sci-biology/cufflinks: Drop debugging flags, fix compatibility with newer samtools, #524252

Package-Manager: portage-2.2.14_rc1/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

5 files changed, 120 insertions, 16 deletions

diff --git a/sci-biology/cufflinks/ChangeLog b/sci-biology/cufflinks/ChangeLog
index 7a6426be6048..044b1c730a93 100644
--- a/sci-biology/cufflinks/ChangeLog
+++ b/sci-biology/cufflinks/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/cufflinks
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/ChangeLog,v 1.8 2014/09/25 16:11:26 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/ChangeLog,v 1.9 2014/10/02 08:01:05 jlec Exp $
+
+*cufflinks-2.2.1-r1 (02 Oct 2014)
+
+  02 Oct 2014; Justin Lecher <jlec@gentoo.org> +cufflinks-2.2.1-r1.ebuild,
+  +files/cufflinks-2.2.1-flags.patch, +files/cufflinks-2.2.1-hts.patch:
+  Drop debugging flags, fix compatibility with newer samtools, #524252
 
 *cufflinks-2.2.1 (25 Sep 2014)
 
diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest
index 616aae46cffc..bc30e466a804 100644
--- a/sci-biology/cufflinks/Manifest
+++ b/sci-biology/cufflinks/Manifest
@@ -4,28 +4,31 @@ Hash: SHA512
 AUX cufflinks-1.3.0-autotools.patch 1270 SHA256 457741f6707097b6baa004c09995526a06553d75ed0018f0ef239001ab9963ff SHA512 2b9efa463f808e1433674f5c351d5e3fb30db7516d3b4fdf4f9d18d010d64a937b227d9271ece581b8f3240cd156f27972ad1073f07ee1761444c2e2681a9d83 WHIRLPOOL 6c02e73bdd41c117ead6252da374811ccb23658a7f3b6fac2abcee0cc189df4f5b1a3106906ddd462c053ddda02f7b41c7b73a985417f6d8db53afc6a29c158c
 AUX cufflinks-1.3.0-boost.patch 52005 SHA256 4fc98a82bb1b283db0eb0b4064ac76237ddd1f5c329d76a4130ec09d7dc7983b SHA512 910c9d1b9b1635a4b3e30b0d377b1f2c192a20e482697da0346a9ecb99e0255ac50c906ff7be2d94446137ed04cfa7705c916dc892e1fc0c5c05c93e950e1d34 WHIRLPOOL a5fc395daccbf248fe819b1c21979fbd0f6168c7227d4774240fa70d58eb75dd479eb418bd181c5c470209f72d52c7913d0dea77d1b6d16716543841bd5a5984
 AUX cufflinks-1.3.0-gcc-4.7.patch 594 SHA256 9dcdde0e56b3ebb3f0325eaba05b0c8f80cab311519d3785956e32bb1c4e0b97 SHA512 fc8b3924af1f24cc57e5890bb22acc1123eb1704948ded6bdf2beb7500ccbe57c12ff3905c235f3ae47dfff19e4205ed266b94a6eef48ce1539cd2c260e37ac6 WHIRLPOOL 196255a59028cadfa6d0575230bb9f602c894db437b34e1f9efb573dbe5d9bdc9bc3f9ed573166aa9fbb070d7d506a447627369bb71d72040d1ab28b358c46fc
+AUX cufflinks-2.2.1-flags.patch 1132 SHA256 3f86cd6ef757bc597bf4a511c119f176d4bb1bc06b3098791849446329f42a2e SHA512 58ea036d55d0b4835a56ea66afc2359bdb3e022f1fda3cab8402e4a2d7c6eab00fae96c739f89a25ca1e7528dad02f20c5c944a198c1eeca245e8995fbaa8f12 WHIRLPOOL 40db49fef766bf43508fc9748b31dce0098fc2cbd330106dd8156ccab39bbad5f5d15027fa126b6fe7eae082a10355319cca1b223e170d3ab99b8f587a8d935f
+AUX cufflinks-2.2.1-hts.patch 422 SHA256 b04b813da21060c5598b48daf95f42a02b92134935912fe10bb61e396aa66426 SHA512 666eff4c5b40916d8b5c6581b0946f2e5dfaf5e1b816b28aaf5f037e5eab78297058699f686108f0dcc4e9aef2e2e6fdbaf05b9c546b11a3e68e7cbae88d6de7 WHIRLPOOL 330fbcf9e879740b951cbb41d2fcb6ac68e02549b33a4f8e0e84956b8b2ced10659a287cab82e1eac6a2b8e3e1496322ab25c6a452a27483d028d351af4730a3
 DIST cufflinks-1.3.0.tar.gz 676660 SHA256 c1e194e30e6ba2e1cbbd35e5f92be59f9fdef95a12079b3141790efbbdbdfd86 SHA512 b493c06b00093958aa3bf4aefa6435b89aa3fa8f90b9adea955b38aaa0301fafe3f028321573855d2af9515f9792a8a9c3851bd9352846131658e54b5a6ac68a WHIRLPOOL 649ed7638bdc655cc38d9c0ec6c81bc464e648e6e684e31af955a424510ee4702e2cec8e3dbfa2d97859ed27e04ff45fe2e07cb0a548c87674337bb94f5352ce
 DIST cufflinks-2.2.1.tar.gz 766280 SHA256 e8316b66177914f14b3a0c317e436d386a46c4c212ca1b2326f89f8a2e08d5ae SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b WHIRLPOOL bd40e6612f3c16466cf14efe706e38663c61d01661f901d9fdb140d0419e47e2ff10515dc7a0ff81da081e87af6d5d393d88cc4d036e8b921491fb5a790ae224
 EBUILD cufflinks-1.3.0-r1.ebuild 978 SHA256 7080262396c6df8b2e47f811e2f70fca41853367206504e9f3f3941ed412637b SHA512 a8b0778e29ba43694045cb6b4cb74d976b070eb15c10ae7ad8933e82b31e53b2aa096cb0f70d1b34658bfb5b59894ad24ae3446a5a879c40781121d00ef8a43a WHIRLPOOL e7e10b72bc8dc6d064cc87c019bf0ba27f1b24bd3f6b6e0fb43501f72edb218e28db814c43bf10bd70889350b81d64a34d32aa9e6d0af86dc01cd97eee2a5691
