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authorJustin Lecher <jlec@gentoo.org>2011-01-10 21:06:27 +0000
committerJustin Lecher <jlec@gentoo.org>2011-01-10 21:06:27 +0000
commita2b0bec7ec5acffa1d21df70c13c98d6c2163c2a (patch)
tree0c0078cc26cf26bfa8dee7357870d4fc2361bb6c /sci-chemistry
parentUpdate description for aqua USE-flag (diff)
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Moved the installation of profile files from sci-chemistry/ccp4-apps to sci-libs/ccp4-libs
(Portage version: 2.2.0_alpha14/cvs/Linux x86_64)
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/ccp4-apps/ChangeLog9
-rw-r--r--sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r5.ebuild448
-rw-r--r--sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r7.ebuild (renamed from sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r6.ebuild)71
3 files changed, 17 insertions, 511 deletions
diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog
index 03bf05871f3a..034d3285dcfb 100644
--- a/sci-chemistry/ccp4-apps/ChangeLog
+++ b/sci-chemistry/ccp4-apps/ChangeLog
@@ -1,6 +1,13 @@
# ChangeLog for sci-chemistry/ccp4-apps
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.19 2011/01/01 08:57:34 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.20 2011/01/10 21:06:26 jlec Exp $
+
+*ccp4-apps-6.1.3-r7 (10 Jan 2011)
+
+ 10 Jan 2011; Justin Lecher <jlec@gentoo.org> -ccp4-apps-6.1.3-r5.ebuild,
+ -ccp4-apps-6.1.3-r6.ebuild, +ccp4-apps-6.1.3-r7.ebuild:
+ Moved the installation of profile files from sci-chemistry/ccp4-apps to
+ sci-libs/ccp4-libs
*ccp4-apps-6.1.3-r6 (01 Jan 2011)
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r5.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r5.ebuild
deleted file mode 100644
index ce5620fff168..000000000000
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r5.ebuild
+++ /dev/null
@@ -1,448 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r5.ebuild,v 1.4 2010/12/31 17:17:35 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit autotools eutils flag-o-matic gnuconfig python toolchain-funcs
-
-MY_P="${PN/-apps}-${PV}"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-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}/${MY_P}-core-src.tar.gz
- http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
-# 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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples X"
-
-X11DEPS="
- x11-libs/libX11
- x11-libs/libXaw
- x11-libs/libXt
- x11-libs/libxdl_view"
-
-TKDEPS="
- >=dev-lang/tk-8.3
- >=dev-tcltk/blt-2.4
- dev-tcltk/iwidgets
- dev-tcltk/itcl
- dev-tcltk/itk
- >=dev-tcltk/tdom-0.8
- dev-tcltk/tkimg
- dev-tcltk/tktreectrl"
-
-SCILIBS="
- ~sci-libs/ccp4-libs-${PV}
- >=sci-libs/ccp4-libs-${PV}-r2
- !>=sci-libs/ccp4-libs-${PV}-r5
- sci-libs/clipper
- =sci-libs/fftw-2*
- sci-libs/mmdb
- virtual/blas
- virtual/lapack"
-
-SCIAPPS="
- sci-chemistry/pdb-extract
- sci-chemistry/pymol
- sci-chemistry/rasmol
- >=sci-chemistry/oasis-4.0-r1"
-
-RDEPEND="
- ${TKDEPS}
- ${SCILIBS}
- app-shells/tcsh
- dev-python/pyxml
- dev-libs/libxml2
- dev-libs/libjwc_c
- dev-libs/libjwc_f
- dev-libs/boehm-gc
- !app-office/sc
- !<sci-chemistry/ccp4-6.1.2
- X? ( ${X11DEPS} )"
-DEPEND="${RDEPEND}
- X? (
- x11-misc/imake
- x11-proto/inputproto
- x11-proto/xextproto
- )"
-PDEPEND="${SCIAPPS}"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- 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 ..."
-
- # it tries to create libdir, bindir etc on live system in configure
- ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
- # We already have sci-chemistry/rasmol
- # Also remember to create the bindir.
- ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch
-
- # libraries come from sci-libs/ccp4-libs
- ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
-
- # coreutils installs a binary called truncate
-# ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch
-# mv ./doc/truncate.doc ./doc/ftruncate.doc || die
-# mv ./html/truncate.html ./html/ftruncate.html || die
-
- # conflicts with media-libs/raptor
-# ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch
-# mv ./doc/rapper.doc ./doc/rappermc.doc || die
-# mv ./html/rapper.html ./html/rappermc.html || die
-
- # We have seperate ebuilds for those
- for bin in molref xia scala imosflm balbes; do
- ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch
- done
-
- # don't configure what is not build
- ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch
-
- # Set python paths correctly
- ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch
-
- # Set python paths correctly
- ccp_patch "${FILESDIR}"/${PV}-pisa.patch
-
- # Set python paths correctly
- ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch
-
- # Fix upstreams code
- ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
- # Update things for oasis 4 usage
- epatch "${WORKDIR}"/${PV}-oasis4.0.patch
- sed 's: oasis : :g' -i src/Makefile.in || die
-
- einfo "Done." # done applying Gentoo patches
- echo
-
- # Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
- sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure
-
- # Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
- pushd src/rapper 2>/dev/null
- sed -i \
- -e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \
- configure.ac
- sed -i \
- -e '/^SUBDIRS/s:libxml2 gc7.0::g' \
- Makefile.am
- sed -i \
- -e '/^rapper_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \
- LOOP/Makefile.am
- sed -i \
- -e "/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I${EPREFIX}/usr/include/gc -I${EPREFIX}/usr/include/libxml2:g" \
- LOOP/Makefile.am
- eautoreconf
- popd 2>/dev/null
-
- gnuconfig_update
-
- python_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py
-}
-
-src_configure() {
- # Build system is broken if we set LDFLAGS
- unset LDFLAGS
-
- # These are broken with ./src/procheck/ps.f
- filter-flags "-floop-*"
-
- # GENTOO_OSNAME can be one of:
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
- # linux_compaq_compilers linux_intel_compilers generic Darwin
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
- if [[ "$(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" \
- -e "s~^\(export CCP4I_TCLTK.*\)/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=${FFLAGS:- -O2}
- export BINSORT_SCR="${T}"
- export CCP4_MASTER="${WORKDIR}"
- export CCP4I_TCLTK="${EPREFIX}/usr/bin"
-
- # Can't use econf, configure rejects unknown options like --prefix
- ./configure \
- $(use_enable X x) \
- --with-shared-libs \
- --with-fftw="${EPREFIX}"/usr \
- --with-warnings \
- --disable-pdb_extract \
- --disable-cctbx \
- --disable-phaser \
- --disable-diffractionImg \
- --disable-clipper \
- --disable-mosflm \
- --disable-mrbump \
- --tmpdir="${TMPDIR}" \
- ${GENTOO_OSNAME} || die "econf failed"
-
- # We do this manually, since disabling the clipper libraries also
- # disables the clipper programs
- pushd src/clipper_progs 2>/dev/null
- econf \
- --prefix="${S}" \
- --bindir="${ED}"/usr/libexec/ccp4/bin \
- --with-ccp4="${S}" \
- --with-clipper="${EPREFIX}"/usr \
- --with-fftw="${EPREFIX}"/usr \
- --with-mmdb="${EPREFIX}"/usr \
- CXX=$(tc-getCXX) \
- || die
- popd 2>/dev/null
-}
-
-src_compile() {
- # fsplit is required for the programs
- pushd lib/src 2>/dev/null
- emake fsplit -j1 || die
- popd 2>/dev/null
-
- # We do this manually, since disabling the clipper libraries also
- # disables the clipper programs
- pushd src/clipper_progs 2>/dev/null
- emake || die
- popd 2>/dev/null
-
- emake -j1 || die "emake failed"
-}
-
-src_install() {
- # Set up variables for build
- source "${S}"/include/ccp4.setup-sh
-
-# make install || die "install failed"
-
- # if we don't make this, a ton of programs fail to install
- mkdir "${S}"/bin || die
-
- # We do this manually, since disabling the clipper libraries also
- # disables the clipper programs
- pushd "${S}"/src/clipper_progs 2>/dev/null
- emake install || die
- popd 2>/dev/null
-
- einstall || die "install failed"
-
- # Fix env
