Version Bump, fix buffer overflow, make gcc46 resistent, fix build failure, #314665,340579,362633

Package-Manager: portage-2.2.0_alpha41/cvs/Linux x86_64

5 files changed, 129 insertions, 25 deletions

diff --git a/sci-biology/arb/ChangeLog b/sci-biology/arb/ChangeLog
index 561f92346f20..06a7796d0602 100644
--- a/sci-biology/arb/ChangeLog
+++ b/sci-biology/arb/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/arb
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/ChangeLog,v 1.4 2010/10/10 21:16:13 ulm Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/ChangeLog,v 1.5 2011/06/20 07:34:40 jlec Exp $
+
+*arb-5.2 (20 Jun 2011)
+
+  20 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/5.1-bfr-overflow.patch,
+  arb-5.1-r1.ebuild, +arb-5.2.ebuild:
+  Version Bump, fix buffer overflow, make gcc46 resistent, fix build failure,
+  #314665,340579,362633
 
   10 Oct 2010; Ulrich Mueller <ulm@gentoo.org> arb-5.1-r1.ebuild:
   Fix openmotif dependency.
diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest
index 43e9facc6f8e..e94104124242 100644
--- a/sci-biology/arb/Manifest
+++ b/sci-biology/arb/Manifest
@@ -1,17 +1,21 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
+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
 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
-EBUILD arb-5.1-r1.ebuild 2129 RMD160 621ffacf9dab93a6dc83b409aa12aac49b388ede SHA1 e86e84dc9745484e5e03018bf8f4dd571a6a9bc7 SHA256 568fcb375d5e02405b11156d84a4fa89526b3bfa04e001ef5a7f09e80f6d185f
-MISC ChangeLog 768 RMD160 1ac9a6c9c8c72673126e27ceb633bfec912e3343 SHA1 b61448f2463937753c3922a2c22e4dd68894f59d SHA256 894ba9fdf6e7c42150182f6b6a8d86f503d61865224a883f9e0a448774088d3f
+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 2133 RMD160 846134ac1d2021ff1fb34a3e31145660c56ea1f2 SHA1 aed62a0169f663fe67c8e823181f1b986255bf7c SHA256 308a9ddffd81f563607a235f0b665f5557f90f65ac2933d85b13a2e08094d15e
+EBUILD arb-5.2.ebuild 1975 RMD160 53033437cc80dfdc888cea3284851078af61217a SHA1 67f603be4094f0a34b2eb22b1a620583d046c45c SHA256 f06963255fc5ba095ec808e5b4d4cd013c654c07c704ac9e2f3f7ace42047423
+MISC ChangeLog 1012 RMD160 66ea07717193261da183007c098f0bac8ff05cfc SHA1 c0a5f172a41bef264b7a64f962f61a154103cfc5 SHA256 b8fcd073a614656718f41e7f65ad74cd2661f650f69e169dffe93929e934c00a
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.16 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAkyyLZEACgkQOeoy/oIi7ux76QCgrwseV0VcXJwquR2Ka+gcUbK/
-9EAAnA7kZFiXf24tH4lV2hNZtTQkEZGW
-=YrLQ
+iEYEARECAAYFAk3++BUACgkQgAnW8HDreRa1FwCfXSoQfzUxeGqEPEMwiah/+VEj
+ZOIAoJvPUmGYbLBxjmgIPHnOQxkJx6hT
+=/Ybd
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/arb/arb-5.1-r1.ebuild b/sci-biology/arb/arb-5.1-r1.ebuild
index e4e232994bef..17520b091f9f 100644
--- a/sci-biology/arb/arb-5.1-r1.ebuild
+++ b/sci-biology/arb/arb-5.1-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/arb-5.1-r1.ebuild,v 1.3 2010/10/10 21:16:13 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/arb-5.1-r1.ebuild,v 1.4 2011/06/20 07:34:40 jlec Exp $
 
