commit: 29bb345f1ea0a356c7e7e4eca3ab3bc405a7d846 Author: Kent Fredric <kentnl <AT> gentoo <DOT> org> AuthorDate: Sun Sep 10 03:20:29 2017 +0000 Commit: Kent Fredric <kentnl <AT> gentoo <DOT> org> CommitDate: Sun Sep 10 03:22:39 2017 +0000 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 00000000000..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 00000000000..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 <kentfred...@gmail.com> +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 <stdio.h> +-#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 <unistd.h> + #include <math.h> +-#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 +
