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

Package-Manager: portage-2.2.0_alpha121/cvs/Linux x86_64

5 files changed, 129 insertions, 22 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/Manifest b/sci-biology/arb/Manifest
index a3b08040c162..dc0adb266204 100644
--- a/sci-biology/arb/Manifest
+++ b/sci-biology/arb/Manifest
@@ -1,22 +1,27 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
+Hash: SHA256
 
-AUX 5.1-bfr-overflow.patch 715 RMD160 6d547f471a31166ac40c0502206c389d649a625d SHA1 64d010c090b83c57bf211810f1760354cca0bed1 SHA256 bedb03c70bd0e4e180f8d6e966bfaf34af32125a1595aae8a994617e6a2f2833
-AUX 5.1-libs.patch 503 RMD160 a32610db2431b84e9195d7481f50be62dfa6e9da SHA1 37792a725b045bc9948e7bcb3883c29d7cabb0ce SHA256 dfa5f131eafbf163b9a3862360694a7b1f9d6231357247c7f18f696c4c4dd983
-AUX 5.2-libpng15.patch 1545 RMD160 86336e2731ec842985ee49611234636230b3356d SHA1 9391a28d2a102d8dd5663f4fd62d18fccd577e9e SHA256 e0fca903aef6c23173a6484717bdbc08e520a47f6f80c589747bddb557169e50
-DIST arb-5.1-glibc2.10.patch.bz2 24659 RMD160 b522f6cd0cdcfe327d43e9b237a154e8261f7db9 SHA1 923c298f21100a6b3d3d8c4007031e1601834701 SHA256 1153e3efe73c1027972ee1b2789ee9841749c0bd2cbb2cc3ad8cd53586ff6f2f
-DIST arb-5.1-linker.patch.bz2 4406 RMD160 b1273f0b5c765c257c905f5945039864f4c6194a SHA1 e7d75c7d56112acc6b79ea13617c8e72ed05a7d8 SHA256 62080367ebd11ed3c9991bfb872e083e2d747264a400178ab0ec11a3502f3d43
-DIST arb-5.1.tgz 9727285 RMD160 8757446e7145faf28382c617fc7fe4b57a857baf SHA1 69696e52bf86eea5213ad9d27be30dd74f1255f3 SHA256 7f0a2411e7b95b94f23c51211461047eb74ffd3dd632552a82425cf903f89dbf
-DIST arb-5.2-linker.patch.bz2 4441 RMD160 7e410bdf330a946bea7746feaabed871305c9cb3 SHA1 cd13e3316c6734094f8e54a554c0c752ef334ff4 SHA256 3b804fca56e920f83b79f7cdfb124769bfa677a3f2216021eed04ba76ac886c6
-DIST arb-5.2.tgz 9729004 RMD160 d9d99d0ebadaa293091ff93f6ca588b2321bd8b0 SHA1 4ee493a16ece5231d46ed1071407c06e733d67c8 SHA256 cd68cfae317aae378da69c4c4ec8036a2babec064896d0b9d845fac2133f6edd
-EBUILD arb-5.1-r1.ebuild 2182 RMD160 9c485ae3017c99c9fee88eebab99930e1e9466b3 SHA1 7a2e02d74a3e7792bce5e84ba2bd5d4646095a89 SHA256 4c1035295ba7fa81312f861f98841bb3068208562766bea43f6b6f12f283a6b9
-EBUILD arb-5.2.ebuild 2111 RMD160 fdd8236f501ff64eafa682521dee133da858b054 SHA1 bf18d8088f0f9922059cb915063d501ed46beab2 SHA256 2a5b24c4e33c233ddadddff01dbe8e886fab08c9d491cd01f7da04e0eaf384ef
-MISC ChangeLog 1469 RMD160 ee4b463f0e06941e59e486eb9ac48a9311b889c3 SHA1 594857a646e4ec198b01f925eb8d8ca0908a722d SHA256 f29f38a276f449432f12ad99e419024b8a10f3310c055e1d161e138b1ad4a872
