sci-biology/infernal: Add patch as binary to prevent CVS magics, #431076

(Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 34 insertions, 21 deletions

diff --git a/sci-biology/infernal/ChangeLog b/sci-biology/infernal/ChangeLog
index 6f499b0a6fa9..49449a02851f 100644
--- a/sci-biology/infernal/ChangeLog
+++ b/sci-biology/infernal/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/infernal
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/infernal/ChangeLog,v 1.14 2013/03/11 15:25:19 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/infernal/ChangeLog,v 1.15 2014/07/06 11:34:46 jlec Exp $
+
+  06 Jul 2014; Justin Lecher <jlec@gentoo.org> infernal-1.0.2-r1.ebuild,
+  +files/infernal-1.0.2-perl-5.16-2.patch,
+  -files/infernal-1.0.2-perl-5.16.patch:
+  Add patch as binary to prevent CVS magics, #431076
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/infernal/files/infernal-1.0.2-perl-5.16.patch b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch
index 9a06ee88d8d1..c96dcae7b296 100644
--- a/sci-biology/infernal/files/infernal-1.0.2-perl-5.16.patch
+++ b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch
@@ -1,10 +1,10 @@
- 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 ++--
+ 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
@@ -30,7 +30,9 @@ index 9136717..e4df233 100644
      foreach $suffix ("aa".."zz") {
  	$name = "$dir/sre$suffix$$";
 diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
-index 045ce36..22268f6 100755
+old mode 100755
+new mode 100644
+index 045ce36..22268f6
 --- a/easel/devkit/autodoc
 +++ b/easel/devkit/autodoc
 @@ -49,8 +49,8 @@
@@ -45,12 +47,14 @@ index 045ce36..22268f6 100755
  
  if ($opt_t) { $show_api_table = 1; }
 diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies
-index a4dc126..b61fa7a 100755
+old mode 100755
+new mode 100644
+index a4dc126..b61fa7a
 --- 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 1.2 2012/07/15 10:26:02 jlec Exp $
+ # SVN $Id$
  
 -require "getopts.pl"
 -&Getopts('1afr');
@@ -60,12 +64,14 @@ index a4dc126..b61fa7a 100755
  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
+old mode 100755
+new mode 100644
+index 81d03de..6201d3d
 --- 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 1.2 2012/07/15 10:26:02 jlec Exp $
+ # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $
  
 -require "getopts.pl";
 -require "importenv.pl";
@@ -96,7 +102,7 @@ index 9c77791..024ed34
 @@ -16,9 +16,9 @@
  #
  # SRE, Thu Mar  1 19:22:57 2007 (Janelia)
- # SVN $Id: infernal-1.0.2-perl-5.16.patch,v 1.2 2012/07/15 10:26:02 jlec Exp $
+ # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $
 -require  "getopts.pl";
 +use Getopt::Std;
  $have_sloccount = 1;
@@ -106,12 +112,14 @@ index 9c77791..024ed34
  if ($opt_s) { $have_sloccount   = 0; }
  
 diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl
-index d1b4a9a..db4378f 100755
+old mode 100755
+new mode 100644
+index d1b4a9a..db4378f
 --- 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 1.2 2012/07/15 10:26:02 jlec Exp $
+ # SVN $Id: driver_report.pl 231 2008-03-25 14:43:57Z eddys $
  
 -require  "getopts.pl";
 -&Getopts('c');
@@ -129,7 +137,7 @@ index 186a392..07026a0
 @@ -10,8 +10,8 @@
  #
  # SRE, Fri Mar  2 08:37:48 2007 [Janelia]
- # SVN $Id: infernal-1.0.2-perl-5.16.patch,v 1.2 2012/07/15 10:26:02 jlec Exp $
+ # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $
 -require  "getopts.pl";
 -&Getopts('c');
 +use Getopt::Std;
diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild
index 6ccfc9790624..db74fcab8de1 100644
--- a/sci-biology/infernal/infernal-1.0.2-r1.ebuild
+++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/infernal/infernal-1.0.2-r1.ebuild,v 1.4 2012/06/25 07:08:17 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/infernal/infernal-1.0.2-r1.ebuild,v 1.5 2014/07/06 11:34:46 jlec Exp $
 
 EAPI=4
 
@@ -22,7 +22,7 @@ src_prepare() {
 	epatch \
 		"${FILESDIR}"/${P}-parallel-build.patch \
 		"${FILESDIR}"/${P}-overflows.patch \
-		"${FILESDIR}"/${P}-perl-5.16.patch \
+		"${FILESDIR}"/${P}-perl-5.16-2.patch \
 		"${FILESDIR}"/${P}-ldflags.patch
 }