diff options
55 files changed, 1990 insertions, 616 deletions
diff --git a/dev-python/Forthon/ChangeLog b/dev-python/Forthon/ChangeLog index 253728161..0bc57f1d7 100644 --- a/dev-python/Forthon/ChangeLog +++ b/dev-python/Forthon/ChangeLog @@ -2,7 +2,13 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*Forthon-0.8.13 (26 Nov 2013) + + 26 Nov 2013; Sébastien Fabbro <bicatali@gentoo.org> +Forthon-0.8.13.ebuild, + -Forthon-0.8.12.ebuild, -files/Forthon-0.8.11-fix_options_parser.patch, + metadata.xml: + dev-python/Forthon: Version bump, keyworded for prefix + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> Forthon-0.8.11.ebuild, metadata.xml: Correct license name - diff --git a/dev-python/Forthon/Forthon-0.8.12.ebuild b/dev-python/Forthon/Forthon-0.8.13.ebuild index a4d068ef8..013179f79 100644 --- a/dev-python/Forthon/Forthon-0.8.12.ebuild +++ b/dev-python/Forthon/Forthon-0.8.13.ebuild @@ -8,12 +8,12 @@ PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) inherit eutils distutils-r1 DESCRIPTION="Python interface generator for Fortran based codes" -HOMEPAGE="http://hifweb.lbl.gov/Forthon http://pypi.python.org/pypi/Forthon" +HOMEPAGE="http://hifweb.lbl.gov/Forthon" SRC_URI="http://hifweb.lbl.gov/${PN}/${P}.tgz" LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="examples" python_prepare_all() { diff --git a/dev-python/Forthon/Manifest b/dev-python/Forthon/Manifest index 1c0b7e8d5..c6bba14f1 100644 --- a/dev-python/Forthon/Manifest +++ b/dev-python/Forthon/Manifest @@ -1 +1 @@ -DIST Forthon-0.8.12.tgz 88767 SHA256 fae70031ecc519bb4547b48fe98513e7b4ae7e1fbaf97ec57cb03d31894ec817 SHA512 e8a2c8f6484ce6410664837d72e29361e416dda7c8b1c0646580c23abcb56df17804287ab15e32aa75c43799c91469c4a1b3da971ed0254e485fca91ecc0c86b WHIRLPOOL bb0b86b555412d9974a60eef338b0137e6175bfd46603beb1e5e1e0108fe5a6019daae671b6973d5ac3d385f43e52caa5638025baabc5db9544c7f772d264786 +DIST Forthon-0.8.13.tgz 89649 SHA256 d10dd393366e28eb0743074f21d56d82085629708862fca14b40c0eb13b123a0 SHA512 06117d0a6743a65d84390f828170c2d681110f6d9912da78402a3b7d611f945f1ece4a475a2cf90aaec605bd604bcf82bf6c1c4635cbea76979c037de206a356 WHIRLPOOL 13ee1b412f027bead726720b97c959a2e9b54aa5d732b1996d3fd61cac7047c0b8ba31cb74781c98eb7b2afb349a1af8b5c07949d01664cebf27046c6d889006 diff --git a/dev-python/Forthon/files/Forthon-0.8.11-fix_options_parser.patch b/dev-python/Forthon/files/Forthon-0.8.11-fix_options_parser.patch deleted file mode 100644 index 6a5bfc122..000000000 --- a/dev-python/Forthon/files/Forthon-0.8.11-fix_options_parser.patch +++ /dev/null @@ -1,17 +0,0 @@ -In order to allow for installation of package for multiple versions of Python -Linux distribution often provide wrappers with correct shebangs tied to specific -Python implementation, e.g. Forthon-2.7, Forthon-python2.7, etc. -This patch fixes logic in Forthon_options to take that into account - -Patch written by Kacper Kowalik <xarthisius@gentoo.org> ---- a/Lib/Forthon_options.py -+++ b/Lib/Forthon_options.py -@@ -92,7 +92,7 @@ class InputError(Exception): - # --- Otherwise ignore the arguments. This is needed since for example this - # --- module may be imported by the compilers module which is used by some - # --- program other than Forthon. --if os.path.basename(sys.argv[0]) == 'Forthon' or sys.argv[0] == '-c': -+if os.path.basename(sys.argv[0]).startswith('Forthon') or sys.argv[0] == '-c': - (options, args) = parser.parse_args() - else: - (options, args) = parser.parse_args(args=[]) diff --git a/dev-python/Forthon/metadata.xml b/dev-python/Forthon/metadata.xml index ef58ee263..114375b99 100644 --- a/dev-python/Forthon/metadata.xml +++ b/dev-python/Forthon/metadata.xml @@ -5,4 +5,15 @@ <email>xarthisius@gentoo.org</email> <name>Kacper Kowalik</name> </maintainer> +<longdescription> + Forthon generates links between Fortran95 and Python. Python is a high + level, object oriented, interactive and scripting language that allows + a flexible and versatile interface to computational tools. The Forthon + package generates the necessary wrapping code which allows access to + the Fortran database and to the Fortran subroutines and + functions. This provides a development package where the + computationally intensive parts of a code can be written in efficient + Fortran, and the high level controlling code can be written in the + much more versatile Python language. +</longdescription> </pkgmetadata> diff --git a/dev-python/emcee/ChangeLog b/dev-python/emcee/ChangeLog index 89f52ada8..387fdcab9 100644 --- a/dev-python/emcee/ChangeLog +++ b/dev-python/emcee/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*emcee-2.0.0 (26 Nov 2013) + + 26 Nov 2013; Sébastien Fabbro <bicatali@gentoo.org> +emcee-2.0.0.ebuild, + metadata.xml: + dev-python/emcee: Version bump + *emcee-1.2.0 (13 Jun 2013) 13 Jun 2013; Justin Lecher <jlec@gentoo.org> -emcee-1.0.1.ebuild, @@ -13,4 +19,3 @@ 20 Apr 2012; Sébastien Fabbro <bicatali@gentoo.org> +emcee-1.0.1.ebuild, +metadata.xml: Initial import - diff --git a/dev-python/emcee/Manifest b/dev-python/emcee/Manifest index bb26a41ba..02b2f1c53 100644 --- a/dev-python/emcee/Manifest +++ b/dev-python/emcee/Manifest @@ -1 +1,2 @@ DIST emcee-1.2.0.tar.gz 22281 SHA256 97c0e342b093f00203aad4f99c0fcdd8a27a0f98d5f8e3b5f2f1f17a1adc1cb7 SHA512 774680b9f43c0b0ed8de73040246a63ddd36cd543b792cc6eb546b5ddcc826b45cc416c118619d5972daaac8bf707338cd05dc2ff9a09a36061cff9fd8f25dfd WHIRLPOOL 24ee8417e7c5d2deca73faa2517fd3304ef16ed7580ee8533cc5987d4d782677926493a761ef0fff061a6018270364f1ef55dd0277ab704404a9d740faaa9a5a +DIST emcee-2.0.0.tar.gz 18774 SHA256 75edb32374afab669877846bd57fc1990a1f48958614b3d349362a2e7110b429 SHA512 5996e22c9ebb231be7e25c6b7f8f396f747bed5d5b64fa7f5c66e5d3c68cfaf6f450e48ccc0af9bc1245a1521afbfcf4da9096fd49a018d5a5d4fbb90a66344a WHIRLPOOL cc8f25808c93c9d95378a213243267f117d7e0c8728d7f8676059d9870acc9bd599d030fa5ce54dd991229e8d95084b7454665e413d9c3ca133834783ba73c01 diff --git a/dev-python/emcee/emcee-2.0.0.ebuild b/dev-python/emcee/emcee-2.0.0.ebuild new file mode 100644 index 000000000..286e957ae --- /dev/null +++ b/dev-python/emcee/emcee-2.0.0.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) + +inherit distutils-r1 + +DESCRIPTION="Python ensemble sampling toolkit for affine-invariant MCMC" +HOMEPAGE="http://danfm.ca/emcee/" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" +DEPEND="${DEPEND}" + +python_test() { + distutils_install_for_testing + ${EPYTHON} -c "import ${PN}; ${PN}.test()" 2>&1 | tee test.log || die + grep -Eq "^(ERROR|FAIL):" test.log && die +} diff --git a/dev-python/emcee/metadata.xml b/dev-python/emcee/metadata.xml index 84d83504b..b4cb18f4a 