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authorDavid Seifert <soap@gentoo.org>2020-11-01 19:36:24 +0100
committerDavid Seifert <soap@gentoo.org>2020-11-01 19:36:24 +0100
commitc76141a9ed378795deac9e8fdd8f9ff5e6b1b91b (patch)
tree286b98a7462614aedaf9131643130db4d5818006 /sci-biology/clustalw-mpi
parentsci-biology/lagan: Port to EAPI 7 (diff)
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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@gentoo.org>
Diffstat (limited to 'sci-biology/clustalw-mpi')
-rw-r--r--sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild (renamed from sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild)19
-rw-r--r--sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch13
-rw-r--r--sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch (renamed from sci-biology/clustalw-mpi/files/0.13-gentoo.patch)0
-rw-r--r--sci-biology/clustalw-mpi/metadata.xml18
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
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
index 6e36061cbb3..6e36061cbb3 100644
--- a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
+++ b/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>sci-biology@gentoo.org</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>sci-biology@gentoo.org</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>