* [gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/
@ 2015-12-28 20:08 Andreas Hüttel
0 siblings, 0 replies; 7+ messages in thread
From: Andreas Hüttel @ 2015-12-28 20:08 UTC (permalink / raw
To: gentoo-commits
commit: 087966e83658833cb4b436d828c3c0d3519cd5e4
Author: Andreas K. Hüttel <dilfridge <AT> gentoo <DOT> org>
AuthorDate: Mon Dec 28 20:02:49 2015 +0000
Commit: Andreas Hüttel <dilfridge <AT> gentoo <DOT> org>
CommitDate: Mon Dec 28 20:08:36 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=087966e8
dev-perl/Bio-SamTools: Version bump; remove old
Package-Manager: portage-2.2.26
...ls-1.390.0-r1.ebuild => Bio-SamTools-1.420.0.ebuild} | 17 +++++++++--------
dev-perl/Bio-SamTools/Manifest | 2 +-
2 files changed, 10 insertions(+), 9 deletions(-)
diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
similarity index 77%
rename from dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild
rename to dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
index 1ad7fbe..68d7383 100644
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
@@ -2,11 +2,10 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
-
-MODULE_AUTHOR=LDS
-MODULE_VERSION=1.39
+EAPI=6
+DIST_AUTHOR=LDS
+DIST_VERSION=1.42
inherit perl-module toolchain-funcs
DESCRIPTION="Read SAM/BAM database files"
@@ -14,20 +13,22 @@ DESCRIPTION="Read SAM/BAM database files"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
+LICENSE="|| ( Apache-2.0 Artistic-2 GPL-1+ )"
RDEPEND="
- sci-biology/bioperl
+ >=sci-biology/bioperl-1.6.9
>=sci-biology/samtools-1
"
DEPEND="${RDEPEND}
virtual/perl-ExtUtils-CBuilder
- dev-perl/Module-Build
+ >=dev-perl/Module-Build-0.420.0
"
-SRC_TEST=do
+DIST_TEST=skip
+# cannot load its own library, fundamentally b0rken
PATCHES=(
- "${FILESDIR}"/${P}-samtools-1.patch
+ "${FILESDIR}"/${PN}-1.390.0-samtools-1.patch
)
src_prepare() {
diff --git a/dev-perl/Bio-SamTools/Manifest b/dev-perl/Bio-SamTools/Manifest
index bf52deb..9143d80 100644
--- a/dev-perl/Bio-SamTools/Manifest
+++ b/dev-perl/Bio-SamTools/Manifest
@@ -1,2 +1,2 @@
-DIST Bio-SamTools-1.39.tar.gz 331515 SHA256 a2baaa0f569c2b49e988978a121fb210fcb35200dcb2f183aa58bb03d711ef4f SHA512 aff502af24239cd64dec3a5a9cb6ab7280661f277cef066f79c87f608112d5870f46ffcc81f3bc2382f48d5247c7ab5de35e4afaa7ca4e286b0323978368d668 WHIRLPOOL db069d76fe386354b8cec60527de6612fc501428e9775e02574955cead3eba55db169697aaacc22c3b4df6475c6ecb72486b94c9b577da1deb42dc5c3791b04f
DIST Bio-SamTools-1.41.tar.gz 338745 SHA256 b5d7ca16c96cc9fbee5daceb3268f36011740fe4de92074c17a729bac57c3077 SHA512 6f822cd219ecf86e95bc3a6bde1aebbe5eb8284b21b07ca919618c1422c37e6d182285d1a5e77848c6d5cea0dc74a51705f6bc1a27d44aeeaaa69f1cea58f147 WHIRLPOOL b651ea5059ea46ab5e31d237d3e52d7936921470bbd04133be70f935a47b913dc7f3b154c14d1af52f0ba2f5afc6878a27d88e4bbf9d39023cf786bca70f6696
+DIST Bio-SamTools-1.42.tar.gz 337821 SHA256 ef4b736e86442ce61f56ddd94befc302ccc4646cae3c45407e107400c703584c SHA512 6a1f95104ce91a800a314c304915af9d6e1cc477c7d5f42b640d0a27b18cd32c4ad9e261cac5556f4863652570a3c573d34245963fc4b9ade067981b2a329271 WHIRLPOOL 5a216e51173ee5a9a930013718452bcbfbcffe1aa1663f50d567daf17378a50135b1b0b6d750c9aece05de268e730faf6c54963823c037559fb50ed95dda32c7
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/
