sci-biology/vienna-rna: Version Bump; move to EAPI=5, new python eclasses; autotools-utils

Package-Manager: portage-2.2.0_alpha162/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

7 files changed, 214 insertions, 6 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index db40e35eadfb..43d90cdc1e91 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/vienna-rna
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.46 2013/01/31 10:57:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.47 2013/02/13 13:13:57 jlec Exp $
+
+*vienna-rna-2.1.1 (13 Feb 2013)
+
+  13 Feb 2013; Justin Lecher <jlec@gentoo.org> +vienna-rna-2.1.1.ebuild,
+  +files/vienna-rna-2.1.1-bindir.patch,
+  +files/vienna-rna-2.1.1-impl-decl.patch, +files/vienna-rna-2.1.1-prll.patch,
+  +files/vienna-rna-2.1.1-setup.py:
+  Version Bump; move to EAPI=5, new python eclasses; autotools-utils
 
   31 Jan 2013; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.5.ebuild,
   metadata.xml:
diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
index 7f257721c8bd..24db0c31bddf 100644
--- a/sci-biology/vienna-rna/Manifest
+++ b/sci-biology/vienna-rna/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
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 AUX vienna-rna-1.7.2-LDFLAGS.patch 978 SHA256 0c7db17c7a1a8a075e26f6b98b19c84a3f98f9ecdaa06755e4e426fcb1b8ce8c SHA512 a5fea1fc9c969d2bde9094b8303ee5d0b77f0570107d403279bcc3884d2925f81789d3d08627caadf92f435bbf369721dbc95e1122bde5741340104526a532b2 WHIRLPOOL 82d3e59c9a399cd352f72477fc9803012ef288e3198b0c69e86ce184cfe75c1c824b149b6ea55771da88180d9d402e1d8ed8444aac1f1bcd9211ded54f15d917
@@ -10,14 +10,20 @@ AUX vienna-rna-1.8.4-implicits.patch 1163 SHA256 f49e60dc866e7844fea32e90b9e91ce
 AUX vienna-rna-1.8.4-jobserver-fix.patch 681 SHA256 bec5248214ba303d85afda03e663f84061258cd06f2f50773011251299a42b84 SHA512 33ddeb32bb5739081b7c9f9d863f9b4760cb72764bd3e5e2181a9859579e76261af31726021bd3c183862ada1bb5e81aa93b380fa44935b82c296a4b79a64b21 WHIRLPOOL 84af3a01b5b38f11e680ee896dcb93f21828da5aa0f021dce672182725d6a0cbe10df26bec8760b9800e972916a66fea02c78a2d1d3a3f24412b29ca326a07d6
 AUX vienna-rna-1.8.4-overflows.patch 740 SHA256 cd977c5acfca05890768893ab5e18fca5fee167dac341e0edd16bc4fd7cd2a08 SHA512 17bed70ff24f452f042dcf14f303941f21e309c96ffcb2ac38a82cc80a85806d9f8a0d9923ca4446ee021d7f156ab82ac402c51f0178aa180f5893720f57c48e WHIRLPOOL 1f6ba4c537658e383768551561002235bb2c2ed948651898cdb5b24857fa2feb6160586e622e40105f01e7962404a1b9473be6a0f509eb93f14135c98782395c
 AUX vienna-rna-1.8.5-setup.py 810 SHA256 91e4caa304aa97430552f2a3a46f57ced23239d55b1a52a658bbcf91e0835f62 SHA512 85587e631ed98c5f10ab4000a6fe4e2ff7f230e11449f3f8d99e578a56e70b15362bb929f2ddf715065197ac22877f6de253fa8e113ddea276a43ad673bca8aa WHIRLPOOL e1fdf83df88c366d8bf0cac5ba1a5b14b37720fc820a9640e91e890de77e0566763643a0a160699985143f1ed3ef37adf2bff29720b053e881557f2bbe3411a3
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+AUX vienna-rna-2.1.1-impl-decl.patch 354 SHA256 9f9005092b060db501b51c37f215f9ca87da53720609ce971c3d9ad6bcf2ea39 SHA512 7c288b4889f11b5cc4e6db5b5db6dfcd70843aa135181e8d819ae86c90faed4a43e08f99b47f418caa23643642e68bf5e153f4d279f7566433af1c9093ec6e8b WHIRLPOOL 02ce683c58e4f5715ab75445d9efeb02c1c104a6faa25b19739dc43931f813d6c7637a6690026d18607da98f2f7a7185ffe3491c237d1f40dd09340dc44c651e
