From 1b35e331c4c8be8f5c5e4e2749362c8802d15d3a Mon Sep 17 00:00:00 2001
From: "Justin Lecher (jlec)" <jlec@j-schmitz.net>
Date: Tue, 9 Jun 2009 23:50:19 +0200
Subject: cctbx should be linkable now

---
 sci-libs/cctbx/ChangeLog                       |   6 +
 sci-libs/cctbx/Manifest                        |   4 +-
 sci-libs/cctbx/cctbx-2009.02.15.2320-r1.ebuild | 195 ------------------------
 sci-libs/cctbx/cctbx-2009.02.15.2320-r3.ebuild | 199 +++++++++++++++++++++++++
 4 files changed, 207 insertions(+), 197 deletions(-)
 delete mode 100644 sci-libs/cctbx/cctbx-2009.02.15.2320-r1.ebuild
 create mode 100644 sci-libs/cctbx/cctbx-2009.02.15.2320-r3.ebuild

(limited to 'sci-libs')

diff --git a/sci-libs/cctbx/ChangeLog b/sci-libs/cctbx/ChangeLog
index 52dffdab3..47593324a 100644
--- a/sci-libs/cctbx/ChangeLog
+++ b/sci-libs/cctbx/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*cctbx-2009.02.15.2320-r3 (09 Jun 2009)
+
+  09 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -cctbx-2009.02.15.2320-r1.ebuild, +cctbx-2009.02.15.2320-r3.ebuild:
+  fixed bad bug which breaks the libs
+
   08 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
   cctbx-2009.02.15.2320-r1.ebuild:
   Hopefully fixed problem with installation
diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest
index 825e45722..21e4c2bac 100644
--- a/sci-libs/cctbx/Manifest
+++ b/sci-libs/cctbx/Manifest
@@ -1,6 +1,6 @@
 AUX 2009.02.15.2320-sandbox-violations-chmod.patch 467 RMD160 11a55d71c9a238cf8c40f1760344c27c65a53922 SHA1 03ce887b4ddaf72310986d97c8add9a7a73c6fb0 SHA256 1c79b9f3bb0215dca39def9b6ba0bdb678022b51345da1567d0f4952951bdcd1
 DIST cctbx-2009.02.15.2320.tar.gz 12800622 RMD160 8d95db0054e8ba9378e46e9d5d2d7b333418eeb4 SHA1 1d3e5aad9d1c4fd6617295fc3346c079e7c758d9 SHA256 336946867246ed3cf7f697dc9bf0cc21443b7fb9600b24696b4d8d3cb5773200
-EBUILD cctbx-2009.02.15.2320-r1.ebuild 5467 RMD160 c7efd88e36165aa6e27584e198fa6710a28f6626 SHA1 74ddd0f842645f6fe6d314aae07d3980b9750591 SHA256 377ba72a4f9aeaf095173a2af2d249209c777550aea82d6d19542c860e88323f
 EBUILD cctbx-2009.02.15.2320-r2.ebuild 4639 RMD160 69285fb2b9ef6207a8338e0ed6b335432b23c825 SHA1 fd65e7d76f45a4152fbfaaf286e14ee315edfc83 SHA256 21db2dcc51a47440950b854aa54e5f7612128bb0446e69a1877330af003668b7
-MISC ChangeLog 1294 RMD160 654a7ecddbc1531f5e5c6f580ce1b8aa19002de8 SHA1 3731cebd730f7311bf63e8cacdcfde3a25f7a5e2 SHA256 3378786bd75d9b55bff5ed49b36e75788d8e7c1dfe19a2a1884f6a2cd7d6c895
+EBUILD cctbx-2009.02.15.2320-r3.ebuild 5677 RMD160 1fd505556d4c2b02ea33a4da0c2494134fcf9c88 SHA1 304f631bcdbb37baf19d1f5ce5210e1b7429d3b3 SHA256 1a932ef54671f97fc40f5affec24b6bc6331df6e68a911583523240d606dab07
+MISC ChangeLog 1501 RMD160 8b2435c8ce96ffb22ff65eb967c982e473879762 SHA1 1756eb00a128e815151fbfc676d2481a846b88eb SHA256 47d4a83db06e93fb9828686bba3046ded3128746058e6a7b92343ad5d23fbb13
