ -35,5 +35,5 @@
+ LINKFLAGS = $(VERS_INF)
+ endif
+
+-libajaxg_la_LDFLAGS = $(LINKFLAGS)
+-libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
++libajaxg_la_LDFLAGS = $(LINKFLAGS) -L../core/
++libajaxg_la_LIBADD = -lajax $(EXTRA_LIBS)
+--- EMBOSS-6.3.1/ajax/acd/Makefile.am 2013-09-11 12:43:11.660199815 +0200
++++ ajax/acd/Makefile.am 2013-09-11 12:44:01.520199945 +0200
+@@ -41,5 +41,5 @@
+ LINKFLAGS = $(VERS_INF)
+ endif
+
+-libacd_la_LDFLAGS = $(LINKFLAGS)
+-libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la
++libacd_la_LDFLAGS = $(LINKFLAGS) -L../core -L../graphics -L../ajaxdb
++libacd_la_LIBADD = -lajax -lajaxg -lajaxdb
+--- EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am 2013-09-11 12:44:10.980199970 +0200
++++ ajax/ajaxdb/Makefile.am 2013-09-11 12:44:40.040200046 +0200
+@@ -37,5 +37,5 @@
+ LINKFLAGS = $(VERS_INF)
+ endif
+
+-libajaxdb_la_LDFLAGS = $(LINKFLAGS)
+-libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
++libajaxdb_la_LDFLAGS = $(LINKFLAGS) -L../core -L../ensembl
++libajaxdb_la_LIBADD = -lajax -lensembl
+--- EMBOSS-6.3.1/configure.in 2013-09-11 13:24:39.720206315 +0200
++++ configure.in 2013-09-11 13:24:58.610206364 +0200
+@@ -319,10 +319,8 @@
+ AX_LIB_MYSQL
+ AX_LIB_POSTGRESQL
+
+-CFLAGS="$CFLAGS $MYSQL_CFLAGS"
+ LIBS="${MYSQL_LIBS} ${LIBS}"
+
+-CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
+ LIBS="$POSTGRESQL_LIBS $LIBS"
+
+
+--- EMBOSS-6.3.1/ajax/core/Makefile.am 2013-09-11 13:47:36.790209912 +0200
++++ ajax/core/Makefile.am 2013-09-11 13:47:40.550209922 +0200
+@@ -65,5 +65,5 @@
+ LINKFLAGS = $(VERS_INF)
+ endif
+
+-libajax_la_LDFLAGS = $(LINKFLAGS)
++libajax_la_LDFLAGS =
+ libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LIBS) $(MYSQL_LIBS)
+--- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 14:03:21.960212381 +0200
++++ nucleus/Makefile.am 2013-09-11 14:03:58.910212478 +0200
+@@ -22,11 +22,14 @@
+ EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+ -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+ else
+-EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
++EXTRA_INCLUDES =
+ endif
+ endif
+
+
++# zap the crap
++PLPLOT_CFLAGS =
++
+ INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \
+ -I$(top_srcdir)/ajax \
+ $(EXTRA_INCLUDES) \
+--- EMBOSS-6.3.1/emboss/Makefile.am 2013-09-11 14:23:50.570215591 +0200
++++ emboss/Makefile.am 2013-09-11 14:24:24.950215680 +0200
+@@ -328,9 +328,7 @@
+
+ LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \
+ ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
+- ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
+- $(EXTRA_LDS) \
+- $(XLIB)
++ ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la
+
+ pkgdata_DATA = emboss.default.template
+ pkgdatadir=$(prefix)/share/$(PACKAGE)
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch
new file mode 100644
index 0000000..ad358e1
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch
@@ -0,0 +1,18 @@
+--- EMBOSS-6.3.1/m4/libtool.m4 2013-09-11 12:03:45.180193633 +0200
++++ m4/libtool.m4 2013-09-11 12:04:19.280193722 +0200
+@@ -4768,13 +4768,13 @@
+ *Sun\ F*) # Sun Fortran 8.3
+ tmp_sharedflag='-G' ;;
+ esac
+- _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
++ _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname -Wl,--as-needed -o $lib'
+
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+- $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
++ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -Wl,--as-needed -o $lib'
+ fi
+
+ case $cc_basename in
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch
similarity index 100%
rename from sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch
rename to sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2013-09-16 18:42 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2013-09-16 18:42 UTC (permalink / raw
To: gentoo-commits
commit: d7612ffdd7f827fbf8c835e8d4465091a6261038
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Sep 16 18:43:18 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Sep 16 18:43:18 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d7612ffd
Mask the 6.6.0 version due to build breakage; add the missing plcol patch copied over from 6.3.1
---
sci-biology/emboss/ChangeLog | 17 ++++
sci-biology/emboss/emboss-6.6.0.ebuild | 14 ++-
sci-biology/emboss/files/emboss-6.6.0_plcol.patch | 112 ++++++++++++++++++++++
3 files changed, 138 insertions(+), 5 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 76a5b35..1d9c10e 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,23 @@
# Copyright 1999-2013 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 $
+ 16 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ 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)
diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
index 4ab7353..1d7b405 100644
--- a/sci-biology/emboss/emboss-6.6.0.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -6,8 +6,11 @@ EAPI="4"
inherit emboss eutils
-EBO_PATCH="4"
-EBOV=${PV/_p*}
+#EBO_PATCH="4"
+#EBOV=${PV/_p*}
+
+EBO_PATCH=""
+EBOV=${PV}
DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
SRC_URI="
@@ -18,7 +21,8 @@ SRC_URI="
##[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
#[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+#KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+KEYWORDS=""
