gentoo resync : 28.07.2021

4 files changed, 66 insertions, 5 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 1af2f0b3689b..74a32cb73e6b 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest
index 105d1d7245df..1b60b19ffe2c 100644
--- a/sci-biology/mosaik/Manifest
+++ b/sci-biology/mosaik/Manifest
@@ -1,7 +1,8 @@
 AUX mosaik-2.2.30-Wformat-security.patch 3296 BLAKE2B f75a4dde6fb88e0175989ff9ddfd6dfd2450eb0df24e4e5f60943fbd9fcc40b798d7d7bca2d57e25c4201f6a7cbf8eb66b2f3573f54fc05b5b3a46e3e01a1ddb SHA512 e72fa7cac8798425ac1dd4d3358bfdff640cc831a01531749ee2fad99f8b53bd64e8c7fcdddce205e9f6dd312cc74376afcba395ab8d508d92416190b7eed1df
 AUX mosaik-2.2.30-fix-build-system.patch 8056 BLAKE2B 4c795e790718dca2a46e25fd67499612ad1226c6e6ad73d7543cd1c1aa1dacabc0ed77ade798b2602d8f661eeb9cd7b033bd8945d4384d01e2d279762f40fa14 SHA512 ed4a6efd9fb2fabd6c24adaa5894fde80024d8ee930450711c07388b62969a41e801f052ee88d7890355f1ddfc5ef9fbb40bfdabfbfae364c64c673ce08958c6
+AUX mosaik-2.2.30-gcc11.patch 1189 BLAKE2B 29b54205cf90bdf0815d16876db32a2109493f659cc06d4f0f3a9dffb3dcc6ef119a0b567197541226cd77ab8a33e8fab5f7d53ee107ff5ec987493e93ac8db8 SHA512 57aed21aca8b1c5c512bd77d7f5bf1a9846b9f30cb72890f614670930139c5ac8817d2b88b5e39c943c604c736a1a27ee91a01c3f0cdd9a534d8b4185cbdfcf6
 AUX mosaik-2.2.30-gcc7.patch 1252 BLAKE2B 896d662807c223cc69eacfa2e1fcb457c696e0d198dfa718f0f7eb9060d9c0491a18017901385227c2c0906e02c61a8fb9a9deb71f228d4c6195cdf0b5696515 SHA512 fc7dd31d2fcce7a4e624e759ee08b8997757bf4ce3ae3f98080e6e6252dfc647de4848f6a736b35090e8c8da37618baaf08e19be9ddfc408bbc5f7200f44cbba
 AUX mosaik-2.2.30-remove-platform-code.patch 399 BLAKE2B ec711a9b112efa87b2811e4545bfc58716393576915f71167ff700ccd809be4fad5e07bac7a5cb7df911615f4c996284cd711c1d1cb62c5a18695e719e6574c6 SHA512 4aec709660b41fb61bb9219a587255a5f416992a4478c2a7eb67374d1425f0a4e0b4d356827a9214e2f2718b635169c95d3288bf10388a74e50d498c39c2f259
 DIST mosaik-2.2.30.tar.gz 4387062 BLAKE2B 6f373aeae4f68be2455556e7f79a5850e25d804bd482d85a846b44f8adaabb2513ffc7ced774f5ead6dbc8fc9dca9d64f76f83bc5b55b1be4073a8cf309e121b SHA512 1acf534e6defc927fc22937a7bae6786e85ab7aa234b4209169f1267f1a9bd68415b441c6aed2e7cd667f694a562017ebc9457251958f77386259ffce9812b10
-EBUILD mosaik-2.2.30.ebuild 1105 BLAKE2B 842b161c8fc0cda9cab8101ca6ae0879cedb191983a61a25d21afe0ef5edb4a87e7e62edad27f2642444c2dc58387328c275f7830abd7917146d6febee812ba5 SHA512 55377965262d7942229a269bc1c0c56ff930d544b422305994f0995ca68d06ea3a1745fb759dc70225ff6b76d338b8761236079eb7107edb6225ae7c6d2f372e
+EBUILD mosaik-2.2.30.ebuild 1133 BLAKE2B 118906af7e1c8b68cdc1f6c7fdc300cca132a648d65ff193aa02a7998b6f4a75dc1b7daa0cb5631f291073ca4285722b10295364c324c0d83d842127ed7e0d86 SHA512 12c9439396bdd4fbbeb713accc60b6189c8bff056eb9b44c963abe97d7a9520bc9765e9f8839ac426be25dcbcbc6cc69d287fb4bfef5a9d3340f6c0048f1e06b