 MISC metadata.xml 438 RMD160 79ad38c94abc71ba32abccdcd670f2f6802c2df3 SHA1 1ebbff28f7e4d135b26b951b6111f6803f78413c SHA256 94d589a2836bffe732cdf993e9b38afc1cde4683a5e5669c44daf6b69595e8da
diff --git a/sci-libs/cctbx/cctbx-2009.02.15.2320-r1.ebuild b/sci-libs/cctbx/cctbx-2009.02.15.2320-r1.ebuild
deleted file mode 100644
index 0ec1e93ce..000000000
--- a/sci-libs/cctbx/cctbx-2009.02.15.2320-r1.ebuild
+++ /dev/null
@@ -1,195 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit toolchain-funcs python eutils
-
-MY_PV="${PV//./_}"
-
-DESCRIPTION="Computational Crystallography Toolbox"
-HOMEPAGE="http://cctbx.sourceforge.net/"
-SRC_URI="http://cci.lbl.gov/cctbx_build/results/${MY_PV}/${PN}_bundle.tar.gz -> ${P}.tar.gz"
-LICENSE="cctbx-2.0"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="minimal openmp threads"
-
-RDEPEND="!minimal? ( ( sci-chemistry/cns )
-		x86? ( sci-chemistry/shelx )
-	 )"
-DEPEND="${RDEPEND}
-	>=dev-util/scons-1.2"
-
-S="${WORKDIR}"
-MY_S="${WORKDIR}"/cctbx_sources
-MY_B="${WORKDIR}"/cctbx_build
-
-pkg_setup() {
-	if use openmp &&
-	[[ $(tc-getCC)$ == *gcc* ]] &&
-	( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
-	! built_with_use sys-devel/gcc openmp )
-	then
-	ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 "
-	ewarn "If you want to build fftw with OpenMP, abort now,"
-	ewarn "and switch CC to an OpenMP capable compiler"
-	fi
-}
-
-src_prepare() {
-	# Wants to chmod /usr/bin/python
-	epatch "${FILESDIR}"/${PV}-sandbox-violations-chmod.patch
-
-	rm -rf "${MY_S}/clipper" "${MY_S}/scons" # "${MY_S}/boost"
-
-	mkdir -p "${MY_S}"/scons/src/ "${MY_S}/boost"
-
-	ln -sf /usr/$(get_libdir)/scons-1.2.0 "${MY_S}"/scons/src/engine || die
-#	ln -sf /usr/include/boost "${MY_S}/boost/"
-}
-
-src_compile() {
-	python_version
-
-	local MYCONF
-	local MAKEOPTS_EXP
-	local OPTS
-	local OPTSLD
-
-	MYCONF="${MY_S}/libtbx/configure.py"
-
-	MAKEOPTS_EXP=${MAKEOPTS/j/j }
-	MAKEOPTS_EXP=${MAKEOPTS_EXP%-l[0-9]*}
-
-	# Get CXXFLAGS in format suitable for substitition into SConscript
-	for i in ${CXXFLAGS}; do
-		OPTS="${OPTS} \"${i}\","
-	done
-
-	# Strip off the last comma
-	OPTS=${OPTS%,}
-
-	# Fix CXXFLAGS
-	sed -i \
-		-e "s:\"-O3\", \"-ffast-math\":${OPTS}:g" \
-		${MY_S}/libtbx/SConscript
-
-	# Get LDFLAGS in format suitable for substitition into SConscript
-	for i in ${LDFLAGS}; do
-		OPTSLD="${OPTSLD} \"${i}\","
-	done
-
-	# Fix LDFLAGS which should be as-needed ready
-	sed -i \
-		-e "s:\"-shared\":${OPTSLD} \"-shared\":g" \
-		${MY_S}/libtbx/SConscript
-
-	# Get compiler in the right way
-	COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-	MYCONF="${MYCONF} --compiler=${COMPILER}"
-
-	# Precompiling python scripts. It is done in upstreams install script. Perhaps use python_mod_compile,
-	# but as this script works we should stick to it.