IUSE+=" minimal"
RDEPEND+=" !sys-devel/cons"
@@ -40,8 +44,8 @@ DOCS+=" FAQ THANKS"
src_prepare() {
[[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch
- epatch "${WORKDIR}"/${PF}.patch
- epatch "${FILESDIR}/${PF}_plcol.patch"
+ # epatch "${WORKDIR}"/${PF}.patch
+ #epatch "${FILESDIR}/${PF}_plcol.patch"
emboss_src_prepare
}
diff --git a/sci-biology/emboss/files/emboss-6.6.0_plcol.patch b/sci-biology/emboss/files/emboss-6.6.0_plcol.patch
new file mode 100644
index 0000000..0f5e592
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.6.0_plcol.patch
@@ -0,0 +1,112 @@
+--- EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2012-07-19 23:29:05.000000000 +0200
++++ /tmp/ajgraph.c 2012-07-19 23:25:00.000000000 +0200
+@@ -1645,14 +1645,14 @@
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+ static void GraphSetPen(ajint colour)
+ {
+- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]);
+- plcol((PLINT)colour);
++ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]);
++ plcol0((PLINT)colour);
+
+ return;
+ }
+
+
+
+--- EMBOSS-6.3.1/plplot/plcore.c 2007-10-24 15:14:43.000000000 +0200
++++ /tmp/plcore.c 2012-07-19 23:25:00.000000000 +0200
+@@ -1709,13 +1709,13 @@
+ if (plsc->zdigmax == 0)
+ plsc->zdigmax = 3;
+
+ /* Switch to graphics mode and set color and arrow style*/
+
+ plgra();
+- plcol(1);
++ plcol0(1);
+
+ plstyl(0, &mk, &sp);
+ plpat(1, &inc, &del);
+
+ plsvect(def_arrow_x, def_arrow_y, 6, 0);
+
+--- EMBOSS-6.3.1/plplot/plstripc.c 2007-05-08 11:09:37.000000000 +0200
++++ /tmp/plstripc.c 2012-07-19 23:25:00.000000000 +0200
+@@ -153,17 +153,17 @@
+
+ plgchr(&sc, &dy);
+ sc = dy = dy/100;
+ plwind(-0.01, 1.01, -0.01, 1.01);
+ for (i=0; i<PEN; i++) {
+ if (mystripc->npts[i] || first) {
+- plcol(mystripc->colline[i]);
++ plcol0(mystripc->colline[i]);
+ pllsty(mystripc->styline[i]);
+ pljoin(mystripc->xlpos, mystripc->ylpos - sc,
+ mystripc->xlpos + 0.1, mystripc->ylpos - sc);
+- plcol(mystripc->collab);
++ plcol0(mystripc->collab);
+ plptex(mystripc->xlpos + 0.11, mystripc->ylpos - sc,
+ 0., 0., 0, mystripc->legline[i]);
+ sc += dy;
+ }
+ }
+ plwind(mystripc->xmin, mystripc->xmax, mystripc->ymin, mystripc->ymax);
+@@ -184,34 +184,34 @@
+ PLFLT x[]={0.,1.,1.,0.}, y[]={0.,0.,1.,1.};
+
+ /* Set up window */
+
+ plvpor(0,1,0,1);
+ plwind(0,1,0,1);
+- plcol(0);plpsty(0);
++ plcol0(0);plpsty(0);
+ plfill(4, &x[0], &y[0]);
+ plvsta();
+
+ /* Draw box and same window dimensions */
+ mystrip->wxmin=mystrip->xmin;
+ mystrip->wxmax=mystrip->xmax;
+ mystrip->wymin=mystrip->ymin;
+ mystrip->wymax=mystrip->ymax; /* FIXME - can exist some redundancy here */
+
+ plwind(mystrip->xmin, mystrip->xmax, mystrip->ymin, mystrip->ymax);
+
+ pllsty(1);
+- plcol(mystrip->colbox);
++ plcol0(mystrip->colbox);
+ plbox(mystrip->xspec, 0.0, 0, mystrip->yspec, 0.0, 0);
+
+- plcol(mystrip->collab);
++ plcol0(mystrip->collab);
+ pllab(mystrip->labx, mystrip->laby, mystrip->labtop);
+
+ for (i=0; i<PEN; i++) {
+ if (mystrip->npts[i] > 0) {
+- plcol(mystrip->colline[i]);pllsty(mystrip->styline[i]);
++ plcol0(mystrip->colline[i]);pllsty(mystrip->styline[i]);
+ plline(mystrip->npts[i], mystrip->x[i], mystrip->y[i]);
+ }
+ }
+
+ plstrip_legend(mystrip,0);
+ }
+@@ -269,13 +269,13 @@
+ if (stripc->xmax - stripc->xmin < stripc->xlen) {
+ if( yasc == 0) {
+
+ /* If user has changed subwindow, make shure we have the correct one */
+ plvsta();
+ plwind(stripc->wxmin, stripc->wxmax, stripc->wymin, stripc->wymax); /* FIXME - can exist some redundancy here */
+- plcol(stripc->colline[p]); pllsty(stripc->styline[p]);
++ plcol0(stripc->colline[p]); pllsty(stripc->styline[p]);
+ if ((stripc->npts[p]-2) < 0)
+ plP_movwor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
+ else
+ plP_movwor(stripc->x[p][stripc->npts[p]-2], stripc->y[p][stripc->npts[p]-2]);
+ plP_drawor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
+ plflush();
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2014-07-04 16:52 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2014-07-04 16:52 UTC (permalink / raw
To: gentoo-commits
commit: 2ff987f23c228b8e4494df4908bbce11f9c3eec0
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 4 16:51:12 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 4 16:51:12 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2ff987f2
sci-biology/emboss-6.3.1_p4-r2: added a patch for 'undefined reference to c_plwid' bug #493724
Package-Manager: portage-2.2.7
---
sci-biology/emboss/ChangeLog | 6 ++++++
sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild | 1 +
.../files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch | 13 +++++++++++++
3 files changed, 20 insertions(+)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 9dd52d9..b047e8c 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,12 @@
# 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 <mmokrejs@fold.natur.cuni.cz>
+ +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 <mmokrejs@fold.natur.cuni.cz>
emboss-6.3.1_p4-r2.ebuild:
sci-biology/emboss-6.3.1_p4-r2: add plplot dependency, trying to get rid of a
diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
index 59a7d49..962d472 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
@@ -42,6 +42,7 @@ src_prepare() {
