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commit: cfb0869296a4156fe8c7c65c6031debaae954463 |
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Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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AuthorDate: Wed Feb 4 08:11:55 2015 +0000 |
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Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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CommitDate: Wed Feb 4 08:13:00 2015 +0000 |
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URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cfb08692 |
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|
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sci-biology/emboss: Drop old |
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|
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Package-Manager: portage-2.2.15 |
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Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> |
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|
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--- |
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sci-biology/emboss/ChangeLog | 3 + |
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sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild | 94 ------ |
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sci-biology/emboss/files/ax_lib_mysql.m4 | 147 ---------- |
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.../emboss/files/emboss-6.3.1_p4-r2_Makefile.patch | 47 --- |
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.../emboss-6.3.1_p4-r2_compilations-paths.patch | 315 --------------------- |
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.../emboss/files/emboss-6.3.1_p4-r2_libtool.patch | 18 -- |
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.../emboss/files/emboss-6.3.1_p4-r2_plcol.patch | 112 -------- |
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...mboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch | 13 - |
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sci-biology/emboss/files/emboss-README.Gentoo-2 | 34 --- |
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9 files changed, 3 insertions(+), 780 deletions(-) |
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|
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diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog |
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index a8d74bc..a6558c1 100644 |
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--- a/sci-biology/emboss/ChangeLog |
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+++ b/sci-biology/emboss/ChangeLog |
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@@ -2,6 +2,9 @@ |
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# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2011/03/09 16:29:05 jlec Exp $ |
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|
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+ 04 Feb 2015; Justin Lecher <jlec@g.o> -emboss-6.3.1_p4-r2.ebuild: |
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+ Drop old |
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+ |
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04 Feb 2015; Justin Lecher <jlec@g.o> metadata.xml: |
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Clean a bit, user readme.gentoo.eclass |
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|
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|
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diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild |
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deleted file mode 100644 |
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index 962d472..0000000 |
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--- a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild |
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+++ /dev/null |
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@@ -1,94 +0,0 @@ |
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-# Copyright 1999-2014 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Header: $ |
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- |
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-EAPI="4" |
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- |
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-inherit emboss eutils |
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- |
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-EBO_PATCH="4" |
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-EBOV=${PV/_p*} |
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- |
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-DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" |
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-SRC_URI=" |
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- ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz |
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- http://dev.gentoo.org/~jlec/distfiles/${PF}.patch.bz2" |
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-##[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" |
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-[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" |
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- |
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-KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" |
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-IUSE+=" minimal" |
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- |
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-RDEPEND+=" !sys-devel/cons" |
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-PDEPEND+=" |
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- !minimal? ( |
