1 |
jlec 12/06/25 07:08:17 |
2 |
|
3 |
Added: infernal-1.0.2-perl-5.16.patch |
4 |
Log: |
5 |
sci-biology/infernal: Fix for perl-5.16, #422561; move to EAPI=4 |
6 |
|
7 |
(Portage version: 2.2.0_alpha110/cvs/Linux x86_64) |
8 |
|
9 |
Revision Changes Path |
10 |
1.1 sci-biology/infernal/files/infernal-1.0.2-perl-5.16.patch |
11 |
|
12 |
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 |
13 |
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 |
14 |
|
15 |
Index: infernal-1.0.2-perl-5.16.patch |
16 |
=================================================================== |
17 |
benchmarks/cmsearch-rmark/sre.pl | 4 +--- |
18 |
easel/devkit/autodoc | 4 ++-- |
19 |
easel/devkit/esl-dependencies | 4 ++-- |
20 |
easel/devkit/sqc | 7 +++---- |
21 |
easel/testsuite/coverage_report.pl | 4 ++-- |
22 |
easel/testsuite/driver_report.pl | 4 ++-- |
23 |
easel/testsuite/valgrind_report.pl | 4 ++-- |
24 |
7 files changed, 14 insertions(+), 17 deletions(-) |
25 |
|
26 |
diff --git a/benchmarks/cmsearch-rmark/sre.pl b/benchmarks/cmsearch-rmark/sre.pl |
27 |
index 9136717..e4df233 100644 |
28 |
--- a/benchmarks/cmsearch-rmark/sre.pl |
29 |
+++ b/benchmarks/cmsearch-rmark/sre.pl |
30 |
@@ -6,8 +6,6 @@ |
31 |
|
32 |
package SRE_perlstuff; |
33 |
|
34 |
-require "importenv.pl"; |
35 |
- |
36 |
# Function: tempname |
37 |
# |
38 |
# Returns a unique temporary filename. |
39 |
@@ -26,7 +24,7 @@ require "importenv.pl"; |
40 |
# |
41 |
sub main'tempname { |
42 |
local ($dir, $name); |
43 |
- if ($TMPDIR) { $dir = $TMPDIR; } else {$dir = "/tmp";} |
44 |
+ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}; } else {$dir = "/tmp";} |
45 |
|
46 |
foreach $suffix ("aa".."zz") { |
47 |
$name = "$dir/sre$suffix$$"; |
48 |
diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc |
49 |
index 045ce36..22268f6 100755 |
50 |
--- a/easel/devkit/autodoc |
51 |
+++ b/easel/devkit/autodoc |
52 |
@@ -49,8 +49,8 @@ |
53 |
# |
54 |
# SRE, Tue Nov 30 19:43:47 2004 |
55 |
|
56 |
-require "getopts.pl"; |
57 |
-&Getopts('n:t'); |
58 |
+use Getopt::Std; |
59 |
+getopts('n:t'); |
60 |
$cfile = shift; |
61 |
|
62 |
if ($opt_t) { $show_api_table = 1; } |
63 |
diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies |
64 |
index a4dc126..b61fa7a 100755 |
65 |
--- a/easel/devkit/esl-dependencies |
66 |
+++ b/easel/devkit/esl-dependencies |
67 |
@@ -13,8 +13,8 @@ |
68 |
# SRE, Mon Jun 11 11:15:31 2007 |
69 |
# SVN $Id: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 jlec Exp $ |
70 |
|
71 |
-require "getopts.pl" |
72 |
-&Getopts('1afr'); |
73 |
+use Getopt::Std; |
74 |
+getopts('1afr'); |
75 |
|
76 |
if ($opt_1) { $show_summary_table = 1; } |
77 |
if ($opt_a) { $list_augfiles = 1; } |
78 |
diff --git a/easel/devkit/sqc b/easel/devkit/sqc |
79 |
index 81d03de..6201d3d 100755 |
80 |
--- a/easel/devkit/sqc |
81 |
+++ b/easel/devkit/sqc |
82 |
@@ -176,12 +176,11 @@ |
83 |
# SRE, Tue Aug 6 11:16:39 2002 |
84 |
# SVN $Id: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 jlec Exp $ |
85 |
|
86 |
-require "getopts.pl"; |
87 |
-require "importenv.pl"; |
88 |
+use Getopt::Std; |
89 |
|
90 |
# Parse our command line |
91 |
# |
92 |
-&Getopts('mp:r:v'); |
93 |
+getopts('mp:r:v'); |
94 |
if ($opt_m) { $do_memtest = 1; } |
95 |
if ($opt_p) { push @prepdirs, $opt_p; } |
96 |
if ($opt_r) { push @olddirs, $opt_r; } |
97 |
@@ -510,7 +509,7 @@ check_ccmalloc_status |
98 |
# |
99 |
sub tempname { |
100 |
my ($dir, $name, $suffix); |
101 |
- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";} |
102 |
+ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";} |
103 |
|
104 |
foreach $suffix ("aa".."zz") { |
105 |
$name = "$dir"."esltmp".$suffix.$$; |
106 |
diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl |
107 |
index 9c77791..024ed34 100755 |
108 |
--- a/easel/testsuite/coverage_report.pl |
109 |
+++ b/easel/testsuite/coverage_report.pl |
110 |
@@ -16,9 +16,9 @@ |
111 |
# |
112 |
# SRE, Thu Mar 1 19:22:57 2007 (Janelia) |
113 |
# SVN $Id: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 jlec Exp $ |
114 |
-require "getopts.pl"; |
115 |
+use Getopt::Std; |
116 |
$have_sloccount = 1; |
117 |
-&Getopts('cs'); |
118 |
+getopts('cs'); |
119 |
if ($opt_c) { $do_recompile = 1; } |
120 |
if ($opt_s) { $have_sloccount = 0; } |
121 |
|
122 |
diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl |
123 |
index d1b4a9a..db4378f 100755 |
124 |
--- a/easel/testsuite/driver_report.pl |
125 |
+++ b/easel/testsuite/driver_report.pl |
126 |
@@ -19,8 +19,8 @@ |
127 |
# SRE, Fri Mar 2 10:01:44 2007 (Janelia) |
128 |
# SVN $Id: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 jlec Exp $ |
129 |
|
130 |
-require "getopts.pl"; |
131 |
-&Getopts('c'); |
132 |
+use Getopt::Std; |
133 |
+getopts('c'); |
134 |
if ($opt_c) { $do_recompile = 1; } |
135 |
|
136 |
if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } |
137 |
diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl |
138 |
index 186a392..07026a0 100755 |
139 |
--- a/easel/testsuite/valgrind_report.pl |
140 |
+++ b/easel/testsuite/valgrind_report.pl |
141 |
@@ -10,8 +10,8 @@ |
142 |
# |
143 |
# SRE, Fri Mar 2 08:37:48 2007 [Janelia] |
144 |
# SVN $Id: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 jlec Exp $ |
145 |
-require "getopts.pl"; |
146 |
-&Getopts('c'); |
147 |
+use Getopt::Std; |
148 |
+getopts('c'); |
149 |
if ($opt_c) { $do_recompile = 1; } |
150 |
|
151 |
if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } |