From 37c6ef284900aec1695de5b39f830b83415792ca Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Fri, 15 Jul 2022 10:23:58 +0200
Subject: sci-biology/uchime: update EAPI 7 -> 8

Signed-off-by: David Seifert <soap@gentoo.org>
---
 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 ------------------------------
 4 files changed, 40 insertions(+), 42 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')

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 e0481aae2c70..000000000000
--- a/sci-biology/uchime/uchime-4.2.40.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2022 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-cxxflags -std=c++14
-
-	cmake_src_configure
-}
-- 
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