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- sci-biology/aaindex |
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- sci-biology/cutg |
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- sci-biology/prints |
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- sci-biology/prosite |
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- sci-biology/rebase |
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- sci-biology/transfac |
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- sci-libs/plplot |
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- )" |
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- |
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-S="${WORKDIR}"/EMBOSS-${EBOV} |
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- |
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-EBO_EXTRA_ECONF="--includedir=${EPREFIX}/usr/include/emboss" |
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- |
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-DOCS+=" FAQ THANKS" |
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- |
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-src_prepare() { |
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- [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch |
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- epatch "${WORKDIR}"/${PF}.patch |
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- epatch "${FILESDIR}/${PF}"_plcol.patch |
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- epatch "${FILESDIR}/${PF}"_compilations-paths.patch |
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- epatch "${FILESDIR}/${PF}"_rename_plwid_to_plwidth.patch |
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- # cp "${FILESDIR}"/ax_lib_mysql.m4 "${S}"/m4/mysql.m4 |
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- emboss_src_prepare |
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- autoreconf -vfi |
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- epatch "${FILESDIR}/${PF}"_libtool.patch |
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-} |
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- |
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-#src_compile() { |
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-# # epatch "${FILESDIR}/${PF}"_Makefile.patch |
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-# sed -i -e "s#GD_LIBS = .*#GD_LIBS =#" Makefile |
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-# sed -i -e "s#^LIBS = .*#LIBS =#" Makefile |
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-# sed -i -e "s#^PLPLOT_LIBS = .*#PLPLOT_LIBS =#" Makefile |
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-# sed -i -e "s#^libnucleus_la_LDFLAGS = .*#libnucleus_la_LDFLAGS = \$(LDFLAGS)#" Makefile |
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-#} |
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- |
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-src_install() { |
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- default |
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- |
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- sed -e "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \ |
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- dodoc README.Gentoo |
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- |
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- # Install env file for setting libplplot and acd files path. |
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- cat <<- EOF > 22emboss |
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- # ACD files location |
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- EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" |
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- EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" |
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- EOF |
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- doenvd 22emboss |
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- |
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- # Clashes #330507, resolved upstream |
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- mv "${ED}"/usr/bin/{digest,pepdigest} || die |
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- |
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- # Remove useless dummy files from the image. |
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- find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files." |
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- |
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- # Move the provided codon files to a different directory. This will avoid |
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- # user confusion and file collisions on case-insensitive file systems (see |
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- # bug #115446). This change is documented in "README.Gentoo". |
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- mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ |
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- die "Failed to move CODON directory." |
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- |
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- # Move the provided restriction enzyme prototypes file to a different name. |
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- # This avoids file collisions with versions of rebase that install their |
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- # own enzyme prototypes file (see bug #118832). |
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- mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ |
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- die "Failed to move enzyme equivalence file." |
