gentoo-mirror/gentoo
1
0
Fork 0
mirror of https://github.com/gentoo-mirror/gentoo.git synced 2026-08-01 11:18:09 -07:00
Code Issues Projects Releases Wiki Activity

sci-biology/mafft: drop 7.305

Browse Source 
Signed-off-by: David Seifert <soap@gentoo.org>
This commit is contained in:
David Seifert
2022-06-25 20:51:03 +02:00
parent 93c7ef79b8
commit 8fd5549edf
3 changed files with 0 additions and 78 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
sci-biology/mafft/Manifest
View File

@@ -1,2 +1 @@
DIST mafft-7.305-without-extensions-src.tgz 458448 BLAKE2B 5d5fa86e6faa472182c5c48f42056d81bbf545db56426969ff44a24146d4189a7650e85ea6e9fa8b40bb613392bf53bc5dea26012a86eb873c18bee91e6fdc41 SHA512 2aa351dd9b329024f183642cd98287239d12a00a2a65937e072560cba54925bed1fab19fafc734d9a5048ff85151560193ddb0796e0d7510d921fafc4553ebb9
DIST mafft-7.490-without-extensions-src.tgz 605510 BLAKE2B f432ea3001f1d9c18cecea50d19f48570ffe7edf56e64088f8854acc1ee17fd7c1696244133f90ae0bf916f4499becfbfa8a770ca51a370219191f2a29f73db4 SHA512 dd87b731fdee48828da93c715ef480de474870de2fa42727e8d34b62bc136fb486dd9079ca2acdf1745f0a621fe4f413e25c05f7534f1673b6f9c1199ce70b8e

8
sci-biology/mafft/files/mafft-7.305-fno-common.patch
View File

@@ -1,8 +0,0 @@
--- a/core/mltaln.h
+++ b/core/mltaln.h
@@ -336,4 +336,4 @@
extern double sueff_global;
extern double lenfaca, lenfacb, lenfacc, lenfacd;
-int maxl, tsize;
+extern int maxl, tsize;

69
sci-biology/mafft/mafft-7.305.ebuild
View File

@@ -1,69 +0,0 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit flag-o-matic toolchain-funcs
EXTENSIONS="-without-extensions"
DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html"
SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
IUSE="threads"
S="${WORKDIR}/${P}${EXTENSIONS}"
PATCHES=( "${FILESDIR}"/${PN}-7.305-fno-common.patch )
src_prepare() {
default
append-cflags -Wno-unused-result
use threads && append-cppflags -Denablemultithread
sed \
-e 's/(PREFIX)\/man/(PREFIX)\/share\/man/' \
-e 's:$(LDFLAGS)::g' \
-e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \
-e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \
-e '/INSTALL/s: -s : :g' \
-i core/Makefile || die
}
src_compile() {
cd core || die
emake \
$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
PREFIX="${EPREFIX}"/usr \
CC="$(tc-getCC)" \
CFLAGS="${CFLAGS}"
}
src_test() {
export MAFFT_BINARIES="${S}"/core
cd test || die
bash ../core/mafft sample > test.fftns2 || die "Tests failed"
bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die "Tests failed"
bash ../core/mafft --globalpair sample > test.gins1 || die "Tests failed"
bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die "Tests failed"
bash ../core/mafft --localpair sample > test.lins1 || die "Tests failed"
bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die "Tests failed"
diff test.fftns2 sample.fftns2 || die "Tests failed"
diff test.fftnsi sample.fftnsi || die "Tests failed"
diff test.gins1 sample.gins1 || die "Tests failed"
diff test.ginsi sample.ginsi || die "Tests failed"
diff test.lins1 sample.lins1 || die "Tests failed"
}
src_install() {
DOCS=( readme )
einstalldocs
cd core || die
emake PREFIX="${ED%/}/usr" install
}