-	${python} "${MY_S}/libtbx/command_line/py_compile_all.py"
-
-	# Additional USE flag usage
-	check_use openmp
-	MYCONF="${MYCONF} --enable-openmp-if-possible=${USE_openmp}"
-	use threads && USEthreads="--enable-boost-threads" && \
-	ewarn "If using boost threads openmp support is disabled"
-
-	MYCONF="${MYCONF} ${USE_threads} --scan-boost"
-
-	mkdir "${MY_B}" && MYCONF="${MYCONF} --current_working_directory=${MY_B}"
-	cd "${MY_B}"
-
-	MYCONF="${MYCONF} --build=release fftw3tbx rstbx smtbx mmtbx"
-	einfo "configuring with ${python} ${MYCONF}"
-
-	${python} ${MYCONF} \
-		|| die "configure failed"
-
-	source setpaths_all.sh
-
-	einfo "compiling with libtbx.scons ${MAKEOPTS_EXP}"
-	libtbx.scons ${MAKEOPTS_EXP} .|| die "make failed"
-}
-
-src_test(){
-	source "${MY_B}"/setpaths_all.sh
-	libtbx.python $(libtbx.show_dist_paths boost_adaptbx)/tst_rational.py && \
-	libtbx.python ${SCITBX_DIST}/run_tests.py ${MAKEOPTS_EXP} && \
-	libtbx.python ${CCTBX_DIST}/run_tests.py  ${MAKEOPTS_EXP} \
-	|| die "test failed"
-}
-
-src_install(){
-
-	# This is what Bill Scott does in the fink package. Do we need this as well?
-#	-e "s:prepend:append:g" \
-
-	find cctbx_build/ -type f -exec \
-	sed -e "s:${MY_S}:/usr/$(get_libdir)/cctbx/cctbx_sources:g" \
-	    -e "s:${MY_B}:/usr/$(get_libdir)/cctbx/cctbx_build:g"  \
-	    -i '{}' \; || die "Fail to correct path"
-
-
-	ebegin "removing unnessary files"
-		rm -r "${S}"/cctbx_sources/scons || die "failed to remove uneeded scons"
-		find "${S}" -type f -name "*.o" -exec rm -f '{}' \; || die "failed to remove uneeded *.o"
-		find "${S}" -type f -name "*.c" -exec rm -f '{}' \; || die "failed to remove uneeded *.c"
-		find "${S}" -type f -name "*.cpp" -exec rm -f '{}' \; || die "failed to remove uneeded *.cpp"
-		find "${S}" -type f -name "*.pyc" -exec rm -f '{}' \; || die "failed to remove uneeded *.pyc"
-	eend
-
-	insinto /usr/$(get_libdir)/${PN}
-	doins -r cctbx_sources cctbx_build || die
-
-# fperms cannot handle wildcards
-	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/*sh && \
-	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/array_family/* && \
-	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/serialization/* && \
-	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/error/* && \
-	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/fftpack/timing/* && \
-	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/lbfgs/* && \
-	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/chiltbx/handle_test && \
-	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/bin/* || \
-	die
-
-
-	insinto /etc/profile.d/
-	newins "${MY_B}"/setpaths.sh 30cctbx.sh && \
-	newins "${MY_B}"/setpaths.csh 30cctbx.csh || \
-	die
-
-	cat >> "${T}"/30cctbx <<- EOF
-	LDPATH="/usr/$(get_libdir)/${PN}/cctbx_build/lib"
-	EOF
-
-	doenvd "${T}"/30cctbx || die
-}
-
-pkg_postinst () {
-	python_mod_optimize /usr/$(get_libdir)/${PN}/cctbx_sources
