sci-biology/arb: Version BUmp; add fix for gcc-4.7, #431228

(Portage version: 2.2.0_alpha121/cvs/Linux x86_64)

4 files changed, 107 insertions, 5 deletions

diff --git a/sci-biology/arb/ChangeLog b/sci-biology/arb/ChangeLog
index ceeeaf8aecd3..068e4e8c8211 100644
--- a/sci-biology/arb/ChangeLog
+++ b/sci-biology/arb/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/arb
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/ChangeLog,v 1.7 2012/03/04 09:55:06 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/ChangeLog,v 1.8 2012/08/14 16:47:19 jlec Exp $
+
+*arb-5.3 (14 Aug 2012)
+
+  14 Aug 2012; Justin Lecher <jlec@gentoo.org> arb-5.2.ebuild,
+  +files/arb-5.2-gcc-47.patch, +arb-5.3.ebuild:
+  Version BUmp; add fix for gcc-4.7, #431228
 
   04 Mar 2012; Justin Lecher <jlec@gentoo.org> arb-5.1-r1.ebuild,
   arb-5.2.ebuild:
diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild
index 55ea8e8a81e7..b843c06f88af 100644
--- a/sci-biology/arb/arb-5.2.ebuild
+++ b/sci-biology/arb/arb-5.2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/arb-5.2.ebuild,v 1.4 2012/03/04 09:55:06 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/arb-5.2.ebuild,v 1.5 2012/08/14 16:47:19 jlec Exp $
 
 EAPI=4
 
@@ -46,12 +46,15 @@ src_prepare() {
 		"${WORKDIR}"/${P}-linker.patch \
 		"${FILESDIR}"/5.1-libs.patch \
 		"${FILESDIR}"/5.1-bfr-overflow.patch \
-		"${FILESDIR}"/${PV}-libpng15.patch
-	sed -i \
+		"${FILESDIR}"/${PV}-libpng15.patch \
+		"${FILESDIR}"/${P}-gcc-47.patch
+	sed \
 		-e 's/all: checks/all:/' \
 		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
 		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
-		"${S}/Makefile" || die
+		-e 's:-O4::g' \
+		-e 's:-pipe::g' \
+		-i "${S}/Makefile" || die
 	cp config.makefile.template config.makefile
 	sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
 	use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
diff --git a/sci-biology/arb/arb-5.3.ebuild b/sci-biology/arb/arb-5.3.ebuild
new file mode 100644
index 000000000000..7cf8503a3780
--- /dev/null
+++ b/sci-biology/arb/arb-5.3.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/arb-5.3.ebuild,v 1.1 2012/08/14 16:47:19 jlec Exp $
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis"
+HOMEPAGE="http://www.arb-home.de/"
+SRC_URI="
+	http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
+	http://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.xz"
+
+SLOT="0"
+LICENSE="arb"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="app-text/sablotron
+	media-libs/libpng
+	media-libs/tiff
+	www-client/lynx
+	x11-libs/libXaw
+	x11-libs/libXpm
+	x11-libs/openmotif:0
+	opengl? (
+		media-libs/glew
+		media-libs/freeglut
+		|| (
+			media-libs/mesa[motif]
+			( media-libs/mesa x11-libs/libGLw ) ) )"
+DEPEND="${CDEPEND}
+	sys-process/time"
+RDEPEND="${CDEPEND}
+	sci-visualization/gnuplot"
+# Recommended: libmotif3 gv xfig xterm treetool java
+
+src_unpack() {
+	unpack ${A}
+	mv arbsrc* ${P}
+}
+
+src_prepare() {
+	epatch \
+		"${WORKDIR}"/${P}-linker.patch \
+		"${FILESDIR}"/5.1-libs.patch \
+		"${FILESDIR}"/5.1-bfr-overflow.patch \
+		"${FILESDIR}"/5.2-libpng15.patch \
+		"${FILESDIR}"/${PN}-5.2-gcc-47.patch
+	sed \
+		-e 's/all: checks/all:/' \
+		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+		-i "${S}/Makefile" || die
+	cp config.makefile.template config.makefile
+	sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
+	use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
+	use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
+	emake ARBHOME="${S}" links
+}
+
+src_compile() {
+	emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile
+	use amd64 && mv arb.tgz arb.64.gentoo.tgz
+	use x86 && mv arb.tgz arb.32.gentoo.tgz
+	ln -s arb.*.tgz arb.tgz || die
+}
+
+src_install() {
+	ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+	cat <<- EOF > "${S}/99${PN}"
+	ARBHOME=/opt/arb
+	PATH=/opt/arb/bin
+	LD_LIBRARY_PATH=/opt/arb/lib
+	EOF
+	doenvd "${S}/99${PN}"
+}
diff --git a/sci-biology/arb/files/arb-5.2-gcc-47.patch b/sci-biology/arb/files/arb-5.2-gcc-47.patch
new file mode 100644
index 000000000000..186e78e450b3
--- /dev/null
+++ b/sci-biology/arb/files/arb-5.2-gcc-47.patch
@@ -0,0 +1,15 @@
+ AWTI/AWTI_import.cxx |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/AWTI/AWTI_import.cxx b/AWTI/AWTI_import.cxx
+index 8e730ac..e3f9ff4 100644
+--- a/AWTI/AWTI_import.cxx
++++ b/AWTI/AWTI_import.cxx
+@@ -12,6 +12,7 @@
+ #include <GEN.hxx>
+ 
+ #include <climits>
++#include <unistd.h>
+ 
+ using namespace std;
+