[gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/, sci-biology/hmmer/files/

[David Seifert]

commit:     cbfe0e33651a8811229d663a9469cc97957b994e
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Feb  6 20:48:01 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Feb  6 21:25:51 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cbfe0e33

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(-)

diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
index dada007..acffd6e 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 983827b..00000000
--- 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 19d38c8..00000000
--- 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 86183e7..00000000
--- 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
-}