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commit: 34b9085a65dbd111a02b71d66e07caad8ec31e32 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Oct 9 15:21:03 2016 +0000 |
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Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de> |
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CommitDate: Sun Oct 9 15:21:03 2016 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=34b9085a |
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|
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sci-biology/hmmer: Remove, latest version in main tree |
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|
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.../hmmer/files/hmmer-3.1_beta2-fix_tests.patch | 12 --- |
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.../hmmer/files/hmmer-3.1_beta2-perl-5.16-2.patch | 90 ---------------------- |
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sci-biology/hmmer/hmmer-3.1_beta2.ebuild | 48 ------------ |
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sci-biology/hmmer/metadata.xml | 8 -- |
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4 files changed, 158 deletions(-) |
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|
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diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix_tests.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix_tests.patch |
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deleted file mode 100644 |
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index 9f4ea12..0000000 |
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--- a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix_tests.patch |
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+++ /dev/null |
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@@ -1,12 +0,0 @@ |
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---- easel/Makefile.in.old 2015-11-19 23:49:53.470244757 +0100 |
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-+++ easel/Makefile.in 2015-11-19 23:52:01.120245091 +0100 |
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-@@ -52,8 +52,7 @@ |
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- SIMDFLAGS= @SIMD_CFLAGS@ |
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- CPPFLAGS = @CPPFLAGS@ |
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- LDFLAGS = @LDFLAGS@ |
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--LIBGSL = @LIBGSL@ |
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--LIBS = @LIBS@ @PTHREAD_LIBS@ |
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-+LIBS = @LIBS@ @LIBGSL@ @PTHREAD_LIBS@ |
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- |
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- # Other tools |
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- # |
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|
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diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-perl-5.16-2.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-perl-5.16-2.patch |
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deleted file mode 100644 |
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index 88a8ea4..0000000 |
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--- a/sci-biology/hmmer/files/hmmer-3.1_beta2-perl-5.16-2.patch |
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+++ /dev/null |
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@@ -1,90 +0,0 @@ |
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---- easel/devkit/autodoc.ori 2015-11-19 23:54:04.170245412 +0100 |
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-+++ easel/devkit/autodoc 2015-11-19 23:54:27.190245472 +0100 |
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-@@ -49,8 +49,8 @@ |
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- # |
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- # SRE, Tue Nov 30 19:43:47 2004 |
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- |
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--require "getopts.pl"; |
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--&Getopts('n:t'); |
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-+use Getopt::Std; |
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-+getopts('n:t'); |
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- $cfile = shift; |
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- |
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- if ($opt_t) { $show_api_table = 1; } |
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---- easel/devkit/esl-dependencies.ori 2015-11-19 23:54:40.830245508 +0100 |
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-+++ easel/devkit/esl-dependencies 2015-11-19 23:55:08.510245580 +0100 |
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-@@ -13,8 +13,8 @@ |
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- # SRE, Mon Jun 11 11:15:31 2007 |
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- # SVN $Id$ |
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- |
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--require "getopts.pl" |
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--&Getopts('1afr'); |
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-+use Getopt::Std; |
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-+getopts('1afr'); |
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- |
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- if ($opt_1) { $show_summary_table = 1; } |
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- if ($opt_a) { $list_augfiles = 1; } |
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---- easel/devkit/sqc.ori 2015-11-19 23:55:15.900245600 +0100 |
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-+++ easel/devkit/sqc 2015-11-19 23:56:16.530245758 +0100 |
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-@@ -674,7 +674,7 @@ |
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- # |
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- sub tempname { |
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- my ($dir, $name, $suffix); |
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-- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";} |
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-+ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";} |
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- |
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- foreach $suffix ("aa".."zz") { |
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- $name = "$dir"."esltmp".$suffix.$$; |
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---- easel/testsuite/coverage_report.pl.ori 2015-11-19 23:56:34.010245804 +0100 |
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-+++ easel/testsuite/coverage_report.pl 2015-11-19 23:57:03.040245879 +0100 |
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-@@ -16,9 +16,9 @@ |
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- # |
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- # SRE, Thu Mar 1 19:22:57 2007 (Janelia) |
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- # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $ |
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--require "getopts.pl"; |
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-+use Getopt::Std; |
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- $have_sloccount = 1; |
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--&Getopts('cs'); |
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-+getopts('cs'); |
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- if ($opt_c) { $do_recompile = 1; } |
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- if ($opt_s) { $have_sloccount = 0; } |
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- |
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---- easel/testsuite/driver_report.pl.ori 2015-11-19 23:57:14.600245910 +0100 |
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-+++ easel/testsuite/driver_report.pl 2015-11-19 23:57:39.310245974 +0100 |
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-@@ -25,8 +25,8 @@ |
