sci-biology/infernal: Fix for perl-5.16, #422561; move to EAPI=4

Package-Manager: portage-2.2.0_alpha110/cvs/Linux x86_64

4 files changed, 167 insertions, 27 deletions

diff --git a/sci-biology/infernal/ChangeLog b/sci-biology/infernal/ChangeLog
index b8fab0ead6e1..38728de4a063 100644
--- a/sci-biology/infernal/ChangeLog
+++ b/sci-biology/infernal/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/infernal
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/infernal/ChangeLog,v 1.10 2011/02/11 13:04:33 hwoarang Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/infernal/ChangeLog,v 1.11 2012/06/25 07:08:17 jlec Exp $
+
+  25 Jun 2012; Justin Lecher <jlec@gentoo.org> infernal-1.0.2-r1.ebuild,
+  +files/infernal-1.0.2-perl-5.16.patch:
+  Fix for perl-5.16, #422561; move to EAPI=4
 
   11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> infernal-1.0.2-r1.ebuild:
   Stable on amd64 wrt bug #353571
diff --git a/sci-biology/infernal/Manifest b/sci-biology/infernal/Manifest
index b513f615a571..418c5af60544 100644
--- a/sci-biology/infernal/Manifest
+++ b/sci-biology/infernal/Manifest
@@ -4,25 +4,17 @@ Hash: SHA512
 AUX infernal-1.0.2-ldflags.patch 440 RMD160 6a9df534b9784f39d768cf62bff406030835ef16 SHA1 c7b796137bef732f84e74d08f1744ec5d150d26f SHA256 397e1fad01f613a4de4679797da5428a8f0d4ebcda0eb68c3044b93d196d6cb0
 AUX infernal-1.0.2-overflows.patch 536 RMD160 fd9434b4291b610053fc0d2a076247eff7799d0c SHA1 8922c7bf904fbf3213231ffc7389645517af1b1b SHA256 ccd5b77323fd769791b1c39f5964fa0a2e29b7710627c16d90eb2b64bb89faa4
 AUX infernal-1.0.2-parallel-build.patch 651 RMD160 4889692cadfd92c96e4b399737374ad7cd401cd1 SHA1 54fadbaca7935c50ec37a1a09318a303de473862 SHA256 5f5aa6fe823640e90bdebe04be99635f1190771df9ea29316d926d3b928878be
+AUX infernal-1.0.2-perl-5.16.patch 4225 RMD160 0bb44e78e6fdbbf87f7cf6698fb948146ee1183e SHA1 7534b0063dd71d3d13cdf31a953f517809c3e937 SHA256 1d88ccec12b1c10dfdd4b96d6e1f9aabba48cbb61bce3e879bbad06b8580c591
 DIST infernal-1.0.2.tar.gz 15205421 RMD160 f56cb970a520b63d60b854f5b397813c342bb81f SHA1 df2454c606eb0f90ab98fc5c988fdd60a6f87903 SHA256 c4f89ac2e865c8b04a53a647703d88f96c31bb1d47d3e06f4b6090d7d15643ad
-EBUILD infernal-1.0.2-r1.ebuild 988 RMD160 b69dea0075c5209df7e6e489bf83888e99ee6324 SHA1 f7d2e6fc6e046db52875227deca7b62f10263ca8 SHA256 10590f5ea77c102385a06a4059a5554d355a9a384c37753e4be4e9f010d6e2fa
+EBUILD infernal-1.0.2-r1.ebuild 1037 RMD160 b363a7eab79f432979508923209b45f6b5effdbe SHA1 ae920cc0b1c81b56cb8e76d47a2233726d3e7ed3 SHA256 f0a9e193e99ac8f10709e0cccfc382f22c34b46f6a2b0e69fd7413b13abd6e31
 EBUILD infernal-1.0.2.ebuild 821 RMD160 a79be76a80f518397d0e25714ab740619ca57e77 SHA1 a520349aac4594219ecb0824905546da1336be83 SHA256 7679a24172fae83d28c7dcec64a6ae9cfdd0204185da8b1170c786f0ddd13570
-MISC ChangeLog 1838 RMD160 5caca96faba02808a156afa3612645016295f0b9 SHA1 5d61683c8e831e949acd543a6e7ff79e7dd0aca2 SHA256 15c79e6fec9ee3645907a319a0099b0de2fed1d934a0da02ee57f14f5ea3ded2
+MISC ChangeLog 1994 RMD160 f468a4d16d9918492090e55c764b4f9d68529e4e SHA1 b58a00672bb7a354cbe4094240c5b4e59c2c2896 SHA256 4c6c7f77c77bb0477860cf6c81d4bb13f8f4d96af8b88dec8093c1040a70a5ec
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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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.patch
new file mode 100644
index 000000000000..b4eeab3ca59d
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16.patch
@@ -0,0 +1,135 @@
+ 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
+index 9136717..e4df233 100644
+--- a/benchmarks/cmsearch-rmark/sre.pl
++++ b/benchmarks/cmsearch-rmark/sre.pl
+@@ -6,8 +6,6 @@
+ 
+ package SRE_perlstuff;
+ 
+-require "importenv.pl";
+-
+ # Function: tempname
+ #
+ # Returns a unique temporary filename. 
+@@ -26,7 +24,7 @@ require "importenv.pl";
+ #
+ sub main'tempname {
+     local ($dir, $name);
+-    if ($TMPDIR) { $dir = $TMPDIR; } else {$dir = "/tmp";}
++    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}; } else {$dir = "/tmp";}
+ 
+     foreach $suffix ("aa".."zz") {
+ 	$name = "$dir/sre$suffix$$";
+diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
+index 045ce36..22268f6 100755
+--- a/easel/devkit/autodoc
++++ b/easel/devkit/autodoc
+@@ -49,8 +49,8 @@
+ #
+ # SRE, Tue Nov 30 19:43:47 2004
+ 
+-require  "getopts.pl";
+-&Getopts('n:t');
++use Getopt::Std;
++getopts('n:t');
+ $cfile = shift;
+ 
+ if ($opt_t) { $show_api_table = 1; }
+diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies
+index a4dc126..b61fa7a 100755
+--- a/easel/devkit/esl-dependencies
++++ b/easel/devkit/esl-dependencies
+@@ -13,8 +13,8 @@
+ # SRE, Mon Jun 11 11:15:31 2007
+ # SVN $Id: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 jlec Exp $
+ 
+-require "getopts.pl"
+-&Getopts('1afr');
++use Getopt::Std;
++getopts('1afr');
+ 
+ if ($opt_1) { $show_summary_table = 1; }
+ if ($opt_a) { $list_augfiles      = 1; }
+diff --git a/easel/devkit/sqc b/easel/devkit/sqc
+index 81d03de..6201d3d 100755
+--- a/easel/devkit/sqc
++++ b/easel/devkit/sqc
+@@ -176,12 +176,11 @@
+ # SRE, Tue Aug  6 11:16:39 2002
+ # SVN $Id: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 jlec Exp $
+ 
+-require "getopts.pl";
+-require "importenv.pl";
++use Getopt::Std;
+ 
+ # Parse our command line
+ #
+-&Getopts('mp:r:v');
++getopts('mp:r:v');
+ if ($opt_m) { $do_memtest = 1;    }
+ if ($opt_p) { push @prepdirs, $opt_p; }
+ if ($opt_r) { push @olddirs,  $opt_r; }
+@@ -510,7 +509,7 @@ check_ccmalloc_status
+ #
+ sub tempname {
+     my ($dir, $name, $suffix);
+-    if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
++    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
+ 
+     foreach $suffix ("aa".."zz") {
+         $name = "$dir"."esltmp".$suffix.$$;
+diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl
+index 9c77791..024ed34 100755
+--- 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: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 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 d1b4a9a..db4378f 100755
+--- 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 1.1 2012/06/25 07:08:17 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
+index 186a392..07026a0 100755
+--- 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: infernal-1.0.2-perl-5.16.patch,v 1.1 2012/06/25 07:08:17 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/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild
index 8c2b8a34e096..6ccfc9790624 100644
--- a/sci-biology/infernal/infernal-1.0.2-r1.ebuild
+++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2011 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/infernal/infernal-1.0.2-r1.ebuild,v 1.3 2011/02/11 13:04:33 hwoarang Exp $
+# $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 $
 