-EAPI="2"
+EAPI=2
 
 inherit eutils toolchain-funcs
 
@@ -11,8 +11,7 @@ HOMEPAGE="http://www.arb-home.de/"
 SRC_URI="
 	http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
 	mirror://gentoo/${P}-glibc2.10.patch.bz2
-	mirror://gentoo/${P}-linker.patch.bz2"
-MY_TAG=6213
+	http://dev.gentoo.org/~jlec/${P}-linker.patch.bz2"
 
 LICENSE="arb"
 SLOT="0"
@@ -21,37 +20,42 @@ KEYWORDS="~amd64 ~x86"
 
 DEPEND="
 	app-text/sablotron
+	media-libs/libpng
+	media-libs/tiff
 	www-client/lynx
-	>=x11-libs/openmotif-2.3:0
-	x11-libs/libXpm
 	x11-libs/libXaw
-	media-libs/tiff
-	media-libs/libpng
-	opengl? ( media-libs/glew
+	x11-libs/libXpm
+	x11-libs/openmotif:0
+	opengl? (
+		media-libs/glew
 		media-libs/freeglut
 		media-libs/mesa[motif] )"
 RDEPEND="${DEPEND}
 	sci-visualization/gnuplot"
 # Recommended: libmotif3 gv xfig xterm treetool java
 
-S="${WORKDIR}/arbsrc_${MY_TAG}"
+src_unpack() {
+	unpack ${A}
+	mv arbsrc* ${P}
+}
 
 src_prepare() {
-	epatch "${WORKDIR}"/${P}-glibc2.10.patch
-	epatch "${WORKDIR}"/${P}-linker.patch
-	epatch "${FILESDIR}"/${PV}-libs.patch
+	epatch \
+		"${WORKDIR}"/${P}-glibc2.10.patch\
+		"${WORKDIR}"/${P}-linker.patch \
+		"${FILESDIR}"/${PV}-libs.patch \
+		"${FILESDIR}"/${PV}-bfr-overflow.patch
 	sed -i \
 		-e 's/all: checks/all:/' \
 		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
-		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CFLAGS}/" \
+		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+		-e 's/--export-dynamic/-Wl,--export-dynamic/g' \
 		"${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 || die
-	# In 5.0; fixed in 5.1
-	# (cd INCLUDE/GL; for i in ../../GL/glAW/*.h; do ln -s $i; done) || die
 }
 
 src_compile() {
diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild
new file mode 100644
index 000000000000..a8267b6d6ac0
--- /dev/null
+++ b/sci-biology/arb/arb-5.2.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2011 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 1.1 2011/06/20 07:34:40 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 -> ${P}.tgz
+	http://dev.gentoo.org/~jlec/${P}-linker.patch.bz2"
+
+SLOT="0"
+LICENSE="arb"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	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] )"
+RDEPEND="${DEPEND}
+	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 \
+		"${FILESDIR}"/5.1-bfr-overflow.patch
+	sed -i \
+		-e 's/all: checks/all:/' \
+		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+		"${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/5.1-bfr-overflow.patch b/sci-biology/arb/files/5.1-bfr-overflow.patch
new file mode 100644
index 000000000000..21d21f5ac17f
--- /dev/null
+++ b/sci-biology/arb/files/5.1-bfr-overflow.patch
@@ -0,0 +1,16 @@
+ ARB_GDE/GDE_HGLfile.cxx |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/ARB_GDE/GDE_HGLfile.cxx b/ARB_GDE/GDE_HGLfile.cxx
+index e353a89..f69635a 100644
+--- a/ARB_GDE/GDE_HGLfile.cxx
++++ b/ARB_GDE/GDE_HGLfile.cxx
+@@ -494,7 +494,7 @@ void ReadGDE(char *filename,NA_Alignment *dataset,int type)
+             if(this_elem->id[0] == '\0')
+                 strncpy(this_elem->id,uniqueID(),79);
+             if(this_elem->short_name[0] == '\0')
+-                strncpy(this_elem->short_name,this_elem->id,79);
++                strncpy(this_elem->short_name,this_elem->id,31);
+             if(this_elem->seqlen == 0)
+                 this_elem->protect=
+                     PROT_BASE_CHANGES+