[gentoo-commits] proj/sci:master commit in: sci-biology/gffread/
commit: 4b61ed2003869365d59797ff40e5e38b18d7a18d
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Wed Mar 2 14:25:58 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Wed Mar 2 14:28:36 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4b61ed20
sci-biology/gffread: bump to 0.12.7
Closes: https://bugs.gentoo.org/832451
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan gentoo.org>
.../gffread/{gffread-0.11.0.ebuild => gffread-0.12.7.ebuild} | 10 +++---
1 file changed, 3 insertions(+), 7 deletions(-)
diff --git a/sci-biology/gffread/gffread-0.11.0.ebuild
b/sci-biology/gffread/gffread-0.12.7.ebuild
similarity index 83%
rename from sci-biology/gffread/gffread-0.11.0.ebuild
rename to sci-biology/gffread/gffread-0.12.7.ebuild
index 871d38d03..9758ccef0 100644
--- a/sci-biology/gffread/gffread-0.11.0.ebuild
+++ b/sci-biology/gffread/gffread-0.12.7.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=7
+EAPI=8
DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract
regions from FASTA"
HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
@@ -12,13 +12,8 @@
SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
src_prepare(){
- src_unpack "${DISTDIR}"/gclib-${PV}.tar.gz
default
sed -e "s/-g -O3/${CXXFLAGS}/" -i Makefile || die
cd .. && ln -s gclib-"${PV}" gclib || die
@@ -30,4 +25,5 @@ src_compile(){
src_install(){
dobin gffread
+ einstalldocs
}
[gentoo-commits] proj/sci:master commit in: sci-biology/gffread/files/, sci-biology/gffread/
commit: e55065dc88a894edab65609ffdd4e275cdcd4bd0
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 11:49:49 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 11:49:49 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e55065dc
sci-biology/gffread: bump to 0.11.0, drop old patch, use sed hackery
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/gffread/files/Makefile.patch | 39 --
...gffread-0.9.12.ebuild => gffread-0.11.0.ebuild} | 25 +++---
2 files changed, 20 insertions(+), 44 deletions(-)
diff --git a/sci-biology/gffread/files/Makefile.patch
b/sci-biology/gffread/files/Makefile.patch
deleted file mode 100644
index 35e6b088e..0
--- a/sci-biology/gffread/files/Makefile.patch
+++ /dev/null
@@ -1,39 +0,0 @@
gffread-0.9.12/Makefile2018-06-26 09:52:26.024747027 +0200
-+++ gffread-0.9.12/Makefile2018-06-26 09:52:41.845177021 +0200
-@@ -1,4 +1,4 @@
--GCLDIR := ../gclib
-+GCLDIR := ../gclib-0.10.2
- SEARCHDIRS := -I. -I${GCLDIR}
-
- SYSTYPE := $(shell uname)
-@@ -10,7 +10,7 @@
- MARCH =
- endif
-
--CC := g++
-+CXX ?= g++
-
- BASEFLAGS := -Wall -Wextra ${SEARCHDIRS} $(MARCH) -D_FILE_OFFSET_BITS=64 \
- -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions
-fno-rtti
-@@ -26,15 +26,17 @@
- GCC45OPTMAIN :=
-
- ifeq ($(findstring release,$(MAKECMDGOALS)),release)
-- CFLAGS := -O2 -DNDEBUG $(BASEFLAGS)
-+ CXXFLAGS ?= -O2
-+ CXXFLAGS += -DNDEBUG $(BASEFLAGS)
- LDFLAGS :=
- else
-- CFLAGS := -g -DDEBUG $(BASEFLAGS)
-- LDFLAGS := -g
-+ CXXFLAGS ?= -g
-+ CXXFLAGS += -DDEBUG $(BASEFLAGS)
-+ LDFLAGS ?= -g
- endif
-
- %.o : %.cpp
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- # C/C++ linker
-
diff --git a/sci-biology/gffread/gffread-0.9.12.ebuild
b/sci-biology/gffread/gffread-0.11.0.ebuild
similarity index 50%
rename from sci-biology/gffread/gffread-0.9.12.ebuild
rename to sci-biology/gffread/gffread-0.11.0.ebuild
index fc60b9a81..bfedb57a5 100644
--- a/sci-biology/gffread/gffread-0.9.12.ebuild
+++ b/sci-biology/gffread/gffread-0.11.0.ebuild
@@ -1,20 +1,35 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
+
+inherit toolchain-funcs
DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract
regions from FASTA"
HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
https://github.com/gpertea/gffread;
SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/gpertea/gclib/archive/v0.10.2.tar.gz ->
gclib-0.10.2.tar.gz"
+ https://github.com/gpertea/gclib/archive/v${PV}.tar.gz ->
gclib-${PV}.tar.gz"
LICENSE="MIT"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}"
-PATCHES=( "${FILESDIR}"/Makefile.patch )
+src_prepare(){
+ src_unpack "${DISTDIR}"/gclib-${PV}.tar.gz
+ default
+ sed -e "s/-g -O3/${CXXFLAGS}/" -i Makefile || die
+ cd .. && ln -s gclib-"${PV}" gclib || die
+}
+
+src_compile(){
+ emake release
+}
+
+src_install(){
+ dobin gffread
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/gffread/files/, sci-biology/gffread/
commit: 75c0f38ac94bb4c86f2c10ef5c0b99227d80cfa9
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Tue Jun 26 07:59:41 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jun 26 07:59:41 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=75c0f38a
sci-biology/gffread: fetch gclib and use during compilation
The soucre tree is not made to use site-wide installed headers from
gclib. I am not going to figure out git commit tag of gclib automagically
bundled into some gffread binary when gffread was released (to make
a dedicated gclib-$commitnr.tar.gz file for Gentoo/Debian/etc. and to
include it into SRC_URI here so gffread could use it.
