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