From feb0daf81d888e9160f9f94502de09b66f2a63fd Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 21 Jun 2020 17:50:24 +0100 Subject: gentoo resync : 21.06.2020 --- dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild | 33 -------- dev-perl/Bio-SamTools/Manifest | 2 - .../files/Bio-SamTools-1.430.0-legacy.patch | 88 ---------------------- 3 files changed, 123 deletions(-) delete mode 100644 dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild delete mode 100644 dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch (limited to 'dev-perl/Bio-SamTools') 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/Manifest b/dev-perl/Bio-SamTools/Manifest index d21de481858c..f36d1f35a96f 100644 --- a/dev-perl/Bio-SamTools/Manifest +++ b/dev-perl/Bio-SamTools/Manifest @@ -1,6 +1,4 @@ AUX Bio-SamTools-1.430.0-legacy-r1.patch 2934 BLAKE2B 17e310aeac8d2548e168c125d498b623fb3ea6ac59da52c9dd7918c4a42a5fe6c3a11488fe67d833f265151330f339e6700bb323e5e6f355a445e58b96546246 SHA512 ac995f9a55e7cac70238f7945f56f91bbbafe207dc55b05115d519737c9a626fa57ccb265c78f028c1a03297bf5916dc60b7d51fe9988b30d27021b03717c750 -AUX Bio-SamTools-1.430.0-legacy.patch 2466 BLAKE2B ab4a384031f4f2b333700e9ddf62d7a8293f88c0390b8f151a6b0657f4f59613f1e33d259f9b575fb8348593dfdc408e4d6168ecba3c3863a856f3ef6abefa9f SHA512 3e886216a966144aa69aa86d3ffa28ee8f9aadec84f760259aad9fcdc09ca69499655e8c3d81a5b39d79fd503f14e0159bdf2422d66458f1e9095b2fb05da26a DIST Bio-SamTools-1.43.tar.gz 340833 BLAKE2B 2b488667b86ef1bedb7cf74dfdcb3abc0302d9f309c1fc3077682bb400c8307f3b7d8fb1a9015a26f9a17f9e9955845d160512aa3273c368b720fe51b4392458 SHA512 cd5bc6213c093f5105399c95278803afcc537bb3d191686cda0193b82fda2580749bf7533791899939a78963fcc0d6b36eabe9c309c9c6816a9849e3c892c41b EBUILD Bio-SamTools-1.430.0-r1.ebuild 785 BLAKE2B ebf4bcc864c98ccf5bbeb62091a8e8a4c960b6d8956b9fc72c5ed802ffbbc382c87c07aef467cc2c21bf811bea1df8aa28e867c14f60cbfec4654cab5329f8ff SHA512 676d31ac906659d14a1addc620a40c846de0e3c73c7b1bfafdef2da60fc97a21e78102d5d2f067af23361eedce9159a07de82c20ac2df79d885a4c1509fee7a2 -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-1.430.0-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 -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 --#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 - #include --#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 - -- cgit v1.2.3