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 DIST ViennaRNA-1.8.5.tar.gz 1306792 SHA256 f4e2d94beaf77165e8321758e4ab0ad1c5d49879cefa12e48b07d09ed2d0ecf9 SHA512 3121bbeb476c1828f2238d32ab4fea724fd17d9108cb38ea76a73b64eda97a36689080faa6745a4cd369178239443eeb68621da0cd96beb55d2bd0b6cb0891de WHIRLPOOL e561f6e3506e85f54974d3bf9def910d404cdc94bb8e184933b90698a083c5c5e40510deec6486737081ca602b560b5409c79a21a517daa2b859c7430abc0fb6
+DIST ViennaRNA-2.1.1.tar.gz 5327215 SHA256 bfea440dface4562d5dfb0a1c83bf226c0697bb18aacae0dc84c555282cedebe SHA512 b272afa1146543b290db605debab2badbdbf04fcdfd6130ed3b10604255476b3472b184e9af8a0bbeaa0def266f1a167c125d6cfd02aa3f7ae463697dc5226d5 WHIRLPOOL 48b6bcd96b2ff2523ba00335cac7fe141b6ed7f037a3192e6c174297266d0f967492a67afaaa6c05f8b28fdc0eb7c9b72d0d9daba286b5dd3dca4456cc058b1f
 EBUILD vienna-rna-1.8.5.ebuild 2890 SHA256 088724bebfc184560535041ddd509d80459e3a3991b1efc7b095f74549b5e047 SHA512 d229dbb7dc2c44fd5181705747e26aa0d6944e17c9694b987d3d9d8a88532ca091c23ae65ad4f0f30f2a6e373e519ce22229fa19dc986d8e0cc6ecb6c3186499 WHIRLPOOL be125d58a63a000a2ab7d901e8adcdbcb811fe2f541d47360951de77bbfa896b305d13c744a70e8b123836ddcb45dbef8d266ef8d1749e94a65156ec69980245
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+EBUILD vienna-rna-2.1.1.ebuild 2728 SHA256 78381c7ff582de36385ed575b66ae412c0f001cd96d108e00f979b196552cf42 SHA512 4e4132f5573fb79340f23258c7b07b1c0efef4f94e9254e30f7e7c55a1d923ce4b11e361dc232fe12ea8712953744d91b521756c9eb6fa2ebe01ae754ddb4e5c WHIRLPOOL 742b1332deaba3a27ade366083fbf713a985087986fa91506edf48efd670cd37a296b791411e1ac9a4a792bb217af9efa4ab48e532b89bac02242b917b66abfb
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diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch
new file mode 100644
index 000000000000..6d35ecea9b0f
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch
@@ -0,0 +1,10 @@
+diff --git a/Utils/Makefile.am b/Utils/Makefile.am
+index f42ebf4..d84a0f1 100644
+--- a/Utils/Makefile.am
++++ b/Utils/Makefile.am
+@@ -1,4 +1,4 @@
+-pkgbindir = $(pkgdatadir)/bin
++pkgbindir = $(prefix)/bin
+ pkgbin_PROGRAMS = b2ct popt
+ 
+ pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
new file mode 100644
index 000000000000..de457f318e8e
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
@@ -0,0 +1,15 @@
+ Readseq/readseq.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/Readseq/readseq.c b/Readseq/readseq.c
+index 8af7b39..56a25ae 100644
+--- a/Readseq/readseq.c
++++ b/Readseq/readseq.c
+@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' 
+ #include <stdio.h>
+ #include <string.h>
+ #include <ctype.h>
++#include <stdlib.h>
+ 
+ #include "ureadseq.h"
+ 
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
new file mode 100644
index 000000000000..ee4aef5c3308
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
@@ -0,0 +1,30 @@
+ Readseq/Makefile | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Readseq/Makefile b/Readseq/Makefile
+index f073aaa..05f2edd 100644
+--- a/Readseq/Makefile
++++ b/Readseq/Makefile
+@@ -6,11 +6,11 @@
+ #
+ 
+ # pick an ANSI C compiler (the default Sun CC is not ANSI)
+-CC=gcc  # Gnu C Compiler
++CC?=gcc  # Gnu C Compiler
+ #CC=cc  # SGI Irix
+ #CC=vcc # some DEC Ultrix
+ 
+-CFLAGS=
++CFLAGS?=
+ #CFLAGS= -DSMALLCHECKSUM  # if you prefer to use a GCG-standard 13 bit checksum
+ #    instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
+ 
+@@ -40,7 +40,7 @@ all: build test
+ 
+ build: $(SOURCES)
+ 	@echo "Compiling readseq..."
