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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 <kentnl@gentoo.org>
This commit is contained in:
Kent Fredric
38
dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r1.ebuild
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38
dev-perl/Bio-SamTools/Bio-SamTools-1.430.0-r1.ebuild
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@@ -0,0 +1,38 @@
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# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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DIST_AUTHOR=LDS
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DIST_VERSION=1.43
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inherit perl-module toolchain-funcs multilib
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DESCRIPTION="Read SAM/BAM database files"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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LICENSE="|| ( Apache-2.0 Artistic-2 GPL-1+ )"
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RDEPEND="
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>=sci-biology/bioperl-1.6.9
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sci-biology/samtools:0.1-legacy=
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"
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DEPEND="
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dev-perl/Module-Build
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sci-biology/samtools:0.1-legacy=
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"
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BDEPEND="${RDEPEND}
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virtual/perl-ExtUtils-CBuilder
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>=dev-perl/Module-Build-0.420.0
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"
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PATCHES=(
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"${FILESDIR}"/${PN}-1.430.0-legacy-r1.patch
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)
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src_configure() {
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tc-export CC
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SAM_LIB="${EPREFIX}/usr/$(get_libdir)/libbam-0.1-legacy.so" \
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SAM_INCLUDE="${EPREFIX}/usr/include/bam-0.1-legacy" \
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perl-module_src_configure
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}
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110
dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy-r1.patch
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110
dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy-r1.patch
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@@ -0,0 +1,110 @@
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From 82942523b2db5143a9da0f9d2f8ec83a26c8d5b0 Mon Sep 17 00:00:00 2001
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From: Kent Fredric <kentfredric@gmail.com>
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Date: Sun, 10 Sep 2017 13:33:32 +1200
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Subject: Fix linking/compiling for bam-0.1-legacy
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---
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Build.PL | 14 +++++++-------
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c_bin/bam2bedgraph.c | 2 +-
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c_bin/makefile | 6 +++---
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lib/Bio/DB/Sam.xs | 6 +++---
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4 files changed, 14 insertions(+), 14 deletions(-)
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diff --git a/Build.PL b/Build.PL
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index 685815f..882f231 100644
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--- a/Build.PL
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+++ b/Build.PL
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@@ -4,11 +4,10 @@ use strict;
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use Module::Build;
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use Module::Load::Conditional qw(can_load);
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-my $HeaderFile = "bam.h";
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-my $LibFile = "libbam.a";
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-my $ReadLine;
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-
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-my ($sam_include,$sam_lib) = find_sam(); # may exit with error here
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+my ($sam_include,$sam_lib) = do {
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+ ($ENV{"SAM_INCLUDE"} || die "SAM_INCLUDE not set"),
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+ ($ENV{"SAM_LIB"} || die "SAM_LIB not set")
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+};
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my $class = Module::Build->subclass(code=><<EOF);
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sub process_c_bin_files {
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@@ -39,7 +38,7 @@ my $build = $class->new(
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dist_abstract => 'Perl interface to SamTools library for DNA sequencing',
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license => 'perl',
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include_dirs => [$sam_include],
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- extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'],
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+ extra_linker_flags => ["-L$sam_lib",'-lbam-0.1-legacy','-lpthread','-lz'],
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extra_compiler_flags=>[
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@@ -67,7 +66,7 @@ $build->add_build_element('c_bin');
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$build->create_build_script;
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exit 0;
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-
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+=for non-gentoo
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sub find_sam {
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my ($sam_include,$sam_lib);
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@@ -162,6 +161,7 @@ sub prompt {
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$ReadLine->addhistory($in) if $in =~ /\S/;
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return $in;
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}
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+=cut
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sub _samtools {
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$ENV{SAMTOOLS} ||
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diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c
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index 298e9a8..91218fa 100644
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--- a/c_bin/bam2bedgraph.c
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+++ b/c_bin/bam2bedgraph.c
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@@ -1,5 +1,5 @@
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#include <stdio.h>
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-#include "sam.h"
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+#include "bam-0.1-legacy/sam.h"
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typedef struct {
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uint32_t ltid;
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diff --git a/c_bin/makefile b/c_bin/makefile
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index 9aef917..0abbb4c 100644
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--- a/c_bin/makefile
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+++ b/c_bin/makefile
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@@ -1,5 +1,5 @@
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-CC= gcc
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-CFLAGS= -g -Wall -O2 -fPIC
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+CC?= gcc
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+CFLAGS?= -g -Wall -O2 -fPIC
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DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
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INCLUDES=
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LIBPATH=
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@@ -14,7 +14,7 @@ PROG= bam2bedgraph
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all:$(PROG)
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bam2bedgraph: bam2bedgraph.o
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- $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam -lpthread -lm -lz
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+ $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam-0.1-legacy -lpthread -lm -lz
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clean:
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rm -f *.o $(PROG)
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diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs
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index 023f655..86410fb 100644
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--- a/lib/Bio/DB/Sam.xs
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+++ b/lib/Bio/DB/Sam.xs
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@@ -25,9 +25,9 @@
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#include <unistd.h>
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#include <math.h>
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-#include "bam.h"
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-#include "khash.h"
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-#include "faidx.h"
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+#include "bam-0.1-legacy/bam.h"
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+#include "bam-0.1-legacy/khash.h"
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+#include "bam-0.1-legacy/faidx.h"
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/* stolen from bam_aux.c */
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#define MAX_REGION 1<<29
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--
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2.26.2
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