sci-biology/allpathslg: Version bump, fix compilation errors with gcc-4.7, #425472

Package-Manager: portage-2.2.0_alpha116/cvs/Linux x86_64

3 files changed, 54 insertions, 12 deletions

diff --git a/sci-biology/allpathslg/ChangeLog b/sci-biology/allpathslg/ChangeLog
index f1b3747e4344..6568253d00ee 100644
--- a/sci-biology/allpathslg/ChangeLog
+++ b/sci-biology/allpathslg/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/allpathslg
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/ChangeLog,v 1.7 2012/05/29 02:51:11 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/ChangeLog,v 1.8 2012/07/09 17:55:40 jlec Exp $
+
+*allpathslg-42337 (09 Jul 2012)
+
+  09 Jul 2012; Justin Lecher <jlec@gentoo.org> +allpathslg-42337.ebuild:
+  Version bump, fix compilation errors with gcc-4.7, #425472
 
 *allpathslg-41839 (29 May 2012)
 
diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
index dcfc14dfb67b..db541700b46f 100644
--- a/sci-biology/allpathslg/Manifest
+++ b/sci-biology/allpathslg/Manifest
@@ -1,16 +1,19 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA256
 
-DIST allpathslg-37578.tar.gz 2511464 RMD160 462febe6efc690d53feaaff9ffb118a0c7e6a134 SHA1 45ca0d5cee312ff77f2c425b6b615dbec0f4726c SHA256 b4fdb6e7cc523cdb2831562bfabdf640dc2eb89f09d626ffeb4d1de358f46056
-DIST allpathslg-41839.tar.gz 2730906 RMD160 3a77abb8ef5a3091dda5b33046ee8762eb7b5e8c SHA1 7b01892856f71eb203760733643c7bbf63d038a1 SHA256 25f3b67d2ce1cde0fa674762da8258f244baefa1593cfc86a5125d9988ddbadd
-EBUILD allpathslg-37578.ebuild 938 RMD160 6bc84531f35c0ae308281f7e51437fdef07039c2 SHA1 323b42fd479529d6dbc81f8f4b562cb4eafb3cd8 SHA256 838d3a1dabcc67d986577592e8a8fa9d1f9529d1797c121dca85112702324bd0
-EBUILD allpathslg-41839.ebuild 903 RMD160 bab7a3ce342d13ec85a14a22555c889c499d9935 SHA1 73afc98d57b1cc0f1222578361132c4a8ebc748e SHA256 4e2122edce43ce1d4171508838e54209631c6edebd15f6d5d4e6f09f416e4a99
-MISC ChangeLog 1307 RMD160 65f7b215399db4cb65af74510b87f4d60081284e SHA1 e0e85116fd94e5b1b6c5ef7100d94a4da3e7a1ef SHA256 c306fe1104aabe735cea57c782e156217071c9c295111d6ffbf0b311b07a2cfd
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+DIST allpathslg-37578.tar.gz 2511464 SHA256 b4fdb6e7cc523cdb2831562bfabdf640dc2eb89f09d626ffeb4d1de358f46056 SHA512 63fd9162e558fdd15958a41bb8ceee3c100d1e933f8c2e02a3ae3cd8f42a7b32240f6863dae7444562257b0444eb894fbc52292861837efcad465fecb257d767 WHIRLPOOL ceb8569e6c56c7d72f102fc6bbf69f8d1022ed3c518407b028a07c4c9adadfe056828b7f4298a74eefbca188033cc1cdc732c79e6d43baf60a7566f7f2fda5d1
+DIST allpathslg-41839.tar.gz 2730906 SHA256 25f3b67d2ce1cde0fa674762da8258f244baefa1593cfc86a5125d9988ddbadd SHA512 9f721ebccea6cb77fb2a201482c4aa4a1dc31e2eba957adf2686eb5e66aae15bdb88da512b8d22fd5baaba95b9b314f7acb5e31838cdc7d519a779b7cb852418 WHIRLPOOL 4e3c4af7ff042d5bc4153bab71ab3404c33907739e6b5ef9ddaa2d7ef19c2ac159d8f31763842a26a06c8995a5e193940925f39109656bd2ba68ea0306886593
+DIST allpathslg-42337.tar.gz 2739498 SHA256 a2c8f64f6ba1705b2331ca07761d189183c6745f8717ffc67ee98e9e3ca3dba6 SHA512 7595fbe14a5029578b57d16f781cbb2a0f0ad6b1af2dd770e2274f8fe2e11d0013fdff12cc85c1be748e769ffb23b7d5fe30920feef38e0e8b947d05b8bda31c WHIRLPOOL 79bda55d49877641eb55630950472a06d8f25db467dbfecde8b4d04c3ce16c071d32dd312fa9a0f72723bf4caa8f9b1d0346acf438b9671b4bed2c0672c788b9
+EBUILD allpathslg-37578.ebuild 938 SHA256 838d3a1dabcc67d986577592e8a8fa9d1f9529d1797c121dca85112702324bd0 SHA512 ab546ed5161e1927fa983de0c41edfc11b19fb588a4f590e8906ab2cde039b0f5798ede2fc3429206d5fe0d30648b81950996a7ae44f8df4690bc08c9cb8e6cc WHIRLPOOL 7a06a5c07efddec8dc129613a7a23bbe7a623c06546ca00f0c3f0bef22dfbec1df6e95a8cdabe800a3a01ad3741dfa908b8702e280b5803451c592765f4c6994
+EBUILD allpathslg-41839.ebuild 903 SHA256 4e2122edce43ce1d4171508838e54209631c6edebd15f6d5d4e6f09f416e4a99 SHA512 1c12c79ee11a986ba8b438b4b52e209e79a7bb2231471925c07079736b29390cb7c961a114485c7db98f826066b6b2814a670876759f972f11c300fccef623dc WHIRLPOOL e2d42eff3cb068e783ecd4db85aa574f128acadac40a88474061604bc9afabb5b09d64e9c9118f5ac876a59994cd8cf80ce14847b3d220c9d4eb4f106f1da53a
+EBUILD allpathslg-42337.ebuild 901 SHA256 f908ece1c5fa94088238ec14f2eec23002d858de9b0bc4fd0f106cc19d33cbf2 SHA512 0430f23dd8ecba31d29dccd0c18008f015a246335f20631bdd4f3d3b598359b0f41b6e1faa60301d6a4dd93cda0279b43cc6496fe749503f8d3995be1d3463ae WHIRLPOOL 5d69f23002143a97925f39e5ca566d518abc0413ab184deb3aadff7c93eb1a0e0b874dbce261065fa37a09e5b6fe4f1d960eeca45579b1457ba3861fb82f1e76
+MISC ChangeLog 1473 SHA256 6aa8cf0c74e1bfd1a3605cd9ecad47578dc01983024d942801db35ed17b217f9 SHA512 aa0b1b4927712047f027589851f0065b911136e339d6c94473595a6058aadb8b12ef8c204eea2ca512e3bf09c493c4905a9e6aff2859c6dd7dd25095d26a97e5 WHIRLPOOL a82f9add49d7d7fd38917ef2238d3018ced688a7c567d51e5e3a87f6c9846bb977d821eefe1ae2e7ba0d2d30aa807be0e292d9df85fd38b91998afb28f0bd84e
+MISC metadata.xml 259 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 SHA512 c3aea4d69d75075af0108a03b7e109cfed6a1fe324f8ccbda3d4e5ca8a5070f1b24ddeb46b64787e10fd22252d867abcee1f31316d602f7e32fe3c990ae60d74 WHIRLPOOL e50da2f26fd4c908446d22da3edb595d60e61d72def374be46440358802a211fc34045b7ad970c4f94b57f7b17ff24cfe64dc94254fea20e047f1fbbbcae0c64
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v1.4.11 (GNU/Linux)
+Version: GnuPG v2.0.19 (GNU/Linux)
+Comment: GPGTools - http://gpgtools.org
 
