gentoo resync : 07.07.2018

6 files changed, 17 insertions, 4 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 9997c5c606d2..66142918b56a 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 2296f9956824..8d1a080b69ee 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,5 +1,5 @@
 DIST biopython-1.68.tar.gz 14445813 BLAKE2B 566931c4e522e95278f7f6a9dc07ecc091dc54b69cdea8bb07603339af4f1fd38e3df87482e97729acb776dd2df19a4e61d49ee7608ec5cb0f24966e28c2e3dd SHA512 0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69
 DIST biopython-1.71.tar.gz 16031832 BLAKE2B 2062065b77fc35ea8a3f09ec967482c233a6e0bbfc7d09187ff5e892848b45fa7bd6d7b6027b38c3d4c9a9c601785521fa7edb91fa960b46c8e49aed91b1f5dc SHA512 003955e92295e98526c88abb573db9bdc37877fc41395551b541e7106ffa603327a36c6f4d999838c0be38b378901235c9dbd7cb7fc25c14a5d7001939fe23bd
 EBUILD biopython-1.68.ebuild 1641 BLAKE2B a66e9c4a4c4987809faa18742b345fad45c6c6e536c1a87dfc552345637f1b7df28426a314df4b2f7e523002229395e978b75548b907f0a7aac6d80ee893d1b3 SHA512 e30c9f8b542ef0508a6fea508461521cbdc140a0c1e1f08eddfaef6dd73c10496f1d2fdc26261c26a5c860ffba845c1e6bb6f82d8722d0c7a1a89253c3a7a7f1
-EBUILD biopython-1.71.ebuild 1623 BLAKE2B 8e9b6b414402fa1317c13cee899a760a51bd45c9bedeff18785681229eceacc4e2e61a8ebe7d801b3716d1b11027cce3dfc16af237fa98c3bcf4bdce410d65bd SHA512 fc968c0003f23ca77244ff41a54cae9ad389a297f70a9ef9b04e79085120a5a5c963c13088140f30fbd971cde10574f6d3a94127acea78881242aa9e4c97b4eb
+EBUILD biopython-1.71.ebuild 1621 BLAKE2B c880eb5d4bde244ee427a576400d5a3fb2703f85fe07a68949a4ff1b0fa7ac1def332cd67b12731bd3629e62ffef318ce55f0768300c20d05eda72fef82a594c SHA512 1c9147003fc3a47e515e94b89bb718e80358db9956382937b9e675240d08608ef57090013a824c7cf504b517697c182385a6073c7cb1e8037a439fde75ca3935
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/biopython/biopython-1.71.ebuild b/sci-biology/biopython/biopython-1.71.ebuild
index f770b57a2a62..73a714248aea 100644
--- a/sci-biology/biopython/biopython-1.71.ebuild
+++ b/sci-biology/biopython/biopython-1.71.ebuild
@@ -13,7 +13,7 @@ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
 LICENSE="HPND"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
 RDEPEND="
diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest
index 57016b548680..4c95c2d9efa8 100644
--- a/sci-biology/cufflinks/Manifest
+++ b/sci-biology/cufflinks/Manifest
@@ -1,9 +1,10 @@
 AUX cufflinks-2.2.1-boost-1.65-tr1-removal.patch 344 BLAKE2B af0287f43bfd37da352fc330e3f6e06d4c6946851c6d8760302078157c8073591ccf7b508e2debf35747837216cc15e952fd7128bca500547cc180061dc2f780 SHA512 774558e93cf57ca9e9361df2271119474c8726573ff4467af4836db863d87ff0f38fe7048c9287227f18d3541891bb7b433b5fa33567616eeecda2bb5b057e9a
 AUX cufflinks-2.2.1-flags.patch 1132 BLAKE2B 675fb86a95425ed0def259b6f316e443eddb0c80a3a4f78e724f85ca3b14e58c29bb59bbc80a61ee7dcfaeb404383ffe0e58669dedc95224913c8d43939fd799 SHA512 58ea036d55d0b4835a56ea66afc2359bdb3e022f1fda3cab8402e4a2d7c6eab00fae96c739f89a25ca1e7528dad02f20c5c944a198c1eeca245e8995fbaa8f12
 AUX cufflinks-2.2.1-format-security.patch 618 BLAKE2B 1a316055af35849333c8ccbd46079a4ee1096becde474151932317bb66f81eff27b80d15306d9432f69a42fa9202a7712f9eff9921b915a92f4094ad2eadc79b SHA512 61a8cfe31988b028636f97db06d6855d9fce4ff3548da70d7e791fde85b38c09376be63714b67a0dc3e112f1d543735a51ebc437fc0b32eff98e9bf13138ff3c
