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commit: c76141a9ed378795deac9e8fdd8f9ff5e6b1b91b |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Nov 1 18:36:24 2020 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Nov 1 18:36:24 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c76141a9 |
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|
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sci-biology/clustalw-mpi: Port to EAPI 7 |
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|
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* Rename USE flags to avoid underscore |
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* Fix building against GCC 10 / -fno-common |
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|
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Closes: https://bugs.gentoo.org/695122 |
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Closes: https://bugs.gentoo.org/706960 |
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Package-Manager: Portage-3.0.8, Repoman-3.0.2 |
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Signed-off-by: David Seifert <soap <AT> gentoo.org> |
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|
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...mpi-0.13-r2.ebuild => clustalw-mpi-0.13-r3.ebuild} | 19 +++++++++++-------- |
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.../files/clustalw-mpi-0.13-fno-common.patch | 13 +++++++++++++ |
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...-gentoo.patch => clustalw-mpi-0.13-makefile.patch} | 0 |
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sci-biology/clustalw-mpi/metadata.xml | 18 ++++++++---------- |
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4 files changed, 32 insertions(+), 18 deletions(-) |
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|
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diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild |
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similarity index 72% |
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rename from sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild |
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rename to sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild |
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index 76d3b80cde3..334c34e78ce 100644 |
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--- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild |
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+++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild |
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@@ -1,7 +1,7 @@ |
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-# Copyright 1999-2017 Gentoo Foundation |
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+# Copyright 1999-2020 Gentoo Authors |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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-EAPI=6 |
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+EAPI=7 |
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|
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inherit toolchain-funcs |
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|
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@@ -12,28 +12,31 @@ SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz" |
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LICENSE="public-domain" |
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SLOT="0" |
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KEYWORDS="~amd64 ~x86" |
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-IUSE="mpi_njtree static_pairalign" |
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+IUSE="mpi-njtree static-pairalign" |
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|
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DEPEND="virtual/mpi" |
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RDEPEND="${DEPEND}" |
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|
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-PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch ) |
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+PATCHES=( |
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+ "${FILESDIR}"/${P}-makefile.patch |
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+ "${FILESDIR}"/${P}-fno-common.patch |
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+) |
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|
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src_prepare() { |
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default |
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|
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- if use mpi_njtree; then |
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+ if use mpi-njtree; then |
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sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \ |
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die "Failed to configure MPI code for NJ trees" |
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fi |
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|
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- if use static_pairalign; then |
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+ if use static-pairalign; then |
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sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \ |
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die "Failed to configure static scheduling for pair alignments" |
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fi |
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} |
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|
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src_install() { |
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- dobin ${PN} |
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- newdoc README.${PN} README |
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+ dobin clustalw-mpi |
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+ newdoc README.clustalw-mpi README |
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} |
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|
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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 |
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new file mode 100644 |
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index 00000000000..da74f0ba172 |
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--- /dev/null |
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+++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch |
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@@ -0,0 +1,13 @@ |
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+--- a/parallel_compare.c |
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++++ b/parallel_compare.c |
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+@@ -74,8 +74,8 @@ |
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+ static sint **accum; |
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+ static sint *diag_index; |
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+ static char *slopes; |
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+-sint ktup,window,wind_gap,signif; |
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+-sint *zza, *zzb, *zzc, *zzd; |
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++extern sint ktup,window,wind_gap,signif; |
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++extern sint *zza, *zzb, *zzc, *zzd; |
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+ extern Boolean percent; |
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+ static void make_p_ptrs(sint *tptr, sint *pl, sint naseq, sint l); |
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+ static void make_n_ptrs(sint *tptr, sint *pl, sint naseq, sint len); |
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|
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diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch |
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similarity index 100% |
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rename from sci-biology/clustalw-mpi/files/0.13-gentoo.patch |
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rename to sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch |
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|
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diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml |
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index 8ab4494152c..ffe2c4efec8 100644 |
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--- a/sci-biology/clustalw-mpi/metadata.xml |
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+++ b/sci-biology/clustalw-mpi/metadata.xml |
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@@ -1,14 +1,12 @@ |
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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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<pkgmetadata> |
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-<maintainer type="project"> |
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- <email>sci-biology@g.o</email> |
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- <name>Gentoo Biology Project</name> |
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-</maintainer> |
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-<use> |
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- <flag name="mpi_njtree">Use MPI (as opposed to serial) code for computing |
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- neighbor-joining trees</flag> |
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- <flag name="static_pairalign">Use static (as opposed to dynamic) scheduling |
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- for pair alignments</flag> |
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-</use> |
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+ <maintainer type="project"> |
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+ <email>sci-biology@g.o</email> |
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+ <name>Gentoo Biology Project</name> |
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+ </maintainer> |
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+ <use> |
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+ <flag name="mpi-njtree">Use MPI (as opposed to serial) code for computing neighbor-joining trees</flag> |
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+ <flag name="static-pairalign">Use static (as opposed to dynamic) scheduling for pair alignments</flag> |
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+ </use> |
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</pkgmetadata> |