From: Kent Fredric Date: Wed, 20 May 2020 17:00:14 +0000 (+1200) Subject: dev-perl/Bio-SamTools: Add fixed version for bug #661112 X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=1442f328453dc90ea24b64ec3abd4e661504f408;p=gentoo.git 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 --- 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 000000000000..861acb6faa27 --- /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 000000000000..ee9bde8fe3d0 --- /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 $class = Module::Build->subclass(code=><new( + dist_abstract => 'Perl interface to SamTools library for DNA sequencing', + license => 'perl', + include_dirs => [$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=>[ + +@@ -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 +- $(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 +-- +2.26.2 +