epatch "${WORKDIR}"/${PF}.patch
epatch "${FILESDIR}/${PF}"_plcol.patch
epatch "${FILESDIR}/${PF}"_compilations-paths.patch
+ epatch "${FILESDIR}/${PF}"_rename_plwid_to_plwidth.patch
# cp "${FILESDIR}"/ax_lib_mysql.m4 "${S}"/m4/mysql.m4
emboss_src_prepare
autoreconf -vfi
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch
new file mode 100644
index 0000000..e66a696
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch
@@ -0,0 +1,13 @@
+--- EMBOSS-6.3.1/ajax/graphics/ajgraph.c.ori 2014-07-04 18:25:18.000000000 +0200
++++ EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2014-07-04 18:25:32.000000000 +0200
+@@ -1329,8 +1329,8 @@
+
+ void ajGraphicsSetPenwidth(float penwidth)
+ {
+- ajDebug("=g= plwid(%.2f) [width]\n", penwidth);
+- plwid((PLINT)penwidth);
++ ajDebug("=g= plwidth(%.2f) [width]\n", penwidth);
++ plwidth((PLINT)penwidth);
+
+ return;
+ }
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
@ 2015-02-04 8:37 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2015-02-04 8:37 UTC (permalink / raw
To: gentoo-commits
commit: cfb0869296a4156fe8c7c65c6031debaae954463
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 4 08:11:55 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 4 08:13:00 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cfb08692
sci-biology/emboss: Drop old
Package-Manager: portage-2.2.15
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
sci-biology/emboss/ChangeLog | 3 +
sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild | 94 ------
sci-biology/emboss/files/ax_lib_mysql.m4 | 147 ----------
.../emboss/files/emboss-6.3.1_p4-r2_Makefile.patch | 47 ---
.../emboss-6.3.1_p4-r2_compilations-paths.patch | 315 ---------------------
.../emboss/files/emboss-6.3.1_p4-r2_libtool.patch | 18 --
.../emboss/files/emboss-6.3.1_p4-r2_plcol.patch | 112 --------
...mboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch | 13 -
sci-biology/emboss/files/emboss-README.Gentoo-2 | 34 ---
9 files changed, 3 insertions(+), 780 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index a8d74bc..a6558c1 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 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 Feb 2015; Justin Lecher <jlec@gentoo.org> -emboss-6.3.1_p4-r2.ebuild:
+ Drop old
+
04 Feb 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
Clean a bit, user readme.gentoo.eclass
diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
deleted file mode 100644
index 962d472..0000000
--- a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
+++ /dev/null
@@ -1,94 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="4"
-
-inherit emboss eutils
-
-EBO_PATCH="4"
-EBOV=${PV/_p*}
-
-DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
-SRC_URI="
- ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
- http://dev.gentoo.org/~jlec/distfiles/${PF}.patch.bz2"
-##[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
-[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
-
-KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-IUSE+=" minimal"
-
-RDEPEND+=" !sys-devel/cons"
-PDEPEND+="
- !minimal? (
- sci-biology/aaindex
- sci-biology/cutg
- sci-biology/prints
- sci-biology/prosite
- sci-biology/rebase
- sci-biology/transfac
- sci-libs/plplot
- )"
-
-S="${WORKDIR}"/EMBOSS-${EBOV}
-
-EBO_EXTRA_ECONF="--includedir=${EPREFIX}/usr/include/emboss"
-
-DOCS+=" FAQ THANKS"
-
-src_prepare() {
- [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch
- epatch "${WORKDIR}"/${PF}.patch
- epatch "${FILESDIR}/${PF}"_plcol.patch
- epatch "${FILESDIR}/${PF}"_compilations-paths.patch
- epatch "${FILESDIR}/${PF}"_rename_plwid_to_plwidth.patch
- # cp "${FILESDIR}"/ax_lib_mysql.m4 "${S}"/m4/mysql.m4
- emboss_src_prepare
- autoreconf -vfi
- epatch "${FILESDIR}/${PF}"_libtool.patch
-}
-
-#src_compile() {
-# # epatch "${FILESDIR}/${PF}"_Makefile.patch
-# sed -i -e "s#GD_LIBS = .*#GD_LIBS =#" Makefile
-# sed -i -e "s#^LIBS = .*#LIBS =#" Makefile
-# sed -i -e "s#^PLPLOT_LIBS = .*#PLPLOT_LIBS =#" Makefile
-# sed -i -e "s#^libnucleus_la_LDFLAGS = .*#libnucleus_la_LDFLAGS = \$(LDFLAGS)#" Makefile
-#}
-
-src_install() {
- default
-
- sed -e "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
- dodoc README.Gentoo
-
- # Install env file for setting libplplot and acd files path.
- cat <<- EOF > 22emboss
- # ACD files location
- EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
- EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
- EOF
- doenvd 22emboss
-
- # Clashes #330507, resolved upstream
- mv "${ED}"/usr/bin/{digest,pepdigest} || die
-
- # Remove useless dummy files from the image.
- find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files."
-
- # Move the provided codon files to a different directory. This will avoid
- # user confusion and file collisions on case-insensitive file systems (see
- # bug #115446). This change is documented in "README.Gentoo".
- mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
- die "Failed to move CODON directory."
-
- # Move the provided restriction enzyme prototypes file to a different name.
- # This avoids file collisions with versions of rebase that install their
- # own enzyme prototypes file (see bug #118832).
- mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
- die "Failed to move enzyme equivalence file."