@ 2016-10-24 13:32 Pacho Ramos
0 siblings, 0 replies; 7+ messages in thread
From: Pacho Ramos @ 2016-10-24 13:32 UTC (permalink / raw
To: gentoo-commits
commit: 1c59326088d72b88e4ecee7ce73d27737024d6c7
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 24 13:06:49 2016 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Mon Oct 24 13:32:36 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1c593260
dev-perl/Bio-SamTools: Set proper slot
Package-Manager: portage-2.3.2
RepoMan-Options: --force
dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
index 68d7383..5443438 100644
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -17,7 +17,7 @@ LICENSE="|| ( Apache-2.0 Artistic-2 GPL-1+ )"
RDEPEND="
>=sci-biology/bioperl-1.6.9
- >=sci-biology/samtools-1
+ >=sci-biology/samtools-1:0
"
DEPEND="${RDEPEND}
virtual/perl-ExtUtils-CBuilder
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/
@ 2016-10-24 13:32 Pacho Ramos
0 siblings, 0 replies; 7+ messages in thread
From: Pacho Ramos @ 2016-10-24 13:32 UTC (permalink / raw
To: gentoo-commits
commit: 61b16ca3665661b434fab1f1ce557335f29fb652
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 24 13:06:18 2016 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Mon Oct 24 13:32:34 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61b16ca3
dev-perl/Bio-SamTools: Drop old
Package-Manager: portage-2.3.2
RepoMan-Options: --force
dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild | 50 -----------------------
dev-perl/Bio-SamTools/Manifest | 1 -
2 files changed, 51 deletions(-)
diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild
deleted file mode 100644
index f38c642..00000000
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-MODULE_AUTHOR=LDS
-MODULE_VERSION=1.41
-
-inherit perl-module toolchain-funcs
-
-DESCRIPTION="Read SAM/BAM database files"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
- >=sci-biology/bioperl-1.6.9
- >=sci-biology/samtools-1
-"
-DEPEND="${RDEPEND}
- virtual/perl-ExtUtils-CBuilder
- >=dev-perl/Module-Build-0.420.0
-"
-
-SRC_TEST=skip
-# cannot load its own library, fundamentally b0rken
-
-PATCHES=(
- "${FILESDIR}"/${PN}-1.390.0-samtools-1.patch
-)
-
-src_prepare() {
- find . -type f -exec chmod +w '{}' + || die
- sed \
- -e 's|my $HeaderFile = "bam.h";|my $HeaderFile = "bam/bam.h";|' \
- -e 's|my $LibFile = "libbam.a";|my $LibFile = "libbam.so";|' \
- -i Build.PL || die
- sed \
- -e 's|#include "bam.h"|#include "bam/bam.h"|' \
- -e 's|#include "sam.h"|#include "bam/sam.h"|' \
- -e 's|#include "khash.h"|#include "htslib/khash.h"|' \
- -e 's|#include "faidx.h"|#include "htslib/faidx.h"|' \
- -i lib/Bio/DB/Sam.xs c_bin/bam2bedgraph.c || die
-
- perl-module_src_prepare
-
- tc-export CC
-}
diff --git a/dev-perl/Bio-SamTools/Manifest b/dev-perl/Bio-SamTools/Manifest
index 9143d80..733a42f 100644
--- a/dev-perl/Bio-SamTools/Manifest
+++ b/dev-perl/Bio-SamTools/Manifest
@@ -1,2 +1 @@
-DIST Bio-SamTools-1.41.tar.gz 338745 SHA256 b5d7ca16c96cc9fbee5daceb3268f36011740fe4de92074c17a729bac57c3077 SHA512 6f822cd219ecf86e95bc3a6bde1aebbe5eb8284b21b07ca919618c1422c37e6d182285d1a5e77848c6d5cea0dc74a51705f6bc1a27d44aeeaaa69f1cea58f147 WHIRLPOOL b651ea5059ea46ab5e31d237d3e52d7936921470bbd04133be70f935a47b913dc7f3b154c14d1af52f0ba2f5afc6878a27d88e4bbf9d39023cf786bca70f6696
