From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1P2oQW-0003Z1-2K for garchives@archives.gentoo.org; Mon, 04 Oct 2010 17:02:12 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 7BB63E079E; Mon, 4 Oct 2010 17:02:10 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 3FAABE07A4 for ; Mon, 4 Oct 2010 17:02:10 +0000 (UTC) Received: from flycatcher.gentoo.org (flycatcher.gentoo.org [81.93.255.6]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id A93171B40C4 for ; Mon, 4 Oct 2010 17:02:09 +0000 (UTC) Received: by flycatcher.gentoo.org (Postfix, from userid 2271) id 40C4120054; Mon, 4 Oct 2010 17:02:08 +0000 (UTC) From: "Kacper Kowalik (xarthisius)" To: gentoo-commits@lists.gentoo.org Reply-To: gentoo-dev@lists.gentoo.org, xarthisius@gentoo.org Subject: [gentoo-commits] gentoo-x86 commit in sci-libs/ccp4-libs: ChangeLog ccp4-libs-6.1.3-r4.ebuild X-VCS-Repository: gentoo-x86 X-VCS-Files: ChangeLog ccp4-libs-6.1.3-r4.ebuild X-VCS-Directories: sci-libs/ccp4-libs X-VCS-Committer: xarthisius X-VCS-Committer-Name: Kacper Kowalik Content-Type: text/plain; charset=utf8 Message-Id: <20101004170208.40C4120054@flycatcher.gentoo.org> Date: Mon, 4 Oct 2010 17:02:08 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: 4247fd14-944a-4507-ad9f-8a123cd49e5f X-Archives-Hash: 5f1af89f47aeb524f3d39786ec765a41 xarthisius 10/10/04 17:02:08 Modified: ChangeLog Added: ccp4-libs-6.1.3-r4.ebuild Log: Fix buffer overflows wrt bug 339706. Thanks to Diego for the report. =20 (Portage version: 2.1.9.13/cvs/Linux x86_64) Revision Changes Path 1.13 sci-libs/ccp4-libs/ChangeLog file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs= /ChangeLog?rev=3D1.13&view=3Dmarkup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs= /ChangeLog?rev=3D1.13&content-type=3Dtext/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs= /ChangeLog?r1=3D1.12&r2=3D1.13 Index: ChangeLog =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D RCS file: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- ChangeLog 16 Jul 2010 10:14:47 -0000 1.12 +++ ChangeLog 4 Oct 2010 17:02:08 -0000 1.13 @@ -1,6 +1,12 @@ # ChangeLog for sci-libs/ccp4-libs # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.12 2= 010/07/16 10:14:47 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.13 2= 010/10/04 17:02:08 xarthisius Exp $ + +*ccp4-libs-6.1.3-r4 (04 Oct 2010) + + 04 Oct 2010; Kacper Kowalik + +files/6.1.3-overflows.patch, +ccp4-libs-6.1.3-r4.ebuild: + Fix buffer overflows wrt bug 339706. Thanks to Diego for the report. =20 16 Jul 2010; Justin Lecher -ccp4-libs-6.1.3.ebuild, -ccp4-libs-6.1.3-r1.ebuild, -ccp4-libs-6.1.3-r2.ebuild: 1.1 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs= /ccp4-libs-6.1.3-r4.ebuild?rev=3D1.1&view=3Dmarkup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs= /ccp4-libs-6.1.3-r4.ebuild?rev=3D1.1&content-type=3Dtext/plain Index: ccp4-libs-6.1.3-r4.ebuild =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D # Copyright 1999-2010 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-r4.= ebuild,v 1.1 2010/10/04 17:02:08 xarthisius Exp $ EAPI=3D"3" inherit fortran eutils gnuconfig multilib toolchain-funcs FORTRAN=3D"g77 gfortran ifc" SRC=3D"ftp://ftp.ccp4.ac.uk/ccp4" #UPDATE=3D"04_03_09" #PATCHDATE=3D"090511" MY_P=3D"${P/-libs}" PATCH_TOT=3D"0" # Here's a little scriptlet to generate this list from the provided # index.patches file # # i=3D1; while read -a line; do [[ ${line//#} !=3D ${line} ]] && continue= ; # echo "PATCH${i}=3D( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done < # index.patches #PATCH1=3D( src/topp_ #topp.f-r1.16.2.5-r1.16.2.6.diff ) #PATCH2=3D( . #configure-r1.372.2.18-r1.372.2.19.diff ) DESCRIPTION=3D"Protein X-ray crystallography toolkit" HOMEPAGE=3D"http://www.ccp4.ac.uk/" SRC_URI=3D"${SRC}/${PV}/${MY_P}-core-src.tar.gz" # patch tarball from upstream [[ -n ${UPDATE} ]] && SRC_URI=3D"${SRC_URI} ${SRC}/${PV}/updates/${P}-sr= c-patch-${UPDATE}.tar.gz" # patches created by us [[ -n ${PATCHDATE} ]] && SRC_URI=3D"${SRC_URI} http://dev.gentooexperime= ntal.