-
- # fix /usr/share/doc/emboss-6.3.1_p4-r1/html to point to /usr/share/doc/emboss-6.3.1_p4-r1/programs/html
- # instead of /usr/share/EMBOSS/doc/html (which does not exist)
-}
diff --git a/sci-biology/emboss/files/ax_lib_mysql.m4 b/sci-biology/emboss/files/ax_lib_mysql.m4
deleted file mode 100644
index e27d755..0000000
--- a/sci-biology/emboss/files/ax_lib_mysql.m4
+++ /dev/null
@@ -1,147 +0,0 @@
-# ===========================================================================
-# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-# AX_LIB_MYSQL([MINIMUM-VERSION])
-#
-# DESCRIPTION
-#
-# This macro provides tests of availability of MySQL client library of
-# particular version or newer.
-#
-# AX_LIB_MYSQL macro takes only one argument which is optional. If there
-# is no required version passed, then macro does not run version test.
-#
-# The --with-mysql option takes one of three possible values:
-#
-# no - do not check for MySQL client library
-#
-# yes - do check for MySQL library in standard locations (mysql_config
-# should be in the PATH)
-#
-# path - complete path to mysql_config utility, use this option if
-# mysql_config can't be found in the PATH
-#
-# This macro calls:
-#
-# AC_SUBST(MYSQL_CFLAGS)
-# AC_SUBST(MYSQL_LDFLAGS)
-# AC_SUBST(MYSQL_VERSION)
-#
-# And sets:
-#
-# HAVE_MYSQL
-#
-# LICENSE
-#
-# Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net>
-#
-# Copying and distribution of this file, with or without modification, are
-# permitted in any medium without royalty provided the copyright notice
-# and this notice are preserved. This file is offered as-is, without any
-# warranty.
-
-#serial 12
-
-AC_DEFUN([AX_LIB_MYSQL],
-[
- AC_ARG_WITH([mysql],
- AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
- [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config]
- ),
- [
- if test "$withval" = "no"; then
- want_mysql="no"
- elif test "$withval" = "yes"; then
- want_mysql="yes"
- else
- want_mysql="yes"
- MYSQL_CONFIG="$withval"
- fi
- ],
- [want_mysql="yes"]
- )
- AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program])
-
- MYSQL_CFLAGS=""
- MYSQL_LDFLAGS=""
- MYSQL_VERSION=""
-
- dnl
- dnl Check MySQL libraries
- dnl
-
- if test "$want_mysql" = "yes"; then
-
- if test -z "$MYSQL_CONFIG" ; then
- AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no])
- fi
-
- if test "$MYSQL_CONFIG" != "no"; then
- MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
- MYSQL_LDFLAGS="`$MYSQL_CONFIG --libs`"
-
- MYSQL_VERSION=`$MYSQL_CONFIG --version`
-
- found_mysql="yes"
- else
- found_mysql="no"
- fi
- fi
-
- dnl
- dnl Check if required version of MySQL is available
- dnl
-
-
- mysql_version_req=ifelse([$1], [], [], [$1])
-
- if test "$found_mysql" = "yes" -a -n "$mysql_version_req"; then
-
- AC_MSG_CHECKING([if MySQL version is >= $mysql_version_req])
-
- dnl Decompose required version string of MySQL
- dnl and calculate its number representation
- mysql_version_req_major=`expr $mysql_version_req : '\([[0-9]]*\)'`
- mysql_version_req_minor=`expr $mysql_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
- mysql_version_req_micro=`expr $mysql_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
- if test "x$mysql_version_req_micro" = "x"; then
- mysql_version_req_micro="0"
- fi
-
- mysql_version_req_number=`expr $mysql_version_req_major \* 1000000 \
- \+ $mysql_version_req_minor \* 1000 \
- \+ $mysql_version_req_micro`
-
- dnl Decompose version string of installed MySQL
- dnl and calculate its number representation
- mysql_version_major=`expr $MYSQL_VERSION : '\([[0-9]]*\)'`
- mysql_version_minor=`expr $MYSQL_VERSION : '[[0-9]]*\.\([[0-9]]*\)'`
- mysql_version_micro=`expr $MYSQL_VERSION : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
- if test "x$mysql_version_micro" = "x"; then
- mysql_version_micro="0"
- fi
-
- mysql_version_number=`expr $mysql_version_major \* 1000000 \
- \+ $mysql_version_minor \* 1000 \
- \+ $mysql_version_micro`
-
- mysql_version_check=`expr $mysql_version_number \>\= $mysql_version_req_number`
- if test "$mysql_version_check" = "1"; then
- AC_MSG_RESULT([yes])
- else
- AC_MSG_RESULT([no])
- fi
- fi
-
- if test "$found_mysql" = "yes" ; then
- AC_DEFINE([HAVE_MYSQL], [1],
- [Define to 1 if MySQL libraries are available])
- fi
-
- AC_SUBST([MYSQL_VERSION])
- AC_SUBST([MYSQL_CFLAGS])
- AC_SUBST([MYSQL_LDFLAGS])
-])
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch
deleted file mode 100644
index 419369e..0000000
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch
+++ /dev/null
@@ -1,47 +0,0 @@
---- EMBOSS-6.3.1/nucleus/Makefile 2013-09-11 14:50:25.140219756 +0200
-+++ nucleus/Makefile 2013-09-11 14:52:00.920220006 +0200
-@@ -165,7 +165,7 @@
- ESYSTEMLIBS =
- EXEEXT =
- FGREP = /bin/grep -F
