* [gentoo-commits] proj/sci:master commit in: sci-biology/gffread/files/, sci-biology/gffread/
@ 2018-06-25 22:23 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2018-06-25 22:23 UTC (permalink / raw
To: gentoo-commits
commit: ea003571ac74c209954bfe016cb6a91319058080
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 25 22:23:40 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 25 22:23:40 2018 +0000
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 000000000..45f8c3ebd
--- /dev/null
+++ b/sci-biology/gffread/files/Makefile.patch
@@ -0,0 +1,39 @@
+--- gffread-0.9.12/Makefile 2018-06-26 00:05:05.298388489 +0200
++++ gffread-0.9.12/Makefile 2018-06-26 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 $@
+
+ # C/C++ linker
+
diff --git a/sci-biology/gffread/gffread-0.9.12.ebuild b/sci-biology/gffread/gffread-0.9.12.ebuild
new file mode 100644
index 000000000..968ebc256
--- /dev/null
+++ b/sci-biology/gffread/gffread-0.9.12.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract regions from FASTA"
+HOMEPAGE="https://github.com/gpertea/gffread"
+SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/gclib"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/Makefile.patch )
diff --git a/sci-biology/gffread/metadata.xml b/sci-biology/gffread/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/gffread/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffread/files/, sci-biology/gffread/
@ 2018-06-26 7:59 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2018-06-26 7:59 UTC (permalink / raw
To: gentoo-commits
commit: 75c0f38ac94bb4c86f2c10ef5c0b99227d80cfa9
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jun 26 07:59:41 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jun 26 07:59:41 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=75c0f38a
sci-biology/gffread: fetch gclib and use during compilation
The soucre tree is not made to use site-wide installed headers from
gclib. I am not going to figure out git commit tag of gclib automagically
bundled into some gffread binary when gffread was released (to make
a dedicated gclib-$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/Makefile 2018-06-26 00:05:05.298388489 +0200
-+++ gffread-0.9.12/Makefile 2018-06-26 00:07:07.461729681 +0200
+--- gffread-0.9.12/Makefile 2018-06-26 09:52:26.024747027 +0200
++++ gffread-0.9.12/Makefile 2018-06-26 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=( "${FILESDIR}"/Makefile.patch )
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffread/files/, sci-biology/gffread/
@ 2019-03-25 11:49 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2019-03-25 11:49 UTC (permalink / raw
To: gentoo-commits
commit: e55065dc88a894edab65609ffdd4e275cdcd4bd0
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 11:49:49 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 11:49:49 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e55065dc
sci-biology/gffread: bump to 0.11.0, drop old patch, use sed hackery
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/gffread/files/Makefile.patch | 39 ----------------------
...gffread-0.9.12.ebuild => gffread-0.11.0.ebuild} | 25 +++++++++++---
2 files changed, 20 insertions(+), 44 deletions(-)
diff --git a/sci-biology/gffread/files/Makefile.patch b/sci-biology/gffread/files/Makefile.patch
deleted file mode 100644
index 35e6b088e..000000000
--- a/sci-biology/gffread/files/Makefile.patch
+++ /dev/null
@@ -1,39 +0,0 @@
---- gffread-0.9.12/Makefile 2018-06-26 09:52:26.024747027 +0200
-+++ gffread-0.9.12/Makefile 2018-06-26 09:52:41.845177021 +0200
-@@ -1,4 +1,4 @@
--GCLDIR := ../gclib
-+GCLDIR := ../gclib-0.10.2
- SEARCHDIRS := -I. -I${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
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
end of thread, other threads:[~2019-03-25 11:50 UTC | newest]
Thread overview: 3+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2018-06-25 22:23 [gentoo-commits] proj/sci:master commit in: sci-biology/gffread/files/, sci-biology/gffread/ Martin Mokrejs
-- strict thread matches above, loose matches on Subject: below --
2018-06-26 7:59 Martin Mokrejs
2019-03-25 11:49 Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox