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|
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 1.2 2012/06/28 16:34:57 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 1.2 2012/06/28 16:34:57 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
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 1.2 2012/06/28 16:34:57 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 1.2 2012/06/28 16:34:57 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
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 1.2 2012/06/28 16:34:57 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) {
|
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