100644 --- a/dev-python/emcee/metadata.xml +++ b/dev-python/emcee/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> +<herd>sci</herd> +<longdescription lang="en"> This provides a set of sparse matrix types for Python, with modules which implement: - Iterative methods for solving linear systems of equations diff --git a/dev-python/pyqtgraph/ChangeLog b/dev-python/pyqtgraph/ChangeLog index bac3994b6..417792d55 100644 --- a/dev-python/pyqtgraph/ChangeLog +++ b/dev-python/pyqtgraph/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*pyqtgraph-0.9.8 (25 Nov 2013) + + 25 Nov 2013; Guillaume Poulin <poulin.guillaume@gmail.com> + +pyqtgraph-0.9.8.ebuild, -pyqtgraph-0.9.7.ebuild: + Update PyQtGraph to 0.9.8. Support of python 3.3 + 07 Sep 2013; Guillaume Poulin <poulin.guillaume@gmail.com> pyqtgraph-0.9.7.ebuild: remove untested keywords diff --git a/dev-python/pyqtgraph/Manifest b/dev-python/pyqtgraph/Manifest index 8e3de3efa..9343219cb 100644 --- a/dev-python/pyqtgraph/Manifest +++ b/dev-python/pyqtgraph/Manifest @@ -1 +1 @@ -DIST pyqtgraph-0.9.7.tar.gz 915620 SHA256 0182c649533f91959a5116ac9b919f66eca5c619bdcce1eb5b6f772eeb18a4df SHA512 59d037d290a6274d6f88327e06cf09709e92b32981dcf536a2014b2accb52a2c5284144c6e1f1434a8530f1d89ca37edaaec20bf7495d1de83753d5c6e09eade WHIRLPOOL 2552a6516fde12fe3f8e43a0130bf8a485a06dd0d9f572584d1997a74ba382cc381fd7d51c4f21ea6760b62a373254e08547e5605c877265648f38cae6638b1e +DIST pyqtgraph-0.9.8.tar.gz 958092 SHA256 257e7de9053c325ea2cce7a93d54ac035276350e5524d065c538e3d48c90d0ba SHA512 66c578fec00bb3fef791bcdaedfc420b7049d1346a5132b7a016d0d016e886381f4e38fe1c39ab4499df50d1cf4f19ef8bfc52ddf20bba8a928a7bf3b5f21e10 WHIRLPOOL 54098f47711fbfed6ce6b429c554effdc1ceed85d86f7da76a04c5583d8b68af26fe1b06e5bafabc064c7e241078e8fd13c452c901a59d77c114f3d4b7c128e7 diff --git a/dev-python/pyqtgraph/pyqtgraph-0.9.7.ebuild b/dev-python/pyqtgraph/pyqtgraph-0.9.8.ebuild index b5325d2ad..f413626d4 100644 --- a/dev-python/pyqtgraph/pyqtgraph-0.9.7.ebuild +++ b/dev-python/pyqtgraph/pyqtgraph-0.9.8.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7,3_2} ) +PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) inherit distutils-r1 diff --git a/eclass/alternatives-2.eclass b/eclass/alternatives-2.eclass index 7908fe21a..3a031ea5e 100644 --- a/eclass/alternatives-2.eclass +++ b/eclass/alternatives-2.eclass @@ -12,7 +12,7 @@ ALTERNATIVES_DIR="/etc/env.d/alternatives" -DEPEND=">=app-admin/eselect-1.3.4-r100" +DEPEND=">=app-admin/eselect-1.3.8-r100" RDEPEND="${DEPEND} !app-admin/eselect-blas !app-admin/eselect-cblas diff --git a/eclass/intel-sdp.eclass b/eclass/intel-sdp.eclass deleted file mode 100644 index f5f01d8d8..000000000 --- a/eclass/intel-sdp.eclass +++ /dev/null @@ -1,497 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/eclass/intel-sdp.eclass,v 1.13 2013/07/19 14:00:50 jlec Exp $ - -# @ECLASS: intel-sdp.eclass -# @MAINTAINER: -# Justin Lecher <jlec@gentoo.org> -# Sci Team <sci@gentoo.org> -# @BLURB: Handling of Intel's Software Development Products package management - -# @ECLASS-VARIABLE: INTEL_DID -# @DEFAULT_UNSET -# @DESCRIPTION: -# The package download ID from Intel. -# To find out its value, see the links to download in -# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx -# -# e.g. 2504 -# -# Must be defined before inheriting the