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xarthisius 10/10/04 17:02:08 |
| 2 |
|
| 3 |
Modified: ChangeLog |
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Added: ccp4-libs-6.1.3-r4.ebuild |
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Log: |
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Fix buffer overflows wrt bug 339706. Thanks to Diego for the report. |
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|
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(Portage version: 2.1.9.13/cvs/Linux x86_64) |
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|
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Revision Changes Path |
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1.13 sci-libs/ccp4-libs/ChangeLog |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.13&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.13&content-type=text/plain |
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diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?r1=1.12&r2=1.13 |
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|
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Index: ChangeLog |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v |
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retrieving revision 1.12 |
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retrieving revision 1.13 |
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diff -u -r1.12 -r1.13 |
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--- ChangeLog 16 Jul 2010 10:14:47 -0000 1.12 |
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+++ ChangeLog 4 Oct 2010 17:02:08 -0000 1.13 |
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@@ -1,6 +1,12 @@ |
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# ChangeLog for sci-libs/ccp4-libs |
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# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 |
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-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.12 2010/07/16 10:14:47 jlec Exp $ |
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+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.13 2010/10/04 17:02:08 xarthisius Exp $ |
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+ |
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+*ccp4-libs-6.1.3-r4 (04 Oct 2010) |
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+ |
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+ 04 Oct 2010; Kacper Kowalik <xarthisius@g.o> |
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+ +files/6.1.3-overflows.patch, +ccp4-libs-6.1.3-r4.ebuild: |
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+ Fix buffer overflows wrt bug 339706. Thanks to Diego for the report. |
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|
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16 Jul 2010; Justin Lecher <jlec@g.o> -ccp4-libs-6.1.3.ebuild, |
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-ccp4-libs-6.1.3-r1.ebuild, -ccp4-libs-6.1.3-r2.ebuild: |
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|
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|
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1.1 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild?rev=1.1&content-type=text/plain |
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|
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Index: ccp4-libs-6.1.3-r4.ebuild |
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=================================================================== |
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# Copyright 1999-2010 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild,v 1.1 2010/10/04 17:02:08 xarthisius Exp $ |
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|
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EAPI="3" |
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|
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inherit fortran eutils gnuconfig multilib toolchain-funcs |
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|
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FORTRAN="g77 gfortran ifc" |
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|
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SRC="ftp://ftp.ccp4.ac.uk/ccp4" |
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|
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#UPDATE="04_03_09" |
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#PATCHDATE="090511" |
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|
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MY_P="${P/-libs}" |
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|
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PATCH_TOT="0" |
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# Here's a little scriptlet to generate this list from the provided |
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# index.patches file |
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# |
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# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue; |
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# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done < |
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# index.patches |
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#PATCH1=( src/topp_ |
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#topp.f-r1.16.2.5-r1.16.2.6.diff ) |
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#PATCH2=( . |
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#configure-r1.372.2.18-r1.372.2.19.diff ) |
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|
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DESCRIPTION="Protein X-ray crystallography toolkit" |
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HOMEPAGE="http://www.ccp4.ac.uk/" |
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SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz" |
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# patch tarball from upstream |
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[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" |
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# patches created by us |
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[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" |
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|
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for i in $(seq $PATCH_TOT); do |
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NAME="PATCH${i}[1]" |
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SRC_URI="${SRC_URI} |
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${SRC}/${PV}/patches/${!NAME}" |
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done |
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|
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LICENSE="ccp4" |
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SLOT="0" |
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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IUSE="" |
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|
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RDEPEND=" |
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media-libs/jpeg:0 |
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app-shells/tcsh |
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!<sci-chemistry/ccp4-6.1.3 |
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sci-libs/cbflib |
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=sci-libs/fftw-2* |
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sci-libs/mmdb |
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sci-libs/monomer-db |
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virtual/lapack |
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virtual/blas" |
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DEPEND="${RDEPEND}" |
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|
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S="${WORKDIR}/${MY_P}" |
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|
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src_prepare() { |
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einfo "Applying upstream patches ..." |
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for patch in $(seq $PATCH_TOT); do |
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base="PATCH${patch}" |
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dir=$(eval echo \${${base}[0]}) |
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p=$(eval echo \${${base}[1]}) |
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pushd "${dir}" >& /dev/null |
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ccp_patch "${DISTDIR}/${p}" |
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popd >& /dev/null |
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done |
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einfo "Done." |
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echo |
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|
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[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch |
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|
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einfo "Applying Gentoo patches ..." |
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# fix buffer overflows wrt bug 339706 |
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ccp_patch "${FILESDIR}"/${PV}-overflows.patch |
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|
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# it tries to create libdir, bindir etc on live system in configure |
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ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch |
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|
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# gerror_ gets defined twice on ppc if you're using gfortran/g95 |
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ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch |
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|
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# make creation of libccif.so smooth |
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ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch |
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|
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# lets try to build libmmdb seperatly |
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ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch |
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|
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# unbundle libjpeg and cbflib |
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ccp_patch "${FILESDIR}"/${PV}-unbundle-libs.patch |
