jlec        12/06/25 07:08:17

  Added:                infernal-1.0.2-perl-5.16.patch
  Log:
  sci-biology/infernal: Fix for perl-5.16, #422561; move to EAPI=4
  
  (Portage version: 2.2.0_alpha110/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-biology/infernal/files/infernal-1.0.2-perl-5.16.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/infernal/files/infernal-1.0.2-perl-5.16.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/infernal/files/infernal-1.0.2-perl-5.16.patch?rev=1.1&content-type=text/plain

Index: infernal-1.0.2-perl-5.16.patch
===================================================================
 benchmarks/cmsearch-rmark/sre.pl   |    4 +---
 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 ++--
 7 files changed, 14 insertions(+), 17 deletions(-)

diff --git a/benchmarks/cmsearch-rmark/sre.pl b/benchmarks/cmsearch-rmark/sre.pl
index 9136717..e4df233 100644
--- a/benchmarks/cmsearch-rmark/sre.pl
+++ b/benchmarks/cmsearch-rmark/sre.pl
@@ -6,8 +6,6 @@
 
 package SRE_perlstuff;
 
-require "importenv.pl";
-
 # Function: tempname
 #
 # Returns a unique temporary filename. 
@@ -26,7 +24,7 @@ require "importenv.pl";
 #
 sub main'tempname {
     local ($dir, $name);
-    if ($TMPDIR) { $dir = $TMPDIR; } else {$dir = "/tmp";}
+    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}; } else {$dir = "/tmp";}
 
     foreach $suffix ("aa".."zz") {
 	$name = "$dir/sre$suffix$$";
diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
index 045ce36..22268f6 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: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 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 81d03de..6201d3d 100755
--- a/easel/devkit/sqc
+++ b/easel/devkit/sqc
@@ -176,12 +176,11 @@
 # SRE, Tue Aug  6 11:16:39 2002
 # SVN $Id: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 jlec Exp $
 
-require "getopts.pl";
-require "importenv.pl";
+use Getopt::Std;
 
 # Parse our command line
 #
-&Getopts('mp:r:v');
+getopts('mp:r:v');
 if ($opt_m) { $do_memtest = 1;    }
 if ($opt_p) { push @prepdirs, $opt_p; }
 if ($opt_r) { push @olddirs,  $opt_r; }
@@ -510,7 +509,7 @@ check_ccmalloc_status
 #
 sub tempname {
     my ($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: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 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 d1b4a9a..db4378f 100755
--- a/easel/testsuite/driver_report.pl
+++ b/easel/testsuite/driver_report.pl
@@ -19,8 +19,8 @@
 # SRE, Fri Mar  2 10:01:44 2007 (Janelia)
 # SVN $Id: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 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: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 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"; }