From bd66fb5f1706d7343b43e10f31debde75ed116d2 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Fri, 26 Jul 2013 11:27:06 +0000 Subject: sci-libs/ccp4-libs: Fix another broken variable (Portage version: 2.2.0_alpha189/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) --- sci-libs/ccp4-libs/ChangeLog | 7 +- sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild | 351 ++++++++++++++++++++++++++ 2 files changed, 357 insertions(+), 1 deletion(-) create mode 100644 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild (limited to 'sci-libs') diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog index 291ac18aa7b7..121574df077d 100644 --- a/sci-libs/ccp4-libs/ChangeLog +++ b/sci-libs/ccp4-libs/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-libs/ccp4-libs # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.58 2013/07/22 06:59:33 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.59 2013/07/26 11:27:05 jlec Exp $ + +*ccp4-libs-6.1.3-r15 (26 Jul 2013) + + 26 Jul 2013; Justin Lecher +ccp4-libs-6.1.3-r15.ebuild: + Fix another broken variable *ccp4-libs-6.1.3-r14 (22 Jul 2013) diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild new file mode 100644 index 000000000000..f98963f8d186 --- /dev/null +++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild @@ -0,0 +1,351 @@ +# Copyright 1999-2013 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-r15.ebuild,v 1.1 2013/07/26 11:27:06 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_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} 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/${!NAME}" +done + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + !=sci-libs/cbflib-0.9.2.2 + sci-libs/fftw:2.1 + sci-libs/mmdb + sci-libs/monomer-db + sci-libs/ssm + virtual/jpeg + virtual/lapack + virtual/blas" +DEPEND="${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 + + 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 ${i} > /dev/null + sed 's:-g::g' -i configure* || die + eautoreconf + popd > /dev/null + done + + ## unbundle libssm + sed -e '/libdir/s:ssm::g' -i Makefile.in || die + find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die +} + +src_configure() { + rm -rf lib/DiffractionImage/{jpg,CBFlib} || die + + # Build system is broken if we set LDFLAGS + userldflags="${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 "${S}"/include/ccp4.setup-sh || die + + # Setup scripts + insinto /etc/profile.d + newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh + newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh + rm -f "${S}"/include/ccp4.setup* + + # 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 "${S}"/include + + dodoc "${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} +} -- cgit v1.2.3-65-gdbad