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- # SRE, Fri Mar 2 10:01:44 2007 (Janelia) |
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- # SVN $Id: driver_report.pl 664 2011-02-27 17:08:36Z eddys $ |
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- |
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--require "getopts.pl"; |
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--&Getopts('c'); |
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-+use Getopt::Std; |
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-+getopts('c'); |
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- if ($opt_c) { $do_recompile = 1; } |
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- |
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- if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } |
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---- easel/testsuite/valgrind_report.pl.ori 2015-11-19 23:57:47.480245996 +0100 |
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-+++ easel/testsuite/valgrind_report.pl 2015-11-19 23:58:03.000246036 +0100 |
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-@@ -10,8 +10,8 @@ |
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- # |
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- # SRE, Fri Mar 2 08:37:48 2007 [Janelia] |
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- # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $ |
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--require "getopts.pl"; |
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--&Getopts('c'); |
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-+use Getopt::Std; |
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-+getopts('c'); |
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- if ($opt_c) { $do_recompile = 1; } |
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- |
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- if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } |
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---- profmark/rocplot.pl.ori 2015-11-19 23:58:12.530246061 +0100 |
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-+++ profmark/rocplot.pl 2015-11-19 23:58:43.090246141 +0100 |
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-@@ -2,8 +2,8 @@ |
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- |
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- $nsearches = 2809; |
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- |
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--require "getopts.pl"; |
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--&Getopts('n:X:x:'); |
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-+use Getopt::Std; |
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-+getopts('n:X:x:'); |
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- |
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- if ($opt_n) { $nsearches = $opt_n; } |
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- if ($opt_X) { |
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|
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diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild |
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deleted file mode 100644 |
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index 880df1e..0000000 |
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--- a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild |
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+++ /dev/null |
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@@ -1,48 +0,0 @@ |
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-# Copyright 1999-2015 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=5 |
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- |
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-inherit eutils |
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- |
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-MY_PV="3.1b2" |
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-DESCRIPTION="Sequence analysis using profile hidden Markov models" |
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-HOMEPAGE="http://hmmer.janelia.org/" |
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-SRC_URI="ftp://selab.janelia.org/pub/software/hmmer3/"${MY_PV}"/"${PN}"-"${MY_PV}".tar.gz" |
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- |
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-LICENSE="GPL-3" |
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-SLOT="0" |
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-IUSE="+cpu_flags_x86_sse mpi +threads gsl static-libs" |
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-KEYWORDS="~amd64" |
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- |
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-DEPEND=" |
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- mpi? ( virtual/mpi ) |
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- gsl? ( >=sci-libs/gsl-1.12 )" |
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-RDEPEND="${DEPEND}" |
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- |
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-S="${WORKDIR}"/"${PN}"-"${MY_PV}" |
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- |
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-src_prepare() { |
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- epatch \ |
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- "${FILESDIR}"/${P}-fix_tests.patch \ |
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- "${FILESDIR}"/${P}-perl-5.16-2.patch |
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-} |
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- |
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-src_configure() { |
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- econf \ |
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- $(use_enable cpu_flags_x86_sse sse) \ |
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- $(use_enable mpi) \ |
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- $(use_enable threads) \ |
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- $(use_with gsl) |
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-} |
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- |
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-src_install() { |
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- default |
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- |
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- use static-libs && dolib.a src/libhmmer.a easel/libeasel.a |
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- |
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- insinto /usr/share/${PN} |
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- doins -r tutorial |
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- dodoc Userguide.pdf |
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-} |
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|
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diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml |
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deleted file mode 100644 |
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index 8417d15..0000000 |
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--- a/sci-biology/hmmer/metadata.xml |
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+++ /dev/null |
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@@ -1,8 +0,0 @@ |
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-<?xml version="1.0" encoding="UTF-8"?> |
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-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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-<pkgmetadata> |
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- <maintainer type="project"> |
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- <email>sci-biology@g.o</email> |
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- <name>Gentoo Biology Project</name> |
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- </maintainer> |
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-</pkgmetadata> |
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