gentoo resync : 16.04.2018

3 files changed, 0 insertions, 111 deletions

diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
deleted file mode 100644
index 2688bc95030a..000000000000
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DIST_AUTHOR=LDS
-DIST_VERSION=1.42
-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-1:0
-"
-DEPEND="${RDEPEND}
-	virtual/perl-ExtUtils-CBuilder
-	>=dev-perl/Module-Build-0.420.0
-"
-
-DIST_TEST=skip
-# cannot load its own library, fundamentally b0rken
-
-PATCHES=(
-	"${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 c3c331e1623e..9130d1cf0d4e 100644
--- a/dev-perl/Bio-SamTools/Manifest
+++ b/dev-perl/Bio-SamTools/Manifest
@@ -1,7 +1,4 @@
-AUX Bio-SamTools-1.390.0-samtools-1.patch 1633 BLAKE2B bba71fe5a80c5275b48cb68c6acfda4591d2f3ef72495ed1b81b4da4673212775076f151660e5a61092858b67b1a4ef9c085977ca7968040b2d98bc4099bc5f9 SHA512 e2c984d76dba66956aeaa81bd803191d71e0084b405745d77d2d00206f6a054d0d378763b46aac89dd2cbd1f6d33ae67a246c707829181d14110f35cd89b9b82
 AUX Bio-SamTools-1.430.0-legacy.patch 2466 BLAKE2B ab4a384031f4f2b333700e9ddf62d7a8293f88c0390b8f151a6b0657f4f59613f1e33d259f9b575fb8348593dfdc408e4d6168ecba3c3863a856f3ef6abefa9f SHA512 3e886216a966144aa69aa86d3ffa28ee8f9aadec84f760259aad9fcdc09ca69499655e8c3d81a5b39d79fd503f14e0159bdf2422d66458f1e9095b2fb05da26a
-DIST Bio-SamTools-1.42.tar.gz 337821 BLAKE2B 21d18bdf8cd3f101dc07cf1bd0d978d949f3dc35ebc5b78cdb3aafff50d8be2a0d2e5999301cb51b5a2314ee6fa93a14f4d6c46431dfdc130f0dd8b0e1a03969 SHA512 6a1f95104ce91a800a314c304915af9d6e1cc477c7d5f42b640d0a27b18cd32c4ad9e261cac5556f4863652570a3c573d34245963fc4b9ade067981b2a329271
 DIST Bio-SamTools-1.43.tar.gz 340833 BLAKE2B 2b488667b86ef1bedb7cf74dfdcb3abc0302d9f309c1fc3077682bb400c8307f3b7d8fb1a9015a26f9a17f9e9955845d160512aa3273c368b720fe51b4392458 SHA512 cd5bc6213c093f5105399c95278803afcc537bb3d191686cda0193b82fda2580749bf7533791899939a78963fcc0d6b36eabe9c309c9c6816a9849e3c892c41b
-EBUILD Bio-SamTools-1.420.0.ebuild 1143 BLAKE2B 8c575b41696907a3a16ef98bbdd430802f20e5b207915e9c7a004a60e8a96f53470a13e99b55bb488ad673ae4f47259cfeec43ede8488d07e7fd4d338bd05b29 SHA512 ecb5a06711da9ef3b85278f690efd331eb9fa477997a5f2319265f6ec57d06c0feeed1500113175938bf86c63872c7d85a4d9f9e781bc8d273fb54d9e903dd32
 EBUILD Bio-SamTools-1.430.0.ebuild 591 BLAKE2B d92daf9d86f1d8a4b60257fd810d012794d41e7082555a89b1fa66f2f2bb65b2585a27d68684d2dd1820dda214905868c752bbcbf3083e32d1797848cfaae4cc SHA512 fe282e0404be9a758e1f42ec9d12ae1dd935aa0f9fca8d07e07f55ae6453b2c615868de859b4e5af9f2195c18b988f0ac8132db0c8c0a880843178bce041b221
 MISC metadata.xml 1642 BLAKE2B 8e00b2305f870d0007a22f366376d77d359df2ab54d279da2c7b791da320f72e7d110956251c3adcddaf8b4b318110b5ff4b6cde4a6cd359cbb403f666c7de93 SHA512 d518abd6c3f99c370ce401f7fce792b2d55d29fc2baccb54f8a32f2e2c385acf3dd7f31f3c3fc0764fb3b754e4bd3378eef0002a0e4d48b2ae2a116c85379c50
diff --git a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch
deleted file mode 100644
index 8e7250c51736..000000000000
--- a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch
+++ /dev/null
@@ -1,59 +0,0 @@
- Build.PL          | 2 +-
- c_bin/makefile    | 6 +++---
- lib/Bio/DB/Sam.xs | 9 ++++++---
- 3 files changed, 10 insertions(+), 7 deletions(-)
-
-diff --git a/Build.PL b/Build.PL
-index 1393e03..cf97ad5 100644
---- a/Build.PL
-+++ b/Build.PL
-@@ -38,7 +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','-lhts','-lpthread','-lz'],
- 
-     extra_compiler_flags=>[
- 
-diff --git a/c_bin/makefile b/c_bin/makefile
-index 9aef917..96a30f2 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 -lhts -lpthread -lm -lz
- 
- clean:
- 	rm -f *.o $(PROG)
-diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs
-index 5ca303b..7f92860 100644
---- a/lib/Bio/DB/Sam.xs
-+++ b/lib/Bio/DB/Sam.xs
-@@ -571,9 +571,12 @@ bama_l_aux(b,...)
-     Bio::DB::Bam::Alignment b
- PROTOTYPE: $;$
- CODE:
--    if (items > 1)
--      b->l_aux = SvIV(ST(1));
--    RETVAL=b->l_aux;
-+    if (items > 1) {
-+      RETVAL = SvIV(ST(1));
-+      }
-+    else {
-+      RETVAL=bam_get_l_aux(b);
-+    }
- OUTPUT:
-     RETVAL
-