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# Copyright 1999-2012 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild,v 1.4 2012/05/21 19:26:43 ranger Exp $ |
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EAPI=3 |
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PYTHON_DEPEND="2" |
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inherit autotools eutils fortran-2 gnuconfig multilib python toolchain-funcs |
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SRC="ftp://ftp.ccp4.ac.uk/ccp4" |
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|
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#UPDATE="04_03_09" |
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#PATCHDATE="090511" |
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MY_P="${P/-libs}" |
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PATCH_TOT="0" |
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DESCRIPTION="Protein X-ray crystallography toolkit - Libraries" |
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HOMEPAGE="http://www.ccp4.ac.uk/" |
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SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz" |
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# patch tarball from upstream |
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[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" |
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# patches created by us |
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[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" |
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for i in $(seq $PATCH_TOT); do |
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NAME="PATCH${i}[1]" |
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SRC_URI="${SRC_URI} |
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${SRC}/${PV}/patches/${!NAME}" |
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done |
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LICENSE="ccp4" |
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SLOT="0" |
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KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux" |
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IUSE="" |
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|
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RDEPEND=" |
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!<sci-chemistry/ccp4-6.1.3 |
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!<sci-chemistry/ccp4-apps-${PV}-r10 |
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app-shells/tcsh |
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dev-lang/tcl |
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>=sci-libs/cbflib-0.9.2.2 |
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sci-libs/fftw:2.1 |
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sci-libs/mmdb |
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sci-libs/monomer-db |
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sci-libs/ssm |
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virtual/fortran |
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virtual/jpeg |
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virtual/lapack |
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virtual/blas" |
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DEPEND="${RDEPEND}" |
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S="${WORKDIR}/${MY_P}" |
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|
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pkg_setup() { |
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fortran-2_pkg_setup |
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python_set_active_version 2 |
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} |
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src_prepare() { |
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einfo "Applying upstream patches ..." |
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for patch in $(seq $PATCH_TOT); do |
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base="PATCH${patch}" |
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dir=$(eval echo \${${base}[0]}) |
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p=$(eval echo \${${base}[1]}) |
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pushd "${dir}" >& /dev/null |
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ccp_patch "${DISTDIR}/${p}" |
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popd >& /dev/null |
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done |
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einfo "Done." |
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echo |
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|
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[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch |
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|
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einfo "Applying Gentoo patches ..." |
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# fix buffer overflows wrt bug 339706 |
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ccp_patch "${FILESDIR}"/${PV}-overflows.patch |
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|
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# it tries to create libdir, bindir etc on live system in configure |
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ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch |
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# gerror_ gets defined twice on ppc if you're using gfortran/g95 |
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ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch |
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|
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# make creation of libccif.so smooth |
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ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch |
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|
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# lets try to build libmmdb seperatly |
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ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch |
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|
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# unbundle libjpeg and cbflib |
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ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch |
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# Fix missing DESTIDR |
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# not installing during build |
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ccp_patch "${FILESDIR}"/${PV}-noinstall.patch |
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sed \ |
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-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \ |
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-i configure || die |
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# Fix upstreams code |
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ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch |
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# use pkg-config to detect BLAS/LAPACK |
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ccp_patch "${FILESDIR}"/${PV}-lapack.patch |
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# proto type changing in version 0.9.2.2 |
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ccp_patch "${FILESDIR}"/${PV}-cbf.patch |
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einfo "Done." # done applying Gentoo patches |
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echo |
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# not needed, we have it extra |
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rm -rf src/rapper/{libxml2,gc7.0} || die |
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|
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sed \ |
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-e "s:/usr:${EPREFIX}/usr:g" \ |
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-e 's:-Wl,-rpath,$CLIB::g' \ |
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-e 's: -rpath $CLIB::g' \ |
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-e 's: -I${srcdir}/include/cpp_c_headers::g' \ |
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-e 's:sleep 1:sleep .2:g' \ |
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-i configure || die |
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gnuconfig_update |
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for i in lib/DiffractionImage src/rapper src/pisa; do |
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pushd ${i} > /dev/null |
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sed 's:-g::g' -i configure* || die |
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eautoreconf |
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popd > /dev/null |
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done |
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## unbundle libssm |
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sed '/libdir/s:ssm::g' -i Makefile.in |
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find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete |
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} |
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src_configure() { |
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rm -rf lib/DiffractionImage/{jpg,CBFlib} || die |
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# Build system is broken if we set LDFLAGS |
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userldflags="${LDFLAGS}" |
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export SHARED_LIB_FLAGS="${LDFLAGS}" |
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unset LDFLAGS |
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# GENTOO_OSNAME can be one of: |
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# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd |
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# linux_compaq_compilers linux_intel_compilers generic Darwin |
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# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers |
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if [[ "$(tc-getFC)" = "ifort" ]]; then |
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if use ia64; then |
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GENTOO_OSNAME="ia64_linux_intel" |
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else |
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# Should be valid for x86, maybe amd64 |
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GENTOO_OSNAME="linux_intel_compilers" |
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fi |
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else |
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# Should be valid for x86 and amd64, at least |
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GENTOO_OSNAME="linux" |
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fi |
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# Sets up env |
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ln -s \ |
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ccp4.setup-bash \ |
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"${S}"/include/ccp4.setup |
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# We agree to the license by emerging this, set in LICENSE |
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sed -i \ |
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-e "s~^\(^agreed=\).*~\1yes~g" \ |
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"${S}"/configure |
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# Fix up variables -- need to reset CCP4_MASTER at install-time |
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sed -i \ |
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-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ |
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-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ |
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-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
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-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
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-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ |
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"${S}"/include/ccp4.setup* |
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|
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# Set up variables for build |
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source "${S}"/include/ccp4.setup-sh |
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export CC=$(tc-getCC) |