--GD_LIBS = -ljpeg -lfontconfig -lfreetype -lz -lm -lgd
-+GD_LIBS =
- GREP = /bin/grep
- HAVE_MEMMOVE =
- HAVE_STRERROR =
-@@ -180,7 +180,7 @@
- LD = /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
- LDFLAGS = -Wl,--as-needed
- LIBOBJS =
--LIBS = -L/usr/lib64/mysql -lmysqlclient -lpthread -lz -lm -lrt -lssl -lcrypto -ldl -lm -lhpdf -lpng16 -L/usr/lib64 -lz -ljpeg -lfontconfig -lfreetype -lz -lm -lgd
-+LIBS =
- LIBTOOL = $(SHELL) $(top_builddir)/libtool
- LIPO =
- LN_S = ln -s
-@@ -219,7 +219,7 @@
- # zap the crap
- PLPLOT_CFLAGS =
- PLPLOT_CPPFLAGS =
--PLPLOT_LIBS = -lplplotd -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lSM -lICE -lX11 -lXext -lgd -lpng -lz -ljpeg -lfreetype -lSM -lICE -lX11 -lXext -lpthread -lLASi -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfreetype -lfontconfig -lhpdf -lm -lcsirocsa -lnistcd -lqsastime -lfreetype
-+PLPLOT_LIBS =
- PNG_CFLAGS = -I/usr/include/libpng16
- PNG_LIBS = -lpng16
- POSIX_MALLOC_THRESHOLD = -DPOSIX_MALLOC_THRESHOLD=10
-@@ -336,7 +336,7 @@
- VERS_INF = -version-info 6:3:0
- LINKFLAGS = $(VERS_INF)
- #LINKFLAGS = $(VERS_INF) $(CYGWIN_LDFLAGS) $(CYGWIN_LIBS)
--libnucleus_la_LDFLAGS = $(LINKFLAGS)
-+libnucleus_la_LDFLAGS = $(LDFLAGS)
- libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd
- all: all-am
-
-@@ -407,7 +407,7 @@
- rm -f $${locs}; \
- }
- libnucleus.la: $(libnucleus_la_OBJECTS) $(libnucleus_la_DEPENDENCIES) $(EXTRA_libnucleus_la_DEPENDENCIES)
-- $(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(libnucleus_la_LIBADD) $(LIBS)
-+ $(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(LIBS)
-
- mostlyclean-compile:
- -rm -f *.$(OBJEXT)
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch
deleted file mode 100644
index 8f87ef9..0000000
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch
+++ /dev/null
@@ -1,315 +0,0 @@
---- EMBOSS-6.3.1/configure.in 2013-09-11 03:55:15.510117066 +0200
-+++ configure.in 2013-09-11 03:48:10.410115955 +0200
-@@ -449,7 +447,8 @@
- if test "`uname -a | grep Darwin`"; then
- OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
- if test ${OSXX} '>' '10.4'; then
-- CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
-+ CPPFLAGS="$CPPFLAGS -I/usr/X11/include"
-+ LDFLAGS="$LDFLAGS -L/usr/X11/lib"
- fi
- fi
- fi
-@@ -461,7 +460,7 @@
- AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
- AC_SUBST(ESYSTEMLIBS)
- AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
--AC_SUBST(PLPLOT_CFLAGS)
-+AC_SUBST(PLPLOT_CPPFLAGS)
- AC_SUBST(PLPLOT_LIBS)
-
-
---- EMBOSS-6.3.1/ajax/graphics/Makefile.am 2013-09-11 03:27:30.110112715 +0200
-+++ ajax/graphics/Makefile.am 2013-09-11 03:58:50.860117628 +0200
-@@ -19,7 +19,7 @@
-
-
- INCLUDES = \
--$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
-+$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core -I$(top_srcdir)/plplot
-
- AJAXGSRC = ajgraph.c ajhist.c
-
---- EMBOSS-6.3.1/ajax/acd/Makefile.am 2013-09-11 03:27:30.110112715 +0200
-+++ ajax/acd/Makefile.am 2013-09-11 03:59:10.310117679 +0200
-@@ -24,7 +24,8 @@
- -I$(top_srcdir)/ajax/core \
- -I$(top_srcdir)/ajax/graphics \
- -I$(top_srcdir)/ajax/ensembl \
---I$(top_srcdir)/ajax/ajaxdb
-+-I$(top_srcdir)/ajax/ajaxdb \
-+-I$(top_srcdir)/plplot
-
- ACDSRC = ajacd.c
-
---- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 03:27:30.110112715 +0200
-+++ nucleus/Makefile.am 2013-09-11 03:59:28.630117727 +0200
-@@ -32,7 +32,7 @@
- $(EXTRA_INCLUDES) \
- -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
- -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
-- -I$(top_srcdir)/ajax/acd
-+ -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
-
- NUCLSRC = embaln.c embcom.c embcons.c embdata.c embdbi.c embdmx.c \
- embdomain.c embest.c embexit.c embgroup.c embiep.c embindex.c \
---- EMBOSS-6.3.1/emboss/Makefile.am 2013-09-11 03:27:30.110112715 +0200
-+++ emboss/Makefile.am 2013-09-11 03:59:46.340117773 +0200
-@@ -89,7 +89,7 @@
- $(EXTRA_INCLUDES) \
- -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
- -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
-- -I$(top_srcdir)/ajax/acd
-+ -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
-
-
- aaindexextract_SOURCES = aaindexextract.c
---- EMBOSS-6.3.1/Makefile.am 2013-09-11 04:19:01.770120791 +0200
-+++ Makefile.am 2013-09-11 04:19:18.460120835 +0200
-@@ -13,8 +13,8 @@
- JEMBOSS_DIR = jemboss
- endif
-
--SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
--DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
-+SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR)
-+DIST_SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR)
-
- # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
-
---- EMBOSS-6.3.1/plplot/Makefile.am 2013-09-11 09:34:44.620170277 +0200
