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author | Justin Lecher (jlec) <jlec@j-schmitz.net> | 2009-10-11 19:06:44 +0200 |
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committer | Justin Lecher (jlec) <jlec@j-schmitz.net> | 2009-10-13 16:11:45 +0200 |
commit | 0acaf2da0d59735fc0640bb5fc557f060e52502b (patch) | |
tree | 9ddca9e6262cb1e689c1102b452fb3555fe9e689 /sci-libs | |
parent | refmac bump to 5.5.106 (diff) | |
download | sci-0acaf2da0d59735fc0640bb5fc557f060e52502b.tar.gz sci-0acaf2da0d59735fc0640bb5fc557f060e52502b.tar.bz2 sci-0acaf2da0d59735fc0640bb5fc557f060e52502b.zip |
cctbx version bump
Diffstat (limited to 'sci-libs')
-rw-r--r-- | sci-libs/cctbx/ChangeLog | 7 | ||||
-rw-r--r-- | sci-libs/cctbx/Manifest | 8 | ||||
-rw-r--r-- | sci-libs/cctbx/cctbx-2009.02.15.2320-r2.ebuild | 15 | ||||
-rw-r--r-- | sci-libs/cctbx/cctbx-2009.02.15.2320-r3.ebuild | 17 | ||||
-rw-r--r-- | sci-libs/cctbx/cctbx-2009.09.28.1034.ebuild | 191 |
5 files changed, 214 insertions, 24 deletions
diff --git a/sci-libs/cctbx/ChangeLog b/sci-libs/cctbx/ChangeLog index 1b3681675..3f709398c 100644 --- a/sci-libs/cctbx/ChangeLog +++ b/sci-libs/cctbx/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*cctbx-2009.09.28.1034 (11 Oct 2009) + + 11 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> + +cctbx-2009.09.28.1034.ebuild: + version bump + sandbox patch is obsolete + 07 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> cctbx-2009.02.15.2320-r3.ebuild: we also depend on shelx for amd64 now diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest index 075fd07b8..6b9f62305 100644 --- a/sci-libs/cctbx/Manifest +++ b/sci-libs/cctbx/Manifest @@ -1,6 +1,8 @@ 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-r2.ebuild 4639 RMD160 69285fb2b9ef6207a8338e0ed6b335432b23c825 SHA1 fd65e7d76f45a4152fbfaaf286e14ee315edfc83 SHA256 21db2dcc51a47440950b854aa54e5f7612128bb0446e69a1877330af003668b7 -EBUILD cctbx-2009.02.15.2320-r3.ebuild 5686 RMD160 f28998a96dace7dc401e1d5d0db4eb405c860200 SHA1 7fd5b8bc2483a3d9892c33254fc365b1c2f0abf8 SHA256 d5d92d72d093955b074823cacdb615f0bdc0ee2aae61fc90aeda15d14b95740e -MISC ChangeLog 1634 RMD160 59d57119125a06d6b6c61f5d28e41ebf7a8b5518 SHA1 c25c2be08a97310f4f75b098d1c96c58700790aa SHA256 6d8ee4f71be586d9ac9b281a70d6d2b53e7315481405ecf68d81573631a9bcc2 +DIST cctbx-2009.09.28.1034.tar.gz 14359425 RMD160 04b932f6dd2665ffd2aa1a21462993ddf0f2e9c4 SHA1 47a529fa596eddc04c93673da16a688617ce07dd SHA256 1714c7a7985c1709baa9786e12dcc24f0073b76e020d194be24fbbf5b4c8504e +EBUILD cctbx-2009.02.15.2320-r2.ebuild 4644 RMD160 6ea87345c030c9c2ec512ac8be9b8c580cb2caa9 SHA1 614dce37aee6ac67b689e50a510dccd3bb81fe59 SHA256 7977fcdf1cac193e7b236ad771dfb047ecf4c2ef77b34aab18d0f1fc894ddeec +EBUILD cctbx-2009.02.15.2320-r3.ebuild 5686 RMD160 7ccf97179ee2540a89052200750675e588075e77 SHA1 8e77b701ab656793b704dc747cf6555b39b34257 SHA256 9d987f67fa1fa2eec9a2b0dfa2784170afe871c97bc94eb3ef1bd600ef0c3d3b +EBUILD cctbx-2009.09.28.1034.ebuild 5687 RMD160 f3bee8d4b39cb82f16f2a536bfcc0d1e878128b0 SHA1 34715892ac4d2d4dcef5139475a7ec88752e41ed SHA256 763ba7237247d87a137686b14e62ee94247a98aca7b015886d1c4e5b585651d7 +MISC ChangeLog 1807 RMD160 e9e011e4ac6482d3efe4130f8959c3e73362358c SHA1 879af48a729f88b5b49cf40c2da63ccf8f900bda SHA256 7622dd891ba98b522f427956766f6b1f59a6d838616d39f1b2647ec0bf09d90c MISC metadata.xml 438 RMD160 79ad38c94abc71ba32abccdcd670f2f6802c2df3 SHA1 1ebbff28f7e4d135b26b951b6111f6803f78413c SHA256 94d589a2836bffe732cdf993e9b38afc1cde4683a5e5669c44daf6b69595e8da diff --git a/sci-libs/cctbx/cctbx-2009.02.15.2320-r2.ebuild b/sci-libs/cctbx/cctbx-2009.02.15.2320-r2.ebuild index 53d6344dc..d165df8a8 100644 --- a/sci-libs/cctbx/cctbx-2009.02.15.2320-r2.ebuild +++ b/sci-libs/cctbx/cctbx-2009.02.15.2320-r2.ebuild @@ -126,7 +126,6 @@ src_test(){ } src_install(){ - local INST_DIR INST_DIR="/usr/${PN}" @@ -182,14 +181,12 @@ pkg_postrm () { } check_use() { - for var in $@; do - if use ${var}; then - printf -v "USE_$var" True - else - printf -v "USE_$var" False - - fi - shift + if use ${var}; then + printf -v "USE_$var" True + else + printf -v "USE_$var" False + fi + shift done } diff --git a/sci-libs/cctbx/cctbx-2009.02.15.2320-r3.ebuild b/sci-libs/cctbx/cctbx-2009.02.15.2320-r3.ebuild index cc6761923..8f884af6c 100644 --- a/sci-libs/cctbx/cctbx-2009.02.15.2320-r3.ebuild +++ b/sci-libs/cctbx/cctbx-2009.02.15.2320-r3.ebuild @@ -127,7 +127,6 @@ src_test(){ } src_install(){ - # This is what Bill Scott does in the fink package. Do we need this as well? # -e "s:prepend:append:g" \ @@ -136,7 +135,6 @@ src_install(){ -e "s:${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 "${S}" -type f -name "*conftest*" -exec rm -f '{}' \; || die "failed to remove uneeded *.o" @@ -161,7 +159,6 @@ src_install(){ chmod 775 "${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 || \ @@ -182,17 +179,13 @@ 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 + 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-2009.09.28.1034.ebuild b/sci-libs/cctbx/cctbx-2009.09.28.1034.ebuild new file mode 100644 index 000000000..2c086e02c --- /dev/null +++ b/sci-libs/cctbx/cctbx-2009.09.28.1034.ebuild @@ -0,0 +1,191 @@ +# 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 -> ${P}.tar.gz" +LICENSE="cctbx-2.0" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="minimal openmp threads" + +RDEPEND="!minimal? ( sci-chemistry/cns + sci-chemistry/shelx )" +DEPEND="${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" ## needs boost 1.39 + + 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 +} |