eclass - -# @ECLASS-VARIABLE: INTEL_DPN -# @DEFAULT_UNSET -# @DESCRIPTION: -# The package name to download from Intel. -# To find out its value, see the links to download in -# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx -# -# e.g. parallel_studio_xe -# -# Must be defined before inheriting the eclass - -# @ECLASS-VARIABLE: INTEL_DPV -# @DEFAULT_UNSET -# @DESCRIPTION: -# The package download version from Intel. -# To find out its value, see the links to download in -# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx -# -# e.g. 2011_sp1_update2 -# -# Must be defined before inheriting the eclass - -# @ECLASS-VARIABLE: INTEL_TARX -# @DEFAULT_UNSET -# @DESCRIPTION: -# The package extention. -# To find out its value, see the links to download in -# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx -# -# e.g. tar.gz -# -# Must be defined before inheriting the eclass -: ${INTEL_TARX:=tgz} - -# @ECLASS-VARIABLE: INTEL_SUBDIR -# @DEFAULT_UNSET -# @DESCRIPTION: -# The package sub-directory where it will end-up in /opt/intel -# To find out its value, you have to do a raw install from the Intel tar ball - -# @ECLASS-VARIABLE: INTEL_SKIP_LICENSE -# @DEFAULT_UNSET -# @DESCRIPTION: -# Possibility to skip the mandatory check for licenses. Only set this if there -# is really no fix. - -# @ECLASS-VARIABLE: INTEL_RPMS_DIR -# @DESCRIPTION: -# Main subdirectory which contains the rpms to extract. -: ${INTEL_RPMS_DIR:=rpm} - -# @ECLASS-VARIABLE: INTEL_X86 -# @DESCRIPTION: -# 32bit arch in rpm names -# -# e.g. i484 -: ${INTEL_X86:=i486} - -# @ECLASS-VARIABLE: INTEL_BIN_RPMS -# @DEFAULT_UNSET -# @DESCRIPTION: -# Functional name of rpm without any version/arch tag -# -# e.g. compilerprof -# -# if the rpm is located in a directory different to INTEL_RPMS_DIR you can -# specify the full path -# -# e.g. CLI_install/rpm/intel-vtune-amplifier-xe-cli - -# @ECLASS-VARIABLE: INTEL_DAT_RPMS -# @DEFAULT_UNSET -# @DESCRIPTION: -# Functional name of rpm of common data which are arch free -# without any version tag -# -# e.g. openmp -# -# if the rpm is located in a directory different to INTEL_RPMS_DIR you can -# specify the full path -# -# e.g. CLI_install/rpm/intel-vtune-amplifier-xe-cli-common - -# @ECLASS-VARIABLE: INTEL_SINGLE_ARCH -# @DESCRIPTION: -# Unset, if only the multilib package will be provided by intel -: ${INTEL_SINGLE_ARCH:=true} - -# @ECLASS-VARIABLE: INTEL_SDP_DB -# @DESCRIPTION: -# Full path to intel registry db -INTEL_SDP_DB="${EROOT%/}"/opt/intel/intel-sdp-products.db - -inherit check-reqs multilib versionator - -_INTEL_PV1=$(get_version_component_range 1) -_INTEL_PV2=$(get_version_component_range 2) -_INTEL_PV3=$(get_version_component_range 3) -_INTEL_PV4=$(get_version_component_range 4) -_INTEL_URI="http://registrationcenter-download.intel.com/irc_nas/${INTEL_DID}/${INTEL_DPN}" - -if [ ${INTEL_SINGLE_ARCH} == true ]; then - SRC_URI=" - amd64? ( multilib? ( ${_INTEL_URI}_${INTEL_DPV}.${INTEL_TARX} ) ) - amd64? ( !multilib? ( ${_INTEL_URI}_${INTEL_DPV}_intel64.${INTEL_TARX} ) ) - x86? ( ${_INTEL_URI}_${INTEL_DPV}_ia32.${INTEL_TARX} )" -else - SRC_URI="${_INTEL_URI}_${INTEL_DPV}.${INTEL_TARX}" -fi - -LICENSE="Intel-SDP" -# Future work, #394411 -#SLOT="${_INTEL_PV1}.