DIST Bio-SamTools-1.42.tar.gz 337821 SHA256 ef4b736e86442ce61f56ddd94befc302ccc4646cae3c45407e107400c703584c SHA512 6a1f95104ce91a800a314c304915af9d6e1cc477c7d5f42b640d0a27b18cd32c4ad9e261cac5556f4863652570a3c573d34245963fc4b9ade067981b2a329271 WHIRLPOOL 5a216e51173ee5a9a930013718452bcbfbcffe1aa1663f50d567daf17378a50135b1b0b6d750c9aece05de268e730faf6c54963823c037559fb50ed95dda32c7
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/
@ 2020-07-03 15:10 Kent Fredric
0 siblings, 0 replies; 7+ messages in thread
From: Kent Fredric @ 2020-07-03 15:10 UTC (permalink / raw
To: gentoo-commits
commit: 821c3144cfab97b5ce23982db8f4fea76a2f3718
Author: Kent Fredric <kentnl <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 3 14:32:54 2020 +0000
Commit: Kent Fredric <kentnl <AT> gentoo <DOT> org>
CommitDate: Fri Jul 3 15:00:08 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=821c3144
dev-perl/Bio-SamTools: -r bump for toolchain fixes
- Don't break when LD=!ccld
- Ensure CFLAGS passed through to compiler
Package-Manager: Portage-2.3.100, Repoman-2.3.22
Signed-off-by: Kent Fredric <kentnl <AT> gentoo.org>
.../Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild | 45 ++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild
new file mode 100644
index 00000000000..ed1ab08f825
--- /dev/null
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DIST_AUTHOR=LDS
+DIST_VERSION=1.43
+inherit perl-module toolchain-funcs multilib
+
+DESCRIPTION="Read SAM/BAM database files"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+LICENSE="|| ( Apache-2.0 Artistic-2 GPL-1+ )"
+
+RDEPEND="
+ >=sci-biology/bioperl-1.6.9
+ sci-biology/samtools:0.1-legacy=
+"
+DEPEND="
+ dev-perl/Module-Build
+ sci-biology/samtools:0.1-legacy=
+"
+BDEPEND="${RDEPEND}
+ virtual/perl-ExtUtils-CBuilder
+ >=dev-perl/Module-Build-0.420.0
+"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-1.430.0-legacy-r1.patch
+)
+
+src_configure() {
+ tc-export CC
+ unset LD
+ if [[ -n "${CCLD}" ]]; then
+ export LD="${CCLD}"
+ fi
+ SAM_LIB="${EPREFIX}/usr/$(get_libdir)/libbam-0.1-legacy.so" \
+ SAM_INCLUDE="${EPREFIX}/usr/include/bam-0.1-legacy" \
+ perl-module_src_configure
+}
+src_compile() {
+ ./Build --config optimize="${CFLAGS}" build || die
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/
@ 2020-08-06 16:40 Kent Fredric
0 siblings, 0 replies; 7+ messages in thread
From: Kent Fredric @ 2020-08-06 16:40 UTC (permalink / raw
To: gentoo-commits
commit: 8a8fdfe14c876fc894455b06f09d805906158615
Author: Kent Fredric <kentnl <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 6 16:14:04 2020 +0000
Commit: Kent Fredric <kentnl <AT> gentoo <DOT> org>
CommitDate: Thu Aug 6 16:38:08 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8a8fdfe1
dev-perl/Bio-SamTools: Cleanup old 1.430.0-r1
Package-Manager: Portage-2.3.103, Repoman-2.3.22
Signed-off-by: Kent Fredric <kentnl <AT> gentoo.org>
.../Bio-SamTools/Bio-SamTools-1.430.0-r1.ebuild | 38 ----------------------
1 file changed, 38 deletions(-)
diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r1.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r1.ebuild
deleted file mode 100644
index 861acb6faa2..00000000000
