From bea948f4cfc46113a18efcc54985f781b351037f Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Mon, 20 Jun 2011 07:34:40 +0000 Subject: 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 --- sci-biology/arb/ChangeLog | 11 ++++- sci-biology/arb/Manifest | 16 +++--- sci-biology/arb/arb-5.1-r1.ebuild | 38 ++++++++------- sci-biology/arb/arb-5.2.ebuild | 73 ++++++++++++++++++++++++++++ sci-biology/arb/files/5.1-bfr-overflow.patch | 16 ++++++ 5 files changed, 129 insertions(+), 25 deletions(-) create mode 100644 sci-biology/arb/arb-5.2.ebuild create mode 100644 sci-biology/arb/files/5.1-bfr-overflow.patch (limited to 'sci-biology') 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 +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 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+ -- cgit v1.2.3-65-gdbad