diff options
Diffstat (limited to 'sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild')
| -rw-r--r-- | sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild | 359 |
1 files changed, 0 insertions, 359 deletions
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild deleted file mode 100644 index dcd741637048..000000000000 --- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild +++ /dev/null @@ -1,359 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -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} https://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/${!NAME}" -done - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="minimal" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - !<sci-chemistry/ccp4-6.1.3 - !<sci-chemistry/ccp4-apps-${PV}-r10 - app-shells/tcsh - dev-lang/tcl:0 - >=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 "${S}"/include/ccp4.setup-sh || die - - if ! use minimal; then - # Setup scripts - insinto /etc/profile.d - newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh - newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh - - # Data - insinto /usr/share/ccp4/data/ - doins -r "${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 - fi - - rm -f "${S}"/include/ccp4.setup* || die - - dodoc "${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} -} |