-+++ plplot/Makefile.am 2013-09-11 09:35:35.820170411 +0200
-@@ -10,26 +10,27 @@
- if AMPNG
-
- if AMPDF
--TESTPDF_CFLAGS = -Wl,-G -lhpdf
-+TESTPDF_LIBS = -Wl,-G -lhpdf
- else
--TESTPDF_CFLAGS = -Wl,-G
-+TESTPDF_LIBS = -Wl,-G
- endif
-
--TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lgd -lpng -lz -lX11 -lm
-+TESTPNG_LIBS = $(TESTPDF_LIBS) -lgd -lpng -lz -lX11 -lm
- else
--TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lX11
-+TESTPNG_LIBS = $(TESTPDF_LIBS) -lX11
- endif
- endif
- endif
-
--AM_CFLAGS = $(TESTPNG_CFLAGS)
-+AM_LIBS = $(TESTPNG_LIBS)
-
- if ISCYGWIN
- CYGWIN_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import
- CYGWIN_LIBS = -lX11 -lgd -lpng -lz
- endif
-
--INCLUDES = $(X_CFLAGS) -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\"
-+INCLUDES = -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\"
-+LIBS = $(AM_LIBS)
-
- PLPLOTSRC = pdfutils.c plargs.c plbox.c plcont.c plcore.c \
- plctrl.c plcvt.c pldtik.c plfill.c plhist.c plline.c plmap.c \
---- EMBOSS-6.3.1/m4/pngdriver.m4 2013-09-11 10:39:07.680180369 +0200
-+++ m4/pngdriver.m4 2013-09-11 10:44:16.000181174 +0200
-@@ -63,7 +63,8 @@
- if test "`uname`" = "SunOS"; then
- AC_CHECK_LIB(iconv, libiconv_close, ICCHECK=1, ICCHECK=0, -L${ALT_HOME}/lib -liconv)
- if test $ICCHECK = "1" ; then
-- LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib -liconv"
-+ LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib"
-+ LIBS="${LIBS} -liconv"
- fi
- LDFLAGS="$LDFLAGS -R$ALT_HOME/lib"
- fi
---- EMBOSS-6.3.1/m4/java.m4 2013-09-11 10:39:03.490180358 +0200
-+++ m4/java.m4 2013-09-11 10:46:08.240181467 +0200
-@@ -180,7 +180,7 @@
-
- if test "$withval" = "yes" ; then
- CFLAGS="$CFLAGS -D_REENTRANT"
-- LDFLAGS="$LDFLAGS -lpthread"
-+ LDFLAGS="$LDFLAGS"
- LIBS="$LIBS -lpthread"
- fi
-
-@@ -192,38 +192,38 @@
-
- if test "$withval" = "linux" ; then
- CFLAGS="$CFLAGS -D_REENTRANT"
-- LDFLAGS="$LDFLAGS -lpthread"
-+ LDFLAGS="$LDFLAGS"
- LIBS="$LIBS -lpthread"
- fi
-
- if test "$withval" = "solaris" ; then
- CFLAGS="$CFLAGS -D_POSIX_C_SOURCE=199506L"
-- LDFLAGS="$LDFLAGS -lpthread"
-+ LDFLAGS="$LDFLAGS"
- LIBS="$LIBS -lpthread"
- fi
- if test "$withval" = "macos" ; then
- CFLAGS="$CFLAGS"
-- LDFLAGS="$LDFLAGS -lpthread"
-+ LDFLAGS="$LDFLAGS"
- LIBS="$LIBS -lpthread"
- fi
- if test "$withval" = "hpux" ; then
- CFLAGS="$CFLAGS -Ae +z -DNATIVE -D_POSIX_C_SOURCE=199506L"
-- LDFLAGS="$LDFLAGS -lpthread"
-+ LDFLAGS="$LDFLAGS"
- LIBS="$LIBS -lpthread"
- fi
- if test "$withval" = "irix" ; then
- CFLAGS="$CFLAGS"
-- LDFLAGS="$LDFLAGS -lpthread"
-+ LDFLAGS="$LDFLAGS"
- LIBS="$LIBS -lpthread"
- fi
- if test "$withval" = "aix" ; then
- CFLAGS="$CFLAGS -D_REENTRANT"
-- LDFLAGS="$LDFLAGS -lpthread"
-+ LDFLAGS="$LDFLAGS"
- LIBS="$LIBS -lpthread"
- fi
- if test "$withval" = "osf" ; then
- CFLAGS="$CFLAGS -D_REENTRANT -D_OSF_SOURCE"
-- LDFLAGS="$LDFLAGS -lpthread"
-+ LDFLAGS="$LDFLAGS"
- LIBS="$LIBS -lpthread"
- fi
- else
---- EMBOSS-6.3.1/m4/mysql.m4 2013-09-11 11:03:07.160184129 +0200
-+++ m4/mysql.m4 2013-09-11 11:04:39.440184370 +0200
-@@ -85,7 +85,6 @@
- AC_MSG_CHECKING([for MySQL libraries])
-
- dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
-- MYSQL_CFLAGS="`$MYSQL_CONFIG --include`"
- MYSQL_LIBS="`$MYSQL_CONFIG --libs`"
-
- MYSQL_VERSION=`$MYSQL_CONFIG --version`
---- EMBOSS-6.3.1/m4/mysql.m4 2013-09-11 11:38:09.330189621 +0200
-+++ m4/mysql.m4 2013-09-11 11:41:02.170190072 +0200
-@@ -170,6 +170,4 @@
- fi
-
- AC_SUBST([MYSQL_VERSION])
-- AC_SUBST([MYSQL_CFLAGS])
-- AC_SUBST([MYSQL_LIBS])
- ])
---- EMBOSS-6.3.1/configure.in 2013-09-11 12:23:17.330196695 +0200
-+++ configure.in 2013-09-11 12:23:21.480196706 +0200
-@@ -8,6 +8,8 @@
- AC_INIT(ajax/core/ajmath.c)
- AM_INIT_AUTOMAKE([EMBOSS],[6.3.1])
-
-+AC_CONFIG_MACRO_DIR([m4])
-+
- # Make sure CFLAGS is defined to stop LT_INIT adding -g
- CFLAGS="$CFLAGS "
-
---- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 12:33:14.260198254 +0200
-+++ nucleus/Makefile.am 2013-09-11 12:33:16.650198260 +0200
-@@ -58,4 +58,4 @@
- endif
-
- libnucleus_la_LDFLAGS = $(LINKFLAGS)
--libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la
-+libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd
---- EMBOSS-6.3.1/ajax/ensembl/Makefile.am 2013-09-11 12:41:06.340199487 +0200
-+++ ajax/ensembl/Makefile.am 2013-09-11 12:41:40.460199577 +0200
-@@ -56,5 +56,5 @@
- LINKFLAGS = $(VERS_INF)
- endif
-
--libensembl_la_LDFLAGS = $(LINKFLAGS)
--libensembl_la_LIBADD = ../core/libajax.la
-+libensembl_la_LDFLAGS = $(LINKFLAGS) -L../core
-+libensembl_la_LIBADD = -lajax
---- EMBOSS-6.3.1/ajax/graphics/Makefile.am 2013-09-11 12:42:17.730199674 +0200
-+++ ajax/graphics/Makefile.am 2013-09-11 12:42:47.000199750 +0200
-@@ -35,5 +35,5 @@
- LINKFLAGS = $(VERS_INF)
