* [gentoo-commits] gentoo-x86 commit in sci-biology/hmmer/files: hmmer-3.0-perl-5.16.patch
@ 2012-06-25 6:23 Justin Lecher (jlec)
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher (jlec) @ 2012-06-25 6:23 UTC (permalink / raw
To: gentoo-commits
jlec 12/06/25 06:23:12
Added: hmmer-3.0-perl-5.16.patch
Log:
sci-biology/hmmer: Fix for build with perl-5.16, #421799; handle static-libs
(Portage version: 2.2.0_alpha110/cvs/Linux x86_64)
Revision Changes Path
1.1 sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.1&content-type=text/plain
Index: hmmer-3.0-perl-5.16.patch
===================================================================
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: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
-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: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
-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
index 9c77791..024ed34 100755
--- 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: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
-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: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
-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
index 186a392..07026a0 100755
--- 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: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
-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) {
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/hmmer/files: hmmer-3.0-perl-5.16.patch
@ 2012-06-28 16:34 Justin Lecher (jlec)
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher (jlec) @ 2012-06-28 16:34 UTC (permalink / raw
To: gentoo-commits
jlec 12/06/28 16:34:57
Modified: hmmer-3.0-perl-5.16.patch
Log:
sci-biology/hmmer: Fix patch, screwed VCS tags, #423983
(Portage version: 2.2.0_alpha114/cvs/Linux x86_64)
Revision Changes Path
1.2 sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?r1=1.1&r2=1.2
Index: hmmer-3.0-perl-5.16.patch
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- hmmer-3.0-perl-5.16.patch 25 Jun 2012 06:23:12 -0000 1.1
+++ hmmer-3.0-perl-5.16.patch 28 Jun 2012 16:34:57 -0000 1.2
@@ -28,7 +28,7 @@
+++ b/easel/devkit/esl-dependencies
@@ -13,8 +13,8 @@
# SRE, Mon Jun 11 11:15:31 2007
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
-require "getopts.pl"
-&Getopts('1afr');
@@ -43,7 +43,7 @@
+++ b/easel/devkit/sqc
@@ -205,12 +205,11 @@
# SRE, Tue Aug 6 11:16:39 2002
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
-require "getopts.pl";
-require "importenv.pl";
@@ -66,13 +66,15 @@
foreach $suffix ("aa".."zz") {
$name = "$dir"."esltmp".$suffix.$$;
diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl
-index 9c77791..024ed34 100755
+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: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
-require "getopts.pl";
+use Getopt::Std;
$have_sloccount = 1;
@@ -87,7 +89,7 @@
+++ b/easel/testsuite/driver_report.pl
@@ -25,8 +25,8 @@
# SRE, Fri Mar 2 10:01:44 2007 (Janelia)
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
-require "getopts.pl";
-&Getopts('c');
@@ -97,13 +99,15 @@
if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; }
diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl
-index 186a392..07026a0 100755
+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: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
-require "getopts.pl";
-&Getopts('c');
+use Getopt::Std;
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/hmmer/files: hmmer-3.0-perl-5.16.patch
@ 2012-06-28 16:36 Justin Lecher (jlec)
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher (jlec) @ 2012-06-28 16:36 UTC (permalink / raw
To: gentoo-commits
jlec 12/06/28 16:36:08
Modified: hmmer-3.0-perl-5.16.patch
Log:
fix patch again
(Portage version: 2.2.0_alpha114/cvs/Linux x86_64)
Revision Changes Path
1.3 sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?r1=1.2&r2=1.3
Index: hmmer-3.0-perl-5.16.patch
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- hmmer-3.0-perl-5.16.patch 28 Jun 2012 16:34:57 -0000 1.2
+++ hmmer-3.0-perl-5.16.patch 28 Jun 2012 16:36:08 -0000 1.3
@@ -28,7 +28,7 @@
+++ b/easel/devkit/esl-dependencies
@@ -13,8 +13,8 @@
