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authorJustin Lecher <jlec@gentoo.org>2015-03-09 13:35:48 +0000
committerJustin Lecher <jlec@gentoo.org>2015-03-09 13:35:48 +0000
commitdbb559d3a6392a1e2c55fd34fdc51487301be956 (patch)
tree7c6a5a1dfa11651d6050e455d614ad7e2ef07fe8 /sci-libs
parentDrop old (diff)
downloadgentoo-2-dbb559d3a6392a1e2c55fd34fdc51487301be956.tar.gz
gentoo-2-dbb559d3a6392a1e2c55fd34fdc51487301be956.tar.bz2
gentoo-2-dbb559d3a6392a1e2c55fd34fdc51487301be956.zip
Drop old
(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Diffstat (limited to 'sci-libs')
-rw-r--r--sci-libs/ccp4-libs/ChangeLog9
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild6
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild348
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.3-r13.ebuild349
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.3-r14.ebuild350
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild10
6 files changed, 15 insertions, 1057 deletions
diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index 75e72fe3dbab..6131f33be497 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -1,6 +1,11 @@
# ChangeLog for sci-libs/ccp4-libs
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.60 2014/10/12 14:46:08 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.61 2015/03/09 13:35:48 jlec Exp $
+
+ 09 Mar 2015; Justin Lecher <jlec@gentoo.org> -ccp4-libs-6.1.3-r12.ebuild,
+ -ccp4-libs-6.1.3-r13.ebuild, -ccp4-libs-6.1.3-r14.ebuild,
+ ccp4-libs-6.1.3-r11.ebuild, ccp4-libs-6.1.3-r15.ebuild:
+ Drop old
12 Oct 2014; Justin Lecher <jlec@gentoo.org> ccp4-libs-6.1.3-r11.ebuild,
ccp4-libs-6.1.3-r12.ebuild, ccp4-libs-6.1.3-r13.ebuild,
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild
index 9ac15932373c..6ce6dc0d77fa 100644
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 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-r11.ebuild,v 1.11 2014/10/12 14:46:08 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild,v 1.12 2015/03/09 13:35:48 jlec Exp $
EAPI=3
@@ -23,7 +23,7 @@ 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"
+ [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
for i in $(seq $PATCH_TOT); do
NAME="PATCH${i}[1]"
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild
deleted file mode 100644
index 7ef561290595..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild
+++ /dev/null
@@ -1,348 +0,0 @@
-# Copyright 1999-2014 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-r12.ebuild,v 1.3 2014/10/12 14:46:08 jlec Exp $
-
-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:0
- 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:^\(.*export CLIBS=\).*:\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 ${file}
- else
- insinto /usr/$(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}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r13.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r13.ebuild
deleted file mode 100644
index a5e63e29a737..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r13.ebuild
+++ /dev/null
@@ -1,349 +0,0 @@
-# Copyright 1999-2014 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-r13.ebuild,v 1.3 2014/10/12 14:46:08 jlec Exp $
-
-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:0
- 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${EPREFIX}/usr/share/ccp4/include:g" \
- -e '/# .*LD_LIBRARY_PATH specifies/,/^$/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}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r14.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r14.ebuild
deleted file mode 100644
index 4cf29537697e..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r14.ebuild
+++ /dev/null
@@ -1,350 +0,0 @@
-# Copyright 1999-2014 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-r14.ebuild,v 1.2 2014/10/12 14:46:08 jlec Exp $
-
-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:0
- 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/$(get_libdir)/font84.dat\":g" \
- -e '/# .*LD_LIBRARY_PATH specifies/,/^$/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}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild
index 95be2810d6d4..a23602876a35 100644
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 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-r15.ebuild,v 1.2 2014/10/12 14:46:08 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild,v 1.3 2015/03/09 13:35:48 jlec Exp $
EAPI=5
-PYTHON_COMPAT=( python{2_6,2_7} )
+PYTHON_COMPAT=( python2_7 )
inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs
@@ -23,7 +23,7 @@ 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"
+ [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
for i in $(seq $PATCH_TOT); do
NAME="PATCH${i}[1]"
@@ -49,7 +49,7 @@ RDEPEND="
sci-libs/mmdb:0
sci-libs/monomer-db
sci-libs/ssm
- virtual/jpeg
+ virtual/jpeg:0=
virtual/lapack
virtual/blas"
DEPEND="${RDEPEND}