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| author |   David Seifert <soap@gentoo.org> | 2022-07-15 10:23:58 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2022-07-15 10:23:58 +0200 |
| commit | 37c6ef284900aec1695de5b39f830b83415792ca (patch) | |
| tree | 5f60014cf1ac45ffa42ca722c1b8d231c6b5f931 /sci-biology | |
| parent | dev-python/jupyter_server_mathjax: Bump to 0.2.6 (diff) | |
| download | gentoo-37c6ef284900aec1695de5b39f830b83415792ca.tar.gz gentoo-37c6ef284900aec1695de5b39f830b83415792ca.tar.bz2 gentoo-37c6ef284900aec1695de5b39f830b83415792ca.zip | |
sci-biology/uchime: update EAPI 7 -> 8
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/uchime/files/CMakeLists.patch | 21 | ||||
| -rw-r--r-- | sci-biology/uchime/files/CMakeLists.txt | 12 | ||||
| -rw-r--r-- | sci-biology/uchime/uchime-4.2.40-r1.ebuild (renamed from sci-biology/uchime/uchime-4.2.40.ebuild) | 21 |
3 files changed, 26 insertions, 28 deletions
diff --git a/sci-biology/uchime/files/CMakeLists.patch b/sci-biology/uchime/files/CMakeLists.patch new file mode 100644 index 000000000000..c33af8c7e827 --- /dev/null +++ b/sci-biology/uchime/files/CMakeLists.patch @@ -0,0 +1,21 @@ +--- /dev/null ++++ b/CMakeLists.txt +@@ -0,0 +1,18 @@ ++cmake_minimum_required(VERSION 2.8.12) ++project(UCHIME LANGUAGES CXX) ++ ++include(GNUInstallDirs) ++ ++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1") ++ ++# "myutils.h: error: reference to byte is ambiguous"" ++# bug #786297 ++set(CMAKE_CXX_STANDARD 14) ++set(CMAKE_CXX_STANDARD_REQUIRED ON) ++set(CMAKE_CXX_EXTENSIONS OFF) ++ ++# Simply copy the source files from the mk script ++add_executable(uchime ++ addtargets2.cpp alignchime.cpp alignchimel.cpp alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp writechhit.cpp) ++ ++INSTALL(TARGETS uchime DESTINATION ${CMAKE_INSTALL_BINDIR}) diff --git a/sci-biology/uchime/files/CMakeLists.txt b/sci-biology/uchime/files/CMakeLists.txt deleted file mode 100644 index a9319293e10b..000000000000 --- a/sci-biology/uchime/files/CMakeLists.txt +++ /dev/null @@ -1,12 +0,0 @@ -cmake_minimum_required(VERSION 2.8.12) -project(UCHIME) - -include(GNUInstallDirs) - -set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1") - -# Simply copy the source files from the mk script -add_executable(uchime - addtargets2.cpp alignchime.cpp alignchimel.cpp alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp writechhit.cpp) - -INSTALL(TARGETS uchime DESTINATION ${CMAKE_INSTALL_BINDIR}) diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild b/sci-biology/uchime/uchime-4.2.40-r1.ebuild index e0481aae2c70..fe35819b5eed 100644 --- a/sci-biology/uchime/uchime-4.2.40.ebuild +++ b/sci-biology/uchime/uchime-4.2.40-r1.ebuild @@ -1,30 +1,19 @@ # Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 + +inherit cmake MY_P="${PN}${PV}_src" -inherit cmake flag-o-matic DESCRIPTION="Fast, accurate chimera detection" HOMEPAGE="https://www.drive5.com/usearch/manual/uchime_algo.html" SRC_URI="https://www.drive5.com/${PN}/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" LICENSE="public-domain" SLOT="0" KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -S="${WORKDIR}"/${MY_P} - -src_prepare() { - cp "${FILESDIR}"/CMakeLists.txt . || die - cmake_src_prepare -} - -src_configure() { - # "myutils.h: error: reference to byte is ambiguous"" - # bug #786297 - append-cxxflags -std=c++14 - - cmake_src_configure -} +PATCHES=( "${FILESDIR}"/CMakeLists.patch ) |