# SRE, Mon Jun 11 11:15:31 2007
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.3 2012/06/28 16:36:08 jlec Exp $
-require "getopts.pl"
-&Getopts('1afr');
@@ -43,7 +43,7 @@
+++ b/easel/devkit/sqc
@@ -205,12 +205,11 @@
# SRE, Tue Aug 6 11:16:39 2002
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.3 2012/06/28 16:36:08 jlec Exp $
-require "getopts.pl";
-require "importenv.pl";
@@ -74,7 +74,7 @@
@@ -16,9 +16,9 @@
#
# SRE, Thu Mar 1 19:22:57 2007 (Janelia)
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.3 2012/06/28 16:36:08 jlec Exp $
-require "getopts.pl";
+use Getopt::Std;
$have_sloccount = 1;
@@ -89,7 +89,7 @@
+++ b/easel/testsuite/driver_report.pl
@@ -25,8 +25,8 @@
# SRE, Fri Mar 2 10:01:44 2007 (Janelia)
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.3 2012/06/28 16:36:08 jlec Exp $
-require "getopts.pl";
-&Getopts('c');
@@ -107,7 +107,7 @@
@@ -10,8 +10,8 @@
#
# SRE, Fri Mar 2 08:37:48 2007 [Janelia]
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.3 2012/06/28 16:36:08 jlec Exp $
-require "getopts.pl";
-&Getopts('c');
+use Getopt::Std;
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/hmmer/files: hmmer-3.0-perl-5.16.patch
@ 2012-06-28 16:38 Justin Lecher (jlec)
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher (jlec) @ 2012-06-28 16:38 UTC (permalink / raw
To: gentoo-commits
jlec 12/06/28 16:38:29
Modified: hmmer-3.0-perl-5.16.patch
Log:
Fix patch
(Portage version: 2.2.0_alpha114/cvs/Linux x86_64)
Revision Changes Path
1.4 sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.4&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.4&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?r1=1.3&r2=1.4
Index: hmmer-3.0-perl-5.16.patch
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- hmmer-3.0-perl-5.16.patch 28 Jun 2012 16:36:08 -0000 1.3
+++ hmmer-3.0-perl-5.16.patch 28 Jun 2012 16:38:29 -0000 1.4
@@ -28,7 +28,7 @@
+++ b/easel/devkit/esl-dependencies
@@ -13,8 +13,8 @@
# SRE, Mon Jun 11 11:15:31 2007
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.3 2012/06/28 16:36:08 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.4 2012/06/28 16:38:29 jlec Exp $
-require "getopts.pl"
-&Getopts('1afr');
@@ -43,7 +43,7 @@
+++ b/easel/devkit/sqc
@@ -205,12 +205,11 @@
# SRE, Tue Aug 6 11:16:39 2002
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.3 2012/06/28 16:36:08 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.4 2012/06/28 16:38:29 jlec Exp $
-require "getopts.pl";
-require "importenv.pl";
@@ -74,7 +74,7 @@
@@ -16,9 +16,9 @@
#
# SRE, Thu Mar 1 19:22:57 2007 (Janelia)
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.3 2012/06/28 16:36:08 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.4 2012/06/28 16:38:29 jlec Exp $
-require "getopts.pl";
+use Getopt::Std;
$have_sloccount = 1;
@@ -89,7 +89,7 @@
+++ b/easel/testsuite/driver_report.pl
@@ -25,8 +25,8 @@
# SRE, Fri Mar 2 10:01:44 2007 (Janelia)
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.3 2012/06/28 16:36:08 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.4 2012/06/28 16:38:29 jlec Exp $
-require "getopts.pl";
-&Getopts('c');
@@ -107,7 +107,7 @@
@@ -10,8 +10,8 @@
#
# SRE, Fri Mar 2 08:37:48 2007 [Janelia]
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.3 2012/06/28 16:36:08 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.4 2012/06/28 16:38:29 jlec Exp $
-require "getopts.pl";
-&Getopts('c');
+use Getopt::Std;
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/hmmer/files: hmmer-3.0-perl-5.16.patch
@ 2012-06-28 16:39 Justin Lecher (jlec)
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher (jlec) @ 2012-06-28 16:39 UTC (permalink / raw
To: gentoo-commits
jlec 12/06/28 16:39:03
Modified: hmmer-3.0-perl-5.16.patch
Log:
Plain patch
Revision Changes Path
1.5 sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.5&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.5&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?r1=1.4&r2=1.5
Index: hmmer-3.0-perl-5.16.patch
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- hmmer-3.0-perl-5.16.patch 28 Jun 2012 16:38:29 -0000 1.4
+++ hmmer-3.0-perl-5.16.patch 28 Jun 2012 16:39:03 -0000 1.5
@@ -28,7 +28,7 @@
+++ b/easel/devkit/esl-dependencies
@@ -13,8 +13,8 @@
