From 162613ec311e1a8019b99fa6dedba870dd7cc7f1 Mon Sep 17 00:00:00 2001 From: "Justin Lecher (jlec)" Date: Wed, 13 May 2009 20:54:08 +0200 Subject: ccp4 upstream patch included -- bug 269504 --- sci-libs/ccp4-libs/ChangeLog | 7 + sci-libs/ccp4-libs/ccp4-libs-6.1.1-r3.ebuild | 205 +++++++++++++++++++++++++++ 2 files changed, 212 insertions(+) create mode 100644 sci-libs/ccp4-libs/ccp4-libs-6.1.1-r3.ebuild (limited to 'sci-libs') diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog index efd97c981..c1bf51d34 100644 --- a/sci-libs/ccp4-libs/ChangeLog +++ b/sci-libs/ccp4-libs/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*ccp4-libs-6.1.1-r3 (13 May 2009) + + 13 May 2009; Justin Lecher (jlec) + +ccp4-libs-6.1.1-r3.ebuild: + Includes upstream updates src files from 03/04/09 + fixes bug 269504 + *ccp4-libs-6.1.1-r2 (29 Apr 2009) 29 Apr 2009; Justin Lecher (jlec) diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r3.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r3.ebuild new file mode 100644 index 000000000..8cf1fa79d --- /dev/null +++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r3.ebuild @@ -0,0 +1,205 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +inherit fortran eutils gnuconfig toolchain-funcs + +FORTRAN="g77 gfortran ifc" + +SRC="ftp://ftp.ccp4.ac.uk/ccp4" + +UPDATE="04_03_09" +PATCHDATE="090511" + +MY_P="${P/-libs}" + +PATCH_TOT="0" +# Here's a little scriptlet to generate this list from the provided +# index.patches file +# +# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue; +# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done < +# index.patches +#PATCH1=( src/topp_ +#topp.f-r1.16.2.5-r1.16.2.6.diff ) +#PATCH2=( . +#configure-r1.372.2.18-r1.372.2.19.diff ) + +DESCRIPTION="Protein X-ray crystallography toolkit" +HOMEPAGE="http://www.ccp4.ac.uk/" +RESTRICT="mirror" +SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz + ${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz + 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/${!NAME}" +done +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="" +RDEPEND="virtual/lapack + virtual/blas + =sci-libs/fftw-2* + app-shells/tcsh + !& /dev/null + ccp_patch "${DISTDIR}/${p}" + popd >& /dev/null + done + einfo "Done." + echo + + epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch + + einfo "Applying Gentoo patches ..." + # These two only needed when attempting to install outside build dir via + # --bindir and --libdir instead of straight copying after build + + # it attempts to install some libraries during the build + #ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch + # hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view + # without this patch when --libdir is set + # Rotgen still needs more patching to find it + #ccp_patch "${FILESDIR}"/add-xdl-libdir.patch + + # it tries to create libdir, bindir etc on live system in configure + ccp_patch "${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 + + einfo "Done." # done applying Gentoo patches + echo + + gnuconfig_update +} + +src_compile() { + # Build system is broken if we set 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 [[ "${FORTRANC}" = "ifc" ]]; then + if use ia64; then + GENTOO_OSNAME="ia64_linux_intel" + else + # Should be valid for x86, maybe amd64 + GENTOO_OSNAME="linux_intel_compilers" + fi + else + # Should be valid for x86 and amd64, at least + GENTOO_OSNAME="linux" + fi + + # Sets up env + ln -s \ + ccp4.setup-bash \ + "${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~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \ + "${S}"/include/ccp4.setup* + + # Set up variables for build + source "${S}"/include/ccp4.setup + + export CC=$(tc-getCC) + export CXX=$(tc-getCXX) + export COPTIM=${CFLAGS} + export CXXOPTIM=${CXXFLAGS} + # Default to -O2 if FFLAGS is unset + export FC=${FORTRANC} + export FOPTIM=${FFLAGS:- -O2} + + # Fix linking + export SHARE_LIB="ld -shared -soname libmmdb.so --whole-archive -o libmmdb.so libmmdb.a ../libccif.a; \ + ld -shared -soname libccp4c.so --whole-archive -o libccp4c.so libccp4c.a ../libccif.a; \ + ld -shared -soname libccp4f.so --whole-archive -o libccp4f.so libccp4f.a libmmdb.a libccp4c.a ../libccif.a -lstdc++ $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')" + + # Can't use econf, configure rejects unknown options like --prefix + ./configure \ + --onlylibs \ + --with-shared-libs \ + --with-fftw=/usr \ + --with-warnings \ + --disable-cctbx \ + --disable-clipper \ + --tmpdir="${TMPDIR}" \ + ${GENTOO_OSNAME} || die "econf failed" + emake -j1 onlylib || die "emake failed" +} + +src_install() { + # Set up variables for build + source "${S}"/include/ccp4.setup + +# Only needed when using --bindir and --libdir + # Needed to avoid errors. Originally tried to make lib and bin + # in configure script, now patched out by dont-make-dirs-in-configure.patch +# dodir /usr/include /usr/$(get_libdir) /usr/bin + +# make install || die "install failed" + einstall || die "install failed" + + # Libs + for file in "${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 + + # Fix libdir in all *.la files + sed -i \ + -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \ + "${D}"/usr/$(get_libdir)/*.la + + # Data + insinto /usr/share/ccp4/data/ + doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die + dodoc "${S}"/lib/data/*.doc + newdoc "${S}"/lib/data/README DATA-README + + # Include files + insinto /usr/include + for i in ccp4 mmdb; do + doins -r "${S}"/include/${i} || die + done +} + +# Epatch wrapper for bulk patching +ccp_patch() { + EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} +} -- cgit v1.2.3-65-gdbad