From cbfe0e33651a8811229d663a9469cc97957b994e Mon Sep 17 00:00:00 2001 From: David Seifert Date: Mon, 6 Feb 2017 21:48:01 +0100 Subject: sci-biology/hmmer: Remove old Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3856 --- sci-biology/hmmer/Manifest | 1 - sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch | 23 ---- .../hmmer/files/hmmer-3.0-perl-5.16-2.patch | 132 --------------------- sci-biology/hmmer/hmmer-3.0.ebuild | 45 ------- 4 files changed, 201 deletions(-) delete mode 100644 sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch delete mode 100644 sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch delete mode 100644 sci-biology/hmmer/hmmer-3.0.ebuild diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest index dada0077d965..acffd6ebc766 100644 --- a/sci-biology/hmmer/Manifest +++ b/sci-biology/hmmer/Manifest @@ -1,3 +1,2 @@ DIST hmmer-2.3.2.tar.gz 1024933 SHA256 d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7 WHIRLPOOL 604cc3f532d6eae3fbca893d991d0714a5a897fbac3059d63fdbebc6221e9321c2b444db2700e7068a11c043c0a7f9f3935617a3aa1878ca06ba18c558d55d40 -DIST hmmer-3.0.tar.gz 3952015 SHA256 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83 SHA512 752f06b0494a87ccd2cf6aa93e622fd02173eaa0df60df0527b3361dcaa2baf2b45a2daf0123217c0029bc9d95e505a92f1e97039eb8b7218b4c4b65ddad1db5 WHIRLPOOL a181ce8ddb016bf1209c83fa754163e9ac653acb51fed13dee8598565d2f058a118fca04229aef7e4e5a79aae86712639b8e43bf7e12c50a8bf22e32be9df658 DIST hmmer-3.1b2.tar.gz 5965253 SHA256 dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536 SHA512 64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771 WHIRLPOOL 0b6d17b5f5efe31873cde93ff33cc5b01c53de8e1daf1ed473ef92d6585f34abcbb31e35e4d02537fbbc2c808131b70a0f51a3832ee332e23246cbc75edc354a diff --git a/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch b/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch deleted file mode 100644 index 983827b0bd46..000000000000 --- a/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch +++ /dev/null @@ -1,23 +0,0 @@ ---- easel/Makefile.in -+++ easel/Makefile.in -@@ -26,8 +26,7 @@ - LDFLAGS = @LDFLAGS@ - SIMDFLAGS= @SIMD_CFLAGS@ - CPPFLAGS = @CPPFLAGS@ --LIBGSL = @LIBGSL@ --LIBS = @LIBS@ @PTHREAD_LIBS@ -+LIBS = @LIBS@ @LIBGSL@ @PTHREAD_LIBS@ - - # Other tools - # -@@ -252,8 +251,8 @@ - else \ - DFILE=${srcdir}/esl_$${BASENAME}.c ;\ - fi;\ -- echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm;\ -- ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm -+ echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS};\ -+ ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS} - - - # install: installs libeasel.a in ${libdir}/ diff --git a/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch b/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch deleted file mode 100644 index 19d38c8e32ed..000000000000 --- a/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch +++ /dev/null @@ -1,132 +0,0 @@ - easel/devkit/autodoc | 4 ++-- - easel/devkit/esl-dependencies | 4 ++-- - easel/devkit/sqc | 7 +++---- - easel/testsuite/coverage_report.pl | 4 ++-- - easel/testsuite/driver_report.pl | 4 ++-- - easel/testsuite/valgrind_report.pl | 4 ++-- - profmark/rocplot.pl | 4 ++-- - 7 files changed, 15 insertions(+), 16 deletions(-) - -diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc -index 16bda4d..f5c5efc 100755 ---- a/easel/devkit/autodoc -+++ b/easel/devkit/autodoc -@@ -49,8 +49,8 @@ - # - # SRE, Tue Nov 30 19:43:47 2004 - --require "getopts.pl"; --&Getopts('n:t'); -+use Getopt::Std; -+getopts('n:t'); - $cfile = shift; - - if ($opt_t) { $show_api_table = 1; } -diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies -index a4dc126..b61fa7a 100755 ---- a/easel/devkit/esl-dependencies -+++ b/easel/devkit/esl-dependencies -@@ -13,8 +13,8 @@ - # SRE, Mon Jun 11 11:15:31 2007 - # SVN $Id$ - --require "getopts.pl" --&Getopts('1afr'); -+use Getopt::Std; -+getopts('1afr'); - - if ($opt_1) { $show_summary_table = 1; } - if ($opt_a) { $list_augfiles = 1; } -diff --git a/easel/devkit/sqc b/easel/devkit/sqc -index af3adf6..0cdb458 100755 ---- a/easel/devkit/sqc -+++ b/easel/devkit/sqc -@@ -205,12 +205,11 @@ - # SRE, Tue Aug 6 11:16:39 2002 - # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $ - --require "getopts.pl"; --require "importenv.pl"; -+use Getopt::Std; - - # Parse our command line - # --&Getopts('v'); -+getopts('v'); - if ($opt_v) { $verbose = 1; } - - -@@ -609,7 +608,7 @@ sub check_valgrind_status - # - sub tempname { - my ($dir, $name, $suffix); -- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";} -+ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";} - - foreach $suffix ("aa".."zz") { - $name = "$dir"."esltmp".$suffix.$$; -diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl -old mode 100755 -new mode 100644 -index 9c77791..024ed34 ---- a/easel/testsuite/coverage_report.pl -+++ b/easel/testsuite/coverage_report.pl -@@ -16,9 +16,9 @@ - # - # SRE, Thu Mar 1 19:22:57 2007 (Janelia) - # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $ --require "getopts.pl"; -+use Getopt::Std; - $have_sloccount = 1; --&Getopts('cs'); -+getopts('cs'); - if ($opt_c) { $do_recompile = 1; } - if ($opt_s) { $have_sloccount = 0; } - -diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl -index 757854d..a9a8902 100755 ---- a/easel/testsuite/driver_report.pl -+++ b/easel/testsuite/driver_report.pl -@@ -25,8 +25,8 @@ - # SRE, Fri Mar 2 10:01:44 2007 (Janelia) - # SVN $Id: driver_report.pl 326 2009-02-28 15:49:07Z eddys $ - --require "getopts.pl"; --&Getopts('c'); -+use Getopt::Std; -+getopts('c'); - if ($opt_c) { $do_recompile = 1; } - - if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } -diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl -old mode 100755 -new mode 100644 -index 186a392..07026a0 ---- a/easel/testsuite/valgrind_report.pl -+++ b/easel/testsuite/valgrind_report.pl -@@ -10,8 +10,8 @@ - # - # SRE, Fri Mar 2 08:37:48 2007 [Janelia] - # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $ --require "getopts.pl"; --&Getopts('c'); -+use Getopt::Std; -+getopts('c'); - if ($opt_c) { $do_recompile = 1; } - - if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } -diff --git a/profmark/rocplot.pl b/profmark/rocplot.pl -index d4c0f67..4e8175a 100755 ---- a/profmark/rocplot.pl -+++ b/profmark/rocplot.pl -@@ -2,8 +2,8 @@ - - $nsearches = 1567; - --require "getopts.pl"; --&Getopts('n:X:x:'); -+use Getopt::Std -+getopts('n:X:x:'); - - if ($opt_n) { $nsearches = $opt_n; } - if ($opt_X) { diff --git a/sci-biology/hmmer/hmmer-3.0.ebuild b/sci-biology/hmmer/hmmer-3.0.ebuild deleted file mode 100644 index 86183e7f9d3a..000000000000 --- a/sci-biology/hmmer/hmmer-3.0.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit eutils - -DESCRIPTION="Sequence analysis using profile hidden Markov models" -HOMEPAGE="http://hmmer.janelia.org/" -SRC_URI="ftp://selab.janelia.org/pub/software/hmmer3/${PV}/${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="+cpu_flags_x86_sse mpi +threads gsl static-libs" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos" - -DEPEND=" - mpi? ( virtual/mpi ) - gsl? ( >=sci-libs/gsl-1.12 )" -RDEPEND="${DEPEND}" - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-fix_tests.patch \ - "${FILESDIR}"/${P}-perl-5.16-2.patch -} - -src_configure() { - econf \ - $(use_enable cpu_flags_x86_sse sse) \ - $(use_enable mpi) \ - $(use_enable threads) \ - $(use_with gsl) -} - -src_install() { - default - - use static-libs && dolib.a src/libhmmer.a easel/libeasel.a - - insinto /usr/share/${PN} - doins -r tutorial - dodoc Userguide.pdf -} -- cgit v1.2.3-65-gdbad