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" for i in $(seq $PATCH_TOT); do NAME=3D"PATCH${i}[1]" SRC_URI=3D"${SRC_URI} ${SRC}/${PV}/patches/${!NAME}" done LICENSE=3D"ccp4" SLOT=3D"0" KEYWORDS=3D"~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE=3D"" RDEPEND=3D" media-libs/jpeg:0 app-shells/tcsh !& /dev/null ccp_patch "${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}"/${PV}-unbundle-libs.patch # Fix missing DESTIDR # not installing during build ccp_patch "${FILESDIR}"/${PV}-noinstall.patch sed \ -e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \ -i configure || die einfo "Done." # done applying Gentoo patches echo 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' \ -i configure || die gnuconfig_update } src_configure() { rm -rf lib/DiffractionImage/{jpg,CBFlib} || die # Build system is broken if we set LDFLAGS userldflags=3D"${LDFLAGS}" export SHARED_LIB_FLAGS=3D"${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 [[ "${FORTRANC}" =3D "ifc" ]]; then if use ia64; then GENTOO_OSNAME=3D"ia64_linux_intel" else # Should be valid for x86, maybe amd64 GENTOO_OSNAME=3D"linux_intel_compilers" fi else # Should be valid for x86 and amd64, at least GENTOO_OSNAME=3D"linux" fi # Sets up env ln -s \ ccp4.setup-bash \ "${S}"/include/ccp4.setup # We agree to the license by emerging this, set in LICENSE sed -i \ -e "s~^\(^agreed=3D\).*~\1yes~g" \ "${S}"/configure # Fix up variables -- need to reset CCP4_MASTER at install-time sed -i \ -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \ -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ "${S}"/include/ccp4.setup* # Set up variables for build source "${S}"/include/ccp4.setup export CC=3D$(tc-getCC) export CXX=3D$(tc-getCXX) export COPTIM=3D${CFLAGS} export CXXOPTIM=3D${CXXFLAGS} # Default to -O2 if FFLAGS is unset export FC=3D${FORTRANC} export FOPTIM=3D${FFLAGS:- -O2} # export CCP4_SCR=3D"${T}" # Fix linking # $(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so= \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=3D1; i<=3DNF; i++) printf= " -L%s", $i}') -lm -lstdc++ && \ export SHARE_LIB=3D"\ $(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=3D1; i<= =3DNF; i++) printf " -L%s", $i}') -lm && \ ${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.= so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c -lmm= db $(gcc-config -L | awk -F: '{for(i=3D1; i<=3DNF; i++) printf " -L%s", $= i}') -lstdc++ -lgfortran -lm" # Can't use econf, configure rejects unknown options like --prefix ./configure \ --onlylibs \ --with-shared-libs \ --with-fftw=3D"${EPREFIX}"/usr \ --with-warnings \ --disable-cctbx \ --disable-clipper \ --tmpdir=3D"${TMPDIR}" \ --bindir=3D"${EPREFIX}"/usr/libexec/ccp4/bin/ \ --libdir=3D"${EPREFIX}"/usr/$(get_libdir) \ ${GENTOO_OSNAME} || die "econf failed" } src_compile() { emake -j1 \ DESTDIR=3D"${ED}" onlylib || die "emake failed" } src_install() { # Set up variables for build source "${S}"/include/ccp4.setup emake -j1 \ DESTDIR=3D"${ED}" \ includedir=3D"${EPREFIX}"/usr/include \ library_includedir=3D"${EPREFIX}"/usr/include \ install || die # Libs for file in "${S}"/lib/*; do if [[ -d ${file} ]]; then continue elif [[ -x ${file} ]]; then dolib.so ${file} || die else insinto /usr/$(get_libdir) doins ${file} || die fi done # Fix libdir in all *.la files sed -i \ -e "s:^\(libdir=3D\).*:\1\'${EPREFIX}/usr/$(get_libdir)\':g" \ "${ED}"/usr/$(get_libdir)/*.la || die # Data insinto /usr/share/ccp4/data/ doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resourc= e,*.york,*.hist,fraglib,reference_structures} || die dodoc "${S}"/lib/data/*.doc || die newdoc "${S}"/lib/data/README DATA-README || die } # Epatch wrapper for bulk patching ccp_patch() { EPATCH_SINGLE_MSG=3D" ${1##*/} ..." epatch ${1} }