commit: 2a866fb9126e4c0a780620e041598cc6d3726ad3 Author: Kent Fredric <kentnl <AT> gentoo <DOT> org> AuthorDate: Sat Jun 20 04:28:41 2020 +0000 Commit: Kent Fredric <kentnl <AT> gentoo <DOT> org> CommitDate: Sat Jun 20 04:28:41 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2a866fb9
dev-perl/Bio-SamTools: Cleanup old 1.430.0 - Unstable(~) eclipsed by 1.430.0-r1 for ~1 month Closes: https://bugs.gentoo.org/661112 Package-Manager: Portage-2.3.100, Repoman-2.3.22 Signed-off-by: Kent Fredric <kentnl <AT> gentoo.org> dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild | 33 -------- .../files/Bio-SamTools-1.430.0-legacy.patch | 88 ---------------------- 2 files changed, 121 deletions(-) diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild deleted file mode 100644 index 1147cec5a48..00000000000 --- a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# 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/files/Bio-SamTools-1.430.0-legacy.patch b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch deleted file mode 100644 index 8464f06a2f0..00000000000 --- a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch +++ /dev/null @@ -1,88 +0,0 @@ -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 -
