You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
gentoo-overlay/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2....

148 lines
4.1 KiB

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$$";
diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
old mode 100755
new mode 100644
index 045ce36..22268f6
--- a/easel/devkit/autodoc
+++ b/easel/devkit/autodoc
@@ -49,8 +49,8 @@
#
# SRE, Tue Nov 30 19:43:47 2004
-require "getopts.pl";
-&Getopts('n:t');
+use Getopt::Std;
+getopts('n:t');
$cfile = shift;
if ($opt_t) { $show_api_table = 1; }
diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies
old mode 100755
new mode 100644
index a4dc126..b61fa7a
--- a/easel/devkit/esl-dependencies
+++ b/easel/devkit/esl-dependencies
@@ -13,8 +13,8 @@
# SRE, Mon Jun 11 11:15:31 2007
# SVN $Id$
-require "getopts.pl"
-&Getopts('1afr');
+use Getopt::Std;
+getopts('1afr');
if ($opt_1) { $show_summary_table = 1; }
if ($opt_a) { $list_augfiles = 1; }
diff --git a/easel/devkit/sqc b/easel/devkit/sqc
old mode 100755
new mode 100644
index 81d03de..6201d3d
--- a/easel/devkit/sqc
+++ b/easel/devkit/sqc
@@ -176,12 +176,11 @@
# SRE, Tue Aug 6 11:16:39 2002
# SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $
-require "getopts.pl";
-require "importenv.pl";
+use Getopt::Std;
# Parse our command line
#
-&Getopts('mp:r:v');
+getopts('mp:r:v');
if ($opt_m) { $do_memtest = 1; }
if ($opt_p) { push @prepdirs, $opt_p; }
if ($opt_r) { push @olddirs, $opt_r; }
@@ -510,7 +509,7 @@ check_ccmalloc_status
#
sub tempname {
my ($dir, $name, $suffix);
- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
+ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
foreach $suffix ("aa".."zz") {
$name = "$dir"."esltmp".$suffix.$$;
diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl
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
old mode 100755
new mode 100644
index d1b4a9a..db4378f
--- 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: driver_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/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"; }