dev-perl/Bio-SamTools: Drop old; restrict version for dep on samtools, #523568

(Portage version: 2.2.13/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

5 files changed, 12 insertions, 115 deletions

diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.330.0.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.330.0.ebuild
deleted file mode 100644
index 7dcbc8844650..000000000000
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.330.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.330.0.ebuild,v 1.1 2012/02/29 08:57:25 robbat2 Exp $
-
-EAPI=4
-
-MODULE_AUTHOR=LDS
-MODULE_VERSION=1.33
-inherit perl-module
-
-DESCRIPTION="Read SAM/BAM database files"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="sci-biology/bioperl
-	>=sci-biology/samtools-0.1.16"
-DEPEND="${RDEPEND}
-	virtual/perl-ExtUtils-CBuilder
-	virtual/perl-Module-Build
-"
-
-SRC_TEST=do
-
-src_prepare() {
-	sed -i -e 's|my $HeaderFile = "bam.h";|my $HeaderFile = "bam/bam.h";|' \
-		-e 's|my $LibFile    = "libbam.a";|my $LibFile    = "libbam.so";|' Build.PL || die
-	sed -i -e 's|#include "bam.h"|#include "bam/bam.h"|' \
-		-e 's|#include "khash.h"|#include "bam/khash.h"|' \
-		-e 's|#include "faidx.h"|#include "bam/faidx.h"|' lib/Bio/DB/Sam.xs || die
-	perl-module_src_prepare
-}
diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.370.0-r1.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.370.0-r1.ebuild
deleted file mode 100644
index 23cc2c4bd75b..000000000000
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.370.0-r1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.370.0-r1.ebuild,v 1.1 2013/01/24 07:58:57 jlec Exp $
-
-EAPI=4
-
-MODULE_AUTHOR=LDS
-MODULE_VERSION=1.37
-inherit perl-module
-
-DESCRIPTION="Read SAM/BAM database files"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="sci-biology/bioperl
-	>=sci-biology/samtools-0.1.16"
-DEPEND="${RDEPEND}
-	virtual/perl-ExtUtils-CBuilder
-	virtual/perl-Module-Build
-"
-
-SRC_TEST=do
-
-src_prepare() {
-	sed \
-		-e 's|my $HeaderFile = "bam.h";|my $HeaderFile = "bam/bam.h";|' \
-		-e 's|my $LibFile    = "libbam.a";|my $LibFile    = "libbam.so";|' \
-		-i Build.PL || die
-	sed \
-		-e 's|#include "bam.h"|#include "bam/bam.h"|' \
-		-e 's|#include "sam.h"|#include "bam/sam.h"|' \
-		-e 's|#include "khash.h"|#include "bam/khash.h"|' \
-		-e 's|#include "faidx.h"|#include "bam/faidx.h"|' \
-		-i lib/Bio/DB/Sam.xs c_bin/bam2bedgraph.c || die
-
-	perl-module_src_prepare
-}
diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.380.0.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.380.0.ebuild
deleted file mode 100644
index e6e399649aec..000000000000
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.380.0.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.380.0.ebuild,v 1.1 2013/08/17 14:02:59 patrick Exp $
-
-EAPI=4
-
-MODULE_AUTHOR=LDS
-MODULE_VERSION=1.38
-inherit perl-module
-
-DESCRIPTION="Read SAM/BAM database files"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="sci-biology/bioperl
-	>=sci-biology/samtools-0.1.16"
-DEPEND="${RDEPEND}
-	virtual/perl-ExtUtils-CBuilder
-	virtual/perl-Module-Build
-"
-
-SRC_TEST=do
-
-src_prepare() {
-	sed \
-		-e 's|my $HeaderFile = "bam.h";|my $HeaderFile = "bam/bam.h";|' \
-		-e 's|my $LibFile    = "libbam.a";|my $LibFile    = "libbam.so";|' \
-		-i Build.PL || die
-	sed \
-		-e 's|#include "bam.h"|#include "bam/bam.h"|' \
-		-e 's|#include "sam.h"|#include "bam/sam.h"|' \
-		-e 's|#include "khash.h"|#include "bam/khash.h"|' \
-		-e 's|#include "faidx.h"|#include "bam/faidx.h"|' \
-		-i lib/Bio/DB/Sam.xs c_bin/bam2bedgraph.c || die
-
-	perl-module_src_prepare
-}
diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild
index 4bce31003650..4ea422c499a0 100644
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild,v 1.1 2014/08/26 19:37:47 axs Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild,v 1.2 2014/09/24 07:52:53 jlec Exp $
 
 EAPI=5
 
@@ -14,8 +14,11 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-RDEPEND="sci-biology/bioperl
-	>=sci-biology/samtools-0.1.16"
+RDEPEND="
+	sci-biology/bioperl
+	>=sci-biology/samtools-0.1.16
+	<sci-biology/samtools-1
+"
 DEPEND="${RDEPEND}
 	virtual/perl-ExtUtils-CBuilder
 	virtual/perl-Module-Build
diff --git a/dev-perl/Bio-SamTools/ChangeLog b/dev-perl/Bio-SamTools/ChangeLog
index 8ccb593f3c0f..fdc3e45e8c3f 100644
--- a/dev-perl/Bio-SamTools/ChangeLog
+++ b/dev-perl/Bio-SamTools/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for dev-perl/Bio-SamTools
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog,v 1.14 2014/08/26 19:37:47 axs Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog,v 1.15 2014/09/24 07:52:53 jlec Exp $
+
+  24 Sep 2014; Justin Lecher <jlec@gentoo.org> -Bio-SamTools-1.330.0.ebuild,
+  -Bio-SamTools-1.370.0-r1.ebuild, -Bio-SamTools-1.380.0.ebuild,
+  Bio-SamTools-1.390.0-r1.ebuild:
+  Drop old; restrict version for dep on samtools, #523568
 
 *Bio-SamTools-1.390.0-r1 (26 Aug 2014)