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@gentoo.org>

2 files changed, 0 insertions, 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 1147cec5a486..000000000000
--- 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 8464f06a2f01..000000000000
--- 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 <kentfredric@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
-