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

[Pacho Ramos]

commit:     61b16ca3665661b434fab1f1ce557335f29fb652
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 24 13:06:18 2016 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Mon Oct 24 13:32:34 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61b16ca3

dev-perl/Bio-SamTools: Drop old

Package-Manager: portage-2.3.2
RepoMan-Options: --force

 dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild | 50 -----------------------
 dev-perl/Bio-SamTools/Manifest                    |  1 -
 2 files changed, 51 deletions(-)

diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild 
b/dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild
deleted file mode 100644
index f38c642..00000000
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-MODULE_AUTHOR=LDS
-MODULE_VERSION=1.41
-
-inherit perl-module toolchain-funcs
-
-DESCRIPTION="Read SAM/BAM database files"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-       >=sci-biology/bioperl-1.6.9
-       >=sci-biology/samtools-1
-"
-DEPEND="${RDEPEND}
-       virtual/perl-ExtUtils-CBuilder
-       >=dev-perl/Module-Build-0.420.0
-"
-
-SRC_TEST=skip
-# cannot load its own library, fundamentally b0rken
-
-PATCHES=(
-       "${FILESDIR}"/${PN}-1.390.0-samtools-1.patch
-)
-
-src_prepare() {
-       find . -type f -exec chmod +w '{}' + || die
-       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 "htslib/khash.h"|' \
-               -e 's|#include "faidx.h"|#include "htslib/faidx.h"|' \
-               -i lib/Bio/DB/Sam.xs c_bin/bam2bedgraph.c || die
-
-       perl-module_src_prepare
-
-       tc-export CC
-}

diff --git a/dev-perl/Bio-SamTools/Manifest b/dev-perl/Bio-SamTools/Manifest
index 9143d80..733a42f 100644
--- a/dev-perl/Bio-SamTools/Manifest
+++ b/dev-perl/Bio-SamTools/Manifest
@@ -1,2 +1 @@
-DIST Bio-SamTools-1.41.tar.gz 338745 SHA256 
b5d7ca16c96cc9fbee5daceb3268f36011740fe4de92074c17a729bac57c3077 SHA512 
6f822cd219ecf86e95bc3a6bde1aebbe5eb8284b21b07ca919618c1422c37e6d182285d1a5e77848c6d5cea0dc74a51705f6bc1a27d44aeeaaa69f1cea58f147
 WHIRLPOOL 
b651ea5059ea46ab5e31d237d3e52d7936921470bbd04133be70f935a47b913dc7f3b154c14d1af52f0ba2f5afc6878a27d88e4bbf9d39023cf786bca70f6696
 DIST Bio-SamTools-1.42.tar.gz 337821 SHA256 
ef4b736e86442ce61f56ddd94befc302ccc4646cae3c45407e107400c703584c SHA512 
6a1f95104ce91a800a314c304915af9d6e1cc477c7d5f42b640d0a27b18cd32c4ad9e261cac5556f4863652570a3c573d34245963fc4b9ade067981b2a329271
 WHIRLPOOL 
5a216e51173ee5a9a930013718452bcbfbcffe1aa1663f50d567daf17378a50135b1b0b6d750c9aece05de268e730faf6c54963823c037559fb50ed95dda32c7