${_INTEL_PV2}" -SLOT="0" -IUSE="examples multilib" - -RESTRICT="mirror" - -RDEPEND="" -DEPEND="app-arch/rpm2targz" - -_INTEL_SDP_YEAR=${INTEL_DPV%_update*} -_INTEL_SDP_YEAR=${INTEL_DPV%_sp*} - -# @ECLASS-VARIABLE: INTEL_SDP_DIR -# @DEFAULT_UNSET -# @DESCRIPTION: -# Full rootless path to installation dir -INTEL_SDP_DIR="opt/intel/${INTEL_SUBDIR}-${_INTEL_SDP_YEAR:-${_INTEL_PV1}}.${_INTEL_PV3}.${_INTEL_PV4}" - -# @ECLASS-VARIABLE: INTEL_SDP_EDIR -# @DEFAULT_UNSET -# @DESCRIPTION: -# Full rooted path to installation dir -INTEL_SDP_EDIR="${EROOT%/}/${INTEL_SDP_DIR}" - -S="${WORKDIR}" - -QA_PREBUILT="${INTEL_SDP_DIR}/*" - -# @ECLASS-VARIABLE: INTEL_ARCH -# @DEFAULT_UNSET -# @DESCRIPTION: -# Intels internal names of the arches; will be set at runtime accordingly -# -# e.g. amd64-multilib -> INTEL_ARCH="intel64 ia32" - -# @FUNCTION: _isdp_link_eclipse_plugins -# @INTERNAL -# @DESCRIPTION: -# Creating necessary links to use intel compiler with eclipse -_isdp_link_eclipse_plugins() { - local c f - pushd ${INTEL_SDP_DIR}/eclipse_support > /dev/null - for c in cdt*; do - local cv=${c#cdt} ev=3.$(( ${cv:0:1} - 1)) - if has_version "dev-util/eclipse-sdk:${ev}"; then - einfo "Linking eclipse (v${ev}) plugin cdt (v${cv})" - for f in cdt${cv}/eclipse/features/*; do - dodir /usr/$(get_libdir)/eclipse-${ev}/features - dosym "${INTEL_SDP_EDIR}"/eclipse_support/${f} \ - /usr/$(get_libdir)/eclipse-${ev}/features/ || die - done - for f in cdt${cv}/eclipse/plugins/*; do - dodir /usr/$(get_libdir)/eclipse-${ev}/plugins - dosym "${INTEL_SDP_EDIR}"/eclipse_support/${f} \ - /usr/$(get_libdir)/eclipse-${ev}/plugins/ || die - done - fi - done - popd > /dev/null -} - -# @FUNCTION: _isdp_big-warning -# @USAGE: [pre-check | test-failed] -# @INTERNAL -# @DESCRIPTION: -# warn user that we really require a license -_isdp_big-warning() { - case ${1} in - pre-check ) - echo "" - ewarn "License file not found!" - ;; - - test-failed ) - echo - ewarn "Function test failed. Most probably due to an invalid license." - ewarn "This means you already tried to bypass the license check once." - ;; - esac - - echo "" - ewarn "Make sure you have recieved the an Intel license." - ewarn "To receive a non-commercial license, you need to register at:" - ewarn "http://software.intel.com/en-us/articles/non-commercial-software-development/" - ewarn "Install the license file into ${INTEL_SDP_EDIR}/licenses/" - - case ${1} in - pre-check ) - ewarn "before proceeding with installation of ${P}" - echo "" - ;; - * ) - echo "" - ;; - esac -} - -# @FUNCTION: _isdp_version_test -# @INTERNAL -# @DESCRIPTION: -# Testing for valid license by asking for version information of the compiler -_isdp_version_test() { - local comp comp_full arch warn - case ${PN} in - ifc ) - debug-print "Testing ifort" - comp=ifort - ;; - icc ) - debug-print "Testing icc" - comp=icc - ;; - *) - die "${PN} is not supported for testing" - ;; - esac - - for arch in ${INTEL_ARCH}; do - case ${EBUILD_PHASE} in - install ) - comp_full="${ED}/${INTEL_SDP_DIR}/bin/${arch}/${comp}" - ;; - postinst ) - comp_full="${INTEL_SDP_EDIR}/bin/${arch}/${comp}" - ;; - * ) - ewarn "Compile test not supported in ${EBUILD_PHASE}" - continue - ;; - esac - - debug-print "LD_LIBRARY_PATH=\"${INTEL_SDP_EDIR}/bin/${arch}/\" \"${comp_full}\" -V" - - LD_LIBRARY_PATH="${INTEL_SDP_EDIR}/bin/${arch}/" "${comp_full}" -V &>/dev/null - [[ $? -ne 0 ]] && warn=yes - done - [[ "${warn}" == "yes" ]] && _isdp_big-warning test-failed -} - -# @FUNCTION: _isdp_run-test -# @INTERNAL -# Test if installed compiler is working -_isdp_run-test() { - if [[ -z ${INTEL_SKIP_LICENSE} ]]; then - case ${PN} in - ifc | icc ) - _isdp_version_test ;; - * ) - debug-print "No test available for ${PN}" - ;; - esac - fi -} - -# @FUNCTION: intel-sdp_pkg_pretend -# @DESCRIPTION: -# @CODE -# * Check that the user has a (valid) license file before going on. -# * Check for space requirements being fullfilled -# @CODE -intel-sdp_pkg_pretend() { - local warn=1 dir dirs ret arch a p - - : ${CHECKREQS_DISK_BUILD:=256M} - check-reqs_pkg_pretend - - if [[ -z ${INTEL_SKIP_LICENSE} ]]; then - if echo ${INTEL_LICENSE_FILE} | grep -q @; then - einfo "Looks like you are using following license server:" - einfo " ${INTEL_LICENSE_FILE}" - return 0 - fi - - dirs=( - "${INTEL_SDP_EDIR}/licenses" - "${INTEL_SDP_EDIR}/Licenses" - "${EPREFIX}/opt/intel/licenses" - ) - for dir in "${dirs[@]}" ; do - ebegin "Checking for a license in: ${dir}" - #maybe use nullglob or [[ $(echo ${dir/*lic) != "${dir}/*lic" ]] - [[ $( ls "${dir}"/*lic 2>/dev/null ) ]]; ret=$? - eend ${ret} - if [[ ${ret} == "0" ]]; then - warn=${ret} - break - fi - done - if [[ ${warn} == "1" ]]; then - _isdp_big-warning pre-check - die "Could not find license file" - fi - else - eqawarn "The ebuild doesn't check for a license!" - eqawarn "This shouldn't be done unless there is a serious reason." - fi -} - -# @FUNCTION: intel-sdp_pkg_setup -# @DESCRIPTION: -# Setting up and sorting some internal variables -intel-sdp_pkg_setup() { - local arch a p - - if use x86; then - arch=${INTEL_X86} - INTEL_ARCH="ia32" - elif use amd64; then - arch=x86_64 - INTEL_ARCH="intel64" - if has_multilib_profile; then - arch="x86_64 ${INTEL_X86}" - INTEL_ARCH="intel64 ia32" - fi - fi - INTEL_RPMS=() - INTEL_RPMS_FULL=() - for p in ${INTEL_BIN_RPMS}; do - for a in ${arch}; do - if [ ${p} == $(basename ${p}) ]; then - INTEL_RPMS+=( intel-${p}-${_INTEL_PV4}-${_INTEL_PV1}.${_INTEL_PV2}-${_INTEL_PV3}.${a}.rpm ) - else - INTEL_RPMS_FULL+=( ${p}-${_INTEL_PV4}-${_INTEL_PV1}.${_INTEL_PV2}-${_INTEL_PV3}.${a}.rpm ) - fi - done - done - for p in ${INTEL_DAT_RPMS}; do - if [ ${p} == $(basename ${p}) ]; then - INTEL_RPMS+=( intel-${p}-${_INTEL_PV4}-${_INTEL_PV1}.${_INTEL_PV2}-${_INTEL_PV3}.noarch.rpm ) - else - INTEL_RPMS_FULL+=( ${p}-${_INTEL_PV4}-${_INTEL_PV1}.${_INTEL_PV2}-${_INTEL_PV3}.noarch.rpm ) - fi - done - - case "${EAPI:-0}" in - 0|1|2|3) intel-sdp_pkg_pretend ;; - esac -} - -# @FUNCTION: intel-sdp_src_unpack -# @DESCRIPTION: -# Unpacking necessary rpms from tarball, extract them and rearrange the output. -intel-sdp_src_unpack() { - local l r subdir rb t list=() debug_list - - for t in ${A}; do - for r in ${INTEL_RPMS[@]}; do - rpmdir=${t%%.*}/${INTEL_RPMS_DIR} - list+=( ${rpmdir}/${r} ) - done - - for r in ${INTEL_RPMS_FULL[@]}; do - list+=( ${t%%.*}/${r} ) - done - - debug_list="$(IFS=$'\n'; echo ${list[@]} )" - - debug-print "Adding to decompression list:" - debug-print ${debug_list} - - tar xvf "${DISTDIR}"/${t} ${list[@]} &> "${T}"/rpm-extraction.log - - for r in ${list[@]}; do - rb=$(basename ${r}) - l=.