commit: 713d9f01f5ae8bf42d35502519fbf1ef854c63f2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 19 23:02:52 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 19 23:02:52 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=713d9f01
sci-biology/hmmer: add updated patches
Package-Manager: portage-2.2.18
.../hmmer/files/hmmer-3.1_beta2-fix_tests.patch | 12 +++
.../hmmer/files/hmmer-3.1_beta2-perl-5.16-2.patch | 90 ++++++++++++++++++++++
2 files changed, 102 insertions(+)
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
new file mode 100644
index 0000000..9f4ea12
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix_tests.patch
@@ -0,0 +1,12 @@
+--- 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
new file mode 100644
index 0000000..88a8ea4
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-perl-5.16-2.patch
@@ -0,0 +1,90 @@
+--- 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) {