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- |
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- # 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 |
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- # instead of /usr/share/EMBOSS/doc/html (which does not exist) |
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-} |
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|
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diff --git a/sci-biology/emboss/files/ax_lib_mysql.m4 b/sci-biology/emboss/files/ax_lib_mysql.m4 |
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deleted file mode 100644 |
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index e27d755..0000000 |
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--- a/sci-biology/emboss/files/ax_lib_mysql.m4 |
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+++ /dev/null |
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@@ -1,147 +0,0 @@ |
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-# =========================================================================== |
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-# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html |
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-# =========================================================================== |
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-# |
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-# SYNOPSIS |
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-# |
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-# AX_LIB_MYSQL([MINIMUM-VERSION]) |
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-# |
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-# DESCRIPTION |
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-# |
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-# This macro provides tests of availability of MySQL client library of |
158 |
-# particular version or newer. |
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-# |
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-# AX_LIB_MYSQL macro takes only one argument which is optional. If there |
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-# is no required version passed, then macro does not run version test. |
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-# |
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-# The --with-mysql option takes one of three possible values: |
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-# |
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-# no - do not check for MySQL client library |
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-# |
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-# yes - do check for MySQL library in standard locations (mysql_config |
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-# should be in the PATH) |
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-# |
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-# path - complete path to mysql_config utility, use this option if |
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-# mysql_config can't be found in the PATH |
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-# |
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-# This macro calls: |
174 |
-# |
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-# AC_SUBST(MYSQL_CFLAGS) |
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-# AC_SUBST(MYSQL_LDFLAGS) |
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-# AC_SUBST(MYSQL_VERSION) |
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-# |
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-# And sets: |
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-# |
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-# HAVE_MYSQL |
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-# |
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-# LICENSE |
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-# |
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-# Copyright (c) 2008 Mateusz Loskot <mateusz@××××××.net> |
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-# |
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-# Copying and distribution of this file, with or without modification, are |
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-# permitted in any medium without royalty provided the copyright notice |
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-# and this notice are preserved. This file is offered as-is, without any |
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-# warranty. |
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- |
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-#serial 12 |
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- |
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-AC_DEFUN([AX_LIB_MYSQL], |
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-[ |
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- AC_ARG_WITH([mysql], |
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- AS_HELP_STRING([--with-mysql=@<:@ARG@:>@], |
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- [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config] |
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- ), |
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- [ |
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- if test "$withval" = "no"; then |
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- want_mysql="no" |
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- elif test "$withval" = "yes"; then |
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- want_mysql="yes" |
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- else |
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- want_mysql="yes" |
