* [gentoo-commits] proj/sci:master commit in: dev-perl/Bio-DB-HTS/
@ 2016-07-29 20:44 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2016-07-29 20:44 UTC (permalink / raw
To: gentoo-commits
commit: 0f0dfd5089d75186aff4f1e557eabedfcf0930e8
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 29 20:44:32 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 29 20:44:32 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0f0dfd50
dev-perl/Bio-DB-HTS: new package, needs more fixes
Package-Manager: portage-2.3.0
dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild | 28 ++++++++++++++++++++++++++++
dev-perl/Bio-DB-HTS/metadata.xml | 12 ++++++++++++
2 files changed, 40 insertions(+)
diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
new file mode 100644
index 0000000..d450118
--- /dev/null
+++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MODULE_AUTHOR="RISHIDEV"
+inherit perl-module multilib toolchain-funcs
+
+DESCRIPTION="Enable rapid access to bgzipped FASTA files"
+
+#LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+ dev-perl/Module-Build
+ sci-libs/htslib"
+
+SRC_TEST="do"
+
+src_prepare(){
+ # https://github.com/Ensembl/Bio-HTS/issues/15
+ # https://github.com/Ensembl/Bio-HTS/issues/30
+ HTSLIB_LIBDIR="${EPREFIX}"/"$(get_libdir)" HTSLIB_INCDIR="/usr/include/htslib" perl-module_src_prepare
+}
diff --git a/dev-perl/Bio-DB-HTS/metadata.xml b/dev-perl/Bio-DB-HTS/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/dev-perl/Bio-DB-HTS/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-perl/Bio-DB-HTS/
@ 2016-09-23 17:29 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2016-09-23 17:29 UTC (permalink / raw
To: gentoo-commits
commit: c4b219b88d7a0e46126a0bb0ca87772ca86bde89
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Sep 23 17:27:42 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Sep 23 17:27:42 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c4b219b8
dev-perl/Bio-DB-HTS: upstream renamed the package, good
Package-Manager: portage-2.3.0
dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
index d450118..e1951cc 100644
--- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
+++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
@@ -4,6 +4,8 @@
EAPI=5
+# this is https://metacpan.org/pod/Bio::DB::HTS and not https://metacpan.org/pod/Bio::HTS
+# this is https://github.com/Ensembl/Bio-DB-HTS
MODULE_AUTHOR="RISHIDEV"
inherit perl-module multilib toolchain-funcs
@@ -24,5 +26,5 @@ SRC_TEST="do"
src_prepare(){
# https://github.com/Ensembl/Bio-HTS/issues/15
# https://github.com/Ensembl/Bio-HTS/issues/30
- HTSLIB_LIBDIR="${EPREFIX}"/"$(get_libdir)" HTSLIB_INCDIR="/usr/include/htslib" perl-module_src_prepare
+ HTSLIB_LIBDIR="${EPREFIX}"/"$(get_libdir)" HTSLIB_INCDIR="${EPREFIX}"/usr/include/htslib perl-module_src_prepare
}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-perl/Bio-DB-HTS/
@ 2016-12-07 16:33 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2016-12-07 16:33 UTC (permalink / raw
To: gentoo-commits
commit: ace9d9a8850aa50ffe6efc2948260a3195017664
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec 7 16:33:02 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec 7 16:33:02 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ace9d9a8
dev-perl/Bio-DB-HTS: new package requiring sci-libs/[static-libs] and using -rpath
Package-Manager: portage-2.3.2
dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild | 19 +++++++++++++------
1 file changed, 13 insertions(+), 6 deletions(-)
diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
index e1951cc..bbc4011 100644
--- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
+++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
@@ -4,8 +4,8 @@
EAPI=5
-# this is https://metacpan.org/pod/Bio::DB::HTS and not https://metacpan.org/pod/Bio::HTS
-# this is https://github.com/Ensembl/Bio-DB-HTS
+# this is https://metacpan.org/pod/Bio::DB::HTS and https://github.com/Ensembl/Bio-DB-HTS
+# this is not https://metacpan.org/pod/Bio::HTS
MODULE_AUTHOR="RISHIDEV"
inherit perl-module multilib toolchain-funcs
@@ -13,18 +13,25 @@ DESCRIPTION="Enable rapid access to bgzipped FASTA files"
#LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
IUSE=""
RDEPEND=""
DEPEND="${RDEPEND}
dev-perl/Module-Build
- sci-libs/htslib"
+ sci-libs/htslib[static-libs]"
SRC_TEST="do"
src_prepare(){
- # https://github.com/Ensembl/Bio-HTS/issues/15
# https://github.com/Ensembl/Bio-HTS/issues/30
- HTSLIB_LIBDIR="${EPREFIX}"/"$(get_libdir)" HTSLIB_INCDIR="${EPREFIX}"/usr/include/htslib perl-module_src_prepare
+ export HTSLIB_LIBDIR="${EPREFIX}"/"$(get_libdir)" # currently ignored
+ export HTSLIB_INCDIR="${EPREFIX}"/usr/include/htslib # currently ignored
+ export HTSLIB_DIR="${EPREFIX}"/usr # useless, Build.PL will not invent /usr/lib64/ is the correct answer
+ perl-module_src_prepare
}
+
+# is the below -rpath acceptable?
