jlec 15/03/16 13:44:11 Modified: ChangeLog Added: ccp4-libs-6.1.3-r16.ebuild Log: Force error on build failure, bug #543028; fix for format-security (Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path 1.63 sci-libs/ccp4-libs/ChangeLog file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.63&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.63&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?r1=1.62&r2=1.63 Index: ChangeLog =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v retrieving revision 1.62 retrieving revision 1.63 diff -u -r1.62 -r1.63 --- ChangeLog 12 Mar 2015 10:07:56 -0000 1.62 +++ ChangeLog 16 Mar 2015 13:44:11 -0000 1.63 @@ -1,6 +1,13 @@ # ChangeLog for sci-libs/ccp4-libs # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.62 2015/03/12 10:07:56 ago Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.63 2015/03/16 13:44:11 jlec Exp $ + +*ccp4-libs-6.1.3-r16 (16 Mar 2015) + + 16 Mar 2015; Justin Lecher <[email protected]> +ccp4-libs-6.1.3-r16.ebuild, + +files/ccp4-libs-6.1.3-force.patch, + +files/ccp4-libs-6.1.3-format-security.patch: + Force error on build failure, bug #543028; fix for format-security 12 Mar 2015; Agostino Sarubbo <[email protected]> ccp4-libs-6.1.3-r15.ebuild: Stable for amd64, wrt bug #542696 1.1 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild?rev=1.1&content-type=text/plain Index: ccp4-libs-6.1.3-r16.ebuild =================================================================== # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild,v 1.1 2015/03/16 13:44:11 jlec Exp $ EAPI=5 PYTHON_COMPAT=( python2_7 ) inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs SRC="ftp://ftp.ccp4.ac.uk/ccp4"; #UPDATE="04_03_09" #PATCHDATE="090511" MY_P="${P/-libs}" PATCH_TOT="0" DESCRIPTION="Protein X-ray crystallography toolkit - Libraries" HOMEPAGE="http://www.ccp4.ac.uk/"; SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz" # patch tarball from upstream [[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" # patches created by us [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"; for i in $(seq $PATCH_TOT); do NAME="PATCH${i}[1]" SRC_URI="${SRC_URI} ${SRC}/${PV}/patches/${!NAME}" done LICENSE="ccp4" SLOT="0" KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" IUSE="" REQUIRED_USE="${PYTHON_REQUIRED_USE}" RDEPEND=" ${PYTHON_DEPS} !<sci-chemistry/ccp4-6.1.3 !<sci-chemistry/ccp4-apps-${PV}-r10 app-shells/tcsh dev-lang/tcl >=sci-libs/cbflib-0.9.2.2 sci-libs/fftw:2.1 sci-libs/mmdb:0 sci-libs/monomer-db sci-libs/ssm virtual/jpeg:0= virtual/lapack virtual/blas" DEPEND="${RDEPEND} virtual/pkgconfig" S="${WORKDIR}/${MY_P}" MAKEOPTS+=" -j1" pkg_setup() { fortran-2_pkg_setup python-single-r1_pkg_setup } src_prepare() { tc-export PKG_CONFIG RANLIB AR sed \ -e "/^AR/s:ar:$(tc-getAR):g" \ -i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die einfo "Applying upstream patches ..." for patch in $(seq $PATCH_TOT); do base="PATCH${patch}" dir=$(eval echo \${${base}[0]}) p=$(eval echo \${${base}[1]}) pushd "${dir}" >& /dev/null ccp_patch "${DISTDIR}/${p}" popd >& /dev/null done einfo "Done." echo [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch einfo "Applying Gentoo patches ..." # fix buffer overflows wrt bug 339706 ccp_patch "${FILESDIR}"/${PV}-overflows.patch # it tries to create libdir, bindir etc on live system in configure ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch # gerror_ gets defined twice on ppc if you're using gfortran/g95 ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch # make creation of libccif.so smooth ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch # lets try to build libmmdb seperatly ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch # unbundle libjpeg and cbflib ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch # Fix missing DESTIDR # not installing during build ccp_patch "${FILESDIR}"/${PV}-noinstall.patch sed \ -e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \ -i configure || die # Fix upstreams code ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch # use pkg-config to detect BLAS/LAPACK ccp_patch "${FILESDIR}"/${PV}-lapack.patch # proto type changing in version 0.9.2.2 ccp_patch "${FILESDIR}"/${PV}-cbf.patch # proto type changing in version 0.9.2.2 ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch ccp_patch "${FILESDIR}"/${P}-force.patch ccp_patch "${FILESDIR}"/${P}-format-security.patch einfo "Done." # done applying Gentoo patches echo # not needed, we have it extra rm -rf src/rapper/{libxml2,gc7.0} || die sed \ -e "s:/usr:${EPREFIX}/usr:g" \ -e 's:-Wl,-rpath,$CLIB::g' \ -e 's: -rpath $CLIB::g' \ -e 's: -I${srcdir}/include/cpp_c_headers::g' \ -e 's:sleep 1:sleep .2:g' \ -i configure || die gnuconfig_update for i in lib/DiffractionImage src/rapper src/pisa; do pushd ${i} > /dev/null sed 's:-g::g' -i configure* || die [[ -f configure.in ]] && mv configure.{in,ac} eautoreconf popd > /dev/null done ## unbundle libssm sed -e '/libdir/s:ssm::g' -i Makefile.in || die find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die } src_configure() { rm -rf lib/DiffractionImage/{jpg,CBFlib} || die # Build system is broken if we set LDFLAGS userldflags="${LDFLAGS}" export SHARED_LIB_FLAGS="${LDFLAGS}" unset LDFLAGS # GENTOO_OSNAME can be one of: # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd # linux_compaq_compilers linux_intel_compilers generic Darwin # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers if [[ "$(tc-getFC)" = "ifort" ]]; then if use ia64; then GENTOO_OSNAME="ia64_linux_intel" else # Should be valid for x86, maybe amd64 GENTOO_OSNAME="linux_intel_compilers" fi else # Should be valid for x86 and amd64, at least GENTOO_OSNAME="linux" fi # Sets up env ln -s \ ccp4.setup-bash \ "${S}"/include/ccp4.setup || die # We agree to the license by emerging this, set in LICENSE sed -i \ -e "s~^\(^agreed=\).