[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustalw/
commit: 3568d2170e8a80c763c729c58f5327947e0261b1 Author: Georgy Yakovlev gentoo org> AuthorDate: Thu Nov 18 23:44:45 2021 + Commit: Georgy Yakovlev gentoo org> CommitDate: Thu Nov 18 23:50:16 2021 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3568d217 sci-biology/clustalw: de-stabilize for ~ppc, bug #823768 Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev gentoo.org> sci-biology/clustalw/clustalw-1.83-r4.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild index 144789f4c2a3..076f16300b3a 100644 --- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild +++ b/sci-biology/clustalw/clustalw-1.83-r4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -11,7 +11,7 @@ SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz"; LICENSE="clustalw" SLOT="1" -KEYWORDS="amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="amd64 ~ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" IUSE="" S="${WORKDIR}"/${PN}${PV}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustalw-mpi/files/, sci-biology/clustalw-mpi/
commit: c76141a9ed378795deac9e8fdd8f9ff5e6b1b91b Author: David Seifert gentoo org> AuthorDate: Sun Nov 1 18:36:24 2020 + Commit: David Seifert gentoo org> CommitDate: Sun Nov 1 18:36:24 2020 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c76141a9 sci-biology/clustalw-mpi: Port to EAPI 7 * Rename USE flags to avoid underscore * Fix building against GCC 10 / -fno-common Closes: https://bugs.gentoo.org/695122 Closes: https://bugs.gentoo.org/706960 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert gentoo.org> ...mpi-0.13-r2.ebuild => clustalw-mpi-0.13-r3.ebuild} | 19 +++ .../files/clustalw-mpi-0.13-fno-common.patch | 13 + ...-gentoo.patch => clustalw-mpi-0.13-makefile.patch} | 0 sci-biology/clustalw-mpi/metadata.xml | 18 -- 4 files changed, 32 insertions(+), 18 deletions(-) diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild similarity index 72% rename from sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild rename to sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild index 76d3b80cde3..334c34e78ce 100644 --- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild +++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit toolchain-funcs @@ -12,28 +12,31 @@ SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz"; LICENSE="public-domain" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="mpi_njtree static_pairalign" +IUSE="mpi-njtree static-pairalign" DEPEND="virtual/mpi" RDEPEND="${DEPEND}" -PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch ) +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-fno-common.patch +) src_prepare() { default - if use mpi_njtree; then + if use mpi-njtree; then sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \ die "Failed to configure MPI code for NJ trees" fi - if use static_pairalign; then + if use static-pairalign; then sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \ die "Failed to configure static scheduling for pair alignments" fi } src_install() { - dobin ${PN} - newdoc README.${PN} README + dobin clustalw-mpi + newdoc README.clustalw-mpi README } diff --git a/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch new file mode 100644 index 000..da74f0ba172 --- /dev/null +++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch @@ -0,0 +1,13 @@ +--- a/parallel_compare.c b/parallel_compare.c +@@ -74,8 +74,8 @@ + static sint **accum; + static sint *diag_index; + static char *slopes; +-sint ktup,window,wind_gap,signif; +-sint *zza, *zzb, *zzc, *zzd; ++extern sint ktup,window,wind_gap,signif; ++extern sint *zza, *zzb, *zzc, *zzd; + extern Boolean percent; + static void make_p_ptrs(sint *tptr, sint *pl, sint naseq, sint l); + static void make_n_ptrs(sint *tptr, sint *pl, sint naseq, sint len); diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch similarity index 100% rename from sci-biology/clustalw-mpi/files/0.13-gentoo.patch rename to sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml index 8ab4494152c..ffe2c4efec8 100644 --- a/sci-biology/clustalw-mpi/metadata.xml +++ b/sci-biology/clustalw-mpi/metadata.xml @@ -1,14 +1,12 @@ http://www.gentoo.org/dtd/metadata.dtd";> - - sci-biol...@gentoo.org - Gentoo Biology Project - - - Use MPI (as opposed to serial) code for computing -neighbor-joining trees - Use static (as opposed to dynamic) scheduling -for pair alignments - + + sci-biol...@gentoo.org + Gentoo Biology Project + + + Use MPI (as opposed to serial) code for computing neighbor-joining trees + Use static (as opposed to dynamic) scheduling for pair alignments +
[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustalw/
