Fix for newer gcc, bug #514654

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-biology/allpathslg/ChangeLog b/sci-biology/allpathslg/ChangeLog
index 5e25459f87bac2fc652400a2de7f0339dd8cb6a1..7640788cf503e9773c1d17a062f6d02ba64d557b 100644 (file)
--- a/sci-biology/allpathslg/ChangeLog
+++ b/sci-biology/allpathslg/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/allpathslg
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/ChangeLog,v 1.16 2013/11/13 02:34:46 patrick Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/ChangeLog,v 1.17 2015/03/31 09:32:52 jlec Exp $
+
+  31 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +files/allpathslg-47093-gcc4.9.patch, allpathslg-47093.ebuild:
+  Fix for newer gcc, bug #514654
 
   13 Nov 2013; Patrick Lauer <patrick@gentoo.org> allpathslg-42337.ebuild,
   allpathslg-47093.ebuild:

diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
index 9466d1fda3683ddb94dcb592642bf105e03880fb..817a5bcf68b36f7a830aca25a3bc5ed6ed2be3c9 100644 (file)
--- a/sci-biology/allpathslg/Manifest
+++ b/sci-biology/allpathslg/Manifest
@@ -1,6 +1,29 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
+AUX allpathslg-47093-gcc4.9.patch 636 SHA256 79c884902131d18074cbe41864f75a37e94fd7fdce6fcec83ab2d205c5b6bccc SHA512 43fec8052bac3b7b8502210c8169aa433379d2aafa90706bc399ebcf3adeafb2e618ceb32cb8906ee0daa58a653fc7d8d8a50fb2e65b8c2d25f34c1131b72680 WHIRLPOOL 247a6ecdda398ee7414c4fd0e07ce6f7a9a3e87966193e43c630a5603ae5e25f7a2d15e41a2e95479386b5976552bbc884d0eff763322a6ce6dd561da7fa766f
 DIST allpathslg-42337.tar.gz 2739498 SHA256 a2c8f64f6ba1705b2331ca07761d189183c6745f8717ffc67ee98e9e3ca3dba6 SHA512 7595fbe14a5029578b57d16f781cbb2a0f0ad6b1af2dd770e2274f8fe2e11d0013fdff12cc85c1be748e769ffb23b7d5fe30920feef38e0e8b947d05b8bda31c WHIRLPOOL 79bda55d49877641eb55630950472a06d8f25db467dbfecde8b4d04c3ce16c071d32dd312fa9a0f72723bf4caa8f9b1d0346acf438b9671b4bed2c0672c788b9
 DIST allpathslg-47093.tar.gz 3057279 SHA256 493e21ae727250ea632b73b61545c32de2d8fb31e6a92605393ebb4af251f828 SHA512 499d23de52cad666fac663eb4a7d770b2129c4f9622f6c808ce30283429b6f67fb343f8712b07c7cb062c429117a0855da960ffc1d2ffb4e7ec2f544ba5a6314 WHIRLPOOL a3bc58dc140be3cddbd44c7035e628c4425bf86bc38592004df21d4dc91958ced9f08d667b43c15c214e53e3098805f368a856e66e5c2049b0e03d043b098ebc
 EBUILD allpathslg-42337.ebuild 908 SHA256 4b2d74839832fab3ecfdce115881f7f0f96f85a74391ce34646a6a9e07bc9e46 SHA512 a99a0f889b68f54b881df263b4444409aab1b6819fefc1c6107294d3a93597eee833e7e0627ca6d9595c7c1dd95e5f4ffe9ba735821da90d1b6a433de2946330 WHIRLPOOL c74ec2dc882a9532127e152dfe308423deb6fecd8c03e4b8dc053965667ee30123071f2e6dcb8699bab1cd2a8e18f39b1b3dafdda416cea6cc091f975491fcaa
-EBUILD allpathslg-47093.ebuild 918 SHA256 accb0065016f28d31a5ae97441154105290709491201c15f022b23adc2726f6a SHA512 5f34e60d75f25fe034e414997c339def385734a44ff8c46855b094cafbf112493a2a1c45e64a5f07ed489cbeb015dc7136dfe9ce5935c82d0e1ab66202a33b18 WHIRLPOOL b5c8613dd5cd07e924d3b1c6aa16bd9c55abba2903608fd8325ecd3c8a68a0fb8e08238ea9131ef18b8a55d60907145d67acd814e2d2ad2bb5ffe17b1c14e173
-MISC ChangeLog 2604 SHA256 a62ededc38c0cbd76b4e87cbfb9dee95e6b77a5a8c55bc43edd9e0243e89f66a SHA512 91880082eb7f38e201de8f71e5c0c8b0886d4a71c05b58cbc638e8707143d32dee40494d9da4280ae1ddedc80ddfbedc9161131bca784143d34fbe00a576292b WHIRLPOOL fc973cf02784727c555c8c49b65d167ff6be50ab53b2ceab30f58dc27f735bcc08e93440c4b49312de8b525c3001f794f47da92c971c045531602afe7de469c8
+EBUILD allpathslg-47093.ebuild 937 SHA256 55c540cf5d60ec4e6d7a2559fcfca000f44ddc2aa5cf14e04e9da507d583fe50 SHA512 cbfe922e2c4119f06fccb9f67c38237ac7b552528e4b898381b4cc26f61052ef7987cfb47c9b541fcf5d99956a50147bbdb5b844269b987313dc1657c741163f WHIRLPOOL 46c3326f8e54a531b9d9a2a80617f2192f94f0c3962f0ecd546224a457298dd4075bbf92a82be6584e6bac4afa08ea4c1e4fb6242dc1abaa416f712a041d6164
+MISC ChangeLog 2747 SHA256 2625fbb0a587a57e3b7ff2ef617ef9bf61c274a14f2919acc86d9445f8edf77f SHA512 df6fb41b1cbcac4545790457e64cfe9c29602d17d009df120dcb3891b77ab512fecb72cc5c61a0d4cfe23f3b53418d0b157bf2f2483dc54e31a3c68f69c9416e WHIRLPOOL 4472ee4bedcdb8de37fc1ada617dba535b061637c89e12c6ff3588da7e75885ef1ebe5c0d2c207122926c82c09c6ab5373e0989197a4b0d2d366ef7e4c31fcbb
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/allpathslg/allpathslg-47093.ebuild b/sci-biology/allpathslg/allpathslg-47093.ebuild
index f1f35b98540c6e8d0d45f7b98a4408f49268ef44..79b87b580ec145e503901b5117341faa81650c3f 100644 (file)
--- a/sci-biology/allpathslg/allpathslg-47093.ebuild
+++ b/sci-biology/allpathslg/allpathslg-47093.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/allpathslg-47093.ebuild,v 1.2 2013/11/13 02:34:46 patrick Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/allpathslg-47093.ebuild,v 1.3 2015/03/31 09:32:52 jlec Exp $
 