- endif
-
--libajaxg_la_LDFLAGS = $(LINKFLAGS)
--libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
-+libajaxg_la_LDFLAGS = $(LINKFLAGS) -L../core/
-+libajaxg_la_LIBADD = -lajax $(EXTRA_LIBS)
---- EMBOSS-6.3.1/ajax/acd/Makefile.am 2013-09-11 12:43:11.660199815 +0200
-+++ ajax/acd/Makefile.am 2013-09-11 12:44:01.520199945 +0200
-@@ -41,5 +41,5 @@
- LINKFLAGS = $(VERS_INF)
- endif
-
--libacd_la_LDFLAGS = $(LINKFLAGS)
--libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la
-+libacd_la_LDFLAGS = $(LINKFLAGS) -L../core -L../graphics -L../ajaxdb
-+libacd_la_LIBADD = -lajax -lajaxg -lajaxdb
---- EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am 2013-09-11 12:44:10.980199970 +0200
-+++ ajax/ajaxdb/Makefile.am 2013-09-11 12:44:40.040200046 +0200
-@@ -37,5 +37,5 @@
- LINKFLAGS = $(VERS_INF)
- endif
-
--libajaxdb_la_LDFLAGS = $(LINKFLAGS)
--libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
-+libajaxdb_la_LDFLAGS = $(LINKFLAGS) -L../core -L../ensembl
-+libajaxdb_la_LIBADD = -lajax -lensembl
---- EMBOSS-6.3.1/configure.in 2013-09-11 13:24:39.720206315 +0200
-+++ configure.in 2013-09-11 13:24:58.610206364 +0200
-@@ -319,10 +319,8 @@
- AX_LIB_MYSQL
- AX_LIB_POSTGRESQL
-
--CFLAGS="$CFLAGS $MYSQL_CFLAGS"
- LIBS="${MYSQL_LIBS} ${LIBS}"
-
--CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
- LIBS="$POSTGRESQL_LIBS $LIBS"
-
-
---- EMBOSS-6.3.1/ajax/core/Makefile.am 2013-09-11 13:47:36.790209912 +0200
-+++ ajax/core/Makefile.am 2013-09-11 13:47:40.550209922 +0200
-@@ -65,5 +65,5 @@
- LINKFLAGS = $(VERS_INF)
- endif
-
--libajax_la_LDFLAGS = $(LINKFLAGS)
-+libajax_la_LDFLAGS =
- libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LIBS) $(MYSQL_LIBS)
---- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 14:03:21.960212381 +0200
-+++ nucleus/Makefile.am 2013-09-11 14:03:58.910212478 +0200
-@@ -22,11 +22,14 @@
- EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
- -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
- else
--EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
-+EXTRA_INCLUDES =
- endif
- endif
-
-
-+# zap the crap
-+PLPLOT_CFLAGS =
-+
- INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \
- -I$(top_srcdir)/ajax \
- $(EXTRA_INCLUDES) \
---- EMBOSS-6.3.1/emboss/Makefile.am 2013-09-11 14:23:50.570215591 +0200
-+++ emboss/Makefile.am 2013-09-11 14:24:24.950215680 +0200
-@@ -328,9 +328,7 @@
-
- LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \
- ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
-- ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
-- $(EXTRA_LDS) \
-- $(XLIB)
-+ ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la
-
- pkgdata_DATA = emboss.default.template
- pkgdatadir=$(prefix)/share/$(PACKAGE)
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch
deleted file mode 100644
index ad358e1..0000000
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- EMBOSS-6.3.1/m4/libtool.m4 2013-09-11 12:03:45.180193633 +0200
-+++ m4/libtool.m4 2013-09-11 12:04:19.280193722 +0200
-@@ -4768,13 +4768,13 @@
- *Sun\ F*) # Sun Fortran 8.3
- tmp_sharedflag='-G' ;;
- esac
-- _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
-+ _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname -Wl,--as-needed -o $lib'
-
- if test "x$supports_anon_versioning" = xyes; then
- _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
- cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
- echo "local: *; };" >> $output_objdir/$libname.ver~
-- $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
-+ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -Wl,--as-needed -o $lib'
- fi
-
- case $cc_basename in
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch
deleted file mode 100644
index 0f5e592..0000000
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch
+++ /dev/null
@@ -1,112 +0,0 @@
---- EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2012-07-19 23:29:05.000000000 +0200
-+++ /tmp/ajgraph.c 2012-07-19 23:25:00.000000000 +0200
-@@ -1645,14 +1645,14 @@
- ** @return [void]
- ** @@
- ******************************************************************************/
-
- static void GraphSetPen(ajint colour)
- {
-- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]);
-- plcol((PLINT)colour);
-+ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]);
-+ plcol0((PLINT)colour);
-
- return;
- }
-
-
-
---- EMBOSS-6.3.1/plplot/plcore.c 2007-10-24 15:14:43.000000000 +0200
-+++ /tmp/plcore.c 2012-07-19 23:25:00.000000000 +0200
-@@ -1709,13 +1709,13 @@
- if (plsc->zdigmax == 0)
- plsc->zdigmax = 3;
-
- /* Switch to graphics mode and set color and arrow style*/
-
- plgra();
-- plcol(1);
-+ plcol0(1);
-
- plstyl(0, &mk, &sp);
- plpat(1, &inc, &del);
-
- plsvect(def_arrow_x, def_arrow_y, 6, 0);
-