commit: 7e1326f6e20d7dce107dd49bc6715ac1974ddb39 Author: Sergei Trofimovich gentoo org> AuthorDate: Sun Jul 19 13:35:17 2020 + Commit: Sergei Trofimovich gentoo org> CommitDate: Sun Jul 19 13:36:54 2020 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7e1326f6 sci-biology/clustalw: keyworded 2.1-r1 for sparc keyworded wrt bug #732334 Package-Manager: Portage-2.3.103, Repoman-2.3.23 RepoMan-Options: --include-arches="sparc" Signed-off-by: Sergei Trofimovich gentoo.org> sci-biology/clustalw/clustalw-2.1-r1.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/clustalw/clustalw-2.1-r1.ebuild b/sci-biology/clustalw/clustalw-2.1-r1.ebuild index 033b3794e81..f42f1ed031b 100644 --- a/sci-biology/clustalw/clustalw-2.1-r1.ebuild +++ b/sci-biology/clustalw/clustalw-2.1-r1.ebuild @@ -9,7 +9,7 @@ SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz"; LICENSE="GPL-3 LGPL-3" SLOT="2" -KEYWORDS="amd64 ~ppc ~ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" IUSE="" src_install() {
[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustalw/
commit: bea04315b1a4c7238213ea0f7ba7904ec78f1f8e Author: Sam James gentoo org> AuthorDate: Fri Jul 17 00:29:48 2020 + Commit: Sam James gentoo org> CommitDate: Fri Jul 17 00:29:48 2020 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bea04315 sci-biology/clustalw: ppc keyworded (bug #732334) Package-Manager: Portage-2.3.103, Repoman-2.3.23 Signed-off-by: Sam James gentoo.org> sci-biology/clustalw/clustalw-2.1-r1.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/clustalw/clustalw-2.1-r1.ebuild b/sci-biology/clustalw/clustalw-2.1-r1.ebuild index aecb3a2ca82..033b3794e81 100644 --- a/sci-biology/clustalw/clustalw-2.1-r1.ebuild +++ b/sci-biology/clustalw/clustalw-2.1-r1.ebuild @@ -9,7 +9,7 @@ SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz"; LICENSE="GPL-3 LGPL-3" SLOT="2" -KEYWORDS="amd64 ~ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="amd64 ~ppc ~ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" IUSE="" src_install() {
[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustalw/
commit: 14f6dddbfa7b7dc66afd35be989238de99341c88 Author: Sergei Trofimovich gentoo org> AuthorDate: Sun Jul 12 12:33:01 2020 + Commit: Sergei Trofimovich gentoo org> CommitDate: Sun Jul 12 12:33:01 2020 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=14f6dddb sci-biology/clustalw: keyworded 2.1-r1 for ppc64 keyworded wrt bug #732334 Package-Manager: Portage-2.3.103, Repoman-2.3.23 RepoMan-Options: --include-arches="ppc64" Signed-off-by: Sergei Trofimovich gentoo.org> sci-biology/clustalw/clustalw-2.1-r1.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/clustalw/clustalw-2.1-r1.ebuild b/sci-biology/clustalw/clustalw-2.1-r1.ebuild index 0b46aeb5bfd..aecb3a2ca82 100644 --- a/sci-biology/clustalw/clustalw-2.1-r1.ebuild +++ b/sci-biology/clustalw/clustalw-2.1-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -9,7 +9,7 @@ SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz"; LICENSE="GPL-3 LGPL-3" SLOT="2" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="amd64 ~ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" IUSE="" src_install() {
[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustalw/
commit: 6eea6820a8ab87cbf3ff6b9d4c09ab0a57072415 Author: Matt Turner gentoo org> AuthorDate: Mon Mar 16 06:27:33 2020 + Commit: Matt Turner gentoo org> CommitDate: Mon Mar 16 06:30:12 2020 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6eea6820 sci-biology/clustalw: Drop alpha keywords Signed-off-by: Matt Turner gentoo.org> sci-biology/clustalw/clustalw-1.83-r4.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild index 6bccfd828e9..144789f4c2a 100644 --- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild +++ b/sci-biology/clustalw/clustalw-1.83-r4.ebuild @@ -11,7 +11,7 @@ SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz"; LICENSE="clustalw" SLOT="1" -KEYWORDS="~alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" IUSE="" S="${WORKDIR}"/${PN}${PV}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustalw-mpi/
commit: 1aac1736236bb22fb135f1154a4fa250a8bbe05a Author: David Seifert gentoo org> AuthorDate: Wed Mar 8 21:35:40 2017 + Commit: David Seifert gentoo org> CommitDate: Wed Mar 8 22:16:27 2017 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1aac1736 sci-biology/clustalw-mpi: Modernise to EAPI 6 Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165 ...lw-mpi-0.13-r1.ebuild => clustalw-mpi-0.13-r2.ebuild} | 16 ++-- 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild similarity index 85% rename from sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild rename to sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild index 7d68b61be5e..76d3b80cde3 100644 --- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild +++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild @@ -1,31 +1,35 @@ # Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -EAPI=4 +EAPI=6 -inherit eutils toolchain-funcs +inherit toolchain-funcs DESCRIPTION="An MPI implemention of the ClustalW general purpose multiple alignment algorithm" HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php"; SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz"; +LICENSE="public-domain" SLOT="0" KEYWORDS="~amd64 ~x86" -LICENSE="public-domain" IUSE="mpi_njtree static_pairalign" DEPEND="virtual/mpi" RDEPEND="${DEPEND}" +PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch ) + src_prepare() { - epatch "${FILESDIR}"/${PV}-gentoo.patch + default + if use mpi_njtree; then sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \ - die "Failed to configure MPI code for NJ trees." + die "Failed to configure MPI code for NJ trees" fi + if use static_pairalign; then sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \ - die "Failed to configure static scheduling for pair alignments." + die "Failed to configure static scheduling for pair alignments" fi }
