gentoo auto-resync : 15:07:2022 - 13:42:19

5 files changed, 29 insertions, 31 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index da0f930bf8e8..7c88bfc04f5c 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
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.ebuild b/sci-biology/uchime/uchime-4.2.40-r1.ebuild
index 9b346f4fbc8d..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 1999-2021 Gentoo Authors
+# 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 "${FILESDIR}"/CMakeLists.txt . || die
-	cmake_src_prepare
-}
-
-src_configure() {
-	# "myutils.h: error: reference to byte is ambiguous""
-	# bug #786297
-	append-cppflags -std=c++14
-
-	cmake_src_configure
-}
+PATCHES=( "${FILESDIR}"/CMakeLists.patch )