* [gentoo-commits] proj/sci:master commit in: sci-biology/oases/, sci-biology/oases/files/
@ 2021-02-02 10:43 Andrew Ammerlaan
0 siblings, 0 replies; 2+ messages in thread
From: Andrew Ammerlaan @ 2021-02-02 10:43 UTC (permalink / raw
To: gentoo-commits
commit: 03d288e4857b3934a4fac6693944c097da515a2b
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Feb 2 10:42:57 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Feb 2 10:42:57 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=03d288e4
sci-biology/oases: EAPI bump, fix patch
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/oases/files/Makefile.patch | 4 ++--
sci-biology/oases/oases-0.2.08.ebuild | 27 +++++++++++++++++----------
sci-biology/oases/oases-9999.ebuild | 24 +++++++++++++-----------
3 files changed, 32 insertions(+), 23 deletions(-)
diff --git a/sci-biology/oases/files/Makefile.patch b/sci-biology/oases/files/Makefile.patch
index 58652b00e..fcd0842ff 100644
--- a/sci-biology/oases/files/Makefile.patch
+++ b/sci-biology/oases/files/Makefile.patch
@@ -1,5 +1,5 @@
---- Makefile.ori 2016-04-10 22:34:31.976222662 +0200
-+++ Makefile 2016-04-10 22:37:49.636225327 +0200
+--- a/Makefile 2016-04-10 22:34:31.976222662 +0200
++++ b/Makefile 2016-04-10 22:37:49.636225327 +0200
@@ -1,8 +1,8 @@
-CC = gcc
-CFLAGS = -Wall
diff --git a/sci-biology/oases/oases-0.2.08.ebuild b/sci-biology/oases/oases-0.2.08.ebuild
index dcd1e83ab..74ad30f59 100644
--- a/sci-biology/oases/oases-0.2.08.ebuild
+++ b/sci-biology/oases/oases-0.2.08.ebuild
@@ -1,28 +1,35 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
-
-inherit eutils
+EAPI=7
DESCRIPTION="De novo transcriptome assembler"
HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"
-SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
- http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
-KEYWORDS=""
+if [ "$PV" == "9999" ]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/dzerbino/oases.git"
+ SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
+else
+ SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+ http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
+ S="${WORKDIR}/oases_0.2.8"
+ KEYWORDS=""
+ # fails to find globals.h, but which globals.h does it want?
+fi
LICENSE="GPL-3"
SLOT="0"
-IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
>=sci-biology/velvet-1.2.08"
-S="${WORKDIR}"/oases_0.2.8
+PATCHES=(
+ "${FILESDIR}/Makefile.patch"
+)
src_prepare(){
- epatch "${FILESDIR}"/Makefile.patch
+ default
sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
}
diff --git a/sci-biology/oases/oases-9999.ebuild b/sci-biology/oases/oases-9999.ebuild
index fbbe6e6dd..74ad30f59 100644
--- a/sci-biology/oases/oases-9999.ebuild
+++ b/sci-biology/oases/oases-9999.ebuild
@@ -1,34 +1,36 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
-
-[ "$PV" == "9999" ] && inherit git-r3
-
-inherit eutils
+EAPI=7
DESCRIPTION="De novo transcriptome assembler"
HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"
if [ "$PV" == "9999" ]; then
+ inherit git-r3
EGIT_REPO_URI="https://github.com/dzerbino/oases.git"
SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
- KEYWORDS=""
else
SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
- http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
- KEYWORDS="~amd64"
+ http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
+ S="${WORKDIR}/oases_0.2.8"
+ KEYWORDS=""
+ # fails to find globals.h, but which globals.h does it want?
fi
LICENSE="GPL-3"
SLOT="0"
-IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
>=sci-biology/velvet-1.2.08"
+PATCHES=(
+ "${FILESDIR}/Makefile.patch"
+)
+
src_prepare(){
- epatch "${FILESDIR}"/Makefile.patch
+ default
+ sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
}
src_install(){
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/oases/, sci-biology/oases/files/
@ 2022-01-25 13:12 Andrew Ammerlaan
0 siblings, 0 replies; 2+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 13:12 UTC (permalink / raw
To: gentoo-commits
commit: acc21d1b10bd722943d3d422baeeadb52098112c
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 13:11:45 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 13:11:45 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=acc21d1b
sci-biology/oases: drop dead package
last update 2015
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/oases/files/Makefile.patch | 15 -------------
sci-biology/oases/metadata.xml | 12 ----------
sci-biology/oases/oases-0.2.08.ebuild | 40 ----------------------------------
sci-biology/oases/oases-9999.ebuild | 40 ----------------------------------
4 files changed, 107 deletions(-)
diff --git a/sci-biology/oases/files/Makefile.patch b/sci-biology/oases/files/Makefile.patch
deleted file mode 100644
index fcd0842ff..000000000
--- a/sci-biology/oases/files/Makefile.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- a/Makefile 2016-04-10 22:34:31.976222662 +0200
-+++ b/Makefile 2016-04-10 22:37:49.636225327 +0200
-@@ -1,8 +1,8 @@
--CC = gcc
--CFLAGS = -Wall
--DEBUG = -g
-+CC ?= gcc
-+CFLAGS ?= -Wall
-+DEBUG ?= -g
- LIBS = -lm
--OPT = -O3
-+#OPT = -O3
- export MAXKMERLENGTH = 64
- export CATEGORIES = 2
- DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/oases/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/oases/oases-0.2.08.ebuild b/sci-biology/oases/oases-0.2.08.ebuild
deleted file mode 100644
index 74ad30f59..000000000
--- a/sci-biology/oases/oases-0.2.08.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="De novo transcriptome assembler"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"
-if [ "$PV" == "9999" ]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/dzerbino/oases.git"
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
-else
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
- http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
- S="${WORKDIR}/oases_0.2.8"
- KEYWORDS=""
- # fails to find globals.h, but which globals.h does it want?
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-
-DEPEND=""
-RDEPEND="${DEPEND}
- >=sci-biology/velvet-1.2.08"
-
-PATCHES=(
- "${FILESDIR}/Makefile.patch"
-)
-
-src_prepare(){
- default
- sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
-}
-
-src_install(){
- dobin oases
- dodoc README.md
- dodoc "${DISTDIR}"/OasesManual.pdf
-}
diff --git a/sci-biology/oases/oases-9999.ebuild b/sci-biology/oases/oases-9999.ebuild
deleted file mode 100644
index 74ad30f59..000000000
--- a/sci-biology/oases/oases-9999.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="De novo transcriptome assembler"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"
-if [ "$PV" == "9999" ]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/dzerbino/oases.git"
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
-else
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
- http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
- S="${WORKDIR}/oases_0.2.8"
- KEYWORDS=""
- # fails to find globals.h, but which globals.h does it want?
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-
-DEPEND=""
-RDEPEND="${DEPEND}
- >=sci-biology/velvet-1.2.08"
-
-PATCHES=(
- "${FILESDIR}/Makefile.patch"
-)
-
-src_prepare(){
- default
- sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
-}
-
-src_install(){
- dobin oases
- dodoc README.md
- dodoc "${DISTDIR}"/OasesManual.pdf
-}
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