Removed old

Package-Manager: portage-2.2.0_alpha15/cvs/Linux x86_64

4 files changed, 9 insertions, 390 deletions

diff --git a/sci-libs/cctbx/ChangeLog b/sci-libs/cctbx/ChangeLog
index d02f78bba108..37d74cd49f71 100644
--- a/sci-libs/cctbx/ChangeLog
+++ b/sci-libs/cctbx/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-libs/cctbx
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.11 2011/01/15 14:44:16 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.12 2011/01/15 15:17:28 jlec Exp $
+
+  15 Jan 2011; Justin Lecher <jlec@gentoo.org>
+  -cctbx-2009.11.01.0123-r1.ebuild, -cctbx-2010.03.29.2334-r2.ebuild:
+  Removed old
 
   15 Jan 2011; Justin Lecher <jlec@gentoo.org>
   files/2010.03.29.2334-boost.patch, cctbx-2010.03.29.2334-r2.ebuild,
diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest
index 24227a21a5d4..9a8f2f217626 100644
--- a/sci-libs/cctbx/Manifest
+++ b/sci-libs/cctbx/Manifest
@@ -6,18 +6,15 @@ AUX 2010.03.29.2334-clipper.patch 2209 RMD160 1bfc13f0834e837a55f0e41554649acd1e
 AUX 2010.03.29.2334-flags.patch 3336 RMD160 fdbb0b71499e00c666629e1ff04b5bdcbe376b13 SHA1 ef97099dbd93727bd356015f22e82480a48e1a0c SHA256 769edb3e5dcb608b54ab4d33c5933b523f73ff62c6cb627c4eb4b1a2086e40b1
 AUX 2010.03.29.2334-soname.patch 5177 RMD160 c6cad498c4edb7046696428008408b126efa954c SHA1 7c5d78110c4270c9ca113ae5ea77c7c2451e2b21 SHA256 dd4ea6dbf34c1b2d9572adec5a33fe6a73b1a99e8c4364123e69382bb161ce74
 AUX 2010.03.29.2334-tst_server.py.patch 774 RMD160 12e1115b2ccc0b6b01b365925bf311d29ef08c7a SHA1 09549cc6103f502777acced13a3ed483d713dfc0 SHA256 df058d16d2dc5beaac9f1a1fbf2e640994c7e881d449eb01ac338dadbfb15ac3
-DIST cctbx-2009.11.01.0123.tar.gz 14604079 RMD160 77cc84d4b9e35e7a87f807d8669efb939b2e82ce SHA1 7db71a62786b82f47999919a9411938b123d5b4d SHA256 31e7f79424360f963c6eae528a9d289db4b53c1f7fe4aa9de71201e9d14bc5af
 DIST cctbx-2010.03.29.2334.tar.gz 15570372 RMD160 e543578dbe6568f5f8f80b3ce7a20b10e01193bc SHA1 1442dbd5d1ef3b91e718dce039a24fc1637104d3 SHA256 e1fae804caaf8593c7a3f32e4544046f4c00293063d9099721578cc8fbd17213
-EBUILD cctbx-2009.11.01.0123-r1.ebuild 5746 RMD160 ea65055c3ecb4f90fea5850349e8d48a6062e792 SHA1 fbb89c8b722375504ae455dbf1511871f09f2df5 SHA256 7f15213ea692197e2b5f6e7a8d350a76d5456ad9b498b5569f510d6e1c1ce604
 EBUILD cctbx-2010.03.29.2334-r1.ebuild 5881 RMD160 deee9422031d740e93c4448d9b192d4a413fccc3 SHA1 3ce9443b9a3756dc090666cd947df0f6bc831b42 SHA256 a879efce871c0d3c1f4771df98e7e0a4835e0e0637605176920dcc50fde8d19c
-EBUILD cctbx-2010.03.29.2334-r2.ebuild 5665 RMD160 7f4866e6bf4fa2e7b2ffa57244b1c4e52ce969d7 SHA1 28b0855d693f323332ca1e922ae7afe5d740eba0 SHA256 f4b691c564fe6017da12002a15274ace64f6ec873b6792b55da73f9cd4041d0b
