[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/files/, dev-perl/Bio-SamTools/, profiles/

2023-05-05 Thread David Seifert 
commit: 6e802f90c6c852f03c1ac87dacb11069265c3b36
Author: David Seifert  gentoo  org>
AuthorDate: Fri May  5 09:19:57 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri May  5 09:19:57 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6e802f90

dev-perl/Bio-SamTools: treeclean

Signed-off-by: David Seifert  gentoo.org>

 .../Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild|  45 -
 dev-perl/Bio-SamTools/Manifest |   1 -
 .../files/Bio-SamTools-1.430.0-legacy-r1.patch | 110 -
 dev-perl/Bio-SamTools/metadata.xml |  32 --
 profiles/package.mask  |   1 -
 5 files changed, 189 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
deleted file mode 100644
index e8109c9688f3..
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r2.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# 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
-
-DESCRIPTION="Read SAM/BAM database files"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-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
-}

diff --git a/dev-perl/Bio-SamTools/Manifest b/dev-perl/Bio-SamTools/Manifest
deleted file mode 100644
index e3b87c7144ed..
--- a/dev-perl/Bio-SamTools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Bio-SamTools-1.43.tar.gz 340833 BLAKE2B 
2b488667b86ef1bedb7cf74dfdcb3abc0302d9f309c1fc3077682bb400c8307f3b7d8fb1a9015a26f9a17f9e9955845d160512aa3273c368b720fe51b4392458
 SHA512 
cd5bc6213c093f5105399c95278803afcc537bb3d191686cda0193b82fda2580749bf7533791899939a78963fcc0d6b36eabe9c309c9c6816a9849e3c892c41b

diff --git a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy-r1.patch 
b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy-r1.patch
deleted file mode 100644
index ee9bde8fe3d0..
--- a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy-r1.patch
+++ /dev/null
@@ -1,110 +0,0 @@
-From 82942523b2db5143a9da0f9d2f8ec83a26c8d5b0 Mon Sep 17 00:00:00 2001
-From: Kent Fredric 
-Date: Sun, 10 Sep 2017 13:33:32 +1200
-Subject: Fix linking/compiling for bam-0.1-legacy
-

- Build.PL | 14 +++---
- c_bin/bam2bedgraph.c |  2 +-
- c_bin/makefile   |  6 +++---
- lib/Bio/DB/Sam.xs|  6 +++---
- 4 files changed, 14 insertions(+), 14 deletions(-)
-
-diff --git a/Build.PL b/Build.PL
-index 685815f..882f231 100644
 a/Build.PL
-+++ b/Build.PL
-@@ -4,11 +4,10 @@ use strict;
- use Module::Build;
- use Module::Load::Conditional qw(can_load);
- 
--my $HeaderFile = "bam.h";
--my $LibFile= "libbam.a";
--my $ReadLine;
--
--my ($sam_include,$sam_lib) = find_sam(); # may exit with error here
-+my ($sam_include,$sam_lib) = do {
-+  ($ENV{"SAM_INCLUDE"} || die "SAM_INCLUDE not set"),
-+  ($ENV{"SAM_LIB"} || die "SAM_LIB not set")
-+};
- 
- my $class = Module::Build->subclass(code=> 'Perl interface to SamTools library for DNA 
sequencing',
- license=> 'perl',
- include_dirs   => [$sam_include],
--extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'],
-+extra_linker_flags => ["-L$sam_lib",'-lbam-0.1-legacy','-lpthread','-lz'],
- 
- extra_compiler_flags=>[
- 
-@@ -67,7 +66,7 @@ $build->add_build_element('c_bin');
- $build->create_build_script;
- 
- exit 0;
--
-+=for non-gentoo
- sub find_sam {
- my ($sam_include,$sam_lib);
- 
-@@ -162,6 +161,7 @@ sub prompt {
- $ReadLine->addhistory($in) if $in =~ /\S/;
- return $in;
- }
-+=cut
- 
- sub _samtools {
- $ENV{SAMTOOLS} ||
-diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c
-index 298e9a8..91218fa 100644
 a/c_bin/bam2bedgraph.c
-+++ b/c_bin/bam2bedgraph.c
-@@ -1,5 +1,5 @@
- #include 
--#include "sam.h"
-+#include "bam-0.1-legacy/sam.h"
- 
- typedef struct {
-   uint32_t ltid;
-diff --git a/c_bin/makefile b/c_bin/makefile
-index 9aef917..0abbb4c 100644
 a/c_bin/makefile
-+++ b/c_bin/makefile
-@@ -1,5 +1,5 @@
--CC=   gcc
--CFLAGS=   -g -Wall -O2 -fPIC
-+CC?=  gcc
-+CFLAGS?=  -g -Wall

