commit: c76141a9ed378795deac9e8fdd8f9ff5e6b1b91b Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Nov 1 18:36:24 2020 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Nov 1 18:36:24 2020 +0000 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 <soap <AT> 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 00000000000..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 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> -<maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> -</maintainer> -<use> - <flag name="mpi_njtree">Use MPI (as opposed to serial) code for computing - neighbor-joining trees</flag> - <flag name="static_pairalign">Use static (as opposed to dynamic) scheduling - for pair alignments</flag> -</use> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="mpi-njtree">Use MPI (as opposed to serial) code for computing neighbor-joining trees</flag> + <flag name="static-pairalign">Use static (as opposed to dynamic) scheduling for pair alignments</flag> + </use> </pkgmetadata>