-EAPI="2"
+EAPI=4
 
 inherit eutils
 
@@ -19,20 +19,29 @@ DEPEND="mpi? ( virtual/mpi )"
 RDEPEND="${DEPEND}"
 
 src_prepare() {
-	epatch "${FILESDIR}"/${P}-parallel-build.patch \
+	epatch \
+		"${FILESDIR}"/${P}-parallel-build.patch \
 		"${FILESDIR}"/${P}-overflows.patch \
+		"${FILESDIR}"/${P}-perl-5.16.patch \
 		"${FILESDIR}"/${P}-ldflags.patch
 }
 
 src_configure() {
-	econf --prefix="${D}/usr" \
+	econf \
+		--prefix="${D}/usr" \
 		$(use_enable mpi)
 }
 
 src_install() {
-	emake install || die
-	(cd documentation/manpages; for i in *; do newman ${i} ${i/.man/.1}; done)
+	default
+
+	pushd documentation/manpages > /dev/null
+	for i in *;
+		do newman ${i} ${i/.man/.1}
+	done
+	popd > /dev/null
+
 	insinto /usr/share/${PN}
-	doins -r benchmarks tutorial intro matrices || die
-	dodoc 00README* Userguide.pdf documentation/release-notes/* || die
+	doins -r benchmarks tutorial intro matrices
+	dodoc 00README* Userguide.pdf documentation/release-notes/*
 }