[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/

2022-03-10 Thread Sam James 
commit: c6a58ad91a44dbb39c621ca2926b370ab0d70ca3
Author: Sam James  gentoo  org>
AuthorDate: Thu Mar 10 05:13:32 2022 +
Commit: Sam James  gentoo  org>
CommitDate: Thu Mar 10 21:10:16 2022 +
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  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
 }

[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/

2021-05-31 Thread Andreas K. Hüttel 
commit: b8f78e0477bce7c9d37fc50677694631d020f917
Author: Andreas K. Hüttel  gentoo  org>
AuthorDate: Sun May 30 21:04:27 2021 +
Commit: Andreas K. Hüttel  gentoo  org>
CommitDate: Mon May 31 20:50:30 2021 +
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  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

[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/

2020-08-06 Thread Kent Fredric 
commit: 8a8fdfe14c876fc894455b06f09d805906158615
Author: Kent Fredric  gentoo  org>
AuthorDate: Thu Aug  6 16:14:04 2020 +
Commit: Kent Fredric  gentoo  org>
CommitDate: Thu Aug  6 16:38:08 2020 +
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  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..000
--- 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
-}

[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/

2020-07-03 Thread Kent Fredric 
commit: 821c3144cfab97b5ce23982db8f4fea76a2f3718
Author: Kent Fredric  gentoo  org>
AuthorDate: Fri Jul  3 14:32:54 2020 +
Commit: Kent Fredric  gentoo  org>
CommitDate: Fri Jul  3 15:00:08 2020 +
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  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 000..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
+}

[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/, dev-perl/Bio-SamTools/files/

2020-06-19 Thread Kent Fredric 
commit: 2a866fb9126e4c0a780620e041598cc6d3726ad3
Author: Kent Fredric  gentoo  org>
AuthorDate: Sat Jun 20 04:28:41 2020 +
Commit: Kent Fredric  gentoo  org>
CommitDate: Sat Jun 20 04:28:41 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2a866fb9

dev-perl/Bio-SamTools: Cleanup old 1.430.0

- Unstable(~) eclipsed by 1.430.0-r1 for ~1 month

Closes: https://bugs.gentoo.org/661112
Package-Manager: Portage-2.3.100, Repoman-2.3.22
Signed-off-by: Kent Fredric  gentoo.org>

 dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild  | 33 
 .../files/Bio-SamTools-1.430.0-legacy.patch| 88 --
 2 files changed, 121 deletions(-)

diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild 
b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild
deleted file mode 100644
index 1147cec5a48..000
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DIST_AUTHOR=LDS
-DIST_VERSION=1.43
-inherit perl-module toolchain-funcs
-
-DESCRIPTION="Read SAM/BAM database files"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-LICENSE="|| ( Apache-2.0 Artistic-2 GPL-1+ )"
-
-RDEPEND="
-   >=sci-biology/bioperl-1.6.9
-   sci-biology/samtools:0.1-legacy=
-"
-DEPEND="${RDEPEND}
-   virtual/perl-ExtUtils-CBuilder
-   >=dev-perl/Module-Build-0.420.0
-"
-
-PATCHES=(
-   "${FILESDIR}"/${PN}-1.430.0-legacy.patch
-)
-
-src_prepare() {
-   perl-module_src_prepare
-   tc-export CC
-}

diff --git a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch 
b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch
deleted file mode 100644
index 8464f06a2f0..000
--- a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch
+++ /dev/null
@@ -1,88 +0,0 @@
-From 74b38ded97f7a1940c3a37b9aec9b3287a3a78bd Mon Sep 17 00:00:00 2001
-From: Kent Fredric 
-Date: Sun, 10 Sep 2017 13:33:32 +1200
-Subject: Fix linking/compiling for bam-0.1-legacy
-

