commit: 34b9085a65dbd111a02b71d66e07caad8ec31e32
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 9 15:21:03 2016 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sun Oct 9 15:21:03 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=34b9085a
sci-biology/hmmer: Remove, latest version in main tree
.../hmmer/files/hmmer-3.1_beta2-fix_tests.patch | 12 ---
.../hmmer/files/hmmer-3.1_beta2-perl-5.16-2.patch | 90 ----------------------
sci-biology/hmmer/hmmer-3.1_beta2.ebuild | 48 ------------
sci-biology/hmmer/metadata.xml | 8 --
4 files changed, 158 deletions(-)
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
deleted file mode 100644
index 9f4ea12..0000000
--- a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix_tests.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- easel/Makefile.in.old 2015-11-19 23:49:53.470244757 +0100
-+++ easel/Makefile.in 2015-11-19 23:52:01.120245091 +0100
-@@ -52,8 +52,7 @@
- SIMDFLAGS= @SIMD_CFLAGS@
- CPPFLAGS = @CPPFLAGS@
- LDFLAGS = @LDFLAGS@
--LIBGSL = @LIBGSL@
--LIBS = @LIBS@ @PTHREAD_LIBS@
-+LIBS = @LIBS@ @LIBGSL@ @PTHREAD_LIBS@
-
- # Other tools
- #
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
deleted file mode 100644
index 88a8ea4..0000000
--- a/sci-biology/hmmer/files/hmmer-3.1_beta2-perl-5.16-2.patch
+++ /dev/null
@@ -1,90 +0,0 @@
---- easel/devkit/autodoc.ori 2015-11-19 23:54:04.170245412 +0100
-+++ easel/devkit/autodoc 2015-11-19 23:54:27.190245472 +0100
-@@ -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; }
---- easel/devkit/esl-dependencies.ori 2015-11-19 23:54:40.830245508 +0100
-+++ easel/devkit/esl-dependencies 2015-11-19 23:55:08.510245580 +0100
-@@ -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) { $list_augfiles = 1; }
---- easel/devkit/sqc.ori 2015-11-19 23:55:15.900245600 +0100
-+++ easel/devkit/sqc 2015-11-19 23:56:16.530245758 +0100
-@@ -674,7 +674,7 @@
- #
- sub tempname {
- my ($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.$$;
---- easel/testsuite/coverage_report.pl.ori 2015-11-19 23:56:34.010245804
+0100
-+++ easel/testsuite/coverage_report.pl 2015-11-19 23:57:03.040245879 +0100
-@@ -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; }
-
---- easel/testsuite/driver_report.pl.ori 2015-11-19 23:57:14.600245910
+0100
-+++ easel/testsuite/driver_report.pl 2015-11-19 23:57:39.310245974 +0100
-@@ -25,8 +25,8 @@
- # SRE, Fri Mar 2 10:01:44 2007 (Janelia)
- # SVN $Id: driver_report.pl 664 2011-02-27 17:08:36Z 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"; }
---- easel/testsuite/valgrind_report.pl.ori 2015-11-19 23:57:47.480245996
+0100
-+++ easel/testsuite/valgrind_report.pl 2015-11-19 23:58:03.000246036 +0100
-@@ -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"; }
---- profmark/rocplot.pl.ori 2015-11-19 23:58:12.530246061 +0100
-+++ profmark/rocplot.pl 2015-11-19 23:58:43.090246141 +0100
-@@ -2,8 +2,8 @@
-
- $nsearches = 2809;
-
--require "getopts.pl";
--&Getopts('n:X:x:');
-+use Getopt::Std;
-+getopts('n:X:x:');
-
- if ($opt_n) { $nsearches = $opt_n; }
- if ($opt_X) {
diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
deleted file mode 100644
index 880df1e..0000000
--- a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils
-
-MY_PV="3.1b2"
-DESCRIPTION="Sequence analysis using profile hidden Markov models"
-HOMEPAGE="http://hmmer.janelia.org/";
-SRC_URI="ftp://selab.janelia.org/pub/software/hmmer3/"${MY_PV}"/"${PN}"-"${MY_PV}".tar.gz";
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+cpu_flags_x86_sse mpi +threads gsl static-libs"
-KEYWORDS="~amd64"
-
-DEPEND="
- mpi? ( virtual/mpi )
- gsl? ( >=sci-libs/gsl-1.12 )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${PN}"-"${MY_PV}"
-
-src_prepare() {
- epatch \
- "${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
-}
diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml
deleted file mode 100644
index 8417d15..0000000
--- a/sci-biology/hmmer/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biol...@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