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|
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# Fix missing DESTIDR |
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# not installing during build |
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ccp_patch "${FILESDIR}"/${PV}-noinstall.patch |
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sed \ |
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-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \ |
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-i configure || die |
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|
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einfo "Done." # done applying Gentoo patches |
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echo |
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|
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sed \ |
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-e "s:/usr:${EPREFIX}/usr:g" \ |
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-e 's:-Wl,-rpath,$CLIB::g' \ |
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-e 's: -rpath $CLIB::g' \ |
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-e 's: -I${srcdir}/include/cpp_c_headers::g' \ |
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-i configure || die |
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|
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gnuconfig_update |
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} |
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|
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src_configure() { |
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|
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rm -rf lib/DiffractionImage/{jpg,CBFlib} || die |
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|
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# Build system is broken if we set LDFLAGS |
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userldflags="${LDFLAGS}" |
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export SHARED_LIB_FLAGS="${LDFLAGS}" |
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unset LDFLAGS |
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|
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# GENTOO_OSNAME can be one of: |
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# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd |
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# linux_compaq_compilers linux_intel_compilers generic Darwin |
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# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers |
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if [[ "${FORTRANC}" = "ifc" ]]; then |
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if use ia64; then |
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GENTOO_OSNAME="ia64_linux_intel" |
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else |
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# Should be valid for x86, maybe amd64 |
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GENTOO_OSNAME="linux_intel_compilers" |
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fi |
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else |
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# Should be valid for x86 and amd64, at least |
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GENTOO_OSNAME="linux" |
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fi |
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|
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# Sets up env |
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ln -s \ |
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ccp4.setup-bash \ |
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"${S}"/include/ccp4.setup |
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|
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# We agree to the license by emerging this, set in LICENSE |
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sed -i \ |
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-e "s~^\(^agreed=\).*~\1yes~g" \ |
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"${S}"/configure |
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|
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# Fix up variables -- need to reset CCP4_MASTER at install-time |
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sed -i \ |
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-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \ |
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-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ |
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"${S}"/include/ccp4.setup* |
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|
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# Set up variables for build |
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source "${S}"/include/ccp4.setup |
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|
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export CC=$(tc-getCC) |
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export CXX=$(tc-getCXX) |
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export COPTIM=${CFLAGS} |
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export CXXOPTIM=${CXXFLAGS} |
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# Default to -O2 if FFLAGS is unset |
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export FC=${FORTRANC} |
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export FOPTIM=${FFLAGS:- -O2} |
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# export CCP4_SCR="${T}" |
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|
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# Fix linking |
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# $(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", $i}') -lm -lstdc++ && \ |
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export SHARE_LIB="\ |
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$(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", $i}') -lm && \ |
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${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c -lmmdb $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm" |
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|
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# Can't use econf, configure rejects unknown options like --prefix |
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./configure \ |
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--onlylibs \ |
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--with-shared-libs \ |
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--with-fftw="${EPREFIX}"/usr \ |
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--with-warnings \ |
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--disable-cctbx \ |
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--disable-clipper \ |
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--tmpdir="${TMPDIR}" \ |
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--bindir="${EPREFIX}"/usr/libexec/ccp4/bin/ \ |
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--libdir="${EPREFIX}"/usr/$(get_libdir) \ |
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${GENTOO_OSNAME} || die "econf failed" |
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} |
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|
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src_compile() { |
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emake -j1 \ |
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DESTDIR="${ED}" onlylib || die "emake failed" |
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} |
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|
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src_install() { |
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# Set up variables for build |
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source "${S}"/include/ccp4.setup |
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|
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emake -j1 \ |
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DESTDIR="${ED}" \ |
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includedir="${EPREFIX}"/usr/include \ |
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library_includedir="${EPREFIX}"/usr/include \ |
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install || die |
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|
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# Libs |
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for file in "${S}"/lib/*; do |
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if [[ -d ${file} ]]; then |
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continue |
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elif [[ -x ${file} ]]; then |
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dolib.so ${file} || die |
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else |
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insinto /usr/$(get_libdir) |
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doins ${file} || die |
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fi |
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done |
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|
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# Fix libdir in all *.la files |
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sed -i \ |
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-e "s:^\(libdir=\).*:\1\'${EPREFIX}/usr/$(get_libdir)\':g" \ |
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"${ED}"/usr/$(get_libdir)/*.la || die |
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|
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# Data |
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insinto /usr/share/ccp4/data/ |
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doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die |
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dodoc "${S}"/lib/data/*.doc || die |
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newdoc "${S}"/lib/data/README DATA-README || die |
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} |
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|
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# Epatch wrapper for bulk patching |
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ccp_patch() { |
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EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} |
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} |
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