- Build.PL | 6 +++---
- c_bin/bam2bedgraph.c | 2 +-
- c_bin/makefile   | 6 +++---
- lib/Bio/DB/Sam.xs| 6 +++---
- 4 files changed, 10 insertions(+), 10 deletions(-)
-
-diff --git a/Build.PL b/Build.PL
-index 685815f..2611759 100644
 a/Build.PL
-+++ b/Build.PL
-@@ -4,8 +4,8 @@ use strict;
- use Module::Build;
- use Module::Load::Conditional qw(can_load);
- 
--my $HeaderFile = "bam.h";
--my $LibFile= "libbam.a";
-+my $HeaderFile = "bam-0.1-legacy/bam.h";
-+my $LibFile= "libbam-0.1-legacy.so";
- my $ReadLine;
- 
- my ($sam_include,$sam_lib) = find_sam(); # may exit with error here
-@@ -39,7 +39,7 @@ my $build = $class->new(
- dist_abstract  => 'Perl interface to SamTools library for DNA 
sequencing',
- license=> 'perl',
- include_dirs   => [$sam_include],
--extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'],
-+extra_linker_flags => ["-L$sam_lib",'-lbam-0.1-legacy','-lpthread','-lz'],
- 
- extra_compiler_flags=>[
- 
-diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c
-index 298e9a8..91218fa 100644
 a/c_bin/bam2bedgraph.c
-+++ b/c_bin/bam2bedgraph.c
-@@ -1,5 +1,5 @@
- #include 
--#include "sam.h"
-+#include "bam-0.1-legacy/sam.h"
- 
- typedef struct {
-   uint32_t ltid;
-diff --git a/c_bin/makefile b/c_bin/makefile
-index 9aef917..0abbb4c 100644
 a/c_bin/makefile
-+++ b/c_bin/makefile
-@@ -1,5 +1,5 @@
--CC=   gcc
--CFLAGS=   -g -Wall -O2 -fPIC
-+CC?=  gcc
-+CFLAGS?=  -g -Wall -O2 -fPIC
- DFLAGS=   -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE 
-D_USE_KNETFILE -D_CURSES_LIB=1
- INCLUDES=
- LIBPATH=
-@@ -14,7 +14,7 @@ PROG=bam2bedgraph
- all:$(PROG)
- 
- bam2bedgraph: bam2bedgraph.o
--  $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam -lpthread -lm -lz
-+  $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam-0.1-legacy 
-lpthread -lm -lz
- 
- clean:
-   rm -f *.o $(PROG)
-diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs
-index 023f655..86410fb 100644
 a/lib/Bio/DB/Sam.xs
-+++ b/lib/Bio/DB/Sam.xs
-@@ -25,9 +25,9 @@
- 
- #include 
- #include 
--#include "bam.h"
--#include "khash.h"
--#include "faidx.h"
-+#include "bam-0.1-legacy/bam.h"
-+#include "bam-0.1-legacy/khash.h"
-+#include "bam-0.1-legacy/faidx.h"
- 
- /* stolen from bam_aux.c */
- #define MAX_REGION 1<<29
--- 
-2.14.1
-

[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/, dev-perl/Bio-SamTools/files/