---- EMBOSS-6.3.1/plplot/plstripc.c 2007-05-08 11:09:37.000000000 +0200
-+++ /tmp/plstripc.c 2012-07-19 23:25:00.000000000 +0200
-@@ -153,17 +153,17 @@
-
- plgchr(&sc, &dy);
- sc = dy = dy/100;
- plwind(-0.01, 1.01, -0.01, 1.01);
- for (i=0; i<PEN; i++) {
- if (mystripc->npts[i] || first) {
-- plcol(mystripc->colline[i]);
-+ plcol0(mystripc->colline[i]);
- pllsty(mystripc->styline[i]);
- pljoin(mystripc->xlpos, mystripc->ylpos - sc,
- mystripc->xlpos + 0.1, mystripc->ylpos - sc);
-- plcol(mystripc->collab);
-+ plcol0(mystripc->collab);
- plptex(mystripc->xlpos + 0.11, mystripc->ylpos - sc,
- 0., 0., 0, mystripc->legline[i]);
- sc += dy;
- }
- }
- plwind(mystripc->xmin, mystripc->xmax, mystripc->ymin, mystripc->ymax);
-@@ -184,34 +184,34 @@
- PLFLT x[]={0.,1.,1.,0.}, y[]={0.,0.,1.,1.};
-
- /* Set up window */
-
- plvpor(0,1,0,1);
- plwind(0,1,0,1);
-- plcol(0);plpsty(0);
-+ plcol0(0);plpsty(0);
- plfill(4, &x[0], &y[0]);
- plvsta();
-
- /* Draw box and same window dimensions */
- mystrip->wxmin=mystrip->xmin;
- mystrip->wxmax=mystrip->xmax;
- mystrip->wymin=mystrip->ymin;
- mystrip->wymax=mystrip->ymax; /* FIXME - can exist some redundancy here */
-
- plwind(mystrip->xmin, mystrip->xmax, mystrip->ymin, mystrip->ymax);
-
- pllsty(1);
-- plcol(mystrip->colbox);
-+ plcol0(mystrip->colbox);
- plbox(mystrip->xspec, 0.0, 0, mystrip->yspec, 0.0, 0);
-
-- plcol(mystrip->collab);
-+ plcol0(mystrip->collab);
- pllab(mystrip->labx, mystrip->laby, mystrip->labtop);
-
- for (i=0; i<PEN; i++) {
- if (mystrip->npts[i] > 0) {
-- plcol(mystrip->colline[i]);pllsty(mystrip->styline[i]);
-+ plcol0(mystrip->colline[i]);pllsty(mystrip->styline[i]);
- plline(mystrip->npts[i], mystrip->x[i], mystrip->y[i]);
- }
- }
-
- plstrip_legend(mystrip,0);
- }
-@@ -269,13 +269,13 @@
- if (stripc->xmax - stripc->xmin < stripc->xlen) {
- if( yasc == 0) {
-
- /* If user has changed subwindow, make shure we have the correct one */
- plvsta();
- plwind(stripc->wxmin, stripc->wxmax, stripc->wymin, stripc->wymax); /* FIXME - can exist some redundancy here */
-- plcol(stripc->colline[p]); pllsty(stripc->styline[p]);
-+ plcol0(stripc->colline[p]); pllsty(stripc->styline[p]);
- if ((stripc->npts[p]-2) < 0)
- plP_movwor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
- else
- plP_movwor(stripc->x[p][stripc->npts[p]-2], stripc->y[p][stripc->npts[p]-2]);
- plP_drawor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
- plflush();
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch
deleted file mode 100644
index e66a696..0000000
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- EMBOSS-6.3.1/ajax/graphics/ajgraph.c.ori 2014-07-04 18:25:18.000000000 +0200
-+++ EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2014-07-04 18:25:32.000000000 +0200
-@@ -1329,8 +1329,8 @@
-
- void ajGraphicsSetPenwidth(float penwidth)
- {
-- ajDebug("=g= plwid(%.2f) [width]\n", penwidth);
-- plwid((PLINT)penwidth);
-+ ajDebug("=g= plwidth(%.2f) [width]\n", penwidth);
-+ plwidth((PLINT)penwidth);
-
- return;
- }
diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-2 b/sci-biology/emboss/files/emboss-README.Gentoo-2
deleted file mode 100644
index 72fa366..0000000
--- a/sci-biology/emboss/files/emboss-README.Gentoo-2
+++ /dev/null
@@ -1,34 +0,0 @@
-Administrating EMBOSS on Gentoo systems
-=======================================
-
-
-Codon data files location
--------------------------
-
-The codon data files that are distributed with EMBOSS are installed in the
-``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
-``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
-these codon files and those installed with the CUTG database. The names of
-these files sometimes vary only by their case. Having both sets of files in
-the same directory is also impossible on systems such as MacOSX, where the
-root filesystem is case insensitive. If you do not have the CUTG database
-installed and want to use the codon files distributed with EMBOSS, you can
-symlink the ``CODONS.orig`` directory to ``CODONS``::
-
- # cd EPREFIX/usr/share/EMBOSS/data
- # ln -s CODONS.orig CODONS
-
-
-Restriction enzymes equivalence file location
----------------------------------------------
-
-The restriction enzymes equivalence file distributed with EMBOSS is installed
-as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
-``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
-collision with the equivalence file provided by the Rebase database. If you do
-not have the Rebase database installed and want to use the equivalence file
-distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
-``embossre.equ``::
-
- # cd EPREFIX/usr/share/EMBOSS/data
- # ln -s embossre.equ.orig embossre.equ
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