${rb}_$(date +'%d%m%y_%H%M%S').log - einfo "Unpacking ${rb}" - rpm2tar -O ${r} | tar xvf - | sed -e \ - "s:^\.:${EROOT#/}:g" > ${l}; assert "unpacking ${r} failed" - mv ${l} opt/intel/ || die "failed moving extract log file" - done - done - - mv opt/intel/* ${INTEL_SDP_DIR} || die "mv to INTEL_SDP_DIR failed" -} - -# @FUNCTION: intel-sdp_src_install -# @DESCRIPTION: -# Install everything -intel-sdp_src_install() { - if [[ -d "${INTEL_SDP_DIR}"/Documentation ]]; then - dodoc -r "${INTEL_SDP_DIR}"/Documentation/* - - ebegin "Cleaning out documentation" - find "${INTEL_SDP_DIR}"/Documentation -delete || die - eend - fi - - if [[ -d "${INTEL_SDP_DIR}"/Samples ]]; then - if use examples ; then - insinto /usr/share/${P}/examples/ - doins -r "${INTEL_SDP_DIR}"/Samples/* - fi - ebegin "Cleaning out examples" - find "${INTEL_SDP_DIR}"/Samples -delete || die - eend - fi - - if [[ -d "${INTEL_SDP_DIR}"/eclipse_support ]]; then - if has eclipse ${IUSE} && use eclipse; then - _isdp_link_eclipse_plugins - else - ebegin "Cleaning out eclipse plugin" - find "${INTEL_SDP_DIR}"/eclipse_support -delete || die - eend - fi - fi - - if [[ -d "${INTEL_SDP_DIR}"/man ]]; then - doman "${INTEL_SDP_DIR}"/man/en_US/man1/* - if has linguas_ja ${IUSE} && use linguas_ja; then - doman -i18n=ja_JP "${INTEL_SDP_DIR}"/man/ja_JP/man1/* - fi - - find "${INTEL_SDP_DIR}"/man -delete || die - fi - - ebegin "Tagging ${PN}" - find opt -name \*sh -type f -exec sed -i \ - -e "s:<.*DIR>:${INTEL_SDP_EDIR}:g" \ - '{}' + || die - eend - - [[ -d "${ED}" ]] || dodir / - mv opt "${ED}"/ || die "moving files failed" - - dodir "${INTEL_SDP_DIR}"/licenses /opt/intel/ism/rm - keepdir "${INTEL_SDP_DIR}"/licenses /opt/intel/ism/rm -} - -# @FUNCTION: intel-sdp_pkg_postinst -# @DESCRIPTION: -# Add things to intel database -intel-sdp_pkg_postinst() { - # add product registry to intel "database" - local l r - for r in ${INTEL_RPMS}; do - l="$(ls -1 ${EROOT%/}/opt/intel/.${r}_*.log | head -n 1)" - echo >> ${INTEL_SDP_DB} \ - "<:${r%-${_INTEL_PV4}*}-${_INTEL_PV4}:${r}:${INTEL_SDP_EDIR}:${l}:>" - done - _isdp_run-test -} - -# @FUNCTION: intel-sdp_pkg_postrm -# @DESCRIPTION: -# Sanitize intel database -intel-sdp_pkg_postrm() { - # remove from intel "database" - if [[ -e ${INTEL_SDP_DB} ]]; then - local r - for r in ${INTEL_RPMS}; do - sed -i \ - -e "/${r}/d" \ - ${INTEL_SDP_DB} - done - fi -} - -EXPORT_FUNCTIONS pkg_setup src_unpack src_install pkg_postinst pkg_postrm -case "${EAPI:-0}" in - 0|1|2|3) ;; - 4|5) EXPORT_FUNCTIONS pkg_pretend ;; - *) die "EAPI=${EAPI} is not supported" ;; -esac diff --git a/licenses/CPC b/licenses/CPC new file mode 100644 index 000000000..d386afe1c --- /dev/null +++ b/licenses/CPC @@ -0,0 +1,41 @@ +The CPC non-profit use licence agreement is an agreement between the +author(s) of a program distributed by the CPC Program Library and the +person who acquires it. By acquiring the program the person is +agreeing to be bound by the terms of this agreement. + + 1. This licence entitles the licensee (one person) and the + licensee's research group to obtain a copy of the source or + executable code and to use the acquired program for academic or + non-profit use within a research group; or, it entitles the + licensee (one company, organisation or computing centre) to + install the program and allow access to the executable code to + members of the licensee's organisation for academic or non-profit + use. No user or site