+# x86_64-pc-linux-gnu-gcc -shared -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/usr/lib -Wl,-rpath,/usr/lib -lhts -lpthread -lz
+# x86_64-pc-linux-gnu-gcc -shared -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/usr/lib -Wl,-rpath,/usr/lib -lhts -lpthread -lz
+
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-perl/Bio-DB-HTS/
@ 2016-12-07 16:33 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2016-12-07 16:33 UTC (permalink / raw
To: gentoo-commits
commit: 1d42c9e4ef15249d22b4b4547d550a385a311671
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec 7 16:33:47 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec 7 16:33:47 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1d42c9e4
dev-perl/Bio-DB-HTS: remove trailing empty line
Package-Manager: portage-2.3.2
dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild | 1 -
1 file changed, 1 deletion(-)
diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
index bbc4011..7550d24 100644
--- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
+++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
@@ -34,4 +34,3 @@ src_prepare(){
# is the below -rpath acceptable?
# x86_64-pc-linux-gnu-gcc -shared -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/usr/lib -Wl,-rpath,/usr/lib -lhts -lpthread -lz
# x86_64-pc-linux-gnu-gcc -shared -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/usr/lib -Wl,-rpath,/usr/lib -lhts -lpthread -lz
-
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-perl/Bio-DB-HTS/
@ 2020-09-22 0:01 Aisha Tammy
0 siblings, 0 replies; 5+ messages in thread
From: Aisha Tammy @ 2020-09-22 0:01 UTC (permalink / raw
To: gentoo-commits
commit: 6e9bf8f7648c9df1f8b59e8c1631148b490f3aac
Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 00:00:58 2020 +0000
Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 00:01:17 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6e9bf8f7
dev-perl/Bio-DB-HTS: drop package
present in ::gentoo
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>
dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild | 35 -------------------------------
dev-perl/Bio-DB-HTS/metadata.xml | 12 -----------
2 files changed, 47 deletions(-)
diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
deleted file mode 100644
index 1e7e6ceca..000000000
--- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-# this is https://metacpan.org/pod/Bio::DB::HTS and https://github.com/Ensembl/Bio-DB-HTS
-# this is not https://metacpan.org/pod/Bio::HTS
-MODULE_AUTHOR="RISHIDEV"
-inherit perl-module multilib toolchain-funcs
-
-DESCRIPTION="Enable rapid access to bgzipped FASTA files"
-
-#LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
- dev-perl/Module-Build
- sci-libs/htslib[static-libs]"
-
-SRC_TEST="do"
-
-src_prepare(){
- # https://github.com/Ensembl/Bio-HTS/issues/30
- export HTSLIB_LIBDIR="${EPREFIX}"/"$(get_libdir)" # currently ignored
- export HTSLIB_INCDIR="${EPREFIX}"/usr/include/htslib # currently ignored
- export HTSLIB_DIR="${EPREFIX}"/usr # useless, Build.PL will not invent /usr/lib64/ is the correct answer
- perl-module_src_prepare
-}
-
-# is the below -rpath acceptable?
-# x86_64-pc-linux-gnu-gcc -shared -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/usr/lib -Wl,-rpath,/usr/lib -lhts -lpthread -lz
-# x86_64-pc-linux-gnu-gcc -shared -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/usr/lib -Wl,-rpath,/usr/lib -lhts -lpthread -lz
diff --git a/dev-perl/Bio-DB-HTS/metadata.xml b/dev-perl/Bio-DB-HTS/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/dev-perl/Bio-DB-HTS/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 5+ messages in thread
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