-iEUEARECAAYFAk/EOaQACgkQ8xSwyhbn2OaiDwCXV7/xItxk7zx4l7h/pdt9oPdf
-CACeLHgyX5nOZ+gl/rNw1WiAC4gQP4g=
-=Qh0U
+iEYEAREIAAYFAk/7GyIACgkQgAnW8HDreRZ1FACfdw5vTexlz1pPPyDCbj2kMrhb
+do4AoNGnEH7rUiVwx/YSZePOMeaxUhmS
+=R6MD
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/allpathslg/allpathslg-42337.ebuild b/sci-biology/allpathslg/allpathslg-42337.ebuild
new file mode 100644
index 000000000000..c86c7de6d62d
--- /dev/null
+++ b/sci-biology/allpathslg/allpathslg-42337.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/allpathslg-42337.ebuild,v 1.1 2012/07/09 17:55:40 jlec Exp $
+
+EAPI=4
+
+inherit autotools flag-o-matic
+
+DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
+HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz"
+
+LICENSE="as-is"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64"
+
+DEPEND="dev-libs/boost
+	>=sys-devel/gcc-4.3.3
+	sci-biology/vaal"
+RDEPEND=""
+
+src_prepare() {
+	sed -i 's/-ggdb3//' configure.ac || die
+	eautoreconf
+}
+
+src_install() {
+	einstall || die
+	# Provided by sci-biology/vaal
+	for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do
+		rm "${D}/usr/bin/$i" || die
+	done
+}