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export CXX=$(tc-getCXX) |
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export COPTIM=${CFLAGS} |
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export CXXOPTIM=${CXXFLAGS} |
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# Default to -O2 if FFLAGS is unset |
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export FC=$(tc-getFC) |
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export FOPTIM=${FFLAGS:- -O2} |
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|
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export SHARE_LIB="\ |
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$(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", $i}') -lm && \ |
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$(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $(pkg-config --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm" |
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# Can't use econf, configure rejects unknown options like --prefix |
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./configure \ |
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--onlylibs \ |
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--with-shared-libs \ |
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--with-fftw="${EPREFIX}/usr" \ |
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--with-warnings \ |
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--disable-cctbx \ |
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--disable-clipper \ |
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--disable-ssm \ |
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--tmpdir="${TMPDIR}" \ |
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--bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \ |
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--libdir="${EPREFIX}/usr/$(get_libdir)" \ |
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${GENTOO_OSNAME} || die "configure failed" |
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} |
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src_compile() { |
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emake -j1 \ |
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DESTDIR="${D}" onlylib || die "emake failed" |
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} |
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src_install() { |
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# Set up variables for build |
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source "${S}"/include/ccp4.setup-sh |
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emake -j1 \ |
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DESTDIR="${D}" \ |
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includedir="${EPREFIX}/usr/include" \ |
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library_includedir="${EPREFIX}/usr/include" \ |
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install || die |
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|
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sed \ |
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-e "330,1000d" \ |
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-i "${S}"/include/ccp4.setup-sh || die |
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|
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sed \ |
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-e "378,1000d" \ |
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-i "${S}"/include/ccp4.setup-csh || die |
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|
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sed \ |
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-e "s:-${PV/-r*/}::g" \ |
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-e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \ |
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-e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \ |
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-e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \ |
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-e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \ |
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-e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \ |
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-e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \ |
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-e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \ |
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-e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \ |
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-e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \ |
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-e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \ |
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-e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \ |
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-e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \ |
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-e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \ |
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-e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \ |
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-e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ |
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-e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ |
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-e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ |
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-e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ |
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-e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ |
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-e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ |
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-e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \ |
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-e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \ |
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-e "s:^\(.*export CLIBS=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ |
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-e "s:^\(.*setenv CLIBS \).*:\1${EPREFIX}/usr/$(get_libdir):g" \ |
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-e "s:^\(.*export CLIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ |
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-e "s:^\(.*setenv CLIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \ |
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-e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ |
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-e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \ |
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-e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \ |
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-e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \ |
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-e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \ |
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-e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \ |
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-e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \ |
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-e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \ |
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-e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ |
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-e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ |
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-e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \ |
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-e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \ |
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-e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \ |
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-e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \ |
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-e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \ |
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-e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \ |
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-e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \ |
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-e "/CCP4_HELPDIR/d" \ |
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-e "/IMOSFLM_VERSION/d" \ |
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-i "${S}"/include/ccp4.setup* || die |
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|
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# Don't check for updates on every sourcing of /etc/profile |
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sed -i \ |
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-e "s:\(eval python.*\):#\1:g" \ |
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"${S}"/include/ccp4.setup* || die |
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|
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# Libs |
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for file in "${S}"/lib/*; do |
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if [[ -d ${file} ]]; then |
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continue |
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elif [[ -x ${file} ]]; then |
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dolib.so ${file} || die |
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else |
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insinto /usr/$(get_libdir) |
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doins ${file} || die |
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fi |
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done |
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|
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rm -f "${ED}"/usr/$(get_libdir)/*.la || die |
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|
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sed \ |
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-e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \ |
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-i "${S}"/include/ccp4.setup-sh || die |
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|
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# Setup scripts |
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insinto /etc/profile.d |
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newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh || die |
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newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh || die |
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rm -f "${S}"/include/ccp4.setup* |
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|
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# Data |
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insinto /usr/share/ccp4/data/ |
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doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die |
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|
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# Environment files, setup scripts, etc. |
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rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die |
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insinto /usr/share/ccp4/ |
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doins -r "${S}"/include || die |
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|
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dodoc "${S}"/lib/data/*.doc || die |
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newdoc "${S}"/lib/data/README DATA-README || die |
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} |
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|
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pkg_postinst() { |
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einfo "The Web browser defaults to firefox. Change CCP4_BROWSER" |
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einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this." |
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} |
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|
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# Epatch wrapper for bulk patching |
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ccp_patch() { |
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EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} |
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} |
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