 EBUILD cctbx-2010.03.29.2334-r3.ebuild 5935 RMD160 e09e5fa8ff0f93bb28df2bbde41fc3a566823ba7 SHA1 0d192b580152f75907c2658cfe789aef18793f56 SHA256 7ee32c30316a692c2917aadc483e6ecc2a216ca339740e26aba4f48fc349d5ea
-MISC ChangeLog 2646 RMD160 2acc4328c920823bafb1be1bb1420bef290ebdb1 SHA1 2bad5692d3cd6f5d84a2a003120cacb92f4ea17d SHA256 303c8284008660d9370b375e6291f284544958609d45308ab651e3384598842a
+MISC ChangeLog 2778 RMD160 e85d6499f7e8ac9860ba26f97c7be66916aef227 SHA1 66e3fbe73601c80a00da4a4cfef3ba10eb8599a4 SHA256 e7b799ba9ceb3c1de3bc85c0390f85c01846e045328efb8b5708b0eadea6eaea
 MISC metadata.xml 767 RMD160 c2fc3bcc534e407e6066ee98beb6878d78a0f6e9 SHA1 a653677e160cf0726e1747b06b5d0cd95e51ac5f SHA256 ef36fc1a1d5d657ba67f88b303f08eef5a1a814d22a2091c07616dc16928e3fa
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.16 (GNU/Linux)
 
-iEYEARECAAYFAk0xssYACgkQgAnW8HDreRa3cgCgoqsGCCXReb7REi4tK75fmJt6
-8AIAoK9hccWlpnuXANhC+SyNSol+uC61
-=D8C8
+iEYEARECAAYFAk0xuo0ACgkQgAnW8HDreRYUDgCgr7WcVDZmUDyOWnJuP3BKjZjD
+IDMAniVp4RSbaCdeIkf3wi6YpFc4WL8Q
+=iMiC
 -----END PGP SIGNATURE-----
diff --git a/sci-libs/cctbx/cctbx-2009.11.01.0123-r1.ebuild b/sci-libs/cctbx/cctbx-2009.11.01.0123-r1.ebuild
deleted file mode 100644
index 059be0cb80e6..000000000000
--- a/sci-libs/cctbx/cctbx-2009.11.01.0123-r1.ebuild
+++ /dev/null
@@ -1,197 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/cctbx-2009.11.01.0123-r1.ebuild,v 1.6 2010/12/29 15:16:29 jlec Exp $
-
-EAPI="3"
-PYTHON_DEPEND="2"
-
-inherit eutils python toolchain-funcs
-
-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 -> ${P}.tar.gz"
-
-LICENSE="cctbx-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+minimal openmp threads"
-
-RDEPEND="
-	>dev-libs/boost-1.39
-	sci-libs/clipper
-	sci-libs/fftw
-	!minimal? (
-		sci-chemistry/cns
-		sci-chemistry/shelx )"
-DEPEND="${RDEPEND}
-	>=dev-util/scons-1.2"
-
-S="${WORKDIR}"
-MY_S="${WORKDIR}"/cctbx_sources
-MY_B="${WORKDIR}"/cctbx_build
-
-pkg_setup() {
-	if use openmp && ! tc-has-openmp; then
-		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 and icc"
-		ewarn "If you want to build ${PN} with OpenMP, abort now,"
-		ewarn "and switch CC to an OpenMP capable compiler"
-	fi
-	python_set_active_version 2
-}
-
-src_prepare() {
-	local opts
-	local optsld
-
-	rm -rf "${MY_S}/scons"
-
-	mkdir -p "${MY_S}"/scons/src/ "${MY_S}/boost"
-
-	ln -sf "${EPREFIX}"/usr/$(get_libdir)/scons-* "${MY_S}"/scons/src/engine || die
-
-	# 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" \
-		${MY_S}/libtbx/SConscript
-}
-
-src_configure() {
-	local compiler
-	local myconf
-
-	myconf="${MY_S}/libtbx/configure.py"
-
-	# 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_optimize, but as this script works we should stick to it.
