* [gentoo-commits] gentoo-x86 commit in sci-biology/shrimp: ChangeLog shrimp-2.0.1.ebuild
@ 2010-07-25 18:01 Andrey Kislyuk (weaver)
0 siblings, 0 replies; 5+ messages in thread
From: Andrey Kislyuk (weaver) @ 2010-07-25 18:01 UTC (permalink / raw
To: gentoo-commits
weaver 10/07/25 18:01:15
Modified: ChangeLog
Added: shrimp-2.0.1.ebuild
Log:
Version bump
(Portage version: 2.2_rc67/cvs/Linux x86_64)
Revision Changes Path
1.9 sci-biology/shrimp/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?rev=1.9&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?rev=1.9&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?r1=1.8&r2=1.9
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- ChangeLog 3 Jan 2010 14:19:01 -0000 1.8
+++ ChangeLog 25 Jul 2010 18:01:15 -0000 1.9
@@ -1,6 +1,11 @@
# ChangeLog for sci-biology/shrimp
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.8 2010/01/03 14:19:01 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.9 2010/07/25 18:01:15 weaver Exp $
+
+*shrimp-2.0.1 (25 Jul 2010)
+
+ 25 Jul 2010; Andrey Kislyuk <weaver@gentoo.org> +shrimp-2.0.1.ebuild:
+ Version bump
03 Jan 2010; Pacho Ramos <pacho@gentoo.org> shrimp-1.3.1.ebuild:
amd64 stable, bug 298764
1.1 sci-biology/shrimp/shrimp-2.0.1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?rev=1.1&content-type=text/plain
Index: shrimp-2.0.1.ebuild
===================================================================
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.1 2010/07/25 18:01:15 weaver Exp $
EAPI="2"
MY_PV=${PV//./_}
DESCRIPTION="SHort Read Mapping Package"
HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
LICENSE="as-is"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
DEPEND="sys-devel/gcc[openmp]"
RDEPEND=""
S="${WORKDIR}/SHRiMP_${MY_PV}"
src_prepare() {
sed -i -e '1 a #include <stdint.h>' common/dag_glue.cpp || die
sed -i -e '1 a CXXFLAGS+= -O3 -mmmx -msse -msse2 -fopenmp' \
-e 's/-static//' "${S}/Makefile" || die
}
src_install() {
rm bin/README
dobin bin/* || die
insinto /usr/share/${PN}
doins -r utils || die
dodoc HISTORY README TODO SPLITTING_AND_MERGING
}
^ permalink raw reply [flat|nested] 5+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/shrimp: ChangeLog shrimp-2.0.1.ebuild
@ 2010-08-09 17:56 Kacper Kowalik (xarthisius)
0 siblings, 0 replies; 5+ messages in thread
From: Kacper Kowalik (xarthisius) @ 2010-08-09 17:56 UTC (permalink / raw
To: gentoo-commits
xarthisius 10/08/09 17:56:29
Modified: ChangeLog shrimp-2.0.1.ebuild
Log:
Respect LDFLAGS wrt bug 331823. Thanks to Diego for report.
(Portage version: 2.1.8.3/cvs/Linux x86_64)
Revision Changes Path
1.10 sci-biology/shrimp/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?rev=1.10&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?rev=1.10&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?r1=1.9&r2=1.10
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- ChangeLog 25 Jul 2010 18:01:15 -0000 1.9
+++ ChangeLog 9 Aug 2010 17:56:29 -0000 1.10
@@ -1,6 +1,9 @@
# ChangeLog for sci-biology/shrimp
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.9 2010/07/25 18:01:15 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.10 2010/08/09 17:56:29 xarthisius Exp $
+
+ 09 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> shrimp-2.0.1.ebuild:
+ Respect LDFLAGS wrt bug 331823. Thanks to Diego for report.