2020-05-20 Thread Kent Fredric 
commit: 1442f328453dc90ea24b64ec3abd4e661504f408
Author: Kent Fredric  gentoo  org>
AuthorDate: Wed May 20 17:00:14 2020 +
Commit: Kent Fredric  gentoo  org>
CommitDate: Wed May 20 17:01:20 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1442f328

dev-perl/Bio-SamTools: Add fixed version for bug #661112

- Reworked patches so the autodetection stuff is nixed, because its
  really silly and doesn't work.
- Paths now computed in ebuild and passed explicitly
- Fix handling of libdir for lib64 re bug #661112, but in a different
  way than proposed by Sławomir Nizio, mostly because I didn't see that
  suggestion until after I'd done all my changes (but also because
  relying on a hardcoded path in the code is also fragile)
- Converted to EAPI7
- Removed unused empty variable assignments

Bug: https://bugs.gentoo.org/661112
Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Kent Fredric  gentoo.org>

 .../Bio-SamTools/Bio-SamTools-1.430.0-r1.ebuild|  38 +++
 .../files/Bio-SamTools-1.430.0-legacy-r1.patch | 110 +
 2 files changed, 148 insertions(+)

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
new file mode 100644
index 000..861acb6faa2
--- /dev/null
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r1.ebuild
@@ -0,0 +1,38 @@
+# 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
+}

diff --git a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy-r1.patch 
b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy-r1.patch
new file mode 100644
index 000..ee9bde8fe3d
--- /dev/null
+++ b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy-r1.patch
@@ -0,0 +1,110 @@
+From 82942523b2db5143a9da0f9d2f8ec83a26c8d5b0 Mon Sep 17 00:00:00 2001
+From: Kent Fredric 
+Date: Sun, 10 Sep 2017 13:33:32 +1200
+Subject: Fix linking/compiling for bam-0.1-legacy
+
+---
+ Build.PL | 14 +++---
+ c_bin/bam2bedgraph.c |  2 +-
+ c_bin/makefile   |  6 +++---
+ lib/Bio/DB/Sam.xs|  6 +++---
+ 4 files changed, 14 insertions(+), 14 deletions(-)
+
+diff --git a/Build.PL b/Build.PL
+index 685815f..882f231 100644
+--- a/Build.PL
 b/Build.PL
+@@ -4,11 +4,10 @@ use strict;
+ use Module::Build;
+ use Module::Load::Conditional qw(can_load);
+ 
+-my $HeaderFile = "bam.h";
+-my $LibFile= "libbam.a";
+-my $ReadLine;
+-
+-my ($sam_include,$sam_lib) = find_sam(); # may exit with error here
++my ($sam_include,$sam_lib) = do {
++  ($ENV{"SAM_INCLUDE"} || die "SAM_INCLUDE not set"),
++  ($ENV{"SAM_LIB"} || die "SAM_LIB not set")
++};
+ 
+ my $class = Module::Build->subclass(code=> 'Perl interface to SamTools library for DNA 
sequencing',
+ license=> 'perl',
+ include_dirs   => [$sam_include],
+-extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'],
++extra_linker_flags => ["-L$sam_lib",'-lbam-0.1-legacy','-lpthread','-lz'],
+ 
+ extra_compiler_flags=>[
+ 
+@@ -67,7 +66,7 @@ $build->add_build_element('c_bin');
+ $build->create_build_script;
+ 
+ exit 0;
+-
++=for non-gentoo
+ sub find_sam {
+ my ($sam_include,$sam_lib);
+ 
+@@ -162,6 +161,7 @@ sub prompt {
+ $ReadLine->addhistory($in) if $in =~ /\S/;
+ return $in;
+ }
++=cut
+ 
+ sub _samtools {
+ $ENV{SAMTOOLS} ||
+diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c
+index 298e9a8..91218fa 100644
+--- a/c_bin/bam2bedgraph.c
 b/c_bin/bam2bedgraph.c
+@@ -1,5 +1,5 @@
+ #include 
+-#include "sam.h"
++#include "bam-0.1-legacy/sam.h"
+ 
+ typedef struct {
+   uint32_t ltid;
+diff --git a/c_bin/makefile b/c_bin/makefile
+index 9aef917..0abbb4c 100644
+--- a/c_bin/makefile
 b/c_bin/makefile
+@@ -1,5 +1,5 @@
+-CC=   gcc
+-CFLAGS=   -g -Wall -O2 -fPIC
++CC?=  gcc
++CFLAGS?=  -g -Wall -O2 -fPIC
+ DFLAGS=   -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE 
-D_USE_KNETFILE -D_CURSES_LIB=1
+ INCLUDES=
+ LIBPATH=
+@@ -14,7 +14,7 @@ PROG=bam2bedgraph
+ all:$(PROG)
+ 
+ bam2bedgraph: bam2bedgraph.o
+-

