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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 - (hide annotations) (download)
Mon Jun 25 07:08:17 2012 UTC (2 years, 5 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 jlec 1.1 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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