* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/
@ 2011-03-10 19:00 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2011-03-10 19:00 UTC (permalink / raw
To: gentoo-commits
commit: de199f658e982402a3512f235b6cbf89034c9e07
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 10 11:24:09 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 10 11:24:09 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de199f65
Move to new embassy-ng.eclass
(Portage version: 2.2.0_alpha26/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 6 ++
sci-biology/emboss/emboss-6.3.1_p4.ebuild | 74 ++---------------------------
2 files changed, 10 insertions(+), 70 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 5d6f872..07931b5 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,12 @@
# 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> emboss-6.3.1_p4.ebuild:
+ Move to new embassy-ng.eclass
+
+ 09 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild:
+ Move to new embassy-ng.eclass
+
09 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild:
EAPI=4 takes three arguments on use_with
diff --git a/sci-biology/emboss/emboss-6.3.1_p4.ebuild b/sci-biology/emboss/emboss-6.3.1_p4.ebuild
index e235c73..d164460 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4.ebuild
@@ -2,82 +2,16 @@
# 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"
+EBO_PATCH="4"
+EBOV="${PV/_p${EBO_PATCH}}"
-inherit autotools eutils
+inherit embassy-ng
-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."
+ embassy-ng_src_install
- dodoc AUTHORS ChangeLog FAQ NEWS README THANKS
sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
dodoc README.Gentoo
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/
@ 2011-03-10 19:00 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2011-03-10 19:00 UTC (permalink / raw
To: gentoo-commits
commit: 14efef1e5b752c4db2299c75526ecdb310c8d2d5
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 10 11:25:14 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 10 11:25:14 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=14efef1e
Removed largefile from local USE description
(Portage version: 2.2.0_alpha26/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 3 +++
sci-biology/emboss/metadata.xml | 3 ---
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 07931b5..29ec8c8 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 $
+ 10 Mar 2011; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ Removed largefile from local USE description
+
10 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild:
Move to new embassy-ng.eclass
diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml
index 747e4ab..b85761d 100644
--- a/sci-biology/emboss/metadata.xml
+++ b/sci-biology/emboss/metadata.xml
@@ -15,7 +15,4 @@
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] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/
@ 2011-03-10 19:00 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2011-03-10 19:00 UTC (permalink / raw
To: gentoo-commits
commit: ce61f2105cdccb307b39948b18f5bc8e27e3b049
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 10 17:46:26 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 10 17:46:26 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ce61f210
Move away from embass-ng_src_install
(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/emboss-6.3.1_p4.ebuild | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/sci-biology/emboss/emboss-6.3.1_p4.ebuild b/sci-biology/emboss/emboss-6.3.1_p4.ebuild
index d164460..c58dc29 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4.ebuild
@@ -10,7 +10,7 @@ inherit embassy-ng
KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
src_install() {
- embassy-ng_src_install
+ default
sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
dodoc README.Gentoo
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/
@ 2011-03-14 9:54 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2011-03-14 9:54 UTC (permalink / raw
To: gentoo-commits
commit: f50dfab518468be47b2498a518f67bbb7f1a9055
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 14 09:30:07 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar 14 09:30:07 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f50dfab5
Ebov not needed to be set anymore
(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 3 +++
sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 1 -
2 files changed, 3 insertions(+), 1 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 6cb9905..b43a3f4 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 $
+ 14 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
+ Ebov not needed to be set anymore
+
*emboss-6.3.1_p4-r1 (11 Mar 2011)
11 Mar 2011; Justin Lecher <jlec@gentoo.org> -emboss-6.3.1_p4.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 64fbd39..e813f42 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
@@ -3,7 +3,6 @@
# $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"
-EBOV="${PV/_p${EBO_PATCH}}"
EBO_ECONF="--includedir=${EPREFIX}/usr/include/emboss"
inherit embassy-ng
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/
@ 2011-03-15 7:16 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2011-03-15 7:16 UTC (permalink / raw
To: gentoo-commits
commit: 4d7583127ec8084cf8fd9bbe64a3bee521325ecc
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 15 07:07:42 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 15 07:07:42 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4d758312
Naming of eclass changed
(Portage version: 2.2.0_alpha26/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 3 +++
sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 2 +-
2 files changed, 4 insertions(+), 1 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index b43a3f4..1ef8cee 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 $
+ 15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
+ Naming of eclass changed
+
14 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
Ebov not needed to be set anymore
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 e813f42..4dd47bf 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
@@ -5,7 +5,7 @@
EBO_PATCH="4"
EBO_ECONF="--includedir=${EPREFIX}/usr/include/emboss"
-inherit embassy-ng
+inherit emboss
KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/
@ 2011-03-15 10:23 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2011-03-15 10:23 UTC (permalink / raw
To: gentoo-commits
commit: 8193c5e162a08714da4a58b3f234406deda78635
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 15 09:20:26 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 15 09:20:26 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8193c5e1
New emboss_src_install used
(Portage version: 2.2.0_alpha27/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 3 +++
sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 10 ++--------
2 files changed, 5 insertions(+), 8 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 1ef8cee..f82cd15 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -3,6 +3,9 @@
# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2011/03/09 16:29:05 jlec Exp $
15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
+ New emboss_src_install used
+
+ 15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
Naming of eclass changed
14 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.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 4dd47bf..becac66 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
@@ -10,7 +10,7 @@ inherit emboss
KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
src_install() {
- default
+ emboss_src_install
sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
dodoc README.Gentoo
@@ -24,17 +24,11 @@ src_install() {
EOF
doenvd 22emboss
- # Symlink preinstalled docs to "/usr/share/doc".
- dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${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."
+ 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
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/
@ 2011-03-20 16:28 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2011-03-20 16:28 UTC (permalink / raw
To: gentoo-commits
commit: ad664b90203371751633ed859665a7236d10fbeb
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 15 11:29:32 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 15 11:29:32 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ad664b90
Straighten ENV
(Portage version: 2.2.0_alpha27/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 3 +++
sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 3 +--
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index f82cd15..84db2c6 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -3,6 +3,9 @@
# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2011/03/09 16:29:05 jlec Exp $
15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
+ Straighten ENV
+
+ 15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
New emboss_src_install used
15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.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 becac66..d8e0747 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
@@ -17,10 +17,9 @@ src_install() {
# 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"
+ EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
EOF
doenvd 22emboss
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/
@ 2011-10-05 7:54 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2011-10-05 7:54 UTC (permalink / raw
To: gentoo-commits
commit: 3f4c507c66c8e30fac868fe849fa0cdb7b4e8c6a
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 24 05:43:56 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Sep 24 05:43:56 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3f4c507c
Use Fedora hosting because unpstream removed the patches
(Portage version: 2.2.0_alpha59/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/emboss/ChangeLog | 3 +++
sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 3 ++-
2 files changed, 5 insertions(+), 1 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index ba5fbee..9e8a431 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 $
+ 24 Sep 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
+ Use Fedora hosting because unpstream removed the patches
+
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
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 15a4d2a..137eab7 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
@@ -13,7 +13,8 @@ DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence ana
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 ${EBO_PATCH} ]] && SRC_URI+=" ftp://${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"
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/
@ 2012-05-22 19:43 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2012-05-22 19:43 UTC (permalink / raw
To: gentoo-commits
commit: 948535c856e9599eb431c511cea5cc101ad80269
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May 22 18:56:17 2012 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May 22 18:56:17 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=948535c8
sci-biology/emboss: Add missing eutils.eclass
(Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/emboss/ChangeLog | 5 ++++-
sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 4 ++--
2 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 9e8a431..ef98d4f 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-biology/emboss
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# 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 $
+ 22 May 2012; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
+ Add missing eutils.eclass
+
24 Sep 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
Use Fedora hosting because unpstream removed the patches
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 137eab7..af8b56f 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 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 emboss
+inherit emboss eutils
EBO_PATCH="4"
EBOV=${PV/_p*}
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/
@ 2014-03-24 2:00 Martin Mokrejs
0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2014-03-24 2:00 UTC (permalink / raw
To: gentoo-commits
commit: b7e0abfff587fc15ab4b91c88575d9dfa35cb691
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 24 01:58:53 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 24 01:58:53 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b7e0abff
sci-biology/emboss-6.3.1_p4-r2: added plplot dependency, trying to get rid of a Makefile.patch using sed hackery
Package-Manager: portage-2.2.7
---
sci-biology/emboss/ChangeLog | 7 ++++++-
sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild | 11 ++++++++---
2 files changed, 14 insertions(+), 4 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 1d9c10e..9dd52d9 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,7 +1,12 @@
# ChangeLog for sci-biology/emboss
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# 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 $
+ 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
+ Makefile.patch using sed hackery
+
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
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 c394dfa..59a7d49 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
@@ -28,6 +28,7 @@ PDEPEND+="
sci-biology/prosite
sci-biology/rebase
sci-biology/transfac
+ sci-libs/plplot
)"
S="${WORKDIR}"/EMBOSS-${EBOV}
@@ -47,9 +48,13 @@ src_prepare() {
epatch "${FILESDIR}/${PF}"_libtool.patch
}
-src_compile() {
- epatch "${FILESDIR}/${PF}"_Makefile.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
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/
@ 2015-02-04 8:37 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2015-02-04 8:37 UTC (permalink / raw
To: gentoo-commits
commit: e10b5e5861fb565df2c4aead9d8a7c272d1b38e4
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 4 08:07:18 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 4 08:07:18 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e10b5e58
sci-biology/emboss: Clean a bit, user readme.gentoo.eclass
Package-Manager: portage-2.2.15
---
sci-biology/emboss/ChangeLog | 5 ++++-
sci-biology/emboss/metadata.xml | 4 ++--
2 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index b047e8c..a8d74bc 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-biology/emboss
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# 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> metadata.xml:
+ Clean a bit, user readme.gentoo.eclass
+
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:
diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml
index b85761d..3af936d 100644
--- a/sci-biology/emboss/metadata.xml
+++ b/sci-biology/emboss/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
- <longdescription>
+ <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
^ permalink raw reply related [flat|nested] 11+ messages in thread
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