Hash: SHA512
AUX 6.0.2-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 SHA1 209fa1bdf1e59b4055177e343b69e487d9183fb3 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61
+AUX 6.1.3-cbf.patch 773 RMD160 02cefee32763fd4e9e58b7cd7ba96655bbc40374 SHA1 0ba77801413f89bc12b62e09799da97aaf1eba0b SHA256 767a2286956471c6dbf0feee9a5726f5170af21cb2dd85c7f45190cab5cce7a0
AUX 6.1.3-ccif-shared.patch 1668 RMD160 803687b13dbe93aaeed8264a73dfe7303b5fcdfb SHA1 3d833aefea874c08e61140613b0a5c75a90e0382 SHA256 57c201ee81e3fd95f174fecfd810ddf12509f0c2bfb1b2f317f893561eb60e3f
AUX 6.1.3-dont-build-mmdb.patch 749 RMD160 2f4b04d07095d464f00522a935cb93c2dae40f4c SHA1 5b82f59ce190cb82601b7af55083b1a5689c9ae0 SHA256 cf73ff7c361ba7ed3e3084a4c298a1e45307a8b0ac7e2704628f3e0f345a9bde
AUX 6.1.3-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
AUX 6.1.3-unbundle-libs-ng2.patch 15485 RMD160 c4b07251ee584fbc66342cd97f15185ebe6eb81c SHA1 39e9824fdcc120bd380aaae7472ba3c4db7fe0fc SHA256 ded20e7e5a3fd347bc852ca119b3cbe6cde22c8acae21d710d69da4ab12fa7a6
AUX 6.1.3-unbundle-libs.patch 9063 RMD160 326af0e6990134546fb2607dae707b94d4588149 SHA1 ef929532e45c12fb168e5fca4eb7fa8c857c376a SHA256 7e5fc919b5204e2d9141f7715afdd8a8b4e3e2a96e2bf95aa00fbd56046f1aa4
DIST ccp4-6.1.3-core-src.tar.gz 242134076 RMD160 e9b7deb0766fb95d5e8946881f20e086f0896fe9 SHA1 ee5ada892694db5dc9b2d7d2330b4ac694f56580 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324
-EBUILD ccp4-libs-6.1.3-r10.ebuild 10921 RMD160 ce2f841dda3d824cf678ad14494301bd95f346fc SHA1 e8f04160c4e7961aa024dfd9c883c41c270c9341 SHA256 42d41935cb8750de35e56373dc073ab5b46bd87141b6d8e36e16de6af4adc460
-EBUILD ccp4-libs-6.1.3-r8.ebuild 10318 RMD160 d232a25df6d160375891c51351af6756a34a9a6c SHA1 c8130be882a3418fd33360f37403423e8657d828 SHA256 06c6108cd9167e5a56687dc1337578446ecf98026bf9de9b464fef36dbd8621d
+EBUILD ccp4-libs-6.1.3-r10.ebuild 10926 RMD160 db87b7c7369813df9bbe182ec3f520537c0d0e21 SHA1 b0988912ce1bcd47bed716ebbde50cebb140f12e SHA256 62b6daf7759bc9bc5873886912359b04dc0ec3d85a02ba08356e77807043219b
+EBUILD ccp4-libs-6.1.3-r11.ebuild 11013 RMD160 a74baf5881ac73c057275848edc15d446e659f52 SHA1 929a5663980c2567f5a194f9879bcccf4bd687e6 SHA256 f1bbc62c095de45f28902a99c2016d8f71f2351df858152a5b69bc5fa74fabc9
+EBUILD ccp4-libs-6.1.3-r8.ebuild 10327 RMD160 40c4481539fa7bac9c4483e36ea845dbcaef1882 SHA1 f639c289ca397043a84474ce5f5aa0088180d815 SHA256 afb16e948de0bcdb1d2dca8d0f1d4e40d2e1e9737c6240b1fefb7a050780383b
EBUILD ccp4-libs-6.1.3-r9.ebuild 10735 RMD160 0316a1d55d3231f8a2e91f461ad527885e92c1f2 SHA1 0fc4d8b31a232da4cc3097664f206fbddfcde6cb SHA256 b9314ba1ca94d7953c37c3cde39abbc02380d1e6383976c5217d95375971f224
-MISC ChangeLog 6407 RMD160 bece4d3fca252f4576dc51fd0d5862ec61960c52 SHA1 6470d8a7fd652838bc8acd49c02d9d27ec8c905b SHA256 8af3490115944d1467d9b550f9ffe7c5a0fae16e2a16ef1b8c241fd4be02c507
+MISC ChangeLog 6635 RMD160 95874c60566d20a1558511f0d4474e8bda00c401 SHA1 be88eee97db3ba3f2426c2e9266789a7436ed7dd SHA256 938af90241e90d7fa8ae2fcd79367b783b7f2b609ae99728c122d9e8998aea5b
MISC metadata.xml 265 RMD160 3147f5f0ce8982e3376bf6f833ee76e01409d813 SHA1 207dd5e946f2f945fbeb9059a945cb9fca736856 SHA256 6206181a1050a92258360204c836a620d6f016d552a4d829b3007242ee0d294f
