commit: 60b0fd58e2765499b9d2a83c3293b7021b05908c Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Jul 25 23:06:31 2021 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Jul 25 23:06:31 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=60b0fd58
sci-biology/mosaik: Fix GCC 11 build Closes: https://bugs.gentoo.org/788331 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch | 60 ++++++++++++++++++++++ sci-biology/mosaik/mosaik-2.2.30.ebuild | 8 +-- 2 files changed, 64 insertions(+), 4 deletions(-) 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 00000000000..918d882983a --- /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 874edba4504..633738b8f4c 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() {