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- MYSQL_CONFIG="$withval" |
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- fi |
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- ], |
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- [want_mysql="yes"] |
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- ) |
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- AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program]) |
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- |
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- MYSQL_CFLAGS="" |
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- MYSQL_LDFLAGS="" |
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- MYSQL_VERSION="" |
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- |
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- dnl |
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- dnl Check MySQL libraries |
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- dnl |
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- |
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- if test "$want_mysql" = "yes"; then |
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- |
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- if test -z "$MYSQL_CONFIG" ; then |
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- AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no]) |
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- fi |
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- |
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- if test "$MYSQL_CONFIG" != "no"; then |
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- MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`" |
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- MYSQL_LDFLAGS="`$MYSQL_CONFIG --libs`" |
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- |
232 |
- MYSQL_VERSION=`$MYSQL_CONFIG --version` |
233 |
- |
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- found_mysql="yes" |
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- else |
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- found_mysql="no" |
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- fi |
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- fi |
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- |
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- dnl |
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- dnl Check if required version of MySQL is available |
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- dnl |
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- |
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- |
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- mysql_version_req=ifelse([$1], [], [], [$1]) |
246 |
- |
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- if test "$found_mysql" = "yes" -a -n "$mysql_version_req"; then |
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- |
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- AC_MSG_CHECKING([if MySQL version is >= $mysql_version_req]) |
250 |
- |
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- dnl Decompose required version string of MySQL |
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- dnl and calculate its number representation |
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- mysql_version_req_major=`expr $mysql_version_req : '\([[0-9]]*\)'` |
254 |
- mysql_version_req_minor=`expr $mysql_version_req : '[[0-9]]*\.\([[0-9]]*\)'` |
255 |
- mysql_version_req_micro=`expr $mysql_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'` |
256 |
- if test "x$mysql_version_req_micro" = "x"; then |
257 |
- mysql_version_req_micro="0" |
258 |
- fi |
259 |
- |
260 |
- mysql_version_req_number=`expr $mysql_version_req_major \* 1000000 \ |
261 |
- \+ $mysql_version_req_minor \* 1000 \ |
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- \+ $mysql_version_req_micro` |
263 |
- |
264 |
- dnl Decompose version string of installed MySQL |
265 |
- dnl and calculate its number representation |
266 |
- mysql_version_major=`expr $MYSQL_VERSION : '\([[0-9]]*\)'` |
267 |
- mysql_version_minor=`expr $MYSQL_VERSION : '[[0-9]]*\.\([[0-9]]*\)'` |
268 |
- mysql_version_micro=`expr $MYSQL_VERSION : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'` |
269 |
- if test "x$mysql_version_micro" = "x"; then |
270 |
- mysql_version_micro="0" |
271 |
- fi |
272 |
- |
273 |
- mysql_version_number=`expr $mysql_version_major \* 1000000 \ |
274 |
- \+ $mysql_version_minor \* 1000 \ |
275 |
- \+ $mysql_version_micro` |
276 |
- |
277 |
- mysql_version_check=`expr $mysql_version_number \>\= $mysql_version_req_number` |
278 |
- if test "$mysql_version_check" = "1"; then |
279 |
- AC_MSG_RESULT([yes]) |
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- else |
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- AC_MSG_RESULT([no]) |
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- fi |
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- fi |
284 |
- |
285 |
- if test "$found_mysql" = "yes" ; then |
286 |
- AC_DEFINE([HAVE_MYSQL], [1], |
287 |
- [Define to 1 if MySQL libraries are available]) |
288 |
- fi |
289 |
- |
290 |
- AC_SUBST([MYSQL_VERSION]) |
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- AC_SUBST([MYSQL_CFLAGS]) |
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- AC_SUBST([MYSQL_LDFLAGS]) |
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-]) |
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|
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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 |
296 |
deleted file mode 100644 |
297 |
index 419369e..0000000 |
298 |
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch |
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+++ /dev/null |
300 |
@@ -1,47 +0,0 @@ |
301 |
