[gentoo-commits] repo/gentoo:master commit in: sci-biology/mafft/files/, sci-biology/mafft/

[David Seifert]

commit:     8fd5549edf07f4c19086252ca389a16720bd3700
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 25 18:51:03 2022 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jun 25 18:51:03 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8fd5549e

sci-biology/mafft: drop 7.305

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/mafft/Manifest                         |  1 -
 .../mafft/files/mafft-7.305-fno-common.patch       |  8 ---
 sci-biology/mafft/mafft-7.305.ebuild               | 69 ----------------------
 3 files changed, 78 deletions(-)

diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index bb9ba76f1c82..1c8c429c954d 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -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

diff --git a/sci-biology/mafft/files/mafft-7.305-fno-common.patch b/sci-biology/mafft/files/mafft-7.305-fno-common.patch
deleted file mode 100644
index 0287b6367f8b..000000000000
--- a/sci-biology/mafft/files/mafft-7.305-fno-common.patch
+++ /dev/null
@@ -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;

diff --git a/sci-biology/mafft/mafft-7.305.ebuild b/sci-biology/mafft/mafft-7.305.ebuild
deleted file mode 100644
index 105b5ce9883e..000000000000
--- a/sci-biology/mafft/mafft-7.305.ebuild
+++ /dev/null
@@ -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
-}