* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mafft/
@ 2016-09-03 23:03 David Seifert
0 siblings, 0 replies; 4+ messages in thread
From: David Seifert @ 2016-09-03 23:03 UTC (permalink / raw
To: gentoo-commits
commit: b68b635822e44c2ef09f7bee420e93887f93e2ea
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 3 23:02:55 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 3 23:03:22 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b68b6358
sci-biology/mafft: Version bump to 7.305
* EAPI=6
Package-Manager: portage-2.3.0
sci-biology/mafft/Manifest | 1 +
sci-biology/mafft/mafft-7.305.ebuild | 69 ++++++++++++++++++++++++++++++++++++
2 files changed, 70 insertions(+)
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index 0f4b923..a3e34ca 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -1,2 +1,3 @@
DIST mafft-7.050-without-extensions-src.tgz 380375 SHA256 29ddb276bfca24f5815acc41f1e640a705bb12c9d29b7c74902ebca68cece7bc SHA512 ffddedcd03f37241b1493a62bf843eb23caa04089bd0182006aa7669f74de27204d324817e22fec1cb4ae11c4c226db5b725d03ba9f73b30a71ca3d38368d73e WHIRLPOOL d46d7d4dfe453bfb54b9e418308772fb063bffce1d6d45d92262bee45504301daff9a6e57ecde41912a6c11852bb64510fb5ba6df04c7e79dc671e7a31444d49
DIST mafft-7.215-without-extensions-src.tgz 393239 SHA256 22099e42274ef0078302d7cb87180880ee5fd64ef15fdcafd8c95d0018191408 SHA512 1a44b968e2f9ac9db5d17487163a38a7138dc784e63b3aa4082ff6a16c8e168edd09948e2cf182bc7a466802d4a07bdd7ab23386e251df13520acdfb69ebdada WHIRLPOOL de43ba4107e3c1149d5ce47085bacc996393a7ef73535777439b7024eea1dce5f28c1b3c7e518f644345b7b5ea5e70fccbcaba18f16ecb9a6f5f5c31a6b5dca4
+DIST mafft-7.305-without-extensions-src.tgz 458448 SHA256 194503ee6dc9826f5098ac0fd9283034dfee8a1be1287def437f5854dea9317e SHA512 2aa351dd9b329024f183642cd98287239d12a00a2a65937e072560cba54925bed1fab19fafc734d9a5048ff85151560193ddb0796e0d7510d921fafc4553ebb9 WHIRLPOOL 85e9cda397853692f737a4e74159e67e0303076c28d94b85d4039ffe17b72c9d852a8af85941eaaa0fd73e0f1cbdbfe5b6a68e8ad5464506fbb38969f137a1b1
diff --git a/sci-biology/mafft/mafft-7.305.ebuild b/sci-biology/mafft/mafft-7.305.ebuild
new file mode 100644
index 00000000..1212659
--- /dev/null
+++ b/sci-biology/mafft/mafft-7.305.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit flag-o-matic toolchain-funcs
+
+EXTENSIONS="-without-extensions"
+
+DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
+HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
+SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="threads"
+
+S="${WORKDIR}/${P}${EXTENSIONS}"
+
+src_prepare() {
+ default
+
+ append-cflags -Wno-unused-result
+ use threads && append-cppflags -Denablemultithread
+
+ sed \
+ -e 's/(PREFIX)\/man/(PREFIX)\/share\/man/' \
+ -e 's:$(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
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mafft/
@ 2018-05-21 17:05 Aaron Bauman
0 siblings, 0 replies; 4+ messages in thread
From: Aaron Bauman @ 2018-05-21 17:05 UTC (permalink / raw
To: gentoo-commits
commit: b8057dabc8b51cfddf3d94aee03b1433e8eccdc0
Author: Michael Mair-Keimberger <m.mairkeimberger <AT> gmail <DOT> com>
AuthorDate: Mon May 21 10:14:17 2018 +0000
Commit: Aaron Bauman <bman <AT> gentoo <DOT> org>
CommitDate: Mon May 21 17:02:31 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b8057dab
sci-biology/mafft: use HTTPs
sci-biology/mafft/mafft-7.050.ebuild | 6 +++---
sci-biology/mafft/mafft-7.215.ebuild | 6 +++---
sci-biology/mafft/mafft-7.305.ebuild | 6 +++---
3 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/sci-biology/mafft/mafft-7.050.ebuild b/sci-biology/mafft/mafft-7.050.ebuild
index 685d78005c7..5da5d12d1b3 100644
--- a/sci-biology/mafft/mafft-7.050.ebuild
+++ b/sci-biology/mafft/mafft-7.050.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -8,8 +8,8 @@ inherit eutils flag-o-matic multilib toolchain-funcs
EXTENSIONS="-without-extensions"
DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+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"
diff --git a/sci-biology/mafft/mafft-7.215.ebuild b/sci-biology/mafft/mafft-7.215.ebuild
index 21761f1378e..05c3d8d5239 100644
--- a/sci-biology/mafft/mafft-7.215.ebuild
+++ b/sci-biology/mafft/mafft-7.215.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -8,8 +8,8 @@ inherit eutils flag-o-matic multilib toolchain-funcs
EXTENSIONS="-without-extensions"
DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+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"
diff --git a/sci-biology/mafft/mafft-7.305.ebuild b/sci-biology/mafft/mafft-7.305.ebuild
index 92925d8342b..9f9f631416b 100644
--- a/sci-biology/mafft/mafft-7.305.ebuild
+++ b/sci-biology/mafft/mafft-7.305.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -8,8 +8,8 @@ inherit flag-o-matic toolchain-funcs
EXTENSIONS="-without-extensions"
DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+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"
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mafft/
@ 2021-01-06 15:09 Fabian Groffen
0 siblings, 0 replies; 4+ messages in thread
From: Fabian Groffen @ 2021-01-06 15:09 UTC (permalink / raw
To: gentoo-commits
commit: 379bdc341c1768897390b09c7211dd18686a9dcb
Author: Fabian Groffen <grobian <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 6 15:08:55 2021 +0000
Commit: Fabian Groffen <grobian <AT> gentoo <DOT> org>
CommitDate: Wed Jan 6 15:08:55 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=379bdc34
sci-biology/mafft: drop x86-macos
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Fabian Groffen <grobian <AT> gentoo.org>
sci-biology/mafft/mafft-7.305.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/mafft/mafft-7.305.ebuild b/sci-biology/mafft/mafft-7.305.ebuild
index f4863892571..105b5ce9883 100644
--- a/sci-biology/mafft/mafft-7.305.ebuild
+++ b/sci-biology/mafft/mafft-7.305.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -13,7 +13,7 @@ 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 ~x86-macos"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
IUSE="threads"
S="${WORKDIR}/${P}${EXTENSIONS}"
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mafft/
@ 2022-06-19 18:04 David Seifert
0 siblings, 0 replies; 4+ messages in thread
From: David Seifert @ 2022-06-19 18:04 UTC (permalink / raw
To: gentoo-commits
commit: 481e43cca963debc0db30e5c751dda55dc4ea5d7
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 19 18:04:28 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 19 18:04:28 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=481e43cc
sci-biology/mafft: add 7.490
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/mafft/Manifest | 1 +
sci-biology/mafft/mafft-7.490.ebuild | 62 ++++++++++++++++++++++++++++++++++++
2 files changed, 63 insertions(+)
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index cc67db0ab402..bb9ba76f1c82 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -1 +1,2 @@
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/mafft-7.490.ebuild b/sci-biology/mafft/mafft-7.490.ebuild
new file mode 100644
index 000000000000..a5ff0a5764d6
--- /dev/null
+++ b/sci-biology/mafft/mafft-7.490.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+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}${EXTENSIONS}-src.tgz"
+S="${WORKDIR}/${P}${EXTENSIONS}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+src_prepare() {
+ default
+
+ 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 $@:g' \
+ -e '/INSTALL/s: -s : :g' \
+ -i core/Makefile || die
+}
+
+src_configure() {
+ append-cflags -Wno-unused-result
+}
+
+src_compile() {
+ emake -C core \
+ PREFIX="${EPREFIX}"/usr \
+ CC="$(tc-getCC)" \
+ CFLAGS="${CFLAGS}"
+}
+
+src_test() {
+ export MAFFT_BINARIES="${S}"/core
+ cd test || die
+ bash ../core/mafft sample > test.fftns2 || die "Tests failed"
+ bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die "Tests failed"
+ bash ../core/mafft --globalpair sample > test.gins1 || die "Tests failed"
+ bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die "Tests failed"
+ bash ../core/mafft --localpair sample > test.lins1 || die "Tests failed"
+ bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die "Tests failed"
+
+ diff test.fftns2 sample.fftns2 || die "Tests failed"
+ diff test.fftnsi sample.fftnsi || die "Tests failed"
+ diff test.gins1 sample.gins1 || die "Tests failed"
+ diff test.ginsi sample.ginsi || die "Tests failed"
+ diff test.lins1 sample.lins1 || die "Tests failed"
+}
+
+src_install() {
+ emake -C core DESTDIR="${D}" STRIP=":" PREFIX="${EPREFIX}"/usr install
+ dodoc readme
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
end of thread, other threads:[~2022-06-19 18:04 UTC | newest]
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