diff options
Diffstat (limited to 'sci-libs/ccp4-libs')
| -rw-r--r-- | sci-libs/ccp4-libs/ChangeLog | 7 | ||||
| -rw-r--r-- | sci-libs/ccp4-libs/Manifest | 29 | ||||
| -rw-r--r-- | sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild | 351 |
3 files changed, 372 insertions, 15 deletions
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 <jlec@gentoo.org> +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/Manifest b/sci-libs/ccp4-libs/Manifest index 98b8e3a2a1b1..d6bac82a661d 100644 --- a/sci-libs/ccp4-libs/Manifest +++ b/sci-libs/ccp4-libs/Manifest @@ -21,22 +21,23 @@ EBUILD ccp4-libs-6.1.3-r11.ebuild 10952 SHA256 432924c4a519d30ec5c4b3c2c4ae5789b EBUILD ccp4-libs-6.1.3-r12.ebuild 11208 SHA256 412fe48c15475489e153712ad460955ecbb461ad02133f5322d03402cd11fa6f SHA512 d34875ff198ae76f07a894781f5c11cd6691ae2a4ab3aa7ffba44a1fff6bd5e4a8310b7d45ab80061290c11523231691049cd210680d8e720433e8f3568eef4b WHIRLPOOL c6a3f614479130299c4fc19b0f858468cfd920e94f48b6f271e052346db8602ed4d2c855e5e81aca71305b4e001c8bb2f926faf3af4212588e23c6e1c1ea196b EBUILD ccp4-libs-6.1.3-r13.ebuild 11034 SHA256 f305a9b2526256b5a1b809d643dcbf424ddb76c828d9e8a09d19d4574fe7821b SHA512 175eefdda01d04187b92cff1773ff293655b8a9dab474c18424e15af0db73b32fd721870f655b6a15966933dedec37c54af7c44f69eec2b63eef7ae314f4c607 WHIRLPOOL 1e812aca1572f7f4717a013af9c3b130d12b9d47ce17ea6a9de4eaec10b52345e093269e865535437d8dc529e1d678af429ddc15714676ff34088a1cf24850ff EBUILD ccp4-libs-6.1.3-r14.ebuild 11109 SHA256 459770e2071828e83af80d520157adcdeca85a67ffe93305ff3f0790e551d127 SHA512 42d250caba108ee4e52ec055b724f4795e992f67b4d39b18a49c16a9164815a27a2be5632ea0a815f54d6b5b783ee106ab1a4bd99e71a42a2e3cd3d55491a652 WHIRLPOOL 7f802c6749ab55b578dc25c10e426df0f6d3a47b40900d147c5409036f613e04eeef5178f7be23d8e2b041dc084dcab6757803fdd97fa5122c9f7309fa245376 -MISC ChangeLog 8723 SHA256 2469c26a3b252aa34b958d27ff90b6b03952d06766f81764d787f033d3403a55 SHA512 9adbbfa60c799f79aac9f81997833cc4a86d680613c26e32f3c5bed0110d4b4a71019063be77271fdb01e57773e80580d83c6157da0a2ad7ee11138ef1d13e04 WHIRLPOOL 16b434afbcd26d8546ed593659fc505e13a621ea200c80c13c43b722e05b4e56d0f3e72b22f570cb983a4d0862ca3c9b512996a91a48448d908ed3e829a79b89 +EBUILD ccp4-libs-6.1.3-r15.ebuild 11190 SHA256 246ab951ddf17cc200ec4e957e331e705722c5bdf0d1e28a24935a8bc78e0523 SHA512 23d4f496c3c2f0eefce3f94c428cbd8b00709b049bff0caa6647a8bb88380d6da6452b9366ed0898b6512ba3bde2a00a82676f129d7a1168300de85e7ebf8725 WHIRLPOOL 3e5bf7e79cefd23ebd6db02a4246f4bc441cca5d7e6e7dcfc1a73f2e1a72515f04acaeb11516b4966875a75677f8e44870bd21ebc8024870f408cc7397658c3e +MISC ChangeLog 8866 SHA256 d57a626537b9f9c0ed171b63ac8014f64a25685b5f8e80db1a6fec5721fdf072 SHA512 892e785d20819be176452b7fddb22b5f15980eefa8bdb75352e07e101a66d43aa1c84dceb2d42647f7f9aacede5890adeac2b5493a8db466671436f27c667d0f WHIRLPOOL ad7ec75cf34e3558f729b2b8339fe85b396ba468bd84f7209b1d68733031b83345e434b2cd0da110ec9b3233a22f4397beea2ffa8254b109b18b4c0475022f91 MISC metadata.xml 272 SHA256 464cdfad7e5470cd4897f4d81fb87220dfdb9b8645f720e2fcf5157a7a75fbec SHA512 3e8682fbb209895927a39021555e3a440c49e61dcce93ea1b13759e067b285c604328cff031843e3aac6528970384c8fdbf15c8edd76a421db111a3981825fa5 WHIRLPOOL fc8d5f3db9db73bb2026ca21c4448107558ac53d568c89c7c6ccc635fde460aec1bbd177a4ad770b20d35693b59fc0721c8d60aea997973db3efd6b3c3777eba -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.20 (GNU/Linux) -iQIcBAEBCgAGBQJR7NhUAAoJELnU8jG9FVirejcP/RKU2iKKhLHFaD7brBjpfW+r 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+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=" + ${PYTHON_DEPS} + !<sci-chemistry/ccp4-6.1.3 + !<sci-chemistry/ccp4-apps-${PV}-r10 + 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/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} +} |