 EAPI=5
 
@@ -22,13 +22,13 @@ DEPEND="
 RDEPEND=""
 
 src_prepare() {
+       epatch "${FILESDIR}"/${P}-gcc4.9.patch
        sed -i 's/-ggdb//' configure.ac || die
        eautoreconf
 }
 
 src_install() {
        default
-#      einstall || die
        # Provided by sci-biology/vaal
        for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do
                rm "${D}/usr/bin/$i" || die

diff --git a/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch b/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch
new file mode 100644 (file)
index 0000000..46e5493
--- /dev/null
+++ b/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch
@@ -0,0 +1,16 @@
+ src/paths/long/VariantCallTools.cc | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/paths/long/VariantCallTools.cc b/src/paths/long/VariantCallTools.cc
+index dfe2787..725878b 100644
+--- a/src/paths/long/VariantCallTools.cc
++++ b/src/paths/long/VariantCallTools.cc
+@@ -1674,7 +1674,7 @@ void EdgesOnRef::FindAllPathsNoLoop(const GraphT& dg, int entrace_edge, int exit
+     int n1 = to_right2[entrace_edge];
+     int n2 = to_left2[exit_edge];
+ 
+-    PartialPath start = {{n1},{}};
++    PartialPath start{{n1},vec<int>{}};
+     stack<PartialPath> visited;
+     visited.push(start);
+     while (! visited.empty()) {