-# -e "s~^\(.*setenv PYTHONPATH .*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \
-# -e "s~^\(.*export PYTHONPATH.*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \
- sed -i \
- -e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1${EPREFIX}/usr~g" \
- -e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
- -e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
- -e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~g" \
- -e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
- -e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
- -e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
- -e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
- -e "s~^\(.*setenv CLIB .*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \
- -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
- -e "s~^\(export CCP4_MASTER.*\)${WORKDIR}~\1${EPREFIX}/usr~g" \
- -e "s~^\(export CCP4.*\$CCP4_MASTER\).*~\1~g" \
- -e "s~^\(export CCP4I_TOP\).*~\1=\$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
- -e "s~^\(export DBCCP4I_TOP\).*~\1=\$CCP4/share/ccp4/dbccp4i~g" \
- -e "s~^\(.*export CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
- -e "s~^\(.*export CLIBD.*\$CCP4\).*~\1/share/ccp4/data~g" \
- -e "s~^\(.*export CLIBD_MON.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
- -e "s~^\(.*export MOLREPLIB.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
- -e "s~^\(.*export CLIB=.*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \
- -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
- -e "/IMOSFLM_VERSION/d" \
- "${S}"/include/ccp4.setup* || die
-
-# -e "s~\$CCP4/share/XIAROOT/setup.sh~\$CCP4/share/ccp4/XIAROOT/setup.sh~g" \
-
- # Don't check for updates on every sourcing of /etc/profile
- sed -i \
- -e "s:\(eval python.*\):#\1:g"
- "${S}"/include/ccp4.setup* || die
-
- # Collision with sci-chemistry/mrbump
- rm -f "${S}"/bin/{mrbump,pydbviewer} || die
-
- # Bins
- exeinto /usr/libexec/ccp4/bin/
- doexe "${S}"/bin/* || die
-
- # Libs
- for file in "${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-bash ccp4.setup.bash || die
- newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh || die
-# newins "${S}"/include/ccp4.setup-zsh ccp4.setup.zsh || die
- newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh || die
- rm -f "${S}"/include/ccp4.setup*
-
- # Environment files, setup scripts, etc.
- insinto /usr/share/ccp4/include
- doins "${S}"/include/* || die
-
- # smartie -- log parsing
- insinto /usr/share/ccp4
- doins -r "${S}"/share/smartie || die
-
- # Install docs and examples
- doman "${S}"/man/cat1/*
-
- mv "${S}"/manual/README "${S}"/manual/README-manual
- dodoc manual/* README CHANGES doc/* examples/README || die
-
- rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.*
- rm "${ED}"/usr/share/doc/${PF}/COPYING.*
-
- dohtml -r "${S}"/html/*
-
- if use examples; then
- for i in data rnase toxd; do
- docinto examples/${i}
- dodoc "${S}"/examples/${i}/*
- done
-
- docinto examples/tutorial
- dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css
- for i in data results; do
- docinto examples/tutorial/${i}
- dodoc "${S}"/examples/tutorial/${i}/*
- done
-
- for i in non-runnable runnable; do
- docinto examples/unix/${i}
- dodoc "${S}"/examples/unix/${i}/*
- done
- fi
- # Needed for ccp4i docs to work
- dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die
- dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die
-
- # Fix overlaps with other packages
- rm -f "${ED}"/usr/share/man/man1/rasmol.1* "${ED}"/usr/lib/font84.dat || die
- mv "${ED}"/usr/share/man/man1/truncate{,-ccp4}.1 || die
- mv "${ED}"/usr/share/man/man1/rapper{,-ccp4}.1 || die
- mv "${ED}"/usr/share/man/man1/sc{,-ccp4}.1 || die
-
- cat >> "${T}"/baubles <<- EOF
- #!${EPREFIX}/bin/bash
- exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py
- EOF
-
- exeinto /usr/libexec/ccp4/bin/
- doexe "${T}"/baubles || die
-}
-
-pkg_postinst() {
- einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
- einfo "in ${EPREFIX}/etc/profile.d/ccp4.setup* to modify this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r6.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r7.ebuild
index de3209a1862a..d293e2fbdef6 100644
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r6.ebuild