*shrimp-2.0.1 (25 Jul 2010)
1.2 sci-biology/shrimp/shrimp-2.0.1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?r1=1.1&r2=1.2
Index: shrimp-2.0.1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- shrimp-2.0.1.ebuild 25 Jul 2010 18:01:15 -0000 1.1
+++ shrimp-2.0.1.ebuild 9 Aug 2010 17:56:29 -0000 1.2
@@ -1,9 +1,11 @@
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.1 2010/07/25 18:01:15 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.2 2010/08/09 17:56:29 xarthisius Exp $
EAPI="2"
+inherit flag-o-matic toolchain-funcs
+
MY_PV=${PV//./_}
DESCRIPTION="SHort Read Mapping Package"
@@ -16,20 +18,27 @@
KEYWORDS="~amd64 ~x86"
DEPEND="sys-devel/gcc[openmp]"
-RDEPEND=""
+RDEPEND="${DEPEND}" # -lgomp
-S="${WORKDIR}/SHRiMP_${MY_PV}"
+S=${WORKDIR}/SHRiMP_${MY_PV}
src_prepare() {
- sed -i -e '1 a #include <stdint.h>' common/dag_glue.cpp || die
- sed -i -e '1 a CXXFLAGS+= -O3 -mmmx -msse -msse2 -fopenmp' \
- -e 's/-static//' "${S}/Makefile" || die
+ sed -i -e '1 a #include <stdint.h>' common/dag_glue.cpp || die #294811
+ # respect LDFLAGS wrt 331823
+ sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
+ -e 's/-static//' Makefile || die
+}
+
+src_compile() {
+ append-flags -fopenmp
+ tc-export CXX
+ emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" || die
}
src_install() {
- rm bin/README
+ rm bin/README || die
dobin bin/* || die
insinto /usr/share/${PN}
doins -r utils || die
- dodoc HISTORY README TODO SPLITTING_AND_MERGING
+ dodoc HISTORY README TODO SPLITTING_AND_MERGING || die
}
^ permalink raw reply [flat|nested] 5+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/shrimp: ChangeLog shrimp-2.0.1.ebuild
@ 2010-08-09 18:19 Kacper Kowalik (xarthisius)
0 siblings, 0 replies; 5+ messages in thread
From: Kacper Kowalik (xarthisius) @ 2010-08-09 18:19 UTC (permalink / raw
To: gentoo-commits
xarthisius 10/08/09 18:19:29
Modified: ChangeLog shrimp-2.0.1.ebuild
Log:
Fix dependency on openmp.
(Portage version: 2.1.8.3/cvs/Linux x86_64)
Revision Changes Path
1.11 sci-biology/shrimp/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?rev=1.11&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?rev=1.11&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?r1=1.10&r2=1.11
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- ChangeLog 9 Aug 2010 17:56:29 -0000 1.10
+++ ChangeLog 9 Aug 2010 18:19:28 -0000 1.11
@@ -1,6 +1,9 @@
# ChangeLog for sci-biology/shrimp
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.10 2010/08/09 17:56:29 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.11 2010/08/09 18:19:28 xarthisius Exp $
+
+ 09 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> shrimp-2.0.1.ebuild:
+ Fix dependency on openmp.
09 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> shrimp-2.0.1.ebuild:
Respect LDFLAGS wrt bug 331823. Thanks to Diego for report.
1.3 sci-biology/shrimp/shrimp-2.0.1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?r1=1.2&r2=1.3
Index: shrimp-2.0.1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- shrimp-2.0.1.ebuild 9 Aug 2010 17:56:29 -0000 1.2
+++ shrimp-2.0.1.ebuild 9 Aug 2010 18:19:28 -0000 1.3
@@ -1,6 +1,6 @@
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.2 2010/08/09 17:56:29 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.3 2010/08/09 18:19:28 xarthisius Exp $
EAPI="2"
@@ -17,11 +17,15 @@
IUSE=""
KEYWORDS="~amd64 ~x86"
-DEPEND="sys-devel/gcc[openmp]"
+DEPEND=">=sys-devel/gcc-4.3[openmp]"
RDEPEND="${DEPEND}" # -lgomp
S=${WORKDIR}/SHRiMP_${MY_PV}
+pkg_setup() {
+ tc-has-openmp || die "At least gcc-4.3 is required for openmp support."