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DIST_AUTHOR=LDS
-DIST_VERSION=1.43
-inherit perl-module toolchain-funcs multilib
-
-DESCRIPTION="Read SAM/BAM database files"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-LICENSE="|| ( Apache-2.0 Artistic-2 GPL-1+ )"
-
-RDEPEND="
- >=sci-biology/bioperl-1.6.9
- sci-biology/samtools:0.1-legacy=
-"
-DEPEND="
- dev-perl/Module-Build
- sci-biology/samtools:0.1-legacy=
-"
-BDEPEND="${RDEPEND}
- virtual/perl-ExtUtils-CBuilder
- >=dev-perl/Module-Build-0.420.0
-"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-1.430.0-legacy-r1.patch
-)
-
-src_configure() {
- tc-export CC
- SAM_LIB="${EPREFIX}/usr/$(get_libdir)/libbam-0.1-legacy.so" \
- SAM_INCLUDE="${EPREFIX}/usr/include/bam-0.1-legacy" \
- perl-module_src_configure
-}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/
@ 2021-05-31 20:50 Andreas K. Hüttel
0 siblings, 0 replies; 7+ messages in thread
From: Andreas K. Hüttel @ 2021-05-31 20:50 UTC (permalink / raw
To: gentoo-commits
commit: b8f78e0477bce7c9d37fc50677694631d020f917
Author: Andreas K. Hüttel <dilfridge <AT> gentoo <DOT> org>
AuthorDate: Sun May 30 21:04:27 2021 +0000
Commit: Andreas K. Hüttel <dilfridge <AT> gentoo <DOT> org>
CommitDate: Mon May 31 20:50:30 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b8f78e04
dev-perl/Bio-SamTools: Declare Perl5 license, as in Debian
Closes: https://bugs.gentoo.org/721220
Package-Manager: Portage-3.0.18, Repoman-3.0.2
Signed-off-by: Andreas K. Hüttel <dilfridge <AT> gentoo.org>
dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild
index ed1ab08f825..b06de25d354 100644
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -11,7 +11,6 @@ DESCRIPTION="Read SAM/BAM database files"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-LICENSE="|| ( Apache-2.0 Artistic-2 GPL-1+ )"
RDEPEND="
>=sci-biology/bioperl-1.6.9
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/
@ 2022-03-10 21:12 Sam James
0 siblings, 0 replies; 7+ messages in thread
From: Sam James @ 2022-03-10 21:12 UTC (permalink / raw
To: gentoo-commits
commit: c6a58ad91a44dbb39c621ca2926b370ab0d70ca3
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 10 05:13:32 2022 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Thu Mar 10 21:10:16 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c6a58ad9
dev-perl/Bio-SamTools: [QA] fix UnusedInherits (multilib)
get_libdir has been built-in since EAPI 6
Signed-off-by: Sam James <sam <AT> gentoo.org>
dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild
index b06de25d3541..e8109c9688f3 100644
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
DIST_AUTHOR=LDS
DIST_VERSION=1.43
-inherit perl-module toolchain-funcs multilib
+inherit perl-module toolchain-funcs
DESCRIPTION="Read SAM/BAM database files"
@@ -39,6 +39,7 @@ src_configure() {
SAM_INCLUDE="${EPREFIX}/usr/include/bam-0.1-legacy" \
perl-module_src_configure
}
+
src_compile() {
./Build --config optimize="${CFLAGS}" build || die
}
^ permalink raw reply related [flat|nested] 7+ messages in thread
end of thread, other threads:[~2022-03-10 21:13 UTC | newest]
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2020-08-06 16:40 Kent Fredric
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