sci-biology/hmmer: Fix for build with perl-5.16, #421799; handle static-libs

(Portage version: 2.2.0_alpha110/cvs/Linux x86_64)

4 files changed, 155 insertions, 18 deletions

diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog
index ad2f907333d8..423104f09bd4 100644
--- a/sci-biology/hmmer/ChangeLog
+++ b/sci-biology/hmmer/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/hmmer
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.31 2010/07/18 11:38:27 fauli Exp $
+# 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 $
+
+  25 Jun 2012; Justin Lecher <jlec@gentoo.org> hmmer-3.0.ebuild,
+  +files/hmmer-3.0-perl-5.16.patch, metadata.xml:
+  Fix for build with perl-5.16, #421799; handle static-libs
 
   18 Jul 2010; Christian Faulhammer <fauli@gentoo.org> hmmer-3.0.ebuild:
   stable x86, bug 328419
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
new file mode 100644
index 000000000000..08144c2885e2
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch
@@ -0,0 +1,128 @@
+ 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 1.1 2012/06/25 06:23:12 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 1.1 2012/06/25 06:23:12 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
+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: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 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 1.1 2012/06/25 06:23:12 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: hmmer-3.0-perl-5.16.patch,v 1.1 2012/06/25 06:23:12 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 bcf126dbdc4e..45a8f1cf4d22 100644
--- a/sci-biology/hmmer/hmmer-3.0.ebuild
+++ b/sci-biology/hmmer/hmmer-3.0.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2010 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 1.4 2010/07/18 11:38:27 fauli Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-3.0.ebuild,v 1.5 2012/06/25 06:23:12 jlec Exp $
 
-EAPI="2"
+EAPI=4
 
 inherit eutils
 
@@ -12,29 +12,34 @@ SRC_URI="ftp://selab.janelia.org/pub/software/hmmer3/${PV}/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE="+sse mpi +threads gsl"
+IUSE="+sse mpi +threads gsl static-libs"
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos"
 
-DEPEND="mpi? ( virtual/mpi )
+DEPEND="
+	mpi? ( virtual/mpi )
 	gsl? ( >=sci-libs/gsl-1.12 )"
 RDEPEND="${DEPEND}"
 
 src_prepare() {
-	epatch "${FILESDIR}"/${P}-fix_tests.patch
+	epatch \
+		"${FILESDIR}"/${P}-fix_tests.patch \
+		"${FILESDIR}"/${P}-perl-5.16.patch
 }
 
 src_configure() {
-	econf $(use_enable sse) \
+	econf \
+		$(use_enable sse) \
 		$(use_enable mpi) \
 		$(use_enable threads) \
 		$(use_with gsl)
 }
 
 src_install() {
-	emake DESTDIR="${D}" install || die
-	dolib src/libhmmer.a || die
-	dolib easel/libeasel.a || die
+	default
+
+	use static-libs && dolib.a src/libhmmer.a easel/libeasel.a
+
 	insinto /usr/share/${PN}
-	doins -r tutorial || die
-	dodoc RELEASE-NOTES Userguide.pdf
+	doins -r tutorial
+	dodoc Userguide.pdf
 }
diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml
index d7cabd4bc1fd..66fa76626615 100644
--- a/sci-biology/hmmer/metadata.xml
+++ b/sci-biology/hmmer/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-biology</herd>
-<use>
-  <flag name='pvm'>Add support for parallel virtual machine
+	<herd>sci-biology</herd>
+	<use>
+		<flag name="pvm">Add support for parallel virtual machine
     (<pkg>sys-cluster/pvm</pkg>)</flag>
-</use>
+	</use>
 </pkgmetadata>