sci-biology/hmmer: Fix patch, screwed VCS tags, #423983

Package-Manager: portage-2.2.0_alpha114/cvs/Linux x86_64

3 files changed, 20 insertions, 13 deletions

diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog
index 423104f09bd4..eed761671330 100644
--- a/sci-biology/hmmer/ChangeLog
+++ b/sci-biology/hmmer/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/hmmer
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.32 2012/06/25 06:23:12 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.33 2012/06/28 16:34:57 jlec Exp $
+
+  28 Jun 2012; Justin Lecher <jlec@gentoo.org> files/hmmer-3.0-perl-5.16.patch:
+  Fix patch, screwed VCS tags, #423983
 
   25 Jun 2012; Justin Lecher <jlec@gentoo.org> hmmer-3.0.ebuild,
   +files/hmmer-3.0-perl-5.16.patch, metadata.xml:
diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
index 1b45cfc4dcf8..5607273e7e3b 100644
--- a/sci-biology/hmmer/Manifest
+++ b/sci-biology/hmmer/Manifest
@@ -2,19 +2,19 @@
 Hash: SHA512
 
 AUX hmmer-3.0-fix_tests.patch 873 RMD160 a41d05e24c4b7a971be14cc9bc25b6f5d9659022 SHA1 e399425bb460c0e94ff1cabf16d0d94d3018edff SHA256 bcf31054c0b646973faa97c27c03dc80c335c43e5e07816a10a65bd596e65d44
-AUX hmmer-3.0-perl-5.16.patch 3824 RMD160 b99be74675657ebe8b2d310411d46441b89555ef SHA1 fced3aedf64bd259acc4993f13fbf0e0ed5e243f SHA256 5bcb970d569eb2f06b3504261e1a24113f4761665c482157e3061b472ba1398c
+AUX hmmer-3.0-perl-5.16.patch 3874 RMD160 c68e8965636abecc6ed3913f1e930fc50fac64df SHA1 344fdd995aaf9c5fa2bd591c444611ea36fa41dc SHA256 14e7c5ecba86939df535653f270b2b1d59ef9f279e2ad5c62d82b83175167d6f
 DIST hmmer-2.3.2.tar.gz 1024933 RMD160 4bf25fc71f332849c76b0a05bca24e88241cee67 SHA1 aa34cb97cbc43ff3bd92dd111ba5677298fe2d40 SHA256 d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4
 DIST hmmer-3.0.tar.gz 3952015 RMD160 681967fd0d2c0104ca9e080688d9652a187a8b45 SHA1 77803c0bdb3ab07b7051a4c68c0564de31940c6d SHA256 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83
 EBUILD hmmer-2.3.2-r1.ebuild 1167 RMD160 d886db50357d8b0dbb7f8e29bb1712d238ce96d7 SHA1 d8097ea91f630ec34745e65457441f21eea39eac SHA256 1271485785e17ec569eb0d365fba45c69b139b07cb10895915e9a5310d2ef670
 EBUILD hmmer-2.3.2-r2.ebuild 1167 RMD160 e848760e79a34acd82231ce5a53de3c6dec454dc SHA1 9f931c5ccf043dab0b0c061401cf569537094da6 SHA256 c20259de9eaf43c769a1a6b84f10da749018e10e32ae2e04e51995f0b4fd00d9
 EBUILD hmmer-3.0.ebuild 1000 RMD160 3e9197ade8b50646505aff0cd94b9e0fb30dfee0 SHA1 ac9f4797cb6c42f36730a6801f97f68b4474630d SHA256 1188a61ba4008cfa292b534088f1db6fdf996928ea722e16588f30eb42dd3882
-MISC ChangeLog 4948 RMD160 ef60ca960b47ae63df5fcb265241832156e83289 SHA1 81c07133ad73f4024ccdb7a709aa26e079194afb SHA256 710b9f07a111f7ca65b1da431d5afc2dbfa9b9c793fadcda217e96e352348355
+MISC ChangeLog 5068 RMD160 70f77e007204762e491221ed922d027f604529e8 SHA1 ce876fa8340d3889cc1674869e89b83fca4c3def SHA256 57f8abeb43779d43022c8bcd5ae76d089c7408eee4d0b935388fd4930e44dfbf
 MISC metadata.xml 280 RMD160 16affdcafcc20790497e60f2c495e9e7a4b061c9 SHA1 474537a46ec5f57c6eb76e74888a8a4784308a0f SHA256 ad90b4124fcc2ef68ba69b1afc073dc2d3178bade4286b8fb83a90df6f0e9843
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 Comment: GPGTools - http://gpgtools.org
 
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-/+YAniez7RxZ6qaWNqyO/5U6qpacD2tj
-=NSc+
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diff --git a/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch b/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch
index 08144c2885e2..c6ba6da03776 100644
--- a/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch
+++ b/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch
@@ -28,7 +28,7 @@ index a4dc126..b61fa7a 100755
 +++ b/easel/devkit/esl-dependencies
 @@ -13,8 +13,8 @@
  # SRE, Mon Jun 11 11:15:31 2007
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
  
 -require "getopts.pl"
 -&Getopts('1afr');
@@ -43,7 +43,7 @@ index af3adf6..0cdb458 100755
 +++ b/easel/devkit/sqc
 @@ -205,12 +205,11 @@
  # SRE, Tue Aug  6 11:16:39 2002
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
  
 -require "getopts.pl";
 -require "importenv.pl";
@@ -66,13 +66,15 @@ index af3adf6..0cdb458 100755
      foreach $suffix ("aa".."zz") {
          $name = "$dir"."esltmp".$suffix.$$;
 diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl
-index 9c77791..024ed34 100755
+old mode 100755
+new mode 100644
+index 9c77791..024ed34
 --- a/easel/testsuite/coverage_report.pl
 +++ b/easel/testsuite/coverage_report.pl
 @@ -16,9 +16,9 @@
  #
  # SRE, Thu Mar  1 19:22:57 2007 (Janelia)
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
 -require  "getopts.pl";
 +use Getopt::Std;
  $have_sloccount = 1;
@@ -87,7 +89,7 @@ index 757854d..a9a8902 100755
 +++ b/easel/testsuite/driver_report.pl
 @@ -25,8 +25,8 @@
  # SRE, Fri Mar  2 10:01:44 2007 (Janelia)
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
  
 -require  "getopts.pl";
 -&Getopts('c');
@@ -97,13 +99,15 @@ index 757854d..a9a8902 100755
  
  if ($ENV{'CC'}       ne "") { $CC       = $ENV{'CC'};       } else { $CC        = "gcc"; } 
 diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl
-index 186a392..07026a0 100755
+old mode 100755
+new mode 100644
+index 186a392..07026a0
 --- a/easel/testsuite/valgrind_report.pl
 +++ b/easel/testsuite/valgrind_report.pl
 @@ -10,8 +10,8 @@
  #
  # SRE, Fri Mar  2 08:37:48 2007 [Janelia]
- # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 jlec Exp $
+ # SVN $Id: hmmer-3.0-perl-5.16.patch,v 1.2 2012/06/28 16:34:57 jlec Exp $
 -require  "getopts.pl";
 -&Getopts('c');
 +use Getopt::Std;