-	$(PYTHON -a) "${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 -a) ${myconf} \
-		|| die "configure failed"
-}
-
-src_compile() {
-	local makeopts_exp
-
-	cd "${MY_B}"
-
-	makeopts_exp=${MAKEOPTS/j/j }
-	makeopts_exp=${makeopts_exp%-l[0-9]*}
-
-	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)/tests/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:${MY_S}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_sources:g" \
-	    -e "s:${MY_B}:${EPREFIX}/usr/$(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 || die
-	newins "${MY_B}"/setpaths.csh 30cctbx.csh || die
-
-	cat >> "${T}"/30cctbx <<- EOF
-	LDPATH="${EPREFIX}/usr/$(get_libdir)/${PN}/cctbx_build/lib"
-	EOF
-
-	doenvd "${T}"/30cctbx || die
-}
-
-pkg_postinst () {
-	python_need_rebuild
-	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-2010.03.29.2334-r2.ebuild b/sci-libs/cctbx/cctbx-2010.03.29.2334-r2.ebuild
deleted file mode 100644
index 5dbdc622d98d..000000000000
--- a/sci-libs/cctbx/cctbx-2010.03.29.2334-r2.ebuild
+++ /dev/null
@@ -1,185 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/cctbx-2010.03.29.2334-r2.ebuild,v 1.4 2011/01/15 14:44:16 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit eutils prefix python toolchain-funcs
-
-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 -> ${P}.tar.gz"
-
-LICENSE="cctbx-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+minimal openmp threads"
-
-RDEPEND="
-	>dev-libs/boost-1.39
-	sci-libs/clipper
-	sci-libs/fftw
-	!minimal? (
-		sci-chemistry/cns
-		sci-chemistry/shelx )"
-DEPEND="${RDEPEND}
-	>=dev-util/scons-1.2"
-
-S="${WORKDIR}"
-MY_S="${WORKDIR}"/cctbx_sources
-MY_B="${WORKDIR}"/cctbx_build
-
-pkg_setup() {
-	if use openmp && ! tc-has-openmp; then
-		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 and icc"
-		ewarn "If you want to build ${PN} with OpenMP, abort now,"
-		ewarn "and switch CC to an OpenMP capable compiler"
-	fi
-	python_set_active_version 2
-}
-
-src_prepare() {
-	local opts
-	local optsld
-
-	epatch \
-		"${FILESDIR}"/${PV}-tst_server.py.patch \
-		"${FILESDIR}"/${PV}-boost.patch \
-		"${FILESDIR}"/${PV}-clipper.patch \
-		"${FILESDIR}"/${PV}-flags.patch \
-		"${FILESDIR}"/${PV}-soname.patch
-
-	eprefixify "${MY_S}"/scitbx/libtbx_refresh.py
-
-	rm -rf "${MY_S}/scons" "${MY_S}/boost" "${MY_S}/PyCifRW"
-	find "${MY_S}/clipper" -name "*.h" -delete
-
-	echo "import os, sys; os.execvp('scons', sys.argv)" > "${MY_S}"/libtbx/command_line/scons.py
-}
-
-src_configure() {
-	local compiler
-	local myconf
-
-	myconf="${MY_S}/libtbx/configure.py"
-
-	compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-	myconf="${myconf} --compiler=${compiler}"
-
-	# 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} ${USE_threads} --scan-boost --use_environment_flags"
-
-	mkdir "${MY_B}" && myconf="${myconf} --current_working_directory=${MY_B}"
-	cd "${MY_B}"
-
-	myconf="${myconf} --build=release fftw3tbx rstbx smtbx mmtbx clipper_adaptbx fable"
-	einfo "configuring with ${python} ${myconf}"
-
-	$(PYTHON) ${myconf} || die "configure failed"
-}
-
-src_compile() {
