* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mothur/
@ 2021-04-05 14:15 David Seifert
0 siblings, 0 replies; 7+ messages in thread
From: David Seifert @ 2021-04-05 14:15 UTC (permalink / raw
To: gentoo-commits
commit: 17ca0e1b3b8cda81f6028b21303d8c64021c2947
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 5 14:14:41 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Apr 5 14:14:41 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=17ca0e1b
sci-biology/mothur: Port to EAPI 7
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/mothur/mothur-1.27.0-r1.ebuild | 35 +++++++++++++++---------------
1 file changed, 17 insertions(+), 18 deletions(-)
diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
index 9e9bf216031..12b628475aa 100644
--- a/sci-biology/mothur/mothur-1.27.0-r1.ebuild
+++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
@@ -1,43 +1,42 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-inherit eutils flag-o-matic fortran-2 toolchain-funcs
+inherit flag-o-matic fortran-2 toolchain-funcs
DESCRIPTION="A suite of algorithms for ecological bioinformatics"
HOMEPAGE="https://www.mothur.org/"
SRC_URI="https://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip"
+S="${WORKDIR}/${PN^}.source"
LICENSE="GPL-3"
SLOT="0"
-IUSE="mpi +readline"
KEYWORDS="amd64 x86"
+IUSE="mpi +readline"
RDEPEND="
sci-biology/uchime
mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
- app-arch/unzip"
+DEPEND="${RDEPEND}"
+BDEPEND="app-arch/unzip"
-S=${WORKDIR}/Mothur.source
+PATCHES=(
+ "${FILESDIR}"/${P}-makefile.patch
+ "${FILESDIR}"/${P}-overflows.patch
+)
-pkg_setup() {
- fortran-2_pkg_setup
- use mpi && export CXX=mpicxx || export CXX=$(tc-getCXX)
+src_configure() {
+ use mpi && export CXX=mpicxx || tc-export CXX
use amd64 && append-cppflags -DBIT_VERSION
}
-src_prepare() {
- epatch \
- "${FILESDIR}"/${P}-makefile.patch \
- "${FILESDIR}"/${P}-overflows.patch
-}
-
src_compile() {
- emake USEMPI=$(usex mpi) USEREADLINE=$(usex readline)
+ emake \
+ USEMPI=$(usex mpi) \
+ USEREADLINE=$(usex readline)
}
src_install() {
- dobin ${PN}
+ dobin mothur
}
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mothur/
@ 2024-12-03 11:14 Sam James
0 siblings, 0 replies; 7+ messages in thread
From: Sam James @ 2024-12-03 11:14 UTC (permalink / raw
To: gentoo-commits
commit: 59a64e369dca3abad2ee62d2f600943613bd30f8
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 3 11:14:07 2024 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Tue Dec 3 11:14:07 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59a64e36
sci-biology/mothur: Stabilize 1.48.0 amd64, #945569
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/mothur/mothur-1.48.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/mothur/mothur-1.48.0.ebuild b/sci-biology/mothur/mothur-1.48.0.ebuild
index 7d54bf273ac0..d4189ee39e9e 100644
--- a/sci-biology/mothur/mothur-1.48.0.ebuild
+++ b/sci-biology/mothur/mothur-1.48.0.ebuild
@@ -11,7 +11,7 @@ SRC_URI="https://github.com/mothur/mothur/archive/refs/tags/v${PV}.tar.gz -> ${P
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="amd64 ~x86"
IUSE="boost gsl hdf5 mpi +readline"
RDEPEND="
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mothur/
@ 2024-03-22 8:49 Sam James
0 siblings, 0 replies; 7+ messages in thread
From: Sam James @ 2024-03-22 8:49 UTC (permalink / raw
To: gentoo-commits
commit: 2186e8d7f1080d3b350e12f7c21d538c07fa14dd
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 22 08:49:27 2024 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Fri Mar 22 08:49:27 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2186e8d7
sci-biology/mothur: uncomment patch...