It is the task for upstream author to properly document required versions
of dependencies and release them properly.
https://github.com/gpertea/gffread/issues/26#issuecomment-400134376
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/gffread/files/Makefile.patch | 6 +++---
sci-biology/gffread/gffread-0.9.12.ebuild | 8 +---
2 files changed, 8 insertions(+), 6 deletions(-)
diff --git a/sci-biology/gffread/files/Makefile.patch
b/sci-biology/gffread/files/Makefile.patch
index 45f8c3ebd..35e6b088e 100644
--- a/sci-biology/gffread/files/Makefile.patch
+++ b/sci-biology/gffread/files/Makefile.patch
@@ -1,8 +1,8 @@
gffread-0.9.12/Makefile2018-06-26 00:05:05.298388489 +0200
-+++ gffread-0.9.12/Makefile2018-06-26 00:07:07.461729681 +0200
+--- gffread-0.9.12/Makefile2018-06-26 09:52:26.024747027 +0200
gffread-0.9.12/Makefile2018-06-26 09:52:41.845177021 +0200
@@ -1,4 +1,4 @@
-GCLDIR := ../gclib
-+GCLDIR := $(EPREFIX)/usr/include/gclib
++GCLDIR := ../gclib-0.10.2
SEARCHDIRS := -I. -I${GCLDIR}
SYSTYPE := $(shell uname)
diff --git a/sci-biology/gffread/gffread-0.9.12.ebuild
b/sci-biology/gffread/gffread-0.9.12.ebuild
index 968ebc256..fc60b9a81 100644
--- a/sci-biology/gffread/gffread-0.9.12.ebuild
+++ b/sci-biology/gffread/gffread-0.9.12.ebuild
@@ -4,15 +4,17 @@
EAPI=6
DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract
regions from FASTA"
-HOMEPAGE="https://github.com/gpertea/gffread;
-SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
+ https://github.com/gpertea/gffread;
+SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+ https://github.com/gpertea/gclib/archive/v0.10.2.tar.gz ->
gclib-0.10.2.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND="sci-biology/gclib"
+DEPEND=""
RDEPEND="${DEPEND}"
PATCHES=( "${FILESDIR}"/Makefile.patch )
[gentoo-commits] proj/sci:master commit in: sci-biology/gffread/files/, sci-biology/gffread/
commit: ea003571ac74c209954bfe016cb6a91319058080
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Jun 25 22:23:40 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Jun 25 22:23:40 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea003571
sci-biology/gffread: new package
Does not compile, will report upstream.
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/gffread/files/Makefile.patch | 39 +++
sci-biology/gffread/gffread-0.9.12.ebuild | 18 ++
sci-biology/gffread/metadata.xml | 12 ++
3 files changed, 69 insertions(+)
diff --git a/sci-biology/gffread/files/Makefile.patch
b/sci-biology/gffread/files/Makefile.patch
new file mode 100644
index 0..45f8c3ebd
--- /dev/null
+++ b/sci-biology/gffread/files/Makefile.patch
@@ -0,0 +1,39 @@
+--- gffread-0.9.12/Makefile2018-06-26 00:05:05.298388489 +0200
gffread-0.9.12/Makefile2018-06-26 00:07:07.461729681 +0200
+@@ -1,4 +1,4 @@
+-GCLDIR := ../gclib
++GCLDIR := $(EPREFIX)/usr/include/gclib
+ SEARCHDIRS := -I. -I${GCLDIR}
+
+ SYSTYPE := $(shell uname)
+@@ -10,7 +10,7 @@
+ MARCH =
+ endif
+
+-CC := g++
++CXX ?= g++
+
+ BASEFLAGS := -Wall -Wextra ${SEARCHDIRS} $(MARCH) -D_FILE_OFFSET_BITS=64 \
+ -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions
-fno-rtti
+@@ -26,15 +26,17 @@
+ GCC45OPTMAIN :=
+
+ ifeq ($(findstring release,$(MAKECMDGOALS)),release)
+- CFLAGS := -O2 -DNDEBUG $(BASEFLAGS)
++ CXXFLAGS ?= -O2
++ CXXFLAGS += -DNDEBUG $(BASEFLAGS)
+ LDFLAGS :=
+ else
+- CFLAGS := -g -DDEBUG $(BASEFLAGS)
+- LDFLAGS := -g
++ CXXFLAGS ?= -g
++ CXXFLAGS += -DDEBUG $(BASEFLAGS)
++ LDFLAGS ?= -g
+ endif
+
+ %.o : %.cpp
+- ${CC} ${CFLAGS} -c $< -o $@
++ ${CXX} ${CXXFLAGS} -c $< -o $@
+
+ # C/C++ linker
+
diff --git a/sci-biology/gffread/gffread-0.9.12.ebuild
b/sci-biology/gffread/gffread-0.9.12.ebuild
new file mode 100644
index 0..968ebc256
--- /dev/null
+++ b/sci-biology/gffread/gffread-0.9.12.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract
regions from FASTA"
+HOMEPAGE="https://github.com/gpertea/gffread;
+SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/gclib"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/Makefile.patch )
diff --git a/sci-biology/gffread/metadata.xml b/sci-biology/gffread/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/sci-biology/gffread/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ mmokr...@fold.natur.cuni.cz
+ Martin Mokrejs
+
+
+ sci-biol...@gentoo.org
+ Gentoo Biology Project
+
+
