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

Package-Manager: portage-2.2.10/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 54 insertions, 29 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/Manifest b/sci-biology/infernal/Manifest
index 7c6f755c8d12..1b240dcceb2f 100644
--- a/sci-biology/infernal/Manifest
+++ b/sci-biology/infernal/Manifest
@@ -1,18 +1,30 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX infernal-1.0.2-ldflags.patch 440 SHA256 397e1fad01f613a4de4679797da5428a8f0d4ebcda0eb68c3044b93d196d6cb0 SHA512 27f9c6ece32f9f6bc1248da55760ff5c03cab4ff61852731d95fe7378726e9040c9e8bd97f1cc2b4a7957a9d69e76e3b7a804f9db1c5606301a413c1acfa1b79 WHIRLPOOL 4a2856e6ea2a213496f74e3d46ab692ed7647346a97f9ceb0e6958a6c17eafe3d02bc1aecb37051615f3444443cc05a611f34eaa859650ed8cc43ccebb654353
 AUX infernal-1.0.2-overflows.patch 536 SHA256 ccd5b77323fd769791b1c39f5964fa0a2e29b7710627c16d90eb2b64bb89faa4 SHA512 facc52c2148904d91f25ad87680f6a7ed93d18c81c4ed67abd6ec09ed305dcc56f12df80174ddea4f050275739ac203d8234bdf81fb9ce82c01f8947a2fef347 WHIRLPOOL 9891674da74182e4e5f18ce7b7536ee95a0bd0600dc5558a069b8c915ca820fbe60254f0c71bf8f2589413bfedc2d9e78c9dd9cb863d4454dfba600f93ca0788
 AUX infernal-1.0.2-parallel-build.patch 651 SHA256 5f5aa6fe823640e90bdebe04be99635f1190771df9ea29316d926d3b928878be SHA512 6f517a438b580e4d8c110f4b5b7b1ff1ddefce357dc07c5b52f8ac43ef5f4093aecd784707744cc3a4c7effe7b76f29e99d8130fe0948e03951fe2ae2cd2a504 WHIRLPOOL 5484684a4cfd1bdfeda2fa27eadba61b0fc809014121ef5532067f159e73229e135ad5a33f03e59e645ca600f5b981b76a62b187f8da720d0ab98cf0066fd5b5
-AUX infernal-1.0.2-perl-5.16.patch 4275 SHA256 488900758fbf2b165c643507f22f764092f1b807b7a2046ff4ddc48f006d8c28 SHA512 82ec4e3b116957b22604c4c614275d7c9b67fb579bc975baaea105b29a42af75a4ad50ecc4ba53069b7934fddefb4ba5265ed0a79c440e476faa5310cfdcf07b WHIRLPOOL 61b9451bce517db28a00684aded637cbfc3a1977e741bc5be12b57b647353e14d1a93d2dec7e719c7c1b8fa1e637f949510d8fd0fde18177f331064c11dc575c
+AUX infernal-1.0.2-perl-5.16-2.patch 4206 SHA256 db663878a8d139f1832ddbec54131c518cdbac1fa8d298e80cee529fb3eddd0f SHA512 9784f31c18f6c53b15c0454d3a41db27c3f433ac3d3030bc113e9f9e8194fb51109de5055d038a3c639b1c4142d6fd0010825df484a857c9f072f43d8cadcb44 WHIRLPOOL d8ce80893fe2abeb537daa0a759a432649f677d9cc9f77ff597b4a1bfb8d90b45ca4bae0043cd0fb889f6a14b0caa90d3d7cec9516f53d24e6b441fbfeb4dfe3
 DIST infernal-1.0.2.tar.gz 15205421 SHA256 c4f89ac2e865c8b04a53a647703d88f96c31bb1d47d3e06f4b6090d7d15643ad SHA512 0399be14c17f053574e95d8c5b9eaf990545795a9268e20f0940e11a8e78fc49beb4b23994e9ea427764fbb29e9b39f6da9cb1d85eb4b56d354057b48515c4af WHIRLPOOL c4fa3326eb1b36252ce41ca1aeca68bed4373061ca6bc2bfc0af62c0805bfa1747272fbf223b8d47194853ae5cbe7af11d47493c258264503ea6aa7b142a6b60
-EBUILD infernal-1.0.2-r1.ebuild 1037 SHA256 f0a9e193e99ac8f10709e0cccfc382f22c34b46f6a2b0e69fd7413b13abd6e31 SHA512 af884bbf4470a4671fcbffb13d9992bf3fc33a4b58d4de0867400246ac7473630506d3cf8e040eeb92e9585a2c5cfe3f2f20ab60d97a33e8998c1c36ba778424 WHIRLPOOL fd9daec4cab9d6b015594d2a6460dfb27d6b7377a699e02dddd6bb5461d64191eb1687cb896d5441645e140510a089f696f0e98e9ccce7eca0f217544000a1d0
-MISC ChangeLog 2364 SHA256 54b27a9927456829bf26ce765b69897594cbcd50884e2a662a91842f83d51d3a SHA512 9d16fc7d56926aee7d7dac78c2a94e92f9cbe1989b7ec9ee9ec2878be82b0ad86909ec43eaac4e20c2f1de5ffb453e255164c1148491473a6f75a058f40e3650 WHIRLPOOL 0d081ada04444bba7b90d43af46b6ba3db33fdd1dfd91c83f7a7b456d7da940a6be24b5ed56b4f5a3501f5d7912f25e00596e2edfe800ee44890973ec7d16dae
+EBUILD infernal-1.0.2-r1.ebuild 1039 SHA256 6cb9be3179e518c0c300a0df99bd383e70cd3091e430a42fcfc04b9e1bf3f15c SHA512 fbef42c39706706333093f6a2aea413844e72bc203ee58f8430748bf254c8254fcd75caa5a9e8960c6ff7716a8be05d91660215c6144a30ebd60de9e7035e265 WHIRLPOOL 4f9bc18dd00181d59015e176251e0f12e46f2c7beedc9db990442f63403cd41ec2fc708e0797255acbe84f983f6a78828790b17a6ce626c79f545ee6093e4852
+MISC ChangeLog 2575 SHA256 98f684e2671e5dcef3a9572874849d0bf01b8794e7ada1611c491816d8b8ef40 SHA512 371c177a61a11365b50244977c04f1d19cd3ae77425b11f29e39cb9e6ecc5a389cd4fcd0e24bf7fc9086874a03b64208ddac40c2d4ecb893296218a490ecc0ae WHIRLPOOL 3e6552a94f52d170421f1bce77fca59259cca376c1043f10e47c3274ba16089fbff2261817b88773d284b0ca0cd2d51e5078a7b43e973e6712197ab546c93a27
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.19 (GNU/Linux)
+Version: GnuPG v2.0
 
-iEYEAREIAAYFAlE992AACgkQgAnW8HDreRaDagCeIGZAeBCZbRVWuS8kHlKrNhkb
-cjsAoIhNy02/4imtWx0IqXSjZCCz1rxH
-=W26g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+=Fvbh
 -----END PGP SIGNATURE-----
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
 }