---- EMBOSS-6.3.1/nucleus/Makefile 2013-09-11 14:50:25.140219756 +0200 |
302 |
-+++ nucleus/Makefile 2013-09-11 14:52:00.920220006 +0200 |
303 |
-@@ -165,7 +165,7 @@ |
304 |
- ESYSTEMLIBS = |
305 |
- EXEEXT = |
306 |
- FGREP = /bin/grep -F |
307 |
--GD_LIBS = -ljpeg -lfontconfig -lfreetype -lz -lm -lgd |
308 |
-+GD_LIBS = |
309 |
- GREP = /bin/grep |
310 |
- HAVE_MEMMOVE = |
311 |
- HAVE_STRERROR = |
312 |
-@@ -180,7 +180,7 @@ |
313 |
- LD = /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 |
314 |
- LDFLAGS = -Wl,--as-needed |
315 |
- LIBOBJS = |
316 |
--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 |
317 |
-+LIBS = |
318 |
- LIBTOOL = $(SHELL) $(top_builddir)/libtool |
319 |
- LIPO = |
320 |
- LN_S = ln -s |
321 |
-@@ -219,7 +219,7 @@ |
322 |
- # zap the crap |
323 |
- PLPLOT_CFLAGS = |
324 |
- PLPLOT_CPPFLAGS = |
325 |
--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 |
326 |
-+PLPLOT_LIBS = |
327 |
- PNG_CFLAGS = -I/usr/include/libpng16 |
328 |
- PNG_LIBS = -lpng16 |
329 |
- POSIX_MALLOC_THRESHOLD = -DPOSIX_MALLOC_THRESHOLD=10 |
330 |
-@@ -336,7 +336,7 @@ |
331 |
- VERS_INF = -version-info 6:3:0 |
332 |
- LINKFLAGS = $(VERS_INF) |
333 |
- #LINKFLAGS = $(VERS_INF) $(CYGWIN_LDFLAGS) $(CYGWIN_LIBS) |
334 |
--libnucleus_la_LDFLAGS = $(LINKFLAGS) |
335 |
-+libnucleus_la_LDFLAGS = $(LDFLAGS) |
336 |
- libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd |
337 |
- all: all-am |
338 |
- |
339 |
-@@ -407,7 +407,7 @@ |
340 |
- rm -f $${locs}; \ |
341 |
- } |
342 |
- libnucleus.la: $(libnucleus_la_OBJECTS) $(libnucleus_la_DEPENDENCIES) $(EXTRA_libnucleus_la_DEPENDENCIES) |
343 |
-- $(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(libnucleus_la_LIBADD) $(LIBS) |
344 |
-+ $(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(LIBS) |
345 |
- |
346 |
- mostlyclean-compile: |
347 |
- -rm -f *.$(OBJEXT) |
348 |
|
349 |
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 |
350 |
deleted file mode 100644 |
351 |
index 8f87ef9..0000000 |
352 |
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch |
353 |
+++ /dev/null |
354 |
@@ -1,315 +0,0 @@ |
355 |
---- EMBOSS-6.3.1/configure.in 2013-09-11 03:55:15.510117066 +0200 |
356 |
-+++ configure.in 2013-09-11 03:48:10.410115955 +0200 |
357 |
-@@ -449,7 +447,8 @@ |
358 |
- if test "`uname -a | grep Darwin`"; then |
359 |
- OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` |
360 |
- if test ${OSXX} '>' '10.4'; then |
361 |
-- CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" |
362 |
-+ CPPFLAGS="$CPPFLAGS -I/usr/X11/include" |
363 |
-+ LDFLAGS="$LDFLAGS -L/usr/X11/lib" |
364 |
- fi |
365 |
- fi |
366 |
- fi |
367 |
-@@ -461,7 +460,7 @@ |
368 |
- AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes") |
369 |
- AC_SUBST(ESYSTEMLIBS) |
370 |
- AC_SUBST(DEFINE_USE_SYSTEM_PCRE) |
371 |
--AC_SUBST(PLPLOT_CFLAGS) |
372 |
-+AC_SUBST(PLPLOT_CPPFLAGS) |
373 |
- AC_SUBST(PLPLOT_LIBS) |
374 |
- |
375 |
- |
376 |
---- EMBOSS-6.3.1/ajax/graphics/Makefile.am 2013-09-11 03:27:30.110112715 +0200 |
377 |
-+++ ajax/graphics/Makefile.am 2013-09-11 03:58:50.860117628 +0200 |
378 |
-@@ -19,7 +19,7 @@ |
379 |
- |
380 |
- |
381 |
- INCLUDES = \ |
382 |
--$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core |
383 |
-+$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core -I$(top_srcdir)/plplot |
384 |
- |
385 |
- AJAXGSRC = ajgraph.c ajhist.c |
386 |
- |
387 |
---- EMBOSS-6.3.1/ajax/acd/Makefile.am 2013-09-11 03:27:30.110112715 +0200 |
388 |
-+++ ajax/acd/Makefile.am 2013-09-11 03:59:10.310117679 +0200 |
389 |
-@@ -24,7 +24,8 @@ |
390 |
- -I$(top_srcdir)/ajax/core \ |
391 |
- -I$(top_srcdir)/ajax/graphics \ |
392 |
- -I$(top_srcdir)/ajax/ensembl \ |
393 |
---I$(top_srcdir)/ajax/ajaxdb |
394 |
-+-I$(top_srcdir)/ajax/ajaxdb \ |
395 |
-+-I$(top_srcdir)/plplot |
396 |
- |
397 |
- ACDSRC = ajacd.c |
398 |
- |
399 |
---- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 03:27:30.110112715 +0200 |
400 |
-+++ nucleus/Makefile.am 2013-09-11 03:59:28.630117727 +0200 |
401 |
-@@ -32,7 +32,7 @@ |
402 |
- $(EXTRA_INCLUDES) \ |
403 |
- -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ |
404 |
- -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ |
405 |
-- -I$(top_srcdir)/ajax/acd |
406 |
-+ -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot |
407 |
- |
408 |
- NUCLSRC = embaln.c embcom.c embcons.c embdata.c embdbi.c embdmx.c \ |
409 |
- embdomain.c embest.c embexit.c embgroup.c embiep.c embindex.c \ |
410 |
---- EMBOSS-6.3.1/emboss/Makefile.am 2013-09-11 03:27:30.110112715 +0200 |
411 |
-+++ emboss/Makefile.am 2013-09-11 03:59:46.340117773 +0200 |
412 |
-@@ -89,7 +89,7 @@ |
413 |
- $(EXTRA_INCLUDES) \ |
414 |
- -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ |
415 |
- -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ |
416 |
-- -I$(top_srcdir)/ajax/acd |
417 |
-+ -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot |
418 |
- |
419 |
- |
420 |
- aaindexextract_SOURCES = aaindexextract.c |
421 |
---- EMBOSS-6.3.1/Makefile.am 2013-09-11 04:19:01.770120791 +0200 |
422 |
-+++ Makefile.am 2013-09-11 04:19:18.460120835 +0200 |
423 |
-@@ -13,8 +13,8 @@ |
424 |
- JEMBOSS_DIR = jemboss |
425 |
- endif |
426 |
- |
427 |
--SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) |
428 |
--DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) |
429 |
-+SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR) |
430 |
-+DIST_SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR) |
431 |
- |
432 |
- # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\" |
433 |
- |
434 |
---- EMBOSS-6.3.1/plplot/Makefile.am 2013-09-11 09:34:44.620170277 +0200 |
435 |
-+++ plplot/Makefile.am 2013-09-11 09:35:35.820170411 +0200 |
436 |
-@@ -10,26 +10,27 @@ |
437 |
- if AMPNG |
438 |
- |
439 |
- if AMPDF |
440 |
--TESTPDF_CFLAGS = -Wl,-G -lhpdf |
441 |
-+TESTPDF_LIBS = -Wl,-G -lhpdf |
442 |
