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
+}
