From: Justin Lecher Date: Wed, 14 Dec 2011 12:20:17 +0000 (+0000) Subject: Fix for changes in cbflib-0.9.2.2 X-Git-Url: http://git.tremily.us/gitweb.cgi?a=commitdiff_plain;h=c5f709cbe7476206b463de563450e2a5f4a19bd5;p=gentoo.git Fix for changes in cbflib-0.9.2.2 Package-Manager: portage-2.2.0_alpha80/cvs/Linux x86_64 --- diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog index 4de4079bba34..cc06b8332777 100644 --- a/sci-libs/ccp4-libs/ChangeLog +++ b/sci-libs/ccp4-libs/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-libs/ccp4-libs # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.43 2011/08/26 14:26:09 hwoarang Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.44 2011/12/14 12:20:17 jlec Exp $ + +*ccp4-libs-6.1.3-r11 (14 Dec 2011) + + 14 Dec 2011; Justin Lecher +files/6.1.3-cbf.patch, + ccp4-libs-6.1.3-r8.ebuild, ccp4-libs-6.1.3-r10.ebuild, + +ccp4-libs-6.1.3-r11.ebuild: + Fix for changes in cbflib-0.9.2.2 26 Aug 2011; Markos Chandras ccp4-libs-6.1.3-r10.ebuild: diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest index a6805e8bc9fa..e822679791a0 100644 --- a/sci-libs/ccp4-libs/Manifest +++ b/sci-libs/ccp4-libs/Manifest @@ -2,6 +2,7 @@ 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 @@ -15,25 +16,16 @@ AUX 6.1.3-unbundle-libs-ng.patch 13925 RMD160 eb96be062a507906f2e1d2659db0663ef0 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.18 (GNU/Linux) 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index 47ca1d014b6c..bd4b1a370bdf 100644 --- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r10.ebuild +++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r10.ebuild @@ -1,6 +1,6 @@ # 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-r10.ebuild,v 1.7 2011/08/26 14:26:09 hwoarang Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r10.ebuild,v 1.8 2011/12/14 12:20:17 jlec Exp $ EAPI=3 @@ -41,7 +41,7 @@ RDEPEND=" !& /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} +} diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r8.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r8.ebuild index 7eaa55c4c5b9..f3bfaffa089c 100644 --- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r8.ebuild +++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r8.ebuild @@ -1,6 +1,6 @@ # 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-r8.ebuild,v 1.5 2011/07/16 12:21:05 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r8.ebuild,v 1.6 2011/12/14 12:20:17 jlec Exp $ EAPI=3 @@ -40,7 +40,7 @@ RDEPEND=" !sci-libs/ssm app-shells/tcsh dev-lang/tcl - sci-libs/cbflib +