- else |
443 |
--TESTPDF_CFLAGS = -Wl,-G |
444 |
-+TESTPDF_LIBS = -Wl,-G |
445 |
- endif |
446 |
- |
447 |
--TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lgd -lpng -lz -lX11 -lm |
448 |
-+TESTPNG_LIBS = $(TESTPDF_LIBS) -lgd -lpng -lz -lX11 -lm |
449 |
- else |
450 |
--TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lX11 |
451 |
-+TESTPNG_LIBS = $(TESTPDF_LIBS) -lX11 |
452 |
- endif |
453 |
- endif |
454 |
- endif |
455 |
- |
456 |
--AM_CFLAGS = $(TESTPNG_CFLAGS) |
457 |
-+AM_LIBS = $(TESTPNG_LIBS) |
458 |
- |
459 |
- if ISCYGWIN |
460 |
- CYGWIN_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import |
461 |
- CYGWIN_LIBS = -lX11 -lgd -lpng -lz |
462 |
- endif |
463 |
- |
464 |
--INCLUDES = $(X_CFLAGS) -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\" |
465 |
-+INCLUDES = -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\" |
466 |
-+LIBS = $(AM_LIBS) |
467 |
- |
468 |
- PLPLOTSRC = pdfutils.c plargs.c plbox.c plcont.c plcore.c \ |
469 |
- plctrl.c plcvt.c pldtik.c plfill.c plhist.c plline.c plmap.c \ |
470 |
---- EMBOSS-6.3.1/m4/pngdriver.m4 2013-09-11 10:39:07.680180369 +0200 |
471 |
-+++ m4/pngdriver.m4 2013-09-11 10:44:16.000181174 +0200 |
472 |
-@@ -63,7 +63,8 @@ |
473 |
- if test "`uname`" = "SunOS"; then |
474 |
- AC_CHECK_LIB(iconv, libiconv_close, ICCHECK=1, ICCHECK=0, -L${ALT_HOME}/lib -liconv) |
475 |
- if test $ICCHECK = "1" ; then |
476 |
-- LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib -liconv" |
477 |
-+ LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib" |
478 |
-+ LIBS="${LIBS} -liconv" |
479 |
- fi |
480 |
- LDFLAGS="$LDFLAGS -R$ALT_HOME/lib" |
481 |
- fi |
482 |
---- EMBOSS-6.3.1/m4/java.m4 2013-09-11 10:39:03.490180358 +0200 |
483 |
-+++ m4/java.m4 2013-09-11 10:46:08.240181467 +0200 |
484 |
-@@ -180,7 +180,7 @@ |
485 |
- |
486 |
- if test "$withval" = "yes" ; then |
487 |
- CFLAGS="$CFLAGS -D_REENTRANT" |
488 |
-- LDFLAGS="$LDFLAGS -lpthread" |
489 |
-+ LDFLAGS="$LDFLAGS" |
490 |
- LIBS="$LIBS -lpthread" |
491 |
- fi |
492 |
- |
493 |
-@@ -192,38 +192,38 @@ |
494 |
- |
495 |
- if test "$withval" = "linux" ; then |
496 |
- CFLAGS="$CFLAGS -D_REENTRANT" |
497 |
-- LDFLAGS="$LDFLAGS -lpthread" |
498 |
-+ LDFLAGS="$LDFLAGS" |
499 |
- LIBS="$LIBS -lpthread" |
500 |
- fi |
501 |
- |
502 |
- if test "$withval" = "solaris" ; then |
503 |
- CFLAGS="$CFLAGS -D_POSIX_C_SOURCE=199506L" |
504 |
-- LDFLAGS="$LDFLAGS -lpthread" |
505 |
-+ LDFLAGS="$LDFLAGS" |
506 |
- LIBS="$LIBS -lpthread" |
507 |
- fi |
508 |
- if test "$withval" = "macos" ; then |
509 |
- CFLAGS="$CFLAGS" |
510 |
-- LDFLAGS="$LDFLAGS -lpthread" |
511 |
-+ LDFLAGS="$LDFLAGS" |
512 |
- LIBS="$LIBS -lpthread" |
513 |
- fi |
514 |
- if test "$withval" = "hpux" ; then |
515 |
- CFLAGS="$CFLAGS -Ae +z -DNATIVE -D_POSIX_C_SOURCE=199506L" |
516 |
-- LDFLAGS="$LDFLAGS -lpthread" |
517 |
-+ LDFLAGS="$LDFLAGS" |
518 |
- LIBS="$LIBS -lpthread" |
519 |
- fi |
520 |
- if test "$withval" = "irix" ; then |
521 |
- CFLAGS="$CFLAGS" |
522 |
-- LDFLAGS="$LDFLAGS -lpthread" |
523 |
-+ LDFLAGS="$LDFLAGS" |
524 |
- LIBS="$LIBS -lpthread" |
525 |
- fi |
526 |
- if test "$withval" = "aix" ; then |
527 |
- CFLAGS="$CFLAGS -D_REENTRANT" |
528 |
-- LDFLAGS="$LDFLAGS -lpthread" |
529 |
-+ LDFLAGS="$LDFLAGS" |
530 |
- LIBS="$LIBS -lpthread" |
531 |
- fi |
532 |
- if test "$withval" = "osf" ; then |
533 |
- CFLAGS="$CFLAGS -D_REENTRANT -D_OSF_SOURCE" |
534 |
-- LDFLAGS="$LDFLAGS -lpthread" |
535 |
-+ LDFLAGS="$LDFLAGS" |
536 |
- LIBS="$LIBS -lpthread" |
537 |
- fi |
538 |
- else |
539 |
---- EMBOSS-6.3.1/m4/mysql.m4 2013-09-11 11:03:07.160184129 +0200 |
540 |
-+++ m4/mysql.m4 2013-09-11 11:04:39.440184370 +0200 |
541 |
-@@ -85,7 +85,6 @@ |
542 |
- AC_MSG_CHECKING([for MySQL libraries]) |
543 |
- |
544 |
- dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`" |
545 |
-- MYSQL_CFLAGS="`$MYSQL_CONFIG --include`" |
546 |
- MYSQL_LIBS="`$MYSQL_CONFIG --libs`" |
547 |
- |
548 |
- MYSQL_VERSION=`$MYSQL_CONFIG --version` |
549 |
---- EMBOSS-6.3.1/m4/mysql.m4 2013-09-11 11:38:09.330189621 +0200 |
550 |
-+++ m4/mysql.m4 2013-09-11 11:41:02.170190072 +0200 |
551 |
-@@ -170,6 +170,4 @@ |
552 |
- fi |
553 |
- |
554 |
- AC_SUBST([MYSQL_VERSION]) |
555 |
-- AC_SUBST([MYSQL_CFLAGS]) |
556 |
-- AC_SUBST([MYSQL_LIBS]) |
557 |
- ]) |
558 |
---- EMBOSS-6.3.1/configure.in 2013-09-11 12:23:17.330196695 +0200 |
559 |
-+++ configure.in 2013-09-11 12:23:21.480196706 +0200 |
560 |
-@@ -8,6 +8,8 @@ |
561 |
- AC_INIT(ajax/core/ajmath.c) |
562 |
- AM_INIT_AUTOMAKE([EMBOSS],[6.3.1]) |
563 |
- |
564 |
-+AC_CONFIG_MACRO_DIR([m4]) |
565 |
-+ |
566 |
- # Make sure CFLAGS is defined to stop LT_INIT adding -g |
567 |
- CFLAGS="$CFLAGS " |
568 |
- |
569 |
---- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 12:33:14.260198254 +0200 |
570 |
-+++ nucleus/Makefile.am 2013-09-11 12:33:16.650198260 +0200 |
571 |
-@@ -58,4 +58,4 @@ |
572 |
- endif |
573 |
- |
574 |
- libnucleus_la_LDFLAGS = $(LINKFLAGS) |
575 |
--libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la |
576 |
-+libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd |
577 |
---- EMBOSS-6.3.1/ajax/ensembl/Makefile.am 2013-09-11 12:41:06.340199487 +0200 |
578 |
-+++ ajax/ensembl/Makefile.am 2013-09-11 12:41:40.460199577 +0200 |
579 |
-@@ -56,5 +56,5 @@ |
580 |
- LINKFLAGS = $(VERS_INF) |
581 |
- endif |
582 |
- |
583 |
--libensembl_la_LDFLAGS = $(LINKFLAGS) |
584 |
--libensembl_la_LIBADD = ../core/libajax.la |
585 |
-+libensembl_la_LDFLAGS = $(LINKFLAGS) -L../core |
586 |
-+libensembl_la_LIBADD = -lajax |
587 |
---- EMBOSS-6.3.1/ajax/graphics/Makefile.am 2013-09-11 12:42:17.730199674 +0200 |
588 |
-+++ ajax/graphics/Makefile.am 2013-09-11 12:42:47.000199750 +0200 |
589 |
-@@ -35,5 +35,5 @@ |
590 |
- LINKFLAGS = $(VERS_INF) |
591 |
- endif |
592 |
- |
593 |
--libajaxg_la_LDFLAGS = $(LINKFLAGS) |
594 |
--libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS) |
595 |
-+libajaxg_la_LDFLAGS = $(LINKFLAGS) -L../core/ |
596 |
-+libajaxg_la_LIBADD = -lajax $(EXTRA_LIBS) |
597 |
---- EMBOSS-6.3.1/ajax/acd/Makefile.am 2013-09-11 12:43:11.660199815 +0200 |
598 |
-+++ ajax/acd/Makefile.am 2013-09-11 12:44:01.520199945 +0200 |
599 |
-@@ -41,5 +41,5 @@ |
600 |
- LINKFLAGS = $(VERS_INF) |
601 |
- endif |
602 |
- |
603 |
--libacd_la_LDFLAGS = $(LINKFLAGS) |
604 |
--libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la |
605 |
-+libacd_la_LDFLAGS = $(LINKFLAGS) -L../core -L../graphics -L../ajaxdb |
606 |
-+libacd_la_LIBADD = -lajax -lajaxg -lajaxdb |
607 |
---- EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am 2013-09-11 12:44:10.980199970 +0200 |
608 |
-+++ ajax/ajaxdb/Makefile.am 2013-09-11 12:44:40.040200046 +0200 |
609 |
-@@ -37,5 +37,5 @@ |
610 |
- LINKFLAGS = $(VERS_INF) |
611 |
- endif |
612 |
- |
613 |
--libajaxdb_la_LDFLAGS = $(LINKFLAGS) |
614 |
--libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la |
615 |
-+libajaxdb_la_LDFLAGS = $(LINKFLAGS) -L../core -L../ensembl |
616 |
-+libajaxdb_la_LIBADD = -lajax -lensembl |
617 |
---- EMBOSS-6.3.1/configure.in 2013-09-11 13:24:39.720206315 +0200 |
618 |
-+++ configure.in 2013-09-11 13:24:58.610206364 +0200 |
619 |
-@@ -319,10 +319,8 @@ |
620 |
- AX_LIB_MYSQL |
621 |
- AX_LIB_POSTGRESQL |
622 |
- |
623 |
--CFLAGS="$CFLAGS $MYSQL_CFLAGS" |
624 |
- LIBS="${MYSQL_LIBS} ${LIBS}" |
625 |
- |
626 |
--CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS" |
627 |
- LIBS="$POSTGRESQL_LIBS $LIBS" |
628 |
- |
629 |
- |
630 |
---- EMBOSS-6.3.1/ajax/core/Makefile.am 2013-09-11 13:47:36.790209912 +0200 |
631 |
-+++ ajax/core/Makefile.am 2013-09-11 13:47:40.550209922 +0200 |
632 |
-@@ -65,5 +65,5 @@ |
633 |
- LINKFLAGS = $(VERS_INF) |
634 |
- endif |
635 |
- |
636 |
--libajax_la_LDFLAGS = $(LINKFLAGS) |
637 |
-+libajax_la_LDFLAGS = |
638 |
- libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LIBS) $(MYSQL_LIBS) |
639 |
---- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 14:03:21.960212381 +0200 |
640 |
-+++ nucleus/Makefile.am 2013-09-11 14:03:58.910212478 +0200 |
641 |
-@@ -22,11 +22,14 @@ |
642 |
- EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ |
643 |
- -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre |
644 |
- else |
645 |
--EXTRA_INCLUDES = $(PLPLOT_CFLAGS) |
646 |
-+EXTRA_INCLUDES = |
647 |
- endif |
648 |
- endif |
649 |
- |
650 |
- |
651 |
-+# zap the crap |
652 |
-+PLPLOT_CFLAGS = |
653 |
-+ |
654 |
- INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \ |
655 |
- -I$(top_srcdir)/ajax \ |
656 |
- $(EXTRA_INCLUDES) \ |
657 |
---- EMBOSS-6.3.1/emboss/Makefile.am 2013-09-11 14:23:50.570215591 +0200 |
658 |
-+++ emboss/Makefile.am 2013-09-11 14:24:24.950215680 +0200 |
659 |
-@@ -328,9 +328,7 @@ |
660 |
- |
661 |
- LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \ |
662 |
- ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \ |
663 |
-- ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \ |
664 |
-- $(EXTRA_LDS) \ |
665 |
-- $(XLIB) |
666 |
-+ ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la |
667 |
- |
668 |
- pkgdata_DATA = emboss.default.template |
669 |
- pkgdatadir=$(prefix)/share/$(PACKAGE) |
670 |
|
671 |
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 |
672 |
deleted file mode 100644 |
673 |
index ad358e1..0000000 |
674 |
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch |
675 |
+++ /dev/null |
676 |
@@ -1,18 +0,0 @@ |
677 |
---- EMBOSS-6.3.1/m4/libtool.m4 2013-09-11 12:03:45.180193633 +0200 |
678 |
-+++ m4/libtool.m4 2013-09-11 12:04:19.280193722 +0200 |
679 |
-@@ -4768,13 +4768,13 @@ |
680 |
- *Sun\ F*) # Sun Fortran 8.3 |
681 |
- tmp_sharedflag='-G' ;; |
682 |
- esac |
683 |
-- _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' |
684 |
-+ _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname -Wl,--as-needed -o $lib' |
685 |
- |
686 |
- if test "x$supports_anon_versioning" = xyes; then |
687 |
- _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~ |
688 |
- cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ |
689 |
- echo "local: *; };" >> $output_objdir/$libname.ver~ |
690 |
-- $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' |
691 |
-+ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -Wl,--as-needed -o $lib' |
692 |
- fi |
693 |
- |
694 |
- case $cc_basename in |
695 |
|
696 |
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 |
697 |
deleted file mode 100644 |
698 |
index 0f5e592..0000000 |
699 |
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch |
700 |
+++ /dev/null |
701 |
@@ -1,112 +0,0 @@ |
702 |
---- EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2012-07-19 23:29:05.000000000 +0200 |
703 |
-+++ /tmp/ajgraph.c 2012-07-19 23:25:00.000000000 +0200 |
704 |
-@@ -1645,14 +1645,14 @@ |
705 |
- ** @return [void] |
706 |
- ** @@ |
707 |
- ******************************************************************************/ |
708 |
- |
709 |
- static void GraphSetPen(ajint colour) |
710 |
- { |
711 |
-- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]); |
712 |
-- plcol((PLINT)colour); |
713 |
-+ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]); |
714 |
-+ plcol0((PLINT)colour); |
715 |
- |
716 |
- return; |
717 |
- } |
718 |
- |
719 |
- |
720 |
- |
721 |
---- EMBOSS-6.3.1/plplot/plcore.c 2007-10-24 15:14:43.000000000 +0200 |
722 |
-+++ /tmp/plcore.c 2012-07-19 23:25:00.000000000 +0200 |
723 |
-@@ -1709,13 +1709,13 @@ |
724 |
- if (plsc->zdigmax == 0) |
725 |
- plsc->zdigmax = 3; |
726 |
- |
727 |
- /* Switch to graphics mode and set color and arrow style*/ |
728 |
- |
729 |
- plgra(); |
730 |
-- plcol(1); |
731 |
-+ plcol0(1); |
732 |
- |
733 |
- plstyl(0, &mk, &sp); |
734 |
- plpat(1, &inc, &del); |
735 |
- |
736 |
- plsvect(def_arrow_x, def_arrow_y, 6, 0); |
737 |
- |
738 |