+EBUILD cufflinks-2.2.1-r1.ebuild 1137 SHA256 27ead30ca1a68f7bb769dfbd8bba8757c1132d4e2b2bc8a8fd8b742a4db47301 SHA512 6b5bb225a88c579c1f9ece0753e9426fb61e9a30b42d89a48647540b694db87459e0a71f2de361746205c1f23c6d8e3004fd54903f768aeed64a3eb1a8358334 WHIRLPOOL f6bed64b4613b0bad124d7931d18413557686339b1e5b974f9e9a5f5bbe1448c632c3257b4fad0f5a6d8e23230542ebe12aa0b1360ee93879a66aa90295b5d5a
 EBUILD cufflinks-2.2.1.ebuild 993 SHA256 384f5f2f2093511226c4ca3413ac6efca8dc8857d7c78a04d2645f2f000003a7 SHA512 d083a5eb12110a05c12de47abeff82436ce2e22269df0926fbfade60d2cf65fa22399655d05fe25b06d8eef42ce5e82bf2fb1b82631adb224fcd97f6c2d327f7 WHIRLPOOL 069b81f8bc333980b0850463171bdf5aab6c4dbd45fb50a3ae1fd4e0a6359c03bfbf3378141e83d6eaeeeadc1517b0c5d7649b307142c890bd3fdfd7a010be3f
-MISC ChangeLog 1582 SHA256 b728482960fb6a325dcfc0e930461684cbef7a05ffd399fc02042830a3a8672f SHA512 892e4d5eea93f793e25e7be9f08e157d6af089493506b54f47c283bb3c6e43a0deb38f0fafd69f4b30766eee4e4ad49d9418b821849624c3043889be50bd95d3 WHIRLPOOL 5ff30fc83c3bccac30f848e7f562b7be46515d78db20ba8fc2d7ede93d6151b42948d6a85a8010da0814c5232cafa9266668eec6151ae4ed9c69676f8bfbe98a
+MISC ChangeLog 1836 SHA256 4fd424df0395f584024fa8fb2bf37a58d4987f1454ee00e720c2d67eda363aa3 SHA512 30283966a3c1363005c4dfae804a7971810535e688911517ddc73c087bd6c99218c5de3b3e90e5d4e84f8b169d2cec0d9591a469405b6544f8e5a2d1f04bb2c2 WHIRLPOOL 33d8c91f3fe40b1b28bc6d42d5622cca554c399eb2efb875edf09410f6e81050d974eb7b72c49a1bd75c6483e80e9d9955fedf811c5abf5ecd922addfa8715ad
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild
new file mode 100644
index 000000000000..e6e79a3c9df0
--- /dev/null
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild,v 1.1 2014/10/02 08:01:05 jlec Exp $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils flag-o-matic toolchain-funcs
+
+DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq"
+HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
+SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="Artistic"
+IUSE="debug"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	|| (
+		(
+		>=sci-biology/samtools-0.1.18
+		sci-libs/htslib
+		)
+		<sci-biology/samtools-1
+		)
+	>=dev-libs/boost-1.47.0:=
+	dev-cpp/eigen:3
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-hts.patch
+	"${FILESDIR}"/${P}-flags.patch
+	)
+
+src_prepare() {
+	append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local myeconfargs=(
+		--disable-optim
+		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/"
+		--with-bam="${EPREFIX}/usr/"
+		$(use_enable debug)
+	)
+	autotools-utils_src_configure
+}
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch
new file mode 100644
index 000000000000..47784088fab9
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch
@@ -0,0 +1,28 @@
+ configure.ac | 7 ++++---
+ 1 file changed, 4 insertions(+), 3 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 96ffbac..e88b8e4 100755
+--- a/configure.ac
++++ b/configure.ac
+@@ -61,7 +61,8 @@ AC_CANONICAL_HOST
+ 
+ # set CFLAGS and CXXFLAGS
+ user_CFLAGS=${CFLAGS}
+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024"
++generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized"
++generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized -ftemplate-depth-1024"
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ #echo "${host_cpu}-${host_os}"
+@@ -106,8 +107,8 @@ AC_ARG_ENABLE(profiling,      [  --enable-profiling        enable profiling with
+ 	  [ext_LDFLAGS="-lprofiler -ltcmalloc"], [])
+ 	  
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}"
+-CXXFLAGS="$CFLAGS"
+-CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
++CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}"
++CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
+ user_LDFLAGS="$LDFLAGS"
+ LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}"
+ 
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch
new file mode 100644
index 000000000000..3b9abd812680
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch
@@ -0,0 +1,16 @@
+ ax_bam.m4 | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/ax_bam.m4 b/ax_bam.m4
+index 7d463b7..95f1bed 100644
+--- a/ax_bam.m4
++++ b/ax_bam.m4
+@@ -189,7 +189,7 @@ if test "x$want_bam" = "xyes"; then
+ 			AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).])
+ 		fi
+ 	else
+-		BAM_LIB="-lbam"
++		BAM_LIB="-lbam -lhts"
+ 		AC_SUBST(BAM_CPPFLAGS)
+ 		AC_SUBST(BAM_LDFLAGS)
+ 		AC_SUBST(BAM_LIB)