-}
-
-pkg_postrm () {
-	python_mod_cleanup /usr/$(get_libdir)/${PN}/cctbx_sources
-}
-
-
-check_use() {
-
-	for var in $@; do
-	if use ${var}; then
-	printf -v "USE_$var" True
-	else
-	printf -v "USE_$var" False
-
-	fi
-	shift
-	done
-}
-
diff --git a/sci-libs/cctbx/cctbx-2009.02.15.2320-r3.ebuild b/sci-libs/cctbx/cctbx-2009.02.15.2320-r3.ebuild
new file mode 100644
index 000000000..2e040fe52
--- /dev/null
+++ b/sci-libs/cctbx/cctbx-2009.02.15.2320-r3.ebuild
@@ -0,0 +1,199 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit toolchain-funcs python eutils
+
+MY_PV="${PV//./_}"
+
+DESCRIPTION="Computational Crystallography Toolbox"
+HOMEPAGE="http://cctbx.sourceforge.net/"
+SRC_URI="http://cci.lbl.gov/cctbx_build/results/${MY_PV}/${PN}_bundle.tar.gz -> ${P}.tar.gz"
+LICENSE="cctbx-2.0"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="minimal openmp threads"
+
+RDEPEND="!minimal? ( ( sci-chemistry/cns )
+		x86? ( sci-chemistry/shelx )
+	 )"
+DEPEND="${RDEPEND}
+	>=dev-util/scons-1.2"
+
+S="${WORKDIR}"
+MY_S="${WORKDIR}"/cctbx_sources
+MY_B="${WORKDIR}"/cctbx_build
+
+pkg_setup() {
+	if use openmp &&
+	[[ $(tc-getCC)$ == *gcc* ]] &&
+	( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
+	! built_with_use sys-devel/gcc openmp )
+	then
+	ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 "
+	ewarn "If you want to build fftw with OpenMP, abort now,"
+	ewarn "and switch CC to an OpenMP capable compiler"
+	fi
+}
+
+src_prepare() {
+	# Wants to chmod /usr/bin/python
+	epatch "${FILESDIR}"/${PV}-sandbox-violations-chmod.patch
+
+	rm -rf "${MY_S}/scons" # "${MY_S}/boost"
+
+	mkdir -p "${MY_S}"/scons/src/ "${MY_S}/boost"
+
+	ln -sf /usr/$(get_libdir)/scons-1.2.0 "${MY_S}"/scons/src/engine || die
+#	ln -sf /usr/include/boost "${MY_S}/boost/"
+}
+
+src_compile() {
+	python_version
+
+	local MYCONF
+	local MAKEOPTS_EXP
+	local OPTS
+	local OPTSLD
+
+	MYCONF="${MY_S}/libtbx/configure.py"
+
+	MAKEOPTS_EXP=${MAKEOPTS/j/j }
+	MAKEOPTS_EXP=${MAKEOPTS_EXP%-l[0-9]*}
+
+	# Get CXXFLAGS in format suitable for substitition into SConscript
+	for i in ${CXXFLAGS}; do
+		OPTS="${OPTS} \"${i}\","
+	done
+
+	# Strip off the last comma
+	OPTS=${OPTS%,}
+
+	# Fix CXXFLAGS
+	sed -i \
+		-e "s:\"-O3\", \"-ffast-math\":${OPTS}:g" \
+		${MY_S}/libtbx/SConscript
+
+	# Get LDFLAGS in format suitable for substitition into SConscript
+	for i in ${LDFLAGS}; do
+		OPTSLD="${OPTSLD} \"${i}\","
+	done
+
+	OPTSLD=${OPTSLD%,}
+
+	# Fix LDFLAGS which should be as-needed ready
+	sed -i \
+		-e "s:\"-shared\":\"-shared\", ${OPTSLD}:g" \
+		${MY_S}/libtbx/SConscript
+
+	# Get compiler in the right way
+	COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
+	MYCONF="${MYCONF} --compiler=${COMPILER}"
+
+	# Precompiling python scripts. It is done in upstreams install script. Perhaps use python_mod_compile,
+	# but as this script works we should stick to it.