# SRE, Mon Jun 11 11:15:31 2007
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.4 2012/06/28 16:38:29 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.5 2012/06/28 16:39:03 jlec Exp $
-require "getopts.pl"
-&Getopts('1afr');
@@ -43,7 +43,7 @@
+++ b/easel/devkit/sqc
@@ -205,12 +205,11 @@
# SRE, Tue Aug 6 11:16:39 2002
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.4 2012/06/28 16:38:29 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.5 2012/06/28 16:39:03 jlec Exp $
-require "getopts.pl";
-require "importenv.pl";
@@ -74,7 +74,7 @@
@@ -16,9 +16,9 @@
#
# SRE, Thu Mar 1 19:22:57 2007 (Janelia)
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.4 2012/06/28 16:38:29 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.5 2012/06/28 16:39:03 jlec Exp $
-require "getopts.pl";
+use Getopt::Std;
$have_sloccount = 1;
@@ -89,7 +89,7 @@
+++ b/easel/testsuite/driver_report.pl
@@ -25,8 +25,8 @@
# SRE, Fri Mar 2 10:01:44 2007 (Janelia)
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.4 2012/06/28 16:38:29 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.5 2012/06/28 16:39:03 jlec Exp $
-require "getopts.pl";
-&Getopts('c');
@@ -107,7 +107,7 @@
@@ -10,8 +10,8 @@
#
# SRE, Fri Mar 2 08:37:48 2007 [Janelia]
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.4 2012/06/28 16:38:29 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.5 2012/06/28 16:39:03 jlec Exp $
-require "getopts.pl";
-&Getopts('c');
+use Getopt::Std;
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/hmmer/files: hmmer-3.0-perl-5.16.patch
@ 2012-06-28 16:47 Justin Lecher (jlec)
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher (jlec) @ 2012-06-28 16:47 UTC (permalink / raw
To: gentoo-commits
jlec 12/06/28 16:47:02
Modified: hmmer-3.0-perl-5.16.patch
Log:
next try
Revision Changes Path
1.6 sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.6&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?rev=1.6&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch?r1=1.5&r2=1.6
Index: hmmer-3.0-perl-5.16.patch
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- hmmer-3.0-perl-5.16.patch 28 Jun 2012 16:39:03 -0000 1.5
+++ hmmer-3.0-perl-5.16.patch 28 Jun 2012 16:47:02 -0000 1.6
@@ -28,7 +28,7 @@
+++ b/easel/devkit/esl-dependencies
@@ -13,8 +13,8 @@
# SRE, Mon Jun 11 11:15:31 2007
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.5 2012/06/28 16:39:03 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.6 2012/06/28 16:47:02 jlec Exp $
-require "getopts.pl"
-&Getopts('1afr');
@@ -43,7 +43,7 @@
+++ b/easel/devkit/sqc
@@ -205,12 +205,11 @@
# SRE, Tue Aug 6 11:16:39 2002
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.5 2012/06/28 16:39:03 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.6 2012/06/28 16:47:02 jlec Exp $
-require "getopts.pl";
-require "importenv.pl";
@@ -74,7 +74,7 @@
@@ -16,9 +16,9 @@
#
# SRE, Thu Mar 1 19:22:57 2007 (Janelia)
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.5 2012/06/28 16:39:03 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.6 2012/06/28 16:47:02 jlec Exp $
-require "getopts.pl";
+use Getopt::Std;
$have_sloccount = 1;
@@ -89,7 +89,7 @@
+++ b/easel/testsuite/driver_report.pl
@@ -25,8 +25,8 @@
# SRE, Fri Mar 2 10:01:44 2007 (Janelia)
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.5 2012/06/28 16:39:03 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.6 2012/06/28 16:47:02 jlec Exp $
-require "getopts.pl";
-&Getopts('c');
@@ -107,7 +107,7 @@
@@ -10,8 +10,8 @@
#
# SRE, Fri Mar 2 08:37:48 2007 [Janelia]
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.5 2012/06/28 16:39:03 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.6 2012/06/28 16:47:02 jlec Exp $
-require "getopts.pl";
-&Getopts('c');
+use Getopt::Std;
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/hmmer/files: hmmer-3.0-perl-5.16.patch
@ 2012-06-28 16:50 Justin Lecher (jlec)
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher (jlec) @ 2012-06-28 16:50 UTC (permalink / raw
To: gentoo-commits
jlec 12/06/28 16:50:49
Removed: hmmer-3.0-perl-5.16.patch
Log:
sci-biology/hmmer: Fix the patch, thanks xarthisius and bonsaikitten for help
(Portage version: 2.2.0_alpha114/cvs/Linux x86_64)
^ permalink raw reply [flat|nested] 7+ messages in thread
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