[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustalw/files/, sci-biology/clustalw/
commit: ee8afc8624d23ec0bd41a5b63ca03ab40973af00 Author: David Seifert gentoo org> AuthorDate: Sat Feb 25 15:16:26 2017 + Commit: David Seifert gentoo org> CommitDate: Sat Feb 25 15:23:58 2017 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ee8afc86 sci-biology/clustalw: Modernise to EAPI 6 Package-Manager: Portage-2.3.3, Repoman-2.3.1 .../{clustalw-1.83-r3.ebuild => clustalw-1.83-r4.ebuild} | 14 +++--- sci-biology/clustalw/files/1.83-as-needed.patch| 4 ++-- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/sci-biology/clustalw/clustalw-1.83-r3.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild similarity index 74% rename from sci-biology/clustalw/clustalw-1.83-r3.ebuild rename to sci-biology/clustalw/clustalw-1.83-r4.ebuild index 6047a08ed4..bf6e6a9c28 100644 --- a/sci-biology/clustalw/clustalw-1.83-r3.ebuild +++ b/sci-biology/clustalw/clustalw-1.83-r4.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ -EAPI=5 +EAPI=6 -inherit eutils toolchain-funcs +inherit toolchain-funcs DESCRIPTION="General purpose multiple alignment program for DNA and proteins" HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/"; @@ -17,8 +17,10 @@ IUSE="" S="${WORKDIR}"/${PN}${PV} +PATCHES=( "${FILESDIR}"/${PV}-as-needed.patch ) + src_prepare() { - epatch "${FILESDIR}"/${PV}-as-needed.patch + default sed \ -e "/^CC/s:cc:$(tc-getCC):g" \ @@ -30,7 +32,5 @@ src_prepare() { src_install() { dobin clustalw - dodoc README clustalv.doc clustalw.doc clustalw.ms - insinto /usr/share/doc/${PF} - doins clustalw_help + dodoc README clustalv.doc clustalw{.doc,.ms,_help} } diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch index 62b4654cdd..9bb35b43f2 100644 --- a/sci-biology/clustalw/files/1.83-as-needed.patch +++ b/sci-biology/clustalw/files/1.83-as-needed.patch @@ -1,5 +1,5 @@ makefile 2003-01-29 09:53:45.0 +0100 -+++ makefile.new 2009-08-17 08:33:16.0 +0200 +--- a/makefile b/makefile @@ -11,11 +11,11 @@ HEADERS = general.h clustalw.h
[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustalw/
commit: 200b406609b2534985901bd7ce1e13a3135b5720 Author: David Seifert gentoo org> AuthorDate: Sat Feb 25 15:11:09 2017 + Commit: David Seifert gentoo org> CommitDate: Sat Feb 25 15:23:50 2017 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=200b4066 sci-biology/clustalw: Modernise to EAPI 6 Package-Manager: Portage-2.3.3, Repoman-2.3.1 .../clustalw/{clustalw-2.1.ebuild => clustalw-2.1-r1.ebuild} | 9 +++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/sci-biology/clustalw/clustalw-2.1.ebuild b/sci-biology/clustalw/clustalw-2.1-r1.ebuild similarity index 75% rename from sci-biology/clustalw/clustalw-2.1.ebuild rename to sci-biology/clustalw/clustalw-2.1-r1.ebuild index 8664ee3108..467cbf3cc8 100644 --- a/sci-biology/clustalw/clustalw-2.1.ebuild +++ b/sci-biology/clustalw/clustalw-2.1-r1.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ -EAPI=4 +EAPI=6 DESCRIPTION="General purpose multiple alignment program for DNA and proteins" HOMEPAGE="http://www.clustal.org/"; @@ -12,3 +12,8 @@ LICENSE="GPL-3 LGPL-3" SLOT="2" KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" IUSE="" + +src_install() { + default + rmdir "${ED%/}"/usr/share/aclocal || die +}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustalw-mpi/
commit: 6a11bee690bba5d3de48be84eca0d7c90508f841 Author: David Seifert gentoo org> AuthorDate: Mon Feb 6 20:48:02 2017 + Commit: David Seifert gentoo org> CommitDate: Mon Feb 6 21:26:17 2017 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6a11bee6 sci-biology/clustalw-mpi: Fix overlong DESCRIPTION Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3856 sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild index 11f1e57..13b04ed 100644 --- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild +++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ @@ -6,7 +6,7 @@ EAPI=4 inherit eutils toolchain-funcs -DESCRIPTION="A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm" +DESCRIPTION="An MPI implemention of the ClustalW general purpose multiple alignment algorithm" HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php"; SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz";