Gentoo Archives: gentoo-commits

From: "Justin Lecher (jlec)" <jlec@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] gentoo-x86 commit in sci-biology/infernal/files: infernal-1.0.2-perl-5.16.patch
Date: Mon, 25 Jun 2012 07:08:38
Message-Id: 20120625070817.6FD542004E@flycatcher.gentoo.org
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"; }