From bd8ca999980e9c0c9ae40a11789c858bb58769e3 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Fri, 15 Jul 2022 13:42:19 +0100 Subject: gentoo auto-resync : 15:07:2022 - 13:42:19 --- sci-biology/uchime/Manifest | 4 ++-- sci-biology/uchime/files/CMakeLists.patch | 21 +++++++++++++++++++++ sci-biology/uchime/files/CMakeLists.txt | 12 ------------ sci-biology/uchime/uchime-4.2.40-r1.ebuild | 19 +++++++++++++++++++ sci-biology/uchime/uchime-4.2.40.ebuild | 30 ------------------------------ 5 files changed, 42 insertions(+), 44 deletions(-) create mode 100644 sci-biology/uchime/files/CMakeLists.patch delete mode 100644 sci-biology/uchime/files/CMakeLists.txt create mode 100644 sci-biology/uchime/uchime-4.2.40-r1.ebuild delete mode 100644 sci-biology/uchime/uchime-4.2.40.ebuild (limited to 'sci-biology/uchime') diff --git a/sci-biology/uchime/Manifest b/sci-biology/uchime/Manifest index ee70a3428de9..5cc58cb44bbc 100644 --- a/sci-biology/uchime/Manifest +++ b/sci-biology/uchime/Manifest @@ -1,4 +1,4 @@ -AUX CMakeLists.txt 589 BLAKE2B 183caf5f107482c410296eee8136271e261696a3c11255960b840bd4db16cf461c386fa7374b3a2afb3fd38e97593ad98f9efc621104106cfe4463939c6d0d31 SHA512 06e9f9c8806c27b268968b28fb6059fc6d52295a5d38635612728ac577656fcfae5eb6b15c63e3e9de57e1c8cac832cd4dff70d8a6f3182358a5eb06eb354642 +AUX CMakeLists.patch 834 BLAKE2B 1d522463bda3a0dca822c59ade24a7443f7e1b5901a091e0a4a5c86221e4fce91ed968229ba752e5980e202b633ea762b5dfeb758b4c83add0ac15706b7bdcb1 SHA512 f4939dc4b211742c8e1b592b13ad2c24cd7efa050b64c8eedaa99d61a8f60f54645c0f97185a33d13976201ac55249bfdf7edabb14f08e8487412d1b63c20841 DIST uchime4.2.40_src.tar.gz 66772 BLAKE2B 9133853d616ab6e1e6a397da78fc846ba00fc70c2c375eb16a98fbdec25ba6034bd1c876b7ec4a99305e76e47cf7984c1aa30b64bdc96e125f661a0150bae060 SHA512 c3afecb23d164d9c3db6229f54faa13120ac4d88132d9aef707f8d043091099db4205ac80f60242920af6efc23813b3e7e4966d562bdb75ff53244fd525e656b -EBUILD uchime-4.2.40.ebuild 654 BLAKE2B d9ddacb096c43c43858f4b4f572304543c7f5ae059fe9c4a8696d1debcd3304af88f360f312fd470ee9f3c733460840537835dfa67a446a18e4bdab6b460a278 SHA512 a7274df383897140b4db99610a2f0fea6b5364799f32b660b78c2e8ef6d9f59b8e629e331629b3b5877380f0e9700967180216e7ad9235f308389c754bc083e9 +EBUILD uchime-4.2.40-r1.ebuild 464 BLAKE2B 24ad55ba2ddb2d67a1411936538938de2d3b0e67af516c372631cd38533abc666a712dc7c42f5056d199f1b5c4dface6f40e010ebb1f6b2e0514630423109ccb SHA512 eb8c6cafee8784f8a29cc4b51e6b2806d8c80332e9ee9ed9bb2db0c01bdb1ee472d606d00d02246a2f277862721e60b30a4d3b83cfb364fe7a3e316281d2f514 MISC metadata.xml 897 BLAKE2B 26b02bb269f1861d54e723709c38bf2f0f14f146f1175cbfa4d9205ae9a9abec9799d782f715a05c79978a033da8b4c4e8a49461c10091855c5dc1b68475fec2 SHA512 951065ffbcd5a5f974669044acb3b6b73cfa99c375f563707a93277752a0b414521a7e4dda3b40b9272d635cf105212b1053c188e141b0d5674ebcd3d48e66ed 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 ${CMAKE_INSTALL_BINDIR}) diff --git a/sci-biology/uchime/uchime-4.2.40-r1.ebuild b/sci-biology/uchime/uchime-4.2.40-r1.ebuild new file mode 100644 index 000000000000..fe35819b5eed --- /dev/null +++ b/sci-biology/uchime/uchime-4.2.40-r1.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +MY_P="${PN}${PV}_src" + +DESCRIPTION="Fast, accurate chimera detection" +HOMEPAGE="https://www.drive5.com/usearch/manual/uchime_algo.html" +SRC_URI="https://www.drive5.com/${PN}/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" + +PATCHES=( "${FILESDIR}"/CMakeLists.patch ) diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild b/sci-biology/uchime/uchime-4.2.40.ebuild deleted file mode 100644 index 9b346f4fbc8d..000000000000 --- a/sci-biology/uchime/uchime-4.2.40.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -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" - -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-cppflags -std=c++14 - - cmake_src_configure -} -- cgit v1.2.3