sci-biology/abyss: Fix compilation with gcc-4.7, #422599; install docs inside /usr/share/doc/, #297205

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

7 files changed, 96 insertions, 13 deletions

diff --git a/sci-biology/abyss/ChangeLog b/sci-biology/abyss/ChangeLog
index 7d16878ef343..2264b549eeea 100644
--- a/sci-biology/abyss/ChangeLog
+++ b/sci-biology/abyss/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/abyss
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/ChangeLog,v 1.12 2012/05/29 02:44:21 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/ChangeLog,v 1.13 2012/06/20 20:48:56 jlec Exp $
+
+*abyss-1.3.4 (20 Jun 2012)
+
+  20 Jun 2012; Justin Lecher <jlec@gentoo.org> abyss-1.3.0.ebuild,
+  abyss-1.3.3.ebuild, +files/abyss-1.3.3-gcc-4.7.patch, +abyss-1.3.4.ebuild,
+  +files/abyss-1.3.4-gcc-4.7.patch:
+  Fix compilation with gcc-4.7, #422599; install docs inside /usr/share/doc/,
+  #297205
 
 *abyss-1.3.3 (29 May 2012)
 
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index 56809c3ef1a9..4ca997ccce71 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1,20 +1,25 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
+AUX abyss-1.3.3-gcc-4.7.patch 388 RMD160 8470d49f06fc25fc87aaca04744063ee93247a01 SHA1 03ea7c1a04c3194f0003635a3c1f9857dd862aeb SHA256 a5f57201cfcffba775003bc2d02aed7263f2fdc03728b75664d5cb3f6af9f977
+AUX abyss-1.3.4-gcc-4.7.patch 388 RMD160 0ae31ceac3ea8f0757f2ae63af3c04515ce5429c SHA1 9ff7256ee3926eb0adb830aefb919300db483220 SHA256 369b2f4e34ee63f8fe3d305ee1995b024d1b850404cf9df565f863a56e7933b0
 DIST abyss-1.2.3.tar.gz 313587 RMD160 a8f9b54a8fc4ab58f372b25183e806abe5a7eea4 SHA1 cebe61a38f13ce822fb3bc719681858e31b8a6e7 SHA256 d4039cc4cd44ebdcbf3107e6d1e80380dfe3817c64a74d8ac64bc717f07e4fd5
 DIST abyss-1.2.7.tar.gz 467831 RMD160 0dbf424fe8c28e0a5dc88cbcef4d1ba79b4924b3 SHA1 84708296878ef0be2c6eedcba9fbf74ade08227a SHA256 2c3bc0b6046dbbfcb9298f91314c4a2979886009a5d5d68178871e3a8b1d11c2
 DIST abyss-1.3.0.tar.gz 509670 RMD160 c1c51dc1a6698452331a362a98a18975196665d1 SHA1 ca067e7b94329f3e0be764a447e77389d94f4b40 SHA256 50ea7d29f442060fa9cb9f794e5b651d99ced38049be3a489c9bbe37288e8012
 DIST abyss-1.3.3.tar.gz 621480 RMD160 74e0f1658c05b6df6bf4ae03c0cd424dd2a89202 SHA1 43985294ba42ee3ed9e8e5eb14d3b1971238a20a SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0
+DIST abyss-1.3.4.tar.gz 640545 RMD160 d4e82fa30987c3e11776507a9b1fd845086d569d SHA1 763dc423054421829011844ceaa5e18dc43f1ca9 SHA256 6b6ccb04baaa9d244dd67d95e1512a934d2e54fd28a539149b6845ed5c496baf
 EBUILD abyss-1.2.3.ebuild 753 RMD160 d7593fdee0b53d44c4ff4f64c21fa4c51bc804b5 SHA1 92891fc0a9bc436654c53e1f8d21a935a1c29ae3 SHA256 693c360bad8e1a93cd2fda81b3471b19af4ba3eeb7bd0b508d2257fb00e7a997
 EBUILD abyss-1.2.7.ebuild 869 RMD160 444d2c991c15d4b5a976e4aed7cd660a97bedd19 SHA1 391ccdc04f83a8e6c21b257894570893a257583c SHA256 7e0052aca03cf180b839de88f367c0c8f39cb913bea27f4faa781dcb448bbf65
-EBUILD abyss-1.3.0.ebuild 873 RMD160 19345465b2c21e0ab3c91e4672550394d28fec6f SHA1 24e29df27379540a5c48c30880dd225ea71a0eb5 SHA256 bdac80ab73066285b7e62c0cee6fabadfd64c59ae2b944154cd30ea916d260fc
-EBUILD abyss-1.3.3.ebuild 873 RMD160 e1e206defde8ab96373ebb19553387e3c99ab71e SHA1 df67583a5595513a586dee3161d52b1b0ea1b9d9 SHA256 dbc2c57194f41caba4820c458c16bf2f11a0310587b4a452a2e02a8a4a7ff1cf
-MISC ChangeLog 1827 RMD160 6178dea2eb7c5fce8b27b9e4cab7ae0e1dc32f82 SHA1 df9aa2f1865edea6e9a00982eec4909606cf1b01 SHA256 8b14c1c8786c97767ce038a6399d53a75e66c709a32560a71901a850e34dac9e
+EBUILD abyss-1.3.0.ebuild 917 RMD160 2216b98ff885351a32efc85d17adf904a93ee3cc SHA1 2b87b7d9c616455be2b6204a6216d5b118670131 SHA256 f96bbd4515d854068ae3633324d031250cdf273919596d6117f9c03465823d28
+EBUILD abyss-1.3.3.ebuild 965 RMD160 c897c10bc71345da338ce9c8420224431c627ab4 SHA1 2734ec1068d105b74f51362398165bea6655d3ba SHA256 4e1f1df4932ef8cc277197bee89405fbf659d9250fa561ae4f55ee511eb6f8cb
+EBUILD abyss-1.3.4.ebuild 965 RMD160 8ca382069e4b1e42d0a2e528b5732bc11e189a36 SHA1 2b580cd1da22918fedf8be96eb9ffe0e73a489c1 SHA256 1ae0cb72d55f806d1fde548b48a954b95d7d4b6df1604d80ddaf41dd735b0889
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 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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diff --git a/sci-biology/abyss/abyss-1.3.0.ebuild b/sci-biology/abyss/abyss-1.3.0.ebuild
index dbb174c71163..4ac14a4e2c49 100644
--- a/sci-biology/abyss/abyss-1.3.0.ebuild
+++ b/sci-biology/abyss/abyss-1.3.0.ebuild
@@ -1,6 +1,6 @@
-# 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/abyss/abyss-1.3.0.ebuild,v 1.1 2011/09/24 21:48:12 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.0.ebuild,v 1.2 2012/06/20 20:48:56 jlec Exp $
 
