From f95222735de42c17a5f62201631307d9fb1ca3a9 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Sat, 22 May 2010 10:04:27 +0000 Subject: Fixes for bug 314053 (Portage version: 2.2_rc67/cvs/Linux x86_64) --- sci-libs/ccp4-libs/ChangeLog | 7 +- sci-libs/ccp4-libs/ccp4-libs-6.1.3-r2.ebuild | 220 +++++++++++++++++++++++++++ 2 files changed, 226 insertions(+), 1 deletion(-) create mode 100644 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r2.ebuild (limited to 'sci-libs') diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog index b7842087914d..05ee496e8104 100644 --- a/sci-libs/ccp4-libs/ChangeLog +++ b/sci-libs/ccp4-libs/ChangeLog @@ -1,6 +1,11 @@ # 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 1.5 2010/04/25 11:31:53 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.6 2010/05/22 10:04:27 jlec Exp $ + +*ccp4-libs-6.1.3-r2 (22 May 2010) + + 22 May 2010; Justin Lecher +ccp4-libs-6.1.3-r2.ebuild: + Fixes for bug 314053 28 Mar 2010; Justin Lecher ccp4-libs-6.1.3-r1.ebuild: Prefix fixes and keywording for ~*-linux diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r2.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r2.ebuild new file mode 100644 index 000000000000..642627419517 --- /dev/null +++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r2.ebuild @@ -0,0 +1,220 @@ +# 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-r2.ebuild,v 1.1 2010/05/22 10:04:27 jlec Exp $ + +EAPI="3" + +inherit fortran eutils gnuconfig toolchain-funcs + +FORTRAN="g77 gfortran ifc" + +SRC="ftp://ftp.ccp4.ac.uk/ccp4" + +#UPDATE="04_03_09" +#PATCHDATE="090511" + +MY_P="${P/-libs}" + +PATCH_TOT="0" +# Here's a little scriptlet to generate this list from the provided +# index.patches file +# +# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue; +# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done < +# index.patches +#PATCH1=( src/topp_ +#topp.f-r1.16.2.5-r1.16.2.6.diff ) +#PATCH2=( . +#configure-r1.372.2.18-r1.372.2.19.diff ) + +DESCRIPTION="Protein X-ray crystallography toolkit" +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.gentooexperimental.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/${!NAME}" +done + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + media-libs/jpeg:0 + app-shells/tcsh + !& /dev/null + ccp_patch "${DISTDIR}/${p}" + popd >& /dev/null + done + einfo "Done." + echo + + [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch + + einfo "Applying Gentoo patches ..." + # 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}"/${PV}-unbundle-libs.patch + + einfo "Done." # done applying Gentoo patches + echo + + sed "s:/usr:${EPREFIX}/usr:g" -i configure || die + + gnuconfig_update +} + +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 [[ "${FORTRANC}" = "ifc" ]]; then + if use ia64; then + GENTOO_OSNAME="ia64_linux_intel" + else + # Should be valid for x86, maybe amd64 + GENTOO_OSNAME="linux_intel_compilers" + fi + else + # Should be valid for x86 and amd64, at least + GENTOO_OSNAME="linux" + fi + + # Sets up env + ln -s \ + ccp4.setup-bash \ + "${S}"/include/ccp4.setup + + # We agree to the license by emerging this, set in LICENSE + sed -i \ + -e "s~^\(^agreed=\).*~\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 "${S}"/include/ccp4.setup + + export CC=$(tc-getCC) + export CXX=$(tc-getCXX) + export COPTIM=${CFLAGS} + export CXXOPTIM=${CXXFLAGS} + # Default to -O2 if FFLAGS is unset + export FC=${FORTRANC} + export FOPTIM=${FFLAGS:- -O2} +# export CCP4_SCR="${T}" + + # Fix linking +# $(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \ + export SHARE_LIB="\ + $(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \ + ${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(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 \ + --tmpdir="${TMPDIR}" \ + ${GENTOO_OSNAME} || die "econf failed" +} + +src_compile() { + emake -j1 onlylib || die "emake failed" +} + +src_install() { + # Set up variables for build + source "${S}"/include/ccp4.setup + + einstall || die "install failed" + + # 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 + + # Bins + exeinto /usr/libexec/ccp4/bin/ + doexe bin/{automask,diff2jpeg,diffdump,printpeaks,superpose} || die + + # Fix libdir in all *.la files + sed -i \ + -e "s:^\(libdir=\).*:\1\'${EPREFIX}/usr/$(get_libdir)\':g" \ + "${ED}"/usr/$(get_libdir)/*.la || die + + # Data + insinto /usr/share/ccp4/data/ + doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die + dodoc "${S}"/lib/data/*.doc + newdoc "${S}"/lib/data/README DATA-README + + # Include files + insinto /usr/include + for i in ccp4; do + doins -r "${S}"/include/${i} || die + done +} + +# Epatch wrapper for bulk patching +ccp_patch() { + EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} +} -- cgit v1.2.3-65-gdbad