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+AUX 5.1-bfr-overflow.patch 715 SHA256 bedb03c70bd0e4e180f8d6e966bfaf34af32125a1595aae8a994617e6a2f2833 SHA512 840dc83a2f6a6c7da05437a72bbc9372a229a18f6de08758141c6ed142a034f4b2954e9a650185fcdcdd5e672cabad32d9b2496098a2369094f502f87143710c WHIRLPOOL 8c7a986da48f147962456ecef668e516b1c14bd60ce7084b59d4dec2ca24d5e785f1e5ecb59ce6a824676736566cfedf8aa19746492aaa1062b584d3c799fb8a
+AUX 5.1-libs.patch 503 SHA256 dfa5f131eafbf163b9a3862360694a7b1f9d6231357247c7f18f696c4c4dd983 SHA512 9130fd43a7a6c43ac5dce56eeb85cabe881ddd12a2786ae0ec73432584d498afb1b7f28514c9d078e6c19f6654f2ef88192e96cac2f4be5a04474f534a2bdcdd WHIRLPOOL e82d5ae89ed7ffab4d26d6ca4049db1ebb9744c2dc41626c219d5263b8e09a27dd8cebb880821e8d4707bdbcf70a02ede760745fbd34567dca72883d937f2dbe
+AUX 5.2-libpng15.patch 1545 SHA256 e0fca903aef6c23173a6484717bdbc08e520a47f6f80c589747bddb557169e50 SHA512 8215bead0ff0d579b43b6c75f82306aacf5248833b13536ec0bbd703433343f2920c2fb68e015ea39b105630c1c06bc45cc9e165f230deddd52e76a2d7f82bdc WHIRLPOOL ad3edfb1db9f6c811fef635e8d1fa03961a8906b253e06a705ee7e712fbb5dfb16b0e1a08af07eb30b6040b61050f53b73c872af09edef3d60c7e2f558ec44a3
+AUX arb-5.2-gcc-47.patch 330 SHA256 994883702df6406e9d44ff4e3b362046428db25735910e211fc15c6e7ccc7b08 SHA512 36b2afbc6c177c44728da92fd596881b5035d5d7b8880fabbdaa360c9f59057816952112bb98ae0fa5b04352ea99b85318f262a6d91001bc177dd1e6069611c0 WHIRLPOOL c7b0ef45be2a567cd2d5c2032fd9195350f71651c8d9dd7269f94d32586b514b0cf4d2857cf4a2b63ff33cee3620cf87403d484214e95c780d28a450ce9d4928
+DIST arb-5.1-glibc2.10.patch.bz2 24659 SHA256 1153e3efe73c1027972ee1b2789ee9841749c0bd2cbb2cc3ad8cd53586ff6f2f
+DIST arb-5.1-linker.patch.bz2 4406 SHA256 62080367ebd11ed3c9991bfb872e083e2d747264a400178ab0ec11a3502f3d43
+DIST arb-5.1.tgz 9727285 SHA256 7f0a2411e7b95b94f23c51211461047eb74ffd3dd632552a82425cf903f89dbf
+DIST arb-5.2-linker.patch.bz2 4441 SHA256 3b804fca56e920f83b79f7cdfb124769bfa677a3f2216021eed04ba76ac886c6 SHA512 6afae76a4b403ad3139abd4535b5da8bbf2d16aa5f49e30c86c8f186ac585de6c789e8fa4e402576a67ce8c58468e626a46bde5cfae5869ea2c046a1492fa903 WHIRLPOOL 95435cfc7f5a530442ad294cb8cd79a666f54cc3c99195e9c05a923e41b0211e5bad7b67cd4d8c5ee37ef30de22fba4472dc8990d95aaf3c8d3edb2d3d26c984
+DIST arb-5.2.tgz 9729004 SHA256 cd68cfae317aae378da69c4c4ec8036a2babec064896d0b9d845fac2133f6edd SHA512 d1f9f7273645af7da0e949971b705303f0715ac98869acc0f75d62bfe88751709f5d5dbbc3079b0abe461ddce8262b165426e347ad28bc28a55cdf6c29b5ff56 WHIRLPOOL ec5422b4b689a77b479231c04d7b5a2f4f0ef23cd06b024920432134132d7c2c5b24c407b2561074a41606e7945ce88970789f5db82e43cc9ef9313ea48c0583
+DIST arb-5.3-linker.patch.xz 3604 SHA256 09580d0c1ff54c4956382cef850aecb9008e62e083f3246604cac72f06d05e95 SHA512 8eb072cd5a3c13b2a6ad0e40f3b155096168dbd70a6e13878d4a62e563903742442373a5e3032d6f78beefe774943fef86f6060e89acd0d18b95a7c0d4a8dec7 WHIRLPOOL f77d767c5b5c911ba3ddc9ef5b3e482cb1975b5d56f50b76166bd4a0b55e251e73eeee46709147207b2f3553d482bab99398d8bd03aef8f0b79928a8a66d0bfe
