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jlec 14/07/06 11:34:47 |
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|
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Added: infernal-1.0.2-perl-5.16-2.patch |
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Removed: infernal-1.0.2-perl-5.16.patch |
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Log: |
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sci-biology/infernal: Add patch as binary to prevent CVS magics, #431076 |
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|
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(Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
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|
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Revision Changes Path |
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1.1 sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch?rev=1.1&content-type=text/plain |
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|
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Index: infernal-1.0.2-perl-5.16-2.patch |
| 17 |
=================================================================== |
| 18 |
benchmarks/cmsearch-rmark/sre.pl | 4 +--- |
| 19 |
easel/devkit/autodoc | 4 ++-- |
| 20 |
easel/devkit/esl-dependencies | 4 ++-- |
| 21 |
easel/devkit/sqc | 7 +++---- |
| 22 |
easel/testsuite/coverage_report.pl | 4 ++-- |
| 23 |
easel/testsuite/driver_report.pl | 4 ++-- |
| 24 |
easel/testsuite/valgrind_report.pl | 4 ++-- |
| 25 |
7 files changed, 14 insertions(+), 17 deletions(-) |
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|
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diff --git a/benchmarks/cmsearch-rmark/sre.pl b/benchmarks/cmsearch-rmark/sre.pl |
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index 9136717..e4df233 100644 |
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--- a/benchmarks/cmsearch-rmark/sre.pl |
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+++ b/benchmarks/cmsearch-rmark/sre.pl |
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@@ -6,8 +6,6 @@ |
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|
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package SRE_perlstuff; |
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|
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-require "importenv.pl"; |
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- |
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# Function: tempname |
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# |
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# Returns a unique temporary filename. |
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@@ -26,7 +24,7 @@ require "importenv.pl"; |
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# |
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sub main'tempname { |
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local ($dir, $name); |
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- if ($TMPDIR) { $dir = $TMPDIR; } else {$dir = "/tmp";} |
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+ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}; } else {$dir = "/tmp";} |
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|
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foreach $suffix ("aa".."zz") { |
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$name = "$dir/sre$suffix$$"; |
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diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc |
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old mode 100755 |
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new mode 100644 |
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index 045ce36..22268f6 |
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--- a/easel/devkit/autodoc |
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+++ b/easel/devkit/autodoc |
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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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diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies |
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old mode 100755 |
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new mode 100644 |
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index a4dc126..b61fa7a |
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--- a/easel/devkit/esl-dependencies |
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+++ b/easel/devkit/esl-dependencies |
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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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diff --git a/easel/devkit/sqc b/easel/devkit/sqc |
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old mode 100755 |
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new mode 100644 |
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index 81d03de..6201d3d |
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--- a/easel/devkit/sqc |
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+++ b/easel/devkit/sqc |
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@@ -176,12 +176,11 @@ |
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# SRE, Tue Aug 6 11:16:39 2002 |
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# SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $ |
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|
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-require "getopts.pl"; |
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-require "importenv.pl"; |
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+use Getopt::Std; |
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|
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# Parse our command line |
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# |
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-&Getopts('mp:r:v'); |
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+getopts('mp:r:v'); |
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if ($opt_m) { $do_memtest = 1; } |
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if ($opt_p) { push @prepdirs, $opt_p; } |
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if ($opt_r) { push @olddirs, $opt_r; } |
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@@ -510,7 +509,7 @@ check_ccmalloc_status |
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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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diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl |
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old mode 100755 |
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new mode 100644 |
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index 9c77791..024ed34 |
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--- a/easel/testsuite/coverage_report.pl |
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+++ b/easel/testsuite/coverage_report.pl |
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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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diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl |
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old mode 100755 |
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new mode 100644 |
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index d1b4a9a..db4378f |
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--- a/easel/testsuite/driver_report.pl |
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+++ b/easel/testsuite/driver_report.pl |
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@@ -19,8 +19,8 @@ |
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# SRE, Fri Mar 2 10:01:44 2007 (Janelia) |
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# SVN $Id: driver_report.pl 231 2008-03-25 14:43:57Z 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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diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl |
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old mode 100755 |
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new mode 100644 |
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index 186a392..07026a0 |
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--- a/easel/testsuite/valgrind_report.pl |
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+++ b/easel/testsuite/valgrind_report.pl |
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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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