 EAPI="4"
 
@@ -31,5 +31,6 @@ src_prepare() {
 
 src_configure() {
 	econf \
+		--docdir="${EPREFIX}/usr/share/doc/${PF}" \
 		$(use_enable openmp)
 }
diff --git a/sci-biology/abyss/abyss-1.3.3.ebuild b/sci-biology/abyss/abyss-1.3.3.ebuild
index edc248a34395..5c372876b248 100644
--- a/sci-biology/abyss/abyss-1.3.3.ebuild
+++ b/sci-biology/abyss/abyss-1.3.3.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild,v 1.1 2012/05/29 02:44:21 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild,v 1.2 2012/06/20 20:48:56 jlec Exp $
 
 EAPI="4"
 
-inherit autotools
+inherit autotools eutils
 
 DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
 HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
@@ -24,6 +24,7 @@ RDEPEND="${DEPEND}"
 # todo: fix automagic mpi toggling
 
 src_prepare() {
+	epatch "${FILESDIR}"/${P}-gcc-4.7.patch
 	sed -i -e "s/-Werror//" configure.ac || die #365195
 	sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
 	eautoreconf
@@ -31,5 +32,6 @@ src_prepare() {
 
 src_configure() {
 	econf \
+		--docdir="${EPREFIX}/usr/share/doc/${PF}" \
 		$(use_enable openmp)
 }
diff --git a/sci-biology/abyss/abyss-1.3.4.ebuild b/sci-biology/abyss/abyss-1.3.4.ebuild
new file mode 100644
index 000000000000..6ce67798ca99
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.3.4.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.4.ebuild,v 1.1 2012/06/20 20:48:56 jlec Exp $
+
+EAPI="4"
+
+inherit autotools eutils
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
+SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	dev-cpp/sparsehash
+	mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-gcc-4.7.patch
+	sed -i -e "s/-Werror//" configure.ac || die #365195
+	sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		--docdir="${EPREFIX}/usr/share/doc/${PF}" \
+		$(use_enable openmp)
+}
diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
new file mode 100644
index 000000000000..42066f7f2152
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ ParseAligns/abyss-fixmate.cc |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
+index 506ea0c..a0a403c 100644
+--- a/ParseAligns/abyss-fixmate.cc
++++ b/ParseAligns/abyss-fixmate.cc
+@@ -15,6 +15,7 @@
+ #include <iterator>
+ #include <sstream>
+ #include <string>
++#include <unistd.h>
+ 
+ using namespace std;
+ 
diff --git a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
new file mode 100644
index 000000000000..c2cc35c31d98
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ ParseAligns/abyss-fixmate.cc |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
+index 1a169cf..36cc05b 100644
+--- a/ParseAligns/abyss-fixmate.cc
++++ b/ParseAligns/abyss-fixmate.cc
+@@ -16,6 +16,7 @@
+ #include <iterator>
+ #include <sstream>
+ #include <string>
++#include <unistd.h>
+ 
+ using namespace std;
+