+DIST arb-5.3.tgz 9543106 SHA256 c40a3f33f39996e3e331fb41acd452e5a20b7e638b856b0b66ea8e07c977abf8 SHA512 faa924b9c6f437f77ed637798c6fe5fe5c2e6a0f2efc9c1f735133fab9c037c7039fc4ef6f6e5b0408fc39ea5c69c747b1887689f4621b608add593d77930282 WHIRLPOOL 9b4723043b4f8b9a68973f49cb7dc8c3cf3558ff646d20f7d4f20f6e4797b6c9a986fdb1dc47178f2c80251db59f61dffd1b01bbdd880f864fc749ef59e62958
+EBUILD arb-5.1-r1.ebuild 2182 SHA256 4c1035295ba7fa81312f861f98841bb3068208562766bea43f6b6f12f283a6b9 SHA512 b2249f3cfb8ca102b91fe9f01e46bd38fe6e770f1754a32bf9d34b3b20a35050ba08f83e3d8a2388e51fb0d301be28c0487bd4b5b08a08e3b104166bac63672e WHIRLPOOL 11587eed69f415c57e17d4a47c37a2e70f5dbafed5a7d139e8b50e5533da0b76bfcacfcde2869abbd4413ab1dc9bfeee61c60941495f3a91585b4b8b6ba477fc
+EBUILD arb-5.2.ebuild 2185 SHA256 cbb5f8c3fe91eeefbc50b82aa68b9235d95a26531acb68df415112ca92137036 SHA512 471e0864d90ede304467bfa58999cbad9209b7d725b7edf78d4934cefea328671c2d39671a14255b10cb39a6fab556cd664466127057c15b97d8223f765bdece WHIRLPOOL 505ab14c32dac664e02223ab59a4d148586db0fb99405bbcd71e7ffbe53e2add18c26f2b3437383fb728e57c6ef22dd7295b7a2f8999a644574f019ff7c74eeb
+EBUILD arb-5.3.ebuild 2149 SHA256 5adcfdd1444804f1b9fdc781a79e1097a2e4ebb0943d0e4e41b0ec41bfd70aa0 SHA512 6a0552cdd37e34d4ecc5238ebf22ed0abeb88114b1c8b7e4d705e063b33f8a0668409f0b5a8336cb64e53d238d1d3cce8cfde90dfab305eb14f6248184af595a WHIRLPOOL 4b6e6277857f8fa5302771121e1aecac04b313747075a6164d19bb29373ec0ee27847f6af826ba1fc991cc035d7852353e6010e5987b069cc449d7e0013a8c2f
+MISC ChangeLog 1650 SHA256 c8255013f46bb70c81b570c1f9eda48c57954537a2784a192da09c4bd2bd2171 SHA512 63046b7c138cdb6ca1e6090b071c07ec9b5269acab944192e4e87cfe58ef1e502e0309d6ec9f4a078161c0ef85af72a5ae7e8244a90650315f7df76184acebb7 WHIRLPOOL 641d2fea812fe1353d2436fbeb616cabd1d23f3af81391ea657eecf2cf618a4a3f5f77050a273f8add653a2488de4107f457b05dd20b0256b088e3dbdcf23031
+MISC metadata.xml 259 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 SHA512 c3aea4d69d75075af0108a03b7e109cfed6a1fe324f8ccbda3d4e5ca8a5070f1b24ddeb46b64787e10fd22252d867abcee1f31316d602f7e32fe3c990ae60d74 WHIRLPOOL e50da2f26fd4c908446d22da3edb595d60e61d72def374be46440358802a211fc34045b7ad970c4f94b57f7b17ff24cfe64dc94254fea20e047f1fbbbcae0c64
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.18 (GNU/Linux)
+Version: GnuPG v2.0.19 (GNU/Linux)
+Comment: GPGTools - http://gpgtools.org
 
-iEYEAREKAAYFAk9TPAAACgkQgAnW8HDreRZXRACggG6/VQvir/G1TMwTq5ZdKJPD
-LcUAoMbqI4X1LnrVMX4WK/cPzVtnV/8U
-=/g5I
+iEYEAREIAAYFAlAqgR4ACgkQgAnW8HDreRbzaACgmQBkY2jsugAI4efgseQhYNeV
+SAoAn2wRIT9z6Qd3lP6o5ZxqVupScw5k
+=W5zr
 -----END PGP SIGNATURE-----
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;
+