+AUX cufflinks-2.2.1-gcc5-make_shared.patch 417 BLAKE2B 99fb3c7135789073089344d0f362088e5d95354b80a43e5a4fd47daa8b38d7c05b18476c491e5945b6b313925e984361915651c0b783c866273eeb4530eb35ea SHA512 81340797fe99aeb0fd118b28f729dfdcfbd3dd1a5efa2a4874a3732a167ad1c8b8d7d3408d1137db35ac5c17319d90dc1351bfd91a15af5c095de746791394d7
 AUX cufflinks-2.2.1-gcc6.patch 344 BLAKE2B 7534c9060e93f074718726e2cbf7df259ba298b447915a4162916977340d33e35a4fddbf3e1b662334b56d42ffb8e0a096c337b465b5952abe27d1248fd6d0f2 SHA512 1e8fc2e717c464e39aecf2c434857e962a809fd2a9f84bfca2b7230d5150d464262b579f1a8c13970767e929562d04994d60002834c98c204e089d2d2a8381c0
 AUX cufflinks-2.2.1-gcc7.patch 4133 BLAKE2B ac2fbf2ebadfe0e90d7163dbd839b2173a3a3a9925b25e2eba8775793545ed8e17e8075c9e562300fa0fae6fd7c35893c8bc892c3e79bd6645b2e3cf51acbdbf SHA512 cbcc2be9e1266e24801dc91ed776aa314761ac682274c103c4f4ad9c37f8ad02b63233f2a16608dd620ca67e89a21028142bdc059cbe5fd2fffdbdb3e38f0af8
 AUX cufflinks-2.2.1-samtools-legacy.patch 1105 BLAKE2B ceeb2236456f30598e0d98ce1eaa4fae908286704fb6912a19ccc008b3d41476b853cacc3fc545450dde7d883593a545110a440c044118875041f56077c963b3 SHA512 80c6eaadcfe6919d61b63efc83d3d618e939c3a1cd5e4977f936c41656a96c7c2dd71a1309d6b0422b1bf248a366643a62f011b30b37b4001efae5da04acaadf
 DIST cufflinks-2.2.1.tar.gz 766280 BLAKE2B 200ca88d15cdfca550a12a39cf69d4c41850532c76840d2a86a21654b317e28c7f35d36ba26105490e75d55c5527dd64da1ef3c14f2d467a60379c234a8e9e60 SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b
-EBUILD cufflinks-2.2.1-r2.ebuild 1260 BLAKE2B d6a462ebb0ab2851622b70796b6fc436784273004623792c40d95ebcaf0bd6116efe9fc4bfc25ea6fdc8fa1a4bd961564bf32c79e96ab055309df52109c0ca7e SHA512 e18f4e22800d944f71bb498fd6d6de827ef1d6dc3a37b4aabfa9d8c253ee4663cdd3ed6758845f755e3061765cdf9dac1d1f52f5d42da5ccd80449f6f667b9b9
+EBUILD cufflinks-2.2.1-r2.ebuild 1303 BLAKE2B 43a7781892fd664ca50d429ee741233ec4e319a8bccda379cc18a36c8447fb65972a07480bc74dde09d964f8e34f15b5e53204d6da2b1ce9af79fbc39d566103 SHA512 45d0d18bc405809d76f26b348ae90fa0fd9453a9ca1632c052ca6354679b65c9c40460bda40b7f50745549df916704cac3b6e4ed1b833cb9114f61ab002b1640
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
index 745baffad99d..3892e03e23b2 100644
--- a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -33,6 +33,7 @@ PATCHES=(
 	"${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch
 	"${FILESDIR}"/${P}-gcc7.patch
 	"${FILESDIR}"/${P}-format-security.patch
+	"${FILESDIR}"/${P}-gcc5-make_shared.patch
 )
 
 src_prepare() {
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch
new file mode 100644
index 000000000000..67a28df10249
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch
@@ -0,0 +1,11 @@
+--- a/src/differential.cpp
++++ b/src/differential.cpp
+@@ -575,7 +575,7 @@
+     boost::mutex::scoped_lock lock(meta_data_lock);
+ #endif
+     pair<SampleDiffMetaDataTable::iterator, bool> p;
+-    p = meta_data_table.insert(make_pair(description, new SampleDifferenceMetaData()));
++    p = meta_data_table.insert(make_pair(description, boost::make_shared<SampleDifferenceMetaData>()));
+     return p.first->second;
+ }
+