gentoo resync : 29.12.2022

3 files changed, 12 insertions, 28 deletions

diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index 4525adca70e4..623b6345d4f9 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -1,4 +1,3 @@
-AUX mafft-7.305-fno-common.patch 185 BLAKE2B 1230b838fa93b560fe0b0d9dd124cec2daf92d1dbcd75e371af92cc070bf62cea23c7c9ee3d87798de70911e4c316e444c875e79b3cf93f757b7a6fdfe2e279b SHA512 fe9de41eaea3bf799065fac88b336ec45af3c5b4d7d5272a477d99165b88c27f7e7765908e7955eaa0a74bb59df10a0ab77b822fd29bebca601d124938f3489d
-DIST mafft-7.305-without-extensions-src.tgz 458448 BLAKE2B 5d5fa86e6faa472182c5c48f42056d81bbf545db56426969ff44a24146d4189a7650e85ea6e9fa8b40bb613392bf53bc5dea26012a86eb873c18bee91e6fdc41 SHA512 2aa351dd9b329024f183642cd98287239d12a00a2a65937e072560cba54925bed1fab19fafc734d9a5048ff85151560193ddb0796e0d7510d921fafc4553ebb9
-EBUILD mafft-7.305.ebuild 2056 BLAKE2B 4d6599082401880abfa483f5fc23b9379dfca2fd410d948138b0005fcd43737b0dd92777d19b606a9c9ef77a03fdb667122eb8d56d053753d3e83452d0a24a6d SHA512 a6fc3af370b4e677d49372aa7c3908e33574cf7eeaf7cb02025c89b8654152a8cb622850d0f28f880f27cbb3e4743933798c9d843060383339c56ddb6b7792c5
+DIST mafft-7.490-without-extensions-src.tgz 605510 BLAKE2B f432ea3001f1d9c18cecea50d19f48570ffe7edf56e64088f8854acc1ee17fd7c1696244133f90ae0bf916f4499becfbfa8a770ca51a370219191f2a29f73db4 SHA512 dd87b731fdee48828da93c715ef480de474870de2fa42727e8d34b62bc136fb486dd9079ca2acdf1745f0a621fe4f413e25c05f7534f1673b6f9c1199ce70b8e
+EBUILD mafft-7.490.ebuild 1864 BLAKE2B 1590550e268ebd45f9a5ea166369c2874e8782c135f38311ac1fc3c10548da7c0630ec13bd0d2062344642b6876734c1a68858d6c545f127cf8e23f7e7eb85a7 SHA512 324e752905d927cd5dc9823e6d40a0c91d9002e4dedc95bf9c7d0463c14d85022f239764400e409416cba8eab7b2c921362f1292ea9327fb175449d304f12a0f
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
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-7.490.ebuild
index 105b5ce9883e..a5ff0a5764d6 100644
--- a/sci-biology/mafft/mafft-7.305.ebuild
+++ b/sci-biology/mafft/mafft-7.490.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 inherit flag-o-matic toolchain-funcs
 
@@ -10,21 +10,15 @@ 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"
+S="${WORKDIR}/${P}${EXTENSIONS}"
 
 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' \
@@ -34,10 +28,12 @@ src_prepare() {
 		-i core/Makefile || die
 }
 
+src_configure() {
+	append-cflags -Wno-unused-result
+}
+
 src_compile() {
-	cd core || die
-	emake \
-		$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
+	emake -C core \
 		PREFIX="${EPREFIX}"/usr \
 		CC="$(tc-getCC)" \
 		CFLAGS="${CFLAGS}"
@@ -61,9 +57,6 @@ src_test() {
 }
 
 src_install() {
-	DOCS=( readme )
-	einstalldocs
-
-	cd core || die
-	emake PREFIX="${ED%/}/usr" install
+	emake -C core DESTDIR="${D}" STRIP=":" PREFIX="${EPREFIX}"/usr install
+	dodoc readme
 }