+	${python} "${MY_S}/libtbx/command_line/py_compile_all.py"
+
+	# Additional USE flag usage
+	check_use openmp
+	MYCONF="${MYCONF} --enable-openmp-if-possible=${USE_openmp}"
+	use threads && USEthreads="--enable-boost-threads" && \
+	ewarn "If using boost threads openmp support is disabled"
+
+	MYCONF="${MYCONF} ${USE_threads} --scan-boost"
+
+	mkdir "${MY_B}" && MYCONF="${MYCONF} --current_working_directory=${MY_B}"
+	cd "${MY_B}"
+
+	MYCONF="${MYCONF} --build=release fftw3tbx rstbx smtbx mmtbx clipper"
+	einfo "configuring with ${python} ${MYCONF}"
+
+	${python} ${MYCONF} \
+		|| die "configure failed"
+
+	source setpaths_all.sh
+
+	einfo "compiling with libtbx.scons ${MAKEOPTS_EXP}"
+	libtbx.scons ${MAKEOPTS_EXP} .|| die "make failed"
+}
+
+src_test(){
+	source "${MY_B}"/setpaths_all.sh
+	libtbx.python $(libtbx.show_dist_paths boost_adaptbx)/tst_rational.py && \
+	libtbx.python ${SCITBX_DIST}/run_tests.py ${MAKEOPTS_EXP} && \
+	libtbx.python ${CCTBX_DIST}/run_tests.py  ${MAKEOPTS_EXP} \
+	|| die "test failed"
+}
+
+src_install(){
+
+	# This is what Bill Scott does in the fink package. Do we need this as well?
+#	-e "s:prepend:append:g" \
+
+	find cctbx_build/ -type f \( -name "*.py" -o -name "*sh" \) -exec \
+	sed -e "s:${MY_S}:/usr/$(get_libdir)/cctbx/cctbx_sources:g" \
+	    -e "s:${MY_B}:/usr/$(get_libdir)/cctbx/cctbx_build:g"  \
+	    -i '{}' \; || die "Fail to correct path"
+
+
+	ebegin "removing unnessary files"
+		rm -r "${S}"/cctbx_sources/scons || die "failed to remove uneeded scons"
+		find "${S}" -type f -name "*conftest*" -exec rm -f '{}' \; || die "failed to remove uneeded *.o"
+		find "${S}" -type f -name "*.o" -exec rm -f '{}' \; || die "failed to remove uneeded *.o"
+		find "${S}" -type f -name "*.c" -exec rm -f '{}' \; || die "failed to remove uneeded *.c"
+		find "${S}" -type f -name "*.cpp" -exec rm -f '{}' \; || die "failed to remove uneeded *.cpp"
+		find "${S}" -type f -name "*.pyc" -exec rm -f '{}' \; || die "failed to remove uneeded *.pyc"
+	eend
+
+	insinto /usr/$(get_libdir)/${PN}
+	doins -r cctbx_sources cctbx_build || die
+
+# fperms cannot handle wildcards
+	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/*sh && \
+	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/lib/* && \
+	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/array_family/* && \
+	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/serialization/* && \
+	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/error/* && \
+	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/fftpack/timing/* && \
+	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/lbfgs/* && \
+	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/chiltbx/handle_test && \
+	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/bin/* || \
+	die
+
+
+	insinto /etc/profile.d/
+	newins "${MY_B}"/setpaths.sh 30cctbx.sh && \
+	newins "${MY_B}"/setpaths.csh 30cctbx.csh || \
+	die
+
+	cat >> "${T}"/30cctbx <<- EOF
+	LDPATH="/usr/$(get_libdir)/${PN}/cctbx_build/lib"
+	EOF
+
+	doenvd "${T}"/30cctbx || die
+}
+
+pkg_postinst () {
+	python_mod_optimize /usr/$(get_libdir)/${PN}/cctbx_sources
+}
+
+pkg_postrm () {
+	python_mod_cleanup /usr/$(get_libdir)/${PN}/cctbx_sources
+}
+
+
+check_use() {
+
+	for var in $@; do
+	if use ${var}; then
+	printf -v "USE_$var" True
+	else
+	printf -v "USE_$var" False
+
+	fi
+	shift
+	done
+}
+
-- 
cgit v1.2.3-65-gdbad