diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/arb/ChangeLog | 11 | ||||
| -rw-r--r-- | sci-biology/arb/arb-5.1-r1.ebuild | 38 | ||||
| -rw-r--r-- | sci-biology/arb/arb-5.2.ebuild | 73 | ||||
| -rw-r--r-- | sci-biology/arb/files/5.1-bfr-overflow.patch | 16 |
4 files changed, 119 insertions, 19 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/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+ |