1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
|
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"; }
|
GitWeb