From: Justin Lecher Date: Sat, 22 May 2010 10:04:27 +0000 (+0000) Subject: Fixes for bug 314053 X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=8fb38b2f8cb8afb703432d7cb2294f7ebee70338;p=gentoo.git Fixes for bug 314053 Package-Manager: portage-2.2_rc67/cvs/Linux x86_64 --- diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog index b7842087914d..05ee496e8104 100644 --- a/sci-libs/ccp4-libs/ChangeLog +++ b/sci-libs/ccp4-libs/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-libs/ccp4-libs # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.5 2010/04/25 11:31:53 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.6 2010/05/22 10:04:27 jlec Exp $ + +*ccp4-libs-6.1.3-r2 (22 May 2010) + + 22 May 2010; Justin Lecher +ccp4-libs-6.1.3-r2.ebuild: + Fixes for bug 314053 28 Mar 2010; Justin Lecher ccp4-libs-6.1.3-r1.ebuild: Prefix fixes and keywording for ~*-linux diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest index 204487384b0b..746bc7557575 100644 --- a/sci-libs/ccp4-libs/Manifest +++ b/sci-libs/ccp4-libs/Manifest @@ -10,13 +10,14 @@ AUX 6.1.3-link-proberly.patch 8282 RMD160 c45d3d1931e6a083c0c96b819aff3f67873659 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-r1.ebuild 6141 RMD160 7b49aedef260644eb31dc5581bffa58f2b452479 SHA1 70c015dc857ee9afc19bdfb8189bcae3c1f57e61 SHA256 54c6997a9ef747c29ae6e1497e83c1f2465ecb9c75cdb73b578caeb89b17dabf +EBUILD ccp4-libs-6.1.3-r2.ebuild 6141 RMD160 3b629dbda585d8391e64701fab362df0edaf4ebd SHA1 e367891a27dd68f6cc6f70f34516d80795e3623b SHA256 356863aa6ef2ed260fc57d00e95929442a816da11c93f8d1477907ba90ac73c6 EBUILD ccp4-libs-6.1.3.ebuild 5892 RMD160 2fb6d639e3201775ba15ed8a27586b69be7707c7 SHA1 c7240c3c925042c04fd112402ac09607ae6448cf SHA256 9fe3acab2d6f59161772fcac0cf45e2150372d3cbb38f7edfafe2d6f47ab5fb8 -MISC ChangeLog 1013 RMD160 f907affc6280e574437adca7234bf4c455be054b SHA1 5492361fe2b05335b1225e02d62e187e25eeddc9 SHA256 a087f06dc3645bf53672ec16b4022d27ccf0ce2efc6eb6a9bf8421bbcd50ed4b +MISC ChangeLog 1147 RMD160 c10b89157cd1fd4eb9acbd44f98ccaa00b2f2d41 SHA1 f7aadd0b714da7e3c2af5b41e67eb1d58aa4d07c SHA256 472ed2ceccc55333a0cfbe4f43084f27c273bca9c6032dc3f07cd81951a096be MISC metadata.xml 306 RMD160 57ba72f54388a666851bda87e52d313d618084e3 SHA1 7d2f57cb3f35eb6d4567b211e01251b5945d4eb2 SHA256 af351be5ead71b377b6fa2fa118fb9aee74129afdc19f736b41596d3033106aa -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux) -iEYEARECAAYFAkvUKC4ACgkQgAnW8HDreRbZ9wCeMBbokioGEhrmZSZ7w31GMrvO -cC4An1s2ws5Nhbkr1iuIVqhOQmqBqIm4 -=4OBb +iEYEARECAAYFAkv3rDAACgkQgAnW8HDreRaveACgr5bFwE4rmiiKrgQtk42VlzGY +Au0AniXt2+DeOyvbaD4BLGaG1ckQs40X +=D6eN -----END PGP SIGNATURE----- diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r2.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r2.ebuild new file mode 100644 index 000000000000..642627419517 --- /dev/null +++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r2.ebuild @@ -0,0 +1,220 @@ +# Copyright 1999-2010 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-r2.ebuild,v 1.1 2010/05/22 10:04:27 jlec Exp $ + +EAPI="3" + +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/" +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/${!NAME}" +done + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + media-libs/jpeg:0 + app-shells/tcsh + !& /dev/null + ccp_patch "${DISTDIR}/${p}" + popd >& /dev/null + done + einfo "Done." + echo + + [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch + + einfo "Applying Gentoo patches ..." + # 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}"/${PV}-unbundle-libs.patch + + einfo "Done." # done applying Gentoo patches + echo + + sed "s:/usr:${EPREFIX}/usr:g" -i configure || die + + gnuconfig_update +} + +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 [[ "${FORTRANC}" = "ifc" ]]; then + if use ia64; then + GENTOO_OSNAME="ia64_linux_intel" + else + # Should be valid for x86, maybe amd64 + GENTOO_OSNAME="linux_intel_compilers" + fi + else + # Should be valid for x86 and amd64, at least + GENTOO_OSNAME="linux" + fi + + # Sets up env + ln -s \ + ccp4.setup-bash \ + "${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${EPREFIX}/usr/bin~g" \ + "${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=${FFLAGS:- -O2} +# export CCP4_SCR="${T}" + + # Fix linking +# $(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \ + export SHARE_LIB="\ + $(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \ + ${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(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 \ + --tmpdir="${TMPDIR}" \ + ${GENTOO_OSNAME} || die "econf failed" +} + +src_compile() { + emake -j1 onlylib || die "emake failed" +} + +src_install() { + # Set up variables for build + source "${S}"/include/ccp4.setup + + 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 + + # Bins + exeinto /usr/libexec/ccp4/bin/ + doexe bin/{automask,diff2jpeg,diffdump,printpeaks,superpose} || die + + # 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 "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die + dodoc "${S}"/lib/data/*.doc + newdoc "${S}"/lib/data/README DATA-README + + # Include files + insinto /usr/include + for i in ccp4; do + doins -r "${S}"/include/${i} || die + done +} + +# Epatch wrapper for bulk patching +ccp_patch() { + EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} +}