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Contents of /sci-biology/infernal/files/infernal-1.0.2-perl-5.16.patch

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Revision 1.1 - (show annotations) (download)
Mon Jun 25 07:08:17 2012 UTC (2 years, 2 months ago) by jlec
Branch: MAIN
sci-biology/infernal: Fix for perl-5.16, #422561; move to EAPI=4

(Portage version: 2.2.0_alpha110/cvs/Linux x86_64)

1 benchmarks/cmsearch-rmark/sre.pl | 4 +---
2 easel/devkit/autodoc | 4 ++--
3 easel/devkit/esl-dependencies | 4 ++--
4 easel/devkit/sqc | 7 +++----
5 easel/testsuite/coverage_report.pl | 4 ++--
6 easel/testsuite/driver_report.pl | 4 ++--
7 easel/testsuite/valgrind_report.pl | 4 ++--
8 7 files changed, 14 insertions(+), 17 deletions(-)
9
10 diff --git a/benchmarks/cmsearch-rmark/sre.pl b/benchmarks/cmsearch-rmark/sre.pl
11 index 9136717..e4df233 100644
12 --- a/benchmarks/cmsearch-rmark/sre.pl
13 +++ b/benchmarks/cmsearch-rmark/sre.pl
14 @@ -6,8 +6,6 @@
15
16 package SRE_perlstuff;
17
18 -require "importenv.pl";
19 -
20 # Function: tempname
21 #
22 # Returns a unique temporary filename.
23 @@ -26,7 +24,7 @@ require "importenv.pl";
24 #
25 sub main'tempname {
26 local ($dir, $name);
27 - if ($TMPDIR) { $dir = $TMPDIR; } else {$dir = "/tmp";}
28 + if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}; } else {$dir = "/tmp";}
29
30 foreach $suffix ("aa".."zz") {
31 $name = "$dir/sre$suffix$$";
32 diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
33 index 045ce36..22268f6 100755
34 --- a/easel/devkit/autodoc
35 +++ b/easel/devkit/autodoc
36 @@ -49,8 +49,8 @@
37 #
38 # SRE, Tue Nov 30 19:43:47 2004
39
40 -require "getopts.pl";
41 -&Getopts('n:t');
42 +use Getopt::Std;
43 +getopts('n:t');
44 $cfile = shift;
45
46 if ($opt_t) { $show_api_table = 1; }
47 diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies
48 index a4dc126..b61fa7a 100755
49 --- a/easel/devkit/esl-dependencies
50 +++ b/easel/devkit/esl-dependencies
51 @@ -13,8 +13,8 @@
52 # SRE, Mon Jun 11 11:15:31 2007
53 # SVN $Id$
54
55 -require "getopts.pl"
56 -&Getopts('1afr');
57 +use Getopt::Std;
58 +getopts('1afr');
59
60 if ($opt_1) { $show_summary_table = 1; }
61 if ($opt_a) { $list_augfiles = 1; }
62 diff --git a/easel/devkit/sqc b/easel/devkit/sqc
63 index 81d03de..6201d3d 100755
64 --- a/easel/devkit/sqc
65 +++ b/easel/devkit/sqc
66 @@ -176,12 +176,11 @@
67 # SRE, Tue Aug 6 11:16:39 2002
68 # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $
69
70 -require "getopts.pl";
71 -require "importenv.pl";
72 +use Getopt::Std;
73
74 # Parse our command line
75 #
76 -&Getopts('mp:r:v');
77 +getopts('mp:r:v');
78 if ($opt_m) { $do_memtest = 1; }
79 if ($opt_p) { push @prepdirs, $opt_p; }
80 if ($opt_r) { push @olddirs, $opt_r; }
81 @@ -510,7 +509,7 @@ check_ccmalloc_status
82 #
83 sub tempname {
84 my ($dir, $name, $suffix);
85 - if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
86 + if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
87
88 foreach $suffix ("aa".."zz") {
89 $name = "$dir"."esltmp".$suffix.$$;
90 diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl
91 index 9c77791..024ed34 100755
92 --- a/easel/testsuite/coverage_report.pl
93 +++ b/easel/testsuite/coverage_report.pl
94 @@ -16,9 +16,9 @@
95 #
96 # SRE, Thu Mar 1 19:22:57 2007 (Janelia)
97 # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $
98 -require "getopts.pl";
99 +use Getopt::Std;
100 $have_sloccount = 1;
101 -&Getopts('cs');
102 +getopts('cs');
103 if ($opt_c) { $do_recompile = 1; }
104 if ($opt_s) { $have_sloccount = 0; }
105
106 diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl
107 index d1b4a9a..db4378f 100755
108 --- a/easel/testsuite/driver_report.pl
109 +++ b/easel/testsuite/driver_report.pl
110 @@ -19,8 +19,8 @@
111 # SRE, Fri Mar 2 10:01:44 2007 (Janelia)
112 # SVN $Id: driver_report.pl 231 2008-03-25 14:43:57Z eddys $
113
114 -require "getopts.pl";
115 -&Getopts('c');
116 +use Getopt::Std;
117 +getopts('c');
118 if ($opt_c) { $do_recompile = 1; }
119
120 if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; }
121 diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl
122 index 186a392..07026a0 100755
123 --- a/easel/testsuite/valgrind_report.pl
124 +++ b/easel/testsuite/valgrind_report.pl
125 @@ -10,8 +10,8 @@
126 #
127 # SRE, Fri Mar 2 08:37:48 2007 [Janelia]
128 # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $
129 -require "getopts.pl";
130 -&Getopts('c');
131 +use Getopt::Std;
132 +getopts('c');
133 if ($opt_c) { $do_recompile = 1; }
134
135 if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; }

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