-	local makeopts_exp
-
-	cd "${MY_B}"
-
-	makeopts_exp=${MAKEOPTS/j/j }
-	makeopts_exp=${makeopts_exp%-l[0-9]*}
-
-	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)/tests/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(){
-#	find cctbx_build/ -type f \( -name "*.py" -o -name "*sh" \) -exec \
-#	sed -e "s:${MY_S}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_sources:g" \
-#	    -e "s:${MY_B}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build:g"  \
-#	    -i '{}' \; || die "Fail to correct path"
-
-	ebegin "removing unnessary files"
-		rm -r "${S}"/cctbx_sources/{clipper,ccp4io,ucs-fonts,TAG} || die "failed to remove uneeded scons"
-		find "${S}" -type f -name "*conftest*" -delete || die "failed to remove uneeded *.o"
-		find "${S}" -type f -name "*.o" -delete || die "failed to remove uneeded *.o"
-		find "${S}" -type f -name "*.c" -delete || die "failed to remove uneeded *.c"
-		find "${S}" -type f -name "*.f" -delete || die "failed to remove uneeded *.c"
-		find "${S}" -type f -name "*.cpp" -delete || die "failed to remove uneeded *.cpp"
-		find "${S}" -type f -name "*.pyc" -delete || die "failed to remove uneeded *.pyc"
-		find "${S}" -type f -name "SCons*" -delete || die "failed to remove uneeded *.pyc"
-		find "${S}" -type f -name "Makefile" -delete || die "failed to remove uneeded *.pyc"
-		find "${S}" -type f -name "config.log" -delete || die "failed to remove uneeded *.pyc"
-		find "${S}" -type d -empty -delete || die
-		find ${MY_B} -maxdepth 1 -type f
-		find ${MY_B} -maxdepth 1 -type f -delete
-	eend
-
-	dobin ${MY_B}/bin/* || die
-	rm -rf ${MY_B}/bin
-	dolib.so ${MY_B}/lib/lib* || die
-	rm -f ${MY_B}/lib/lib*
-
-	insinto /usr/include
-	doins -r ${MY_B}/include/* || die
-	rm -rf ${MY_B}/include
-
-	insinto /usr/libexec/${PN}
-	doins -r ${MY_B}/* || die
-	find "${ED}"/usr/libexec/${PN} -type f -exec chmod 755 '{}' \;
-
-	cd ${MY_S}
-	insinto $(python_get_sitedir)
-	doins -r * || die
-	exeinto $(python_get_sitedir)
-	doexe ${MY_B}/lib/* || die
-	rm -rvf ${MY_B}/lib
-
-	sed \
-		-e "/PYTHONPATH/s:${MY_S}:$(python_get_sitedir):g" \
-		-e "/PYTHONPATH/s:${MY_B}:$(python_get_sitedir):g" \
-		-e "/LD_LIBRARY_PATH/s:${MY_B}/lib:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "/PATH/s:${MY_B}/bin:${EPREFIX}/usr/bin:g" \
-		-e "/PATH/s:${MY_B}/exe:${EPREFIX}/usr/bin:g" \
-		-e "/exec/s:${MY_S}:$(python_get_sitedir):g" \
-		-e "/LIBTBX_BUILD/s:${MY_B}:/usr:g" \
-		-i "${ED}"/usr/bin/* || die
-
-}
-
-pkg_postinst () {
-	python_need_rebuild
-	python_mod_optimize boost_adaptbx cbflib_adaptbx ccp4io_adaptbx cctbx chiltbx clipper_adaptbx crys3d fable fftw3tbx gltbx iotbx libtbx mmtbx omptbx rstbx scitbx smtbx spotfinder tntbx
-}
-
-pkg_postrm () {
-	python_mod_cleanup boost_adaptbx cbflib_adaptbx ccp4io_adaptbx cctbx chiltbx clipper_adaptbx crys3d fable fftw3tbx gltbx iotbx libtbx mmtbx omptbx rstbx scitbx smtbx spotfinder tntbx
-}
-
-check_use() {
-	for var in $@; do
-		if use ${var}; then
-			printf -v "USE_$var" True
-		else
-			printf -v "USE_$var" False
-		fi
-	shift
-	done
-}