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

[Kent Fredric]

commit:     1442f328453dc90ea24b64ec3abd4e661504f408
Author:     Kent Fredric <kentnl <AT> gentoo <DOT> org>
AuthorDate: Wed May 20 17:00:14 2020 +0000
Commit:     Kent Fredric <kentnl <AT> gentoo <DOT> org>
CommitDate: Wed May 20 17:01:20 2020 +0000
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 <kentnl <AT> 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 00000000000..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 00000000000..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 <kentfredric@×××××.com>
+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=><<EOF);
+     sub process_c_bin_files {
+@@ -39,7 +38,7 @@ 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=>[
+ 
+@@ -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 {
+     $ENV{SAMTOOLS} ||
+diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c
+index 298e9a8..91218fa 100644
+--- a/c_bin/bam2bedgraph.c
++++ b/c_bin/bam2bedgraph.c
+@@ -1,5 +1,5 @@
+ #include <stdio.h>
+-#include "sam.h"
++#include "bam-0.1-legacy/sam.h"
+ 
+ typedef struct {
+   uint32_t ltid;
+diff --git a/c_bin/makefile b/c_bin/makefile
+index 9aef917..0abbb4c 100644
+--- a/c_bin/makefile
++++ b/c_bin/makefile
+@@ -1,5 +1,5 @@
+-CC=		gcc
+-CFLAGS=		-g -Wall -O2 -fPIC
++CC?=		gcc
++CFLAGS?=		-g -Wall -O2 -fPIC
+ DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
+ INCLUDES=
+ LIBPATH=
+@@ -14,7 +14,7 @@ PROG=		bam2bedgraph
+ all:$(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
+-- 
+2.26.2
+