[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/files/, dev-perl/Bio-SamTools/

2017-09-09 Thread Kent Fredric 
commit: 29bb345f1ea0a356c7e7e4eca3ab3bc405a7d846
Author: Kent Fredric  gentoo  org>
AuthorDate: Sun Sep 10 03:20:29 2017 +
Commit: Kent Fredric  gentoo  org>
CommitDate: Sun Sep 10 03:22:39 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=29bb345f

dev-perl/Bio-SamTools: Bump to version 1.430.0

- Links against samtools:0.1-legacy series, as even though this code
  previously attempted to use 1.0+, closer inspection indicated
  incomplete linking, missing symbols, and failing tests introduced
  by this attempt. Additionally, upstream EXPLICITLY STATE the lack of
  current support for samtools 1.0

- Restores DIST_TEST as I can now test they work

- Fold swathe of sed commands into patch

Upstream:
- Ship some test files requried for tests to pass

Closes: https://bugs.gentoo.org/611970
Closes: https://bugs.gentoo.org/604950
Package-Manager: Portage-2.3.6, Repoman-2.3.2

 dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild  | 33 
 dev-perl/Bio-SamTools/Manifest |  1 +
 .../files/Bio-SamTools-1.430.0-legacy.patch| 88 ++
 3 files changed, 122 insertions(+)

diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild 
b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild
new file mode 100644
index 000..1147cec5a48
--- /dev/null
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DIST_AUTHOR=LDS
+DIST_VERSION=1.43
+inherit perl-module toolchain-funcs
+
+DESCRIPTION="Read SAM/BAM database files"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+LICENSE="|| ( Apache-2.0 Artistic-2 GPL-1+ )"
+
+RDEPEND="
+   >=sci-biology/bioperl-1.6.9
+   sci-biology/samtools:0.1-legacy=
+"
+DEPEND="${RDEPEND}
+   virtual/perl-ExtUtils-CBuilder
+   >=dev-perl/Module-Build-0.420.0
+"
+
+PATCHES=(
+   "${FILESDIR}"/${PN}-1.430.0-legacy.patch
+)
+
+src_prepare() {
+   perl-module_src_prepare
+   tc-export CC
+}

diff --git a/dev-perl/Bio-SamTools/Manifest b/dev-perl/Bio-SamTools/Manifest
index 733a42f0cc5..f379ea7e384 100644
--- a/dev-perl/Bio-SamTools/Manifest
+++ b/dev-perl/Bio-SamTools/Manifest
@@ -1 +1,2 @@
 DIST Bio-SamTools-1.42.tar.gz 337821 SHA256 
ef4b736e86442ce61f56ddd94befc302ccc4646cae3c45407e107400c703584c SHA512 
6a1f95104ce91a800a314c304915af9d6e1cc477c7d5f42b640d0a27b18cd32c4ad9e261cac5556f4863652570a3c573d34245963fc4b9ade067981b2a329271
 WHIRLPOOL 
5a216e51173ee5a9a930013718452bcbfbcffe1aa1663f50d567daf17378a50135b1b0b6d750c9aece05de268e730faf6c54963823c037559fb50ed95dda32c7
+DIST Bio-SamTools-1.43.tar.gz 340833 SHA256 
7085ee5e97ad75dbbebd8583072d67b2b06d29e7a9f9741c9ac58dabe300d3fd SHA512 
cd5bc6213c093f5105399c95278803afcc537bb3d191686cda0193b82fda2580749bf7533791899939a78963fcc0d6b36eabe9c309c9c6816a9849e3c892c41b
 WHIRLPOOL 
cd5ece1f08e2b4c8c64c4d289abc7a7035c18f725c28df4e9ac0319efdabb2137864b6d0b692928469c4c48010bf0ab823990a2074cef4c1a87707f5fd3f31e4