+-	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
++	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c
+ 
+ # if using NCBI, uncomment these lines in place of build: above
+ #build: $(SOURCES)
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py
new file mode 100644
index 000000000000..57f6b712ba3d
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py
@@ -0,0 +1,27 @@
+from distutils.core import setup, Extension
+import os
+import sys
+ 
+old_filename = os.path.join("Perl", "RNA.py")
+new_filename = os.path.join("Perl", "__init__.py")
+if os.path.exists(old_filename):
+    os.rename(old_filename, new_filename)
+ 
+extra_link_args = []
+ 
+extension = Extension("_RNA",
+                      ["Perl/RNA_wrap.c"],
+                      libraries=['RNA'],
+                      library_dirs=['lib'],
+                      extra_link_args=extra_link_args
+                      )
+ 
+setup(name="RNA",
+      version="2.1.1",
+      description="Vienna RNA",
+      author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna",
+      url="http://www.tbi.univie.ac.at/RNA/",
+      package_dir = {'RNA':'Perl'},
+      packages = ['RNA'],
+      ext_modules=[extension],
+      )
diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild
new file mode 100644
index 000000000000..3872a6eab80e
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild,v 1.1 2013/02/13 13:13:57 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_5,2_6,2_7} )
+DISTUTILS_OPTIONAL=true
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs
+
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
+SRC_URI="http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="vienna-rna"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE="doc openmp python static-libs"
+
+DEPEND="
+	dev-lang/perl
+	media-libs/gd
+	doc? ( dev-texlive/texlive-latex )
+	python? (
+		${PYTHON_DEPS}
+		dev-lang/swig )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ViennaRNA-${PV}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-bindir.patch
+	"${FILESDIR}"/${P}-prll.patch
+	"${FILESDIR}"/${P}-impl-decl.patch
+)
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+src_prepare() {
+	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
+	sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || die
+
+	autotools-utils_src_prepare
+
+	if use python; then
+		cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py || die
+		PATCHES=()
+		distutils-r1_src_prepare
+	fi
+}
+
+src_configure() {
+	local myeconfargs=(
+		--with-cluster
+		$(use_enable openmp) )
+
+	use doc || \
+		myeconfargs+=(
+			--without-doc-pdf
+			--without-doc-html
+			--without-doc
+			)
+	autotools-utils_src_configure
+	sed \
+		-e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
+		-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
+		-i RNAforester/g2-0.70/Makefile || die
+	sed \
+		-e "s:CC=gcc:CC=$(tc-getCC):" \
+		-e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \
+		-i Readseq/Makefile || die
+	use python && distutils-r1_src_configure
+}
+
+src_compile() {
+	autotools-utils_src_compile
+	autotools-utils_src_compile -C Readseq build CC=$(tc-getCC)
+
+	# TODO: Add (optional?) support for the NCBI toolkit.
+	if use python; then
+		pushd Perl > /dev/null
+			mv RNA_wrap.c{,-perl} || die
+			swig -python RNA.i || die
+		popd > /dev/null
+		distutils-r1_src_compile
+		mv Perl/RNA_wrap.c{-perl,} || die
+	fi
+}
+
+src_test() {
+	autotools-utils_src_compile -C Perl check
+	autotools-utils_src_compile -C Readseq test
+}
+
+src_install() {
+	autotools-utils_src_install
+
+	if ! use static-libs; then
+		rm -f "${ED}"/usr/$(get_libdir)/*.a || die
+	fi
+
+	newbin Readseq/readseq readseq-vienna
+	dodoc Readseq/Readseq.help
+	newdoc Readseq/Readme README.readseq
+	newdoc Readseq/Formats Formats.readseq
+
+	# remove perlocal.pod to avoid file collisions (see #240358)
+	fixlocalpod || die "Failed to remove perlocal.pod"
+	use python && distutils-r1_src_install
+}