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--- /dev/null
+# Copyright 1999-2011 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-r11.ebuild,v 1.1 2011/12/14 12:20:17 jlec Exp $
+
+EAPI=3
+
+PYTHON_DEPEND="2"
+
+inherit autotools eutils fortran-2 gnuconfig multilib python 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.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/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+ !<sci-chemistry/ccp4-6.1.3
+ !<sci-chemistry/ccp4-apps-${PVR}
+ app-shells/tcsh
+ dev-lang/tcl
+ >=sci-libs/cbflib-0.9.2.2
+ sci-libs/fftw:2.1
+ sci-libs/mmdb
+ sci-libs/monomer-db
+ sci-libs/ssm
+ virtual/fortran
+ virtual/jpeg
+ virtual/lapack
+ virtual/blas"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+ fortran-2_pkg_setup
+ python_set_active_version 2
+}
+
+src_prepare() {
+ 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
+
+ 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 ${i} > /dev/null
+ sed 's:-g::g' -i configure* || die
+ eautoreconf
+ popd > /dev/null
+ done
+
+ ## unbundle libssm
+ sed '/libdir/s:ssm::g' -i Makefile.in
+ find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete
+}
+
+src_configure() {
+ rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
+
+ # Build system is broken if we set LDFLAGS
+ userldflags="${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
+
+ # 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~^\(export CCP4_MASTER.*\)/.*~\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*
+
+ # 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 $(pkg-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)" \
+ ${GENTOO_OSNAME} || die "econf failed"
+}
+
+src_compile() {
+ emake -j1 \
+ DESTDIR="${D}" onlylib || die "emake failed"
+}
+
+src_install() {
+ # Set up variables for build
+ source "${S}"/include/ccp4.setup-sh
+
+ emake -j1 \
+ DESTDIR="${D}" \
+ includedir="${EPREFIX}/usr/include" \
+ library_includedir="${EPREFIX}/usr/include" \
+ install || die
+
+ 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:^\(.*export CLIBS=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+ -e "s:^\(.*setenv CLIBS \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+ -e "s:^\(.*export CLIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+ -e "s:^\(.*setenv CLIB \).*:\1${EPREFIX}/usr/$(get_libdir):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${EPREFIX}/usr/share/ccp4/include:g" \
+ -e '/# .*LD_LIBRARY_PATH specifies/,/^$/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 ${file} || die
+ else
+ insinto /usr/$(get_libdir)
+ doins ${file} || die
+ fi
+ done
+
+ sed \
+ -e 's:test "LD_LIBRARY_PATH":test "$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 || die
+ newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh || die
+ rm -f "${S}"/include/ccp4.setup*
+
+ # 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 "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
+
+ # Environment files, setup scripts, etc.
+ rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die
+ insinto /usr/share/ccp4/
+ doins -r "${S}"/include || die
+
+ dodoc "${S}"/lib/data/*.doc || die
+ newdoc "${S}"/lib/data/README DATA-README || die
+}
+
+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}
+}
projects / gentoo.git / commitdiff