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r7.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-chemistry/ccp4-apps/ccp4-apps-6.1.3-r6.ebuild,v 1.1 2011/01/01 08:57:34 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r7.ebuild,v 1.1 2011/01/10 21:06:27 jlec Exp $
EAPI="3"
@@ -67,9 +67,9 @@ TKDEPS="
SCILIBS="
~sci-libs/ccp4-libs-${PV}
- >=sci-libs/ccp4-libs-${PV}-r5
+ >=sci-libs/ccp4-libs-${PVR}
sci-libs/clipper
- =sci-libs/fftw-2*
+ sci-libs/fftw:2.1
sci-libs/mmdb
virtual/blas
virtual/lapack"
@@ -90,7 +90,7 @@ RDEPEND="
dev-libs/libjwc_f
dev-libs/boehm-gc
!app-office/sc
- !<sci-chemistry/ccp4-6.1.2
+ !<sci-chemistry/ccp4-6.1.3
X? ( ${X11DEPS} )"
DEPEND="${RDEPEND}
X? (
@@ -235,7 +235,6 @@ src_configure() {
-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" \
- -e "s~^\(export CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
"${S}"/include/ccp4.setup*
# Set up variables for build
@@ -256,7 +255,7 @@ src_configure() {
./configure \
$(use_enable X x) \
--with-shared-libs \
- --with-fftw="${EPREFIX}"/usr \
+ --with-fftw="${EPREFIX}/usr" \
--with-warnings \
--disable-pdb_extract \
--disable-cctbx \
@@ -275,11 +274,10 @@ src_configure() {
--prefix="${S}" \
--bindir="${ED}"/usr/libexec/ccp4/bin \
--with-ccp4="${S}" \
- --with-clipper="${EPREFIX}"/usr \
- --with-fftw="${EPREFIX}"/usr \
- --with-mmdb="${EPREFIX}"/usr \
- CXX=$(tc-getCXX) \
- || die
+ --with-clipper="${EPREFIX}/usr" \
+ --with-fftw="${EPREFIX}/usr" \
+ --with-mmdb="${EPREFIX}/usr" \
+ CXX=$(tc-getCXX)
popd 2>/dev/null
}
@@ -302,8 +300,6 @@ src_install() {
# Set up variables for build
source "${S}"/include/ccp4.setup-sh
-# make install || die "install failed"
-
# if we don't make this, a ton of programs fail to install
mkdir "${S}"/bin || die
@@ -315,40 +311,6 @@ src_install() {
einstall || die "install failed"
- # Fix env
-# -e "s~^\(.*setenv PYTHONPATH .*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \
-# -e "s~^\(.*export PYTHONPATH.*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \
- sed -i \
- -e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1${EPREFIX}/usr~g" \
- -e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
- -e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
- -e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~g" \
- -e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
- -e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
- -e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
- -e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
- -e "s~^\(.*setenv CLIB .*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \
- -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
- -e "s~^\(export CCP4_MASTER.*\)${WORKDIR}~\1${EPREFIX}/usr~g" \
- -e "s~^\(export CCP4.*\$CCP4_MASTER\).*~\1~g" \
- -e "s~^\(export CCP4I_TOP\).*~\1=\$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
- -e "s~^\(export DBCCP4I_TOP\).*~\1=\$CCP4/share/ccp4/dbccp4i~g" \
- -e "s~^\(.*export CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
- -e "s~^\(.*export CLIBD.*\$CCP4\).*~\1/share/ccp4/data~g" \
- -e "s~^\(.*export CLIBD_MON.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
- -e "s~^\(.*export MOLREPLIB.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
- -e "s~^\(.*export CLIB=.*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \
- -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
- -e "/IMOSFLM_VERSION/d" \
- "${S}"/include/ccp4.setup* || die
-
-# -e "s~\$CCP4/share/XIAROOT/setup.sh~\$CCP4/share/ccp4/XIAROOT/setup.sh~g" \
-
- # Don't check for updates on every sourcing of /etc/profile
- sed -i \
- -e "s:\(eval python.*\):#\1:g"
- "${S}"/include/ccp4.setup* || die
-
# Collision with sci-chemistry/mrbump
rm -f "${S}"/bin/{mrbump,pydbviewer} || die
@@ -368,16 +330,6 @@ src_install() {
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 "${S}"/include/ccp4.setup-bash ccp4.setup.bash || die
- newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh || die
-# newins "${S}"/include/ccp4.setup-zsh ccp4.setup.zsh || die
- newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh || die
rm -f "${S}"/include/ccp4.setup*
# smartie -- log parsing
@@ -432,11 +384,6 @@ src_install() {
doexe "${T}"/baubles || die
}
-pkg_postinst() {
- einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
- einfo "in ${EPREFIX}/etc/profile.d/ccp4.setup* to modify this."
-}
-
# Epatch wrapper for bulk patching
ccp_patch() {
EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}