| 1 |
easel/devkit/autodoc | 4 ++--
|
| 2 |
easel/devkit/esl-dependencies | 4 ++--
|
| 3 |
easel/devkit/sqc | 7 +++----
|
| 4 |
easel/testsuite/coverage_report.pl | 4 ++--
|
| 5 |
easel/testsuite/driver_report.pl | 4 ++--
|
| 6 |
easel/testsuite/valgrind_report.pl | 4 ++--
|
| 7 |
profmark/rocplot.pl | 4 ++--
|
| 8 |
7 files changed, 15 insertions(+), 16 deletions(-)
|
| 9 |
|
| 10 |
diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
|
| 11 |
index 16bda4d..f5c5efc 100755
|
| 12 |
--- a/easel/devkit/autodoc
|
| 13 |
+++ b/easel/devkit/autodoc
|
| 14 |
@@ -49,8 +49,8 @@
|
| 15 |
#
|
| 16 |
# SRE, Tue Nov 30 19:43:47 2004
|
| 17 |
|
| 18 |
-require "getopts.pl";
|
| 19 |
-&Getopts('n:t');
|
| 20 |
+use Getopt::Std;
|
| 21 |
+getopts('n:t');
|
| 22 |
$cfile = shift;
|
| 23 |
|
| 24 |
if ($opt_t) { $show_api_table = 1; }
|
| 25 |
diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies
|
| 26 |
index a4dc126..b61fa7a 100755
|
| 27 |
--- a/easel/devkit/esl-dependencies
|
| 28 |
+++ b/easel/devkit/esl-dependencies
|
| 29 |
@@ -13,8 +13,8 @@
|
| 30 |
# SRE, Mon Jun 11 11:15:31 2007
|
| 31 |
# SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.6 2012/06/28 16:47:02 jlec Exp $
|
| 32 |
|
| 33 |
-require "getopts.pl"
|
| 34 |
-&Getopts('1afr');
|
| 35 |
+use Getopt::Std;
|
| 36 |
+getopts('1afr');
|
| 37 |
|
| 38 |
if ($opt_1) { $show_summary_table = 1; }
|
| 39 |
if ($opt_a) { $list_augfiles = 1; }
|
| 40 |
diff --git a/easel/devkit/sqc b/easel/devkit/sqc
|
| 41 |
index af3adf6..0cdb458 100755
|
| 42 |
--- a/easel/devkit/sqc
|
| 43 |
+++ b/easel/devkit/sqc
|
| 44 |
@@ -205,12 +205,11 @@
|
| 45 |
# SRE, Tue Aug 6 11:16:39 2002
|
| 46 |
# SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.6 2012/06/28 16:47:02 jlec Exp $
|
| 47 |
|
| 48 |
-require "getopts.pl";
|
| 49 |
-require "importenv.pl";
|
| 50 |
+use Getopt::Std;
|
| 51 |
|
| 52 |
# Parse our command line
|
| 53 |
#
|
| 54 |
-&Getopts('v');
|
| 55 |
+getopts('v');
|
| 56 |
if ($opt_v) { $verbose = 1; }
|
| 57 |
|
| 58 |
|
| 59 |
@@ -609,7 +608,7 @@ sub check_valgrind_status
|
| 60 |
#
|
| 61 |
sub tempname {
|
| 62 |
my ($dir, $name, $suffix);
|
| 63 |
- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
|
| 64 |
+ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
|
| 65 |
|
| 66 |
foreach $suffix ("aa".."zz") {
|
| 67 |
$name = "$dir"."esltmp".$suffix.$$;
|
| 68 |
diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl
|
| 69 |
old mode 100755
|
| 70 |
new mode 100644
|
| 71 |
index 9c77791..024ed34
|
| 72 |
--- a/easel/testsuite/coverage_report.pl
|
| 73 |
+++ b/easel/testsuite/coverage_report.pl
|
| 74 |
@@ -16,9 +16,9 @@
|
| 75 |
#
|
| 76 |
# SRE, Thu Mar 1 19:22:57 2007 (Janelia)
|
| 77 |
# SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.6 2012/06/28 16:47:02 jlec Exp $
|
| 78 |
-require "getopts.pl";
|
| 79 |
+use Getopt::Std;
|
| 80 |
$have_sloccount = 1;
|
| 81 |
-&Getopts('cs');
|
| 82 |
+getopts('cs');
|
| 83 |
if ($opt_c) { $do_recompile = 1; }
|
| 84 |
if ($opt_s) { $have_sloccount = 0; }
|
| 85 |
|
| 86 |
diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl
|
| 87 |
index 757854d..a9a8902 100755
|
| 88 |
--- a/easel/testsuite/driver_report.pl
|
| 89 |
+++ b/easel/testsuite/driver_report.pl
|
| 90 |
@@ -25,8 +25,8 @@
|
| 91 |
# SRE, Fri Mar 2 10:01:44 2007 (Janelia)
|
| 92 |
# SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.6 2012/06/28 16:47:02 jlec Exp $
|
| 93 |
|
| 94 |
-require "getopts.pl";
|
| 95 |
-&Getopts('c');
|
| 96 |
+use Getopt::Std;
|
| 97 |
+getopts('c');
|
| 98 |
if ($opt_c) { $do_recompile = 1; }
|
| 99 |
|
| 100 |
if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; }
|
| 101 |
diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl
|
| 102 |
old mode 100755
|
| 103 |
new mode 100644
|
| 104 |
index 186a392..07026a0
|
| 105 |
--- a/easel/testsuite/valgrind_report.pl
|
| 106 |
+++ b/easel/testsuite/valgrind_report.pl
|
| 107 |
@@ -10,8 +10,8 @@
|
| 108 |
#
|
| 109 |
# SRE, Fri Mar 2 08:37:48 2007 [Janelia]
|
| 110 |
# SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.6 2012/06/28 16:47:02 jlec Exp $
|
| 111 |
-require "getopts.pl";
|
| 112 |
-&Getopts('c');
|
| 113 |
+use Getopt::Std;
|
| 114 |
+getopts('c');
|
| 115 |
if ($opt_c) { $do_recompile = 1; }
|
| 116 |
|
| 117 |
if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; }
|
| 118 |
diff --git a/profmark/rocplot.pl b/profmark/rocplot.pl
|
| 119 |
index d4c0f67..4e8175a 100755
|
| 120 |
--- a/profmark/rocplot.pl
|
| 121 |
+++ b/profmark/rocplot.pl
|
| 122 |
@@ -2,8 +2,8 @@
|
| 123 |
|
| 124 |
$nsearches = 1567;
|
| 125 |
|
| 126 |
-require "getopts.pl";
|
| 127 |
-&Getopts('n:X:x:');
|
| 128 |
+use Getopt::Std
|
| 129 |
+getopts('n:X:x:');
|
| 130 |
|
| 131 |
if ($opt_n) { $nsearches = $opt_n; }
|
| 132 |
if ($opt_X) {
|
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