Closes: https://bugs.gentoo.org/927495
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/mothur/mothur-1.48.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/mothur/mothur-1.48.0.ebuild b/sci-biology/mothur/mothur-1.48.0.ebuild
index 869b0bae718b..7d54bf273ac0 100644
--- a/sci-biology/mothur/mothur-1.48.0.ebuild
+++ b/sci-biology/mothur/mothur-1.48.0.ebuild
@@ -24,7 +24,7 @@ RDEPEND="
DEPEND="${RDEPEND}"
PATCHES=(
- #"${FILESDIR}"/${PN}-1.48.0-build.patch
+ "${FILESDIR}"/${PN}-1.48.0-build.patch
)
src_configure() {
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mothur/
@ 2022-07-30 8:35 Sam James
0 siblings, 0 replies; 7+ messages in thread
From: Sam James @ 2022-07-30 8:35 UTC (permalink / raw
To: gentoo-commits
commit: 77c21552c350ad0843d6a5cfe17353c4d1c2a23f
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 30 08:35:11 2022 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Jul 30 08:35:11 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=77c21552
sci-biology/mothur: add github upstream metadata
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/mothur/metadata.xml | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml
index ccdff086e20b..fc926cc4aa42 100644
--- a/sci-biology/mothur/metadata.xml
+++ b/sci-biology/mothur/metadata.xml
@@ -1,8 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">mothur/mothur</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mothur/
@ 2018-05-21 17:05 Aaron Bauman
0 siblings, 0 replies; 7+ messages in thread
From: Aaron Bauman @ 2018-05-21 17:05 UTC (permalink / raw
To: gentoo-commits
commit: 1eb2ddf01f1ad34b00265cf46e5a4e6b3d82b1e7
Author: Michael Mair-Keimberger <m.mairkeimberger <AT> gmail <DOT> com>
AuthorDate: Mon May 21 10:13:08 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=1eb2ddf0
sci-biology/mothur: use HTTPs
sci-biology/mothur/mothur-1.27.0-r1.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
index d12d3c9b439..9e9bf216031 100644
--- a/sci-biology/mothur/mothur-1.27.0-r1.ebuild
+++ b/sci-biology/mothur/mothur-1.27.0-r1.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
@@ -6,8 +6,8 @@ EAPI=5
inherit eutils flag-o-matic fortran-2 toolchain-funcs
DESCRIPTION="A suite of algorithms for ecological bioinformatics"
-HOMEPAGE="http://www.mothur.org/"
-SRC_URI="http://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip"
+HOMEPAGE="https://www.mothur.org/"
+SRC_URI="https://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip"
LICENSE="GPL-3"
SLOT="0"
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mothur/
@ 2015-09-25 18:45 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2015-09-25 18:45 UTC (permalink / raw
To: gentoo-commits
commit: 06eacdf47da231ea1e9beebcad176a8fda063afe
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Sep 25 18:40:53 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Sep 25 18:40:53 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=06eacdf4
sci-biology/mothur: Drop old
Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/mothur/Manifest | 1 -
sci-biology/mothur/mothur-1.6.0.ebuild | 33 ---------------------------------
2 files changed, 34 deletions(-)
diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest
index e0cf36a..1ed7618 100644
--- a/sci-biology/mothur/Manifest
+++ b/sci-biology/mothur/Manifest
@@ -1,2 +1 @@
DIST mothur-1.27.0.zip 7095054 SHA256 7521d0dfc849dc9ef707bf83032e471966914b9833247c49e5d30b8d9281a6c7 SHA512 81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5 WHIRLPOOL 32e5c9c2be6e593b2dbc64be38c49b4dec3ea048cd3c972cf948136b394608a2dc168be58b7fb500a17fc6a152b7777fcd09b3f9fb3bf60c7dd92d043a4bf361
-DIST mothur-1.6.0.zip 465292 SHA256 75583a204d199ddcf9b845fc0adbaf240d7b1f08584fed5e6465982f68ffe121 SHA512 f775ff64991f00423108f295eca640f5c5d85a38e01b31af44ddf91f8897968e934f79899a21606dfd81fdc3e91751df277237e94d56d74f862e472e8da3386c WHIRLPOOL 31ca8decceb38ebd17f15c5f937df70b501833311cbf1aec794bb174d409a0c01e77abb399347781ad820c06411e56c566382a32818a0c57214aad2ad16cc132
diff --git a/sci-biology/mothur/mothur-1.6.0.ebuild b/sci-biology/mothur/mothur-1.6.0.ebuild
deleted file mode 100644
index 034f6fa..0000000
--- a/sci-biology/mothur/mothur-1.6.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit toolchain-funcs
-
-DESCRIPTION="A suite of algorithms for ecological bioinformatics"
-HOMEPAGE="http://www.mothur.org/"
-SRC_URI="mirror://gentoo/${P}.zip"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-S="${WORKDIR}/mothur-v.${PV}"
-
-src_prepare() {
- sed \
- -e 's/CC_OPTIONS =.*$/CC_OPTIONS = ${CXXFLAGS} /' \
- -e 's|CC = g++|CC = '$(tc-getCXX)'|' \
- -e '/^LNK_OPTIONS/s:$:${LDFLAGS}:g' \
- -i makefile || die
-}
-
-src_install() {
- dobin ${PN}
-}
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mothur/
@ 2015-09-25 14:23 Agostino Sarubbo
0 siblings, 0 replies; 7+ messages in thread
From: Agostino Sarubbo @ 2015-09-25 14:23 UTC (permalink / raw
To: gentoo-commits
commit: 9f365a9d5634350da97913fd8a45374b24b3127d
Author: Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Fri Sep 25 14:23:11 2015 +0000
Commit: Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Fri Sep 25 14:23:11 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9f365a9d
sci-biology/mothur: x86 stable wrt bug #556066
Package-Manager: portage-2.2.20.1
RepoMan-Options: --include-arches="x86"
sci-biology/mothur/mothur-1.27.0-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
index 3de23de..dcdf23f 100644
--- a/sci-biology/mothur/mothur-1.27.0-r1.ebuild
+++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
@@ -13,7 +13,7 @@ SRC_URI="http://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip"
LICENSE="GPL-3"
SLOT="0"
IUSE="mpi +readline"
-KEYWORDS="amd64 ~x86"
+KEYWORDS="amd64 x86"
RDEPEND="
sci-biology/uchime
^ permalink raw reply related [flat|nested] 7+ messages in thread
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