3 files changed, 8 insertions, 136 deletions
diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog
index eee879e0d978..112de0d3bb44 100644
--- a/sci-biology/hmmer/ChangeLog
+++ b/sci-biology/hmmer/ChangeLog
@@ -1,6 +1,10 @@
 # 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 1.35 2012/06/28 16:38:29 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.36 2012/06/28 16:50:49 jlec Exp $
+
+  28 Jun 2012; Justin Lecher <jlec@gentoo.org> hmmer-3.0.ebuild,
+  -files/hmmer-3.0-perl-5.16.patch:
+  Fix the patch, thanks xarthisius and bonsaikitten for help
 
   28 Jun 2012; Justin Lecher <jlec@gentoo.org> files/hmmer-3.0-perl-5.16.patch:
   Fix patch, screwed VCS tags, #423983
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
deleted file mode 100644
index bc9a92d8d3be..000000000000
--- a/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch
+++ /dev/null
@@ -1,132 +0,0 @@
- 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 ++--
- profmark/rocplot.pl                |    4 ++--
- 7 files changed, 15 insertions(+), 16 deletions(-)
-
-diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
-index 16bda4d..f5c5efc 100755
---- a/easel/devkit/autodoc
-+++ b/easel/devkit/autodoc
-@@ -49,8 +49,8 @@
- #
- # SRE, Tue Nov 30 19:43:47 2004
- 
--require  "getopts.pl";
--&Getopts('n:t');
-+use Getopt::Std;
-+getopts('n:t');
- $cfile = shift;
- 
- if ($opt_t) { $show_api_table = 1; }
-diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies
-index a4dc126..b61fa7a 100755
---- a/easel/devkit/esl-dependencies
-+++ 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 1.6 2012/06/28 16:47:02 jlec Exp $
- 
--require "getopts.pl"
--&Getopts('1afr');
-+use Getopt::Std;
-+getopts('1afr');
- 
- if ($opt_1) { $show_summary_table = 1; }
- if ($opt_a) { $list_augfiles      = 1; }
-diff --git a/easel/devkit/sqc b/easel/devkit/sqc
-index af3adf6..0cdb458 100755
---- a/easel/devkit/sqc
-+++ 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 1.6 2012/06/28 16:47:02 jlec Exp $
- 
--require "getopts.pl";
--require "importenv.pl";
-+use Getopt::Std;
- 
- # Parse our command line
- #
--&Getopts('v');
-+getopts('v');
- if ($opt_v) { $verbose = 1;           }
- 
- 
-@@ -609,7 +608,7 @@ sub check_valgrind_status
- #
- sub tempname {
-     my ($dir, $name, $suffix);
--    if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
-+    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
- 
-     foreach $suffix ("aa".."zz") {
-         $name = "$dir"."esltmp".$suffix.$$;
-diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl
-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 1.6 2012/06/28 16:47:02 jlec Exp $
--require  "getopts.pl";
-+use Getopt::Std;
- $have_sloccount = 1;
--&Getopts('cs');
-+getopts('cs');
- if ($opt_c) { $do_recompile     = 1; }
- if ($opt_s) { $have_sloccount   = 0; }
- 
-diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl
-index 757854d..a9a8902 100755
---- a/easel/testsuite/driver_report.pl
-+++ 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 1.6 2012/06/28 16:47:02 jlec Exp $
- 
--require  "getopts.pl";
--&Getopts('c');
-+use Getopt::Std;
-+getopts('c');
- if ($opt_c) { $do_recompile = 1; }
- 
- if ($ENV{'CC'}       ne "") { $CC       = $ENV{'CC'};       } else { $CC        = "gcc"; } 
-diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl
-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 1.6 2012/06/28 16:47:02 jlec Exp $
--require  "getopts.pl";
--&Getopts('c');
-+use Getopt::Std;
-+getopts('c');
- if ($opt_c) { $do_recompile = 1; }
- 
- if ($ENV{'CC'}     ne "") { $CC     = $ENV{'CC'};     } else { $CC       = "gcc"; } 
-diff --git a/profmark/rocplot.pl b/profmark/rocplot.pl
-index d4c0f67..4e8175a 100755
---- a/profmark/rocplot.pl
-+++ b/profmark/rocplot.pl
-@@ -2,8 +2,8 @@
- 
- $nsearches = 1567;
- 
--require "getopts.pl";
--&Getopts('n:X:x:');
-+use Getopt::Std
-+getopts('n:X:x:');
- 
- if ($opt_n) { $nsearches = $opt_n; }
- if ($opt_X) { 
diff --git a/sci-biology/hmmer/hmmer-3.0.ebuild b/sci-biology/hmmer/hmmer-3.0.ebuild
index 45a8f1cf4d22..989273b3eb1f 100644
--- a/sci-biology/hmmer/hmmer-3.0.ebuild
+++ b/sci-biology/hmmer/hmmer-3.0.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2012 Gentoo Foundation
+## Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-3.0.ebuild,v 1.5 2012/06/25 06:23:12 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-3.0.ebuild,v 1.6 2012/06/28 16:50:49 jlec Exp $
 
 EAPI=4
 
@@ -23,7 +23,7 @@ RDEPEND="${DEPEND}"
 src_prepare() {
 	epatch \
 		"${FILESDIR}"/${P}-fix_tests.patch \
-		"${FILESDIR}"/${P}-perl-5.16.patch
+		"${FILESDIR}"/${P}-perl-5.16-2.patch
 }
 
 src_configure() {