diff --git a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch 
b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch
new file mode 100644
index 000..8464f06a2f0
--- /dev/null
+++ b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch
@@ -0,0 +1,88 @@
+From 74b38ded97f7a1940c3a37b9aec9b3287a3a78bd Mon Sep 17 00:00:00 2001
+From: Kent Fredric 
+Date: Sun, 10 Sep 2017 13:33:32 +1200
+Subject: Fix linking/compiling for bam-0.1-legacy
+
+---
+ Build.PL | 6 +++---
+ c_bin/bam2bedgraph.c | 2 +-
+ c_bin/makefile   | 6 +++---
+ lib/Bio/DB/Sam.xs| 6 +++---
+ 4 files changed, 10 insertions(+), 10 deletions(-)
+
+diff --git a/Build.PL b/Build.PL
+index 685815f..2611759 100644
+--- a/Build.PL
 b/Build.PL
+@@ -4,8 +4,8 @@ use strict;
+ use Module::Build;
+ use Module::Load::Conditional qw(can_load);
+ 
+-my $HeaderFile = "bam.h";
+-my $LibFile= "libbam.a";
++my $HeaderFile = "bam-0.1-legacy/bam.h";
++my $LibFile= "libbam-0.1-legacy.so";
+ my $ReadLine;
+ 
+ my ($sam_include,$sam_lib) = find_sam(); # may exit with error here
+@@ -39,7 +39,7 @@ my $build = $class->new(
+ dist_abstract  => 'Perl interface to SamTools library for DNA 
sequencing',
+ license=> 'perl',
+ include_dirs   => [$sam_include],
+-extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'],
++extra_linker_flags => ["-L$sam_lib",'-lbam-0.1-legacy','-lpthread','-lz'],
+ 
+ extra_compiler_flags=>[
+ 
+diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c
+index 298e9a8..91218fa 100644
+--- a/c_bin/bam2bedgraph.c
 b/c_bin/bam2bedgraph.c
+@@ -1,5 +1,5 @@
+ #include 
+-#include "sam.h"
++#include "bam-0.1-legacy/sam.h"
+ 
+ typedef struct {
+   uint32_t ltid;
+diff --git a/c_bin/makefile b/c_bin/makefile
+index 9aef917..0abbb4c 100644
+--- a/c_bin/makefile
 b/c_bin/makefile
+@@ -1,5 +1,5 @@

[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/

2016-10-24 Thread Pacho Ramos 
commit: 1c59326088d72b88e4ecee7ce73d27737024d6c7
Author: Pacho Ramos  gentoo  org>
AuthorDate: Mon Oct 24 13:06:49 2016 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Mon Oct 24 13:32:36 2016 +
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

[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/

2016-10-24 Thread Pacho Ramos 
commit: 61b16ca3665661b434fab1f1ce557335f29fb652
Author: Pacho Ramos  gentoo  org>
AuthorDate: Mon Oct 24 13:06:18 2016 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Mon Oct 24 13:32:34 2016 +
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..
--- 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

[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-SamTools/

2015-12-28 Thread Andreas Hüttel 
commit: 087966e83658833cb4b436d828c3c0d3519cd5e4
Author: Andreas K. Hüttel  gentoo  org>
AuthorDate: Mon Dec 28 20:02:49 2015 +
Commit: Andreas Hüttel  gentoo  org>
CommitDate: Mon Dec 28 20:08:36 2015 +
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