 MISC metadata.xml 414 BLAKE2B dadc852f08ed1944b4433e741d8f3c9f9296ecae8772df46193a89591fba8f3346b5b10d1a7227ba78071cc6e3639544a9f23ee61f79ee595bd10155bf6dfd0d SHA512 b38d4852ceabaa543c162eb26a54a76ba83b9d8f2e1520ec0ef16a07f49ddce9835caa5e16883f9755c99e3dba75e9ab689d254bafef92a859d251a53ff0d42f
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch
new file mode 100644
index 000000000000..918d882983a3
--- /dev/null
+++ b/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch
@@ -0,0 +1,60 @@
+--- a/CommonSource/DataStructures/UnorderedMap.h
++++ b/CommonSource/DataStructures/UnorderedMap.h
+@@ -42,13 +42,9 @@
+ 
+ #else // all decent C++ compilers
+ 
+-#ifdef WIN32
+ #include <unordered_map>
+-#else // Linux
+-#include <tr1/unordered_map>
+-#endif
+ 
+-using namespace std::tr1;
++using namespace std;
+ 
+ #endif
+ 
+--- a/CommonSource/DataStructures/UnorderedSet.h
++++ b/CommonSource/DataStructures/UnorderedSet.h
+@@ -42,13 +42,9 @@
+ 
+ #else // all decent C++ compilers
+ 
+-#ifdef WIN32
+ #include <unordered_set>
+-#else // Linux
+-#include <tr1/unordered_set>
+-#endif
+ 
+-using namespace std::tr1;
++using namespace std;
+ 
+ #endif
+ 
+--- a/CommonSource/Utilities/RegexUtilities.h
++++ b/CommonSource/Utilities/RegexUtilities.h
+@@ -12,10 +12,7 @@
+ #define REGEXUTILITIES_H_
+ 
+ #include <iostream>
+-#ifdef WIN32
+ #include <regex>
+-using namespace std::tr1;
+-#endif
+ #include <string>
+ #include <vector>
+ #include <cstdlib>
+--- a/MosaikBuild/MosaikBuild.h
++++ b/MosaikBuild/MosaikBuild.h
+@@ -15,10 +15,7 @@
+ #include <iostream>
+ #include <fstream>
+ #include <map>
+-#ifdef WIN32
+ #include <regex>
+-using namespace std::tr1;
+-#endif
+ #include <set>
+ #include <sstream>
+ #include "ColorspaceUtilities.h"
diff --git a/sci-biology/mosaik/mosaik-2.2.30.ebuild b/sci-biology/mosaik/mosaik-2.2.30.ebuild
index 874edba4504d..633738b8f4c2 100644
--- a/sci-biology/mosaik/mosaik-2.2.30.ebuild
+++ b/sci-biology/mosaik/mosaik-2.2.30.ebuild
@@ -1,25 +1,25 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit flag-o-matic toolchain-funcs vcs-snapshot
 
 DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
 HOMEPAGE="https://github.com/wanpinglee/MOSAIK"
 SRC_URI="https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd76a6d65001e4e67.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${P}/src"
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
-S="${WORKDIR}/${P}/src"
-
 PATCHES=(
 	"${FILESDIR}"/${P}-remove-platform-code.patch
 	"${FILESDIR}"/${P}-fix-build-system.patch
 	"${FILESDIR}"/${P}-Wformat-security.patch
 	"${FILESDIR}"/${P}-gcc7.patch
+	"${FILESDIR}"/${P}-gcc11.patch
 )
 
 src_configure() {