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Thu, 7 Jul 2022 19:58:17 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 19A3F501 for ; Thu, 7 Jul 2022 19:58:14 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1657223832.13297a735a8c0e36ab552d244f4935d21400d310.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/t-coffee/, sci-biology/t-coffee/files/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch sci-biology/t-coffee/t-coffee-11.00-r2.ebuild sci-biology/t-coffee/t-coffee-11.00-r3.ebuild X-VCS-Directories: sci-biology/t-coffee/ sci-biology/t-coffee/files/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 13297a735a8c0e36ab552d244f4935d21400d310 X-VCS-Branch: master Date: Thu, 7 Jul 2022 19:58:14 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 73b7e132-1226-4662-8b81-1c436d740ed2 X-Archives-Hash: 1eed0d0003b88baeaefdc9d7158003d0 commit: 13297a735a8c0e36ab552d244f4935d21400d310 Author: David Seifert gentoo org> AuthorDate: Thu Jul 7 19:57:12 2022 +0000 Commit: David Seifert gentoo org> CommitDate: Thu Jul 7 19:57:12 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=13297a73 sci-biology/t-coffee: update EAPI 6 -> 8 Signed-off-by: David Seifert gentoo.org> .../t-coffee/files/t-coffee-11.00-makefile.patch | 19 +++++++++++++++ ...ee-11.00-r2.ebuild => t-coffee-11.00-r3.ebuild} | 27 ++++++++-------------- 2 files changed, 29 insertions(+), 17 deletions(-) diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch b/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch new file mode 100644 index 000000000000..b7a6d9e17a5e --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch @@ -0,0 +1,19 @@ +--- a/t_coffee_source/makefile ++++ b/t_coffee_source/makefile +@@ -1,14 +1,12 @@ +-CC=g++ +-CFLAGS=-O3 -Wno-write-strings + SOURCES := $(shell find . -type f -name *.c) + OBJECTS := $(SOURCES:.c=.o) + DEPS := $(OBJECTS:.o=.deps) + + t_coffee: $(OBJECTS) +- @echo " Linking..."; $(CC) $^ -o t_coffee -lm ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $^ -o t_coffee -lm $(LIBS) + + %.o: %.c +- @echo " CC $<"; $(CC) $(CFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $< ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $< + + -include $(DEPS) + diff --git a/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild similarity index 66% rename from sci-biology/t-coffee/t-coffee-11.00-r2.ebuild rename to sci-biology/t-coffee/t-coffee-11.00-r3.ebuild index df1859afb208..0064cc319f47 100644 --- a/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild +++ b/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -inherit toolchain-funcs +inherit flag-o-matic toolchain-funcs MY_HASH="4466924" MY_PV="${PV}.${MY_HASH}" @@ -12,6 +12,7 @@ MY_P="${PN^^}_distribution_Version_${MY_PV}" DESCRIPTION="A multiple sequence alignment package" HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" SRC_URI="http://www.tcoffee.org/Packages/Beta/Latest/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" LICENSE="GPL-2" SLOT="0" @@ -20,35 +21,27 @@ KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" RDEPEND=" sci-biology/clustalw sci-chemistry/tm-align" -DEPEND="" -S="${WORKDIR}/${MY_P}" PATCHES=( "${FILESDIR}"/${P}-mayhem.patch "${FILESDIR}"/${P}-set_proper_dir_permissions.patch "${FILESDIR}"/${P}-cxx11.patch "${FILESDIR}"/${P}-gcc7.patch + "${FILESDIR}"/${P}-makefile.patch ) -src_prepare() { - default - sed \ - -e '/@/s:.*;:\t:g' \ - -e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \ - -i t_coffee_source/makefile || die +src_configure() { + tc-export CXX + append-cxxflags -Wno-write-strings -Wno-unused-result } src_compile() { - emake \ - V=1 \ - CC="$(tc-getCXX)" \ - CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \ - -C t_coffee_source t_coffee + emake -C t_coffee_source t_coffee } src_install() { dobin t_coffee_source/t_coffee - insinto /usr/share/${PN} + insinto /usr/share/t-coffee doins -r example }