+}
+
src_prepare() {
sed -i -e '1 a #include <stdint.h>' common/dag_glue.cpp || die #294811
# respect LDFLAGS wrt 331823
^ permalink raw reply [flat|nested] 5+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/shrimp: ChangeLog shrimp-2.0.1.ebuild
@ 2011-02-27 20:16 Markos Chandras (hwoarang)
0 siblings, 0 replies; 5+ messages in thread
From: Markos Chandras (hwoarang) @ 2011-02-27 20:16 UTC (permalink / raw
To: gentoo-commits
hwoarang 11/02/27 20:16:10
Modified: ChangeLog shrimp-2.0.1.ebuild
Log:
Stable on amd64 wrt bug #353563
(Portage version: 2.1.9.41/cvs/Linux x86_64)
Revision Changes Path
1.13 sci-biology/shrimp/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?rev=1.13&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?rev=1.13&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?r1=1.12&r2=1.13
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- ChangeLog 3 Feb 2011 00:13:49 -0000 1.12
+++ ChangeLog 27 Feb 2011 20:16:10 -0000 1.13
@@ -1,6 +1,9 @@
# ChangeLog for sci-biology/shrimp
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.12 2011/02/03 00:13:49 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.13 2011/02/27 20:16:10 hwoarang Exp $
+
+ 27 Feb 2011; Markos Chandras <hwoarang@gentoo.org> shrimp-2.0.1.ebuild:
+ Stable on amd64 wrt bug #353563
*shrimp-2.1.0 (03 Feb 2011)
1.4 sci-biology/shrimp/shrimp-2.0.1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?rev=1.4&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?rev=1.4&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?r1=1.3&r2=1.4
Index: shrimp-2.0.1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- shrimp-2.0.1.ebuild 9 Aug 2010 18:19:28 -0000 1.3
+++ shrimp-2.0.1.ebuild 27 Feb 2011 20:16:10 -0000 1.4
@@ -1,6 +1,6 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.3 2010/08/09 18:19:28 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.4 2011/02/27 20:16:10 hwoarang Exp $
EAPI="2"
@@ -15,7 +15,7 @@
LICENSE="as-is"
SLOT="0"
IUSE=""
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="amd64 ~x86"
DEPEND=">=sys-devel/gcc-4.3[openmp]"
RDEPEND="${DEPEND}" # -lgomp
^ permalink raw reply [flat|nested] 5+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/shrimp: ChangeLog shrimp-2.0.1.ebuild
@ 2011-03-07 15:33 Thomas Kahle (tomka)
0 siblings, 0 replies; 5+ messages in thread
From: Thomas Kahle (tomka) @ 2011-03-07 15:33 UTC (permalink / raw
To: gentoo-commits
tomka 11/03/07 15:33:02
Modified: ChangeLog shrimp-2.0.1.ebuild
Log:
x86 stable per bug 353563
(Portage version: 2.1.9.42/cvs/Linux i686)
Revision Changes Path
1.14 sci-biology/shrimp/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?rev=1.14&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?rev=1.14&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/ChangeLog?r1=1.13&r2=1.14
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- ChangeLog 27 Feb 2011 20:16:10 -0000 1.13
+++ ChangeLog 7 Mar 2011 15:33:02 -0000 1.14
@@ -1,6 +1,9 @@
# ChangeLog for sci-biology/shrimp
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.13 2011/02/27 20:16:10 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.14 2011/03/07 15:33:02 tomka Exp $
+
+ 07 Mar 2011; Thomas Kahle <tomka@gentoo.org> shrimp-2.0.1.ebuild:
+ x86 stable per bug 353563
27 Feb 2011; Markos Chandras <hwoarang@gentoo.org> shrimp-2.0.1.ebuild:
Stable on amd64 wrt bug #353563
1.5 sci-biology/shrimp/shrimp-2.0.1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?rev=1.5&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?rev=1.5&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild?r1=1.4&r2=1.5
Index: shrimp-2.0.1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- shrimp-2.0.1.ebuild 27 Feb 2011 20:16:10 -0000 1.4
+++ shrimp-2.0.1.ebuild 7 Mar 2011 15:33:02 -0000 1.5
@@ -1,6 +1,6 @@
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.4 2011/02/27 20:16:10 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.5 2011/03/07 15:33:02 tomka Exp $
EAPI="2"
@@ -15,7 +15,7 @@
LICENSE="as-is"
SLOT="0"
IUSE=""
-KEYWORDS="amd64 ~x86"
+KEYWORDS="amd64 x86"
DEPEND=">=sys-devel/gcc-4.3[openmp]"
RDEPEND="${DEPEND}" # -lgomp
^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2011-03-07 15:33 UTC | newest]
Thread overview: 5+ messages (download: mbox.gz follow: Atom feed
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2010-08-09 18:19 [gentoo-commits] gentoo-x86 commit in sci-biology/shrimp: ChangeLog shrimp-2.0.1.ebuild Kacper Kowalik (xarthisius)
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2011-03-07 15:33 Thomas Kahle (tomka)
2011-02-27 20:16 Markos Chandras (hwoarang)
2010-08-09 17:56 Kacper Kowalik (xarthisius)
2010-07-25 18:01 Andrey Kislyuk (weaver)
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