---- EMBOSS-6.3.1/plplot/plstripc.c 2007-05-08 11:09:37.000000000 +0200 |
739 |
-+++ /tmp/plstripc.c 2012-07-19 23:25:00.000000000 +0200 |
740 |
-@@ -153,17 +153,17 @@ |
741 |
- |
742 |
- plgchr(&sc, &dy); |
743 |
- sc = dy = dy/100; |
744 |
- plwind(-0.01, 1.01, -0.01, 1.01); |
745 |
- for (i=0; i<PEN; i++) { |
746 |
- if (mystripc->npts[i] || first) { |
747 |
-- plcol(mystripc->colline[i]); |
748 |
-+ plcol0(mystripc->colline[i]); |
749 |
- pllsty(mystripc->styline[i]); |
750 |
- pljoin(mystripc->xlpos, mystripc->ylpos - sc, |
751 |
- mystripc->xlpos + 0.1, mystripc->ylpos - sc); |
752 |
-- plcol(mystripc->collab); |
753 |
-+ plcol0(mystripc->collab); |
754 |
- plptex(mystripc->xlpos + 0.11, mystripc->ylpos - sc, |
755 |
- 0., 0., 0, mystripc->legline[i]); |
756 |
- sc += dy; |
757 |
- } |
758 |
- } |
759 |
- plwind(mystripc->xmin, mystripc->xmax, mystripc->ymin, mystripc->ymax); |
760 |
-@@ -184,34 +184,34 @@ |
761 |
- PLFLT x[]={0.,1.,1.,0.}, y[]={0.,0.,1.,1.}; |
762 |
- |
763 |
- /* Set up window */ |
764 |
- |
765 |
- plvpor(0,1,0,1); |
766 |
- plwind(0,1,0,1); |
767 |
-- plcol(0);plpsty(0); |
768 |
-+ plcol0(0);plpsty(0); |
769 |
- plfill(4, &x[0], &y[0]); |
770 |
- plvsta(); |
771 |
- |
772 |
- /* Draw box and same window dimensions */ |
773 |
- mystrip->wxmin=mystrip->xmin; |
774 |
- mystrip->wxmax=mystrip->xmax; |
775 |
- mystrip->wymin=mystrip->ymin; |
776 |
- mystrip->wymax=mystrip->ymax; /* FIXME - can exist some redundancy here */ |
777 |
- |
778 |
- plwind(mystrip->xmin, mystrip->xmax, mystrip->ymin, mystrip->ymax); |
779 |
- |
780 |
- pllsty(1); |
781 |
-- plcol(mystrip->colbox); |
782 |
-+ plcol0(mystrip->colbox); |
783 |
- plbox(mystrip->xspec, 0.0, 0, mystrip->yspec, 0.0, 0); |
784 |
- |
785 |
-- plcol(mystrip->collab); |
786 |
-+ plcol0(mystrip->collab); |
787 |
- pllab(mystrip->labx, mystrip->laby, mystrip->labtop); |
788 |
- |
789 |
- for (i=0; i<PEN; i++) { |
790 |
- if (mystrip->npts[i] > 0) { |
791 |
-- plcol(mystrip->colline[i]);pllsty(mystrip->styline[i]); |
792 |
-+ plcol0(mystrip->colline[i]);pllsty(mystrip->styline[i]); |
793 |
- plline(mystrip->npts[i], mystrip->x[i], mystrip->y[i]); |
794 |
- } |
795 |
- } |
796 |
- |
797 |
- plstrip_legend(mystrip,0); |
798 |
- } |
799 |
-@@ -269,13 +269,13 @@ |
800 |
- if (stripc->xmax - stripc->xmin < stripc->xlen) { |
801 |
- if( yasc == 0) { |
802 |
- |
803 |
- /* If user has changed subwindow, make shure we have the correct one */ |
804 |
- plvsta(); |
805 |
- plwind(stripc->wxmin, stripc->wxmax, stripc->wymin, stripc->wymax); /* FIXME - can exist some redundancy here */ |
806 |
-- plcol(stripc->colline[p]); pllsty(stripc->styline[p]); |
807 |
-+ plcol0(stripc->colline[p]); pllsty(stripc->styline[p]); |
808 |
- if ((stripc->npts[p]-2) < 0) |
809 |
- plP_movwor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]); |
810 |
- else |
811 |
- plP_movwor(stripc->x[p][stripc->npts[p]-2], stripc->y[p][stripc->npts[p]-2]); |
812 |
- plP_drawor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]); |
813 |
- plflush(); |
814 |
|
815 |
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 |
816 |
deleted file mode 100644 |
817 |
index e66a696..0000000 |
818 |
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch |
819 |
+++ /dev/null |
820 |
@@ -1,13 +0,0 @@ |
821 |
---- EMBOSS-6.3.1/ajax/graphics/ajgraph.c.ori 2014-07-04 18:25:18.000000000 +0200 |
822 |
-+++ EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2014-07-04 18:25:32.000000000 +0200 |
823 |
-@@ -1329,8 +1329,8 @@ |
824 |
- |
825 |
- void ajGraphicsSetPenwidth(float penwidth) |
826 |
- { |
827 |
-- ajDebug("=g= plwid(%.2f) [width]\n", penwidth); |
828 |
-- plwid((PLINT)penwidth); |
829 |
-+ ajDebug("=g= plwidth(%.2f) [width]\n", penwidth); |
830 |
-+ plwidth((PLINT)penwidth); |
831 |
- |
832 |
- return; |
833 |
- } |
834 |
|
835 |
diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-2 b/sci-biology/emboss/files/emboss-README.Gentoo-2 |
836 |
deleted file mode 100644 |
837 |
index 72fa366..0000000 |
838 |
--- a/sci-biology/emboss/files/emboss-README.Gentoo-2 |
839 |
+++ /dev/null |
840 |
@@ -1,34 +0,0 @@ |
841 |
-Administrating EMBOSS on Gentoo systems |
842 |
-======================================= |
843 |
- |
844 |
- |
845 |
-Codon data files location |
846 |
-------------------------- |
847 |
- |
848 |
-The codon data files that are distributed with EMBOSS are installed in the |
849 |
-``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual |
850 |
-``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between |
851 |
-these codon files and those installed with the CUTG database. The names of |
852 |
-these files sometimes vary only by their case. Having both sets of files in |
853 |
-the same directory is also impossible on systems such as MacOSX, where the |
854 |
-root filesystem is case insensitive. If you do not have the CUTG database |
855 |
-installed and want to use the codon files distributed with EMBOSS, you can |
856 |
-symlink the ``CODONS.orig`` directory to ``CODONS``:: |
857 |
- |
858 |
- # cd EPREFIX/usr/share/EMBOSS/data |
859 |
- # ln -s CODONS.orig CODONS |
860 |
- |
861 |
- |
862 |
-Restriction enzymes equivalence file location |
863 |
---------------------------------------------- |
864 |
- |
865 |
-The restriction enzymes equivalence file distributed with EMBOSS is installed |
866 |
-as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual |
867 |
-``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file |
868 |
-collision with the equivalence file provided by the Rebase database. If you do |
869 |
-not have the Rebase database installed and want to use the equivalence file |
870 |
-distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to |
871 |
-``embossre.equ``:: |
872 |
- |
873 |
- # cd EPREFIX/usr/share/EMBOSS/data |
874 |
- # ln -s embossre.equ.orig embossre.equ |