*~\1yes~g" \ "${S}"/configure || die # Fix up variables -- need to reset CCP4_MASTER at install-time sed -i \ -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ "${S}"/include/ccp4.setup* || die # Set up variables for build source "${S}"/include/ccp4.setup-sh export CC=$(tc-getCC) export CXX=$(tc-getCXX) export COPTIM=${CFLAGS} export CXXOPTIM=${CXXFLAGS} # Default to -O2 if FFLAGS is unset export FC=$(tc-getFC) export FOPTIM=${FFLAGS:- -O2} export SHARE_LIB="\ $(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \ $(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm" # Can't use econf, configure rejects unknown options like --prefix ./configure \ --onlylibs \ --with-shared-libs \ --with-fftw="${EPREFIX}/usr" \ --with-warnings \ --disable-cctbx \ --disable-clipper \ --disable-ssm \ --tmpdir="${TMPDIR}" \ --bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \ --libdir="${EPREFIX}/usr/$(get_libdir)" \ ${GENTOO_OSNAME} || die "configure failed" } src_compile() { emake DESTDIR="${D}" onlylib } src_install() { # Set up variables for build source "${S}"/include/ccp4.setup-sh emake \ DESTDIR="${D}" \ includedir="${EPREFIX}/usr/include" \ library_includedir="${EPREFIX}/usr/include" \ install sed \ -e "330,1000d" \ -i "${S}"/include/ccp4.setup-sh || die sed \ -e "378,1000d" \ -i "${S}"/include/ccp4.setup-csh || die sed \ -e "s:-${PV/-r*/}::g" \ -e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \ -e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \ -e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \ -e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \ -e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \ -e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \ -e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \ -e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \ -e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \ -e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \ -e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \ -e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \ -e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \ -e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \ -e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ -e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ -e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ -e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ -e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ -e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ -e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \ -e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \ -e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ -e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \ -e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \ -e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \ -e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \ -e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \ -e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \ -e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \ -e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ -e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ -e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \ -e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \ -e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \ -e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \ -e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \ -e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \ -e "s:\$CLIB/font84.dat:\"${EPREFIX}/usr/$(get_libdir)/font84.dat\":g" \ -e "s:\$CLIB/cif_mmdic.lib:\"${EPREFIX}/usr/$(get_libdir)/cif_mmdic.lib\":g" \ -e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \ -e '/CLIB=/d' \ -e '/CLIB /d' \ -e '/CLIBS=/d' \ -e '/CLIBS /d' \ -e "/alias/d" \ -e "/CCP4_HELPDIR/d" \ -e "/IMOSFLM_VERSION/d" \ -i "${S}"/include/ccp4.setup* || die # Don't check for updates on every sourcing of /etc/profile sed -i \ -e "s:\(eval python.*\):#\1:g" \ "${S}"/include/ccp4.setup* || die # Libs for file in "${S}"/lib/*; do if [[ -d ${file} ]]; then continue elif [[ -x ${file} ]]; then dolib.so ${file} else insinto /usr/$(get_libdir) doins ${file} fi done prune_libtool_files sed \ -e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \ -i "${S}"/include/ccp4.setup-sh || die # Setup scripts insinto /etc/profile.d newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh rm -f "${S}"/include/ccp4.setup* # Data insinto /usr/share/ccp4/data/ doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} # Environment files, setup scripts, etc. rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die insinto /usr/share/ccp4/ doins -r "${S}"/include dodoc "${S}"/lib/data/*.doc newdoc "${S}"/lib/data/README DATA-README } pkg_postinst() { einfo "The Web browser defaults to firefox. Change CCP4_BROWSER" einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this." } # Epatch wrapper for bulk patching ccp_patch() { EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} }