will re-distribute the source code or + executable code to a third party in original or modified form + without the written permission of the author. + + 2. Publications which result from using the acquired program will + reference the article in Computer Physics Communications which + describes the program. + + 3. This licence does not permit any commercial (profit-making or + proprietary) use or re-licensing or re-distributions. Persons + interested in for-profit use should contact the author. + + 4. To the extent permissible under applicable laws, no + responsibility is assumed and is hereby disclaimed by Elsevier for + any injury and/or damage to persons or property as a result of any + actual or alleged libelous statements, infringement of + intellectual property or privacy rights, or products liability, + whether resulting from negligence or otherwise, including without + limitation from any use or operation of any ideas, instructions, + procedures, products or methods contained in the material therein. + Access to this site is provided on an "as is" basis, and Elsevier + does not warrant that the information or software contained herein + is complete or accurate or free from error. + + This information or software is provided by its creators or + authors as a service to Elsevier subscribers on an "as is" basis, + and if downloaded by the subscriber should be checked for defects + or viruses before being used. Unless noted otherwise, the creators + or authors retain copyright and other proprietary rights. diff --git a/profiles/package.mask b/profiles/package.mask index 306ba64a0..8f48c44aa 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -56,6 +56,7 @@ >=sys-cluster/nullmpi-9999 >=sci-physics/espresso-9999 >=sci-physics/espresso++-9999 +>=sci-physics/tauola-9999 ~sci-chemistry/gromacs-4.5.9999 ~sci-chemistry/gromacs-4.6.9999 ~sci-chemistry/gromacs-9999 @@ -64,6 +65,7 @@ >=sci-chemistry/votca-csgapps-9999 ~sci-visualization/gnuplot-4.6.9999 ~sci-visualization/gnuplot-4.7.9999 +>=sci-visualization/yt-9999 ~sci-chemistry/burrow-owl-9999_pre15 >=sci-chemistry/pymol-apbs-plugin-9999 >=sci-chemistry/coot-9999 diff --git a/sci-biology/mne-python/Manifest b/sci-biology/mne-python/Manifest new file mode 100644 index 000000000..38d6e3b27 --- /dev/null +++ b/sci-biology/mne-python/Manifest @@ -0,0 +1 @@ +DIST v0.7.zip 58120981 SHA256 26711803c8068adc7f3c06997b6bd1e076fea170e9f87af3b488c51eb6e3caa9 SHA512 1221038daa9687e358c7b51aed969c0174e5ea979e35c2e2663a5d2795b751f837bb8e1f45fd12251f713b6b69a5c5086e8f07d417e23abfa4302562f271f774 WHIRLPOOL a44c067c02270285103ad978d2d1afbf46972ad39eeec77548d78bb1515bd4a22fca713c2e814d5b462b09ce3caad2696deda1b09f67ed9f3c8f0a74de3fdaee diff --git a/sci-biology/mne-python/mne-python-0.7.ebuild b/sci-biology/mne-python/mne-python-0.7.ebuild new file mode 100644 index 000000000..ad1fa8b95 --- /dev/null +++ b/sci-biology/mne-python/mne-python-0.7.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="5" + +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit distutils-r1 virtualx + +DESCRIPTION="Python package for MEG and EEG data analysis" +HOMEPAGE="http://martinos.org/mne/mne-python.html" +SRC_URI="https://github.com/mne-tools/mne-python/archive/v${PV}.zip" + +LICENSE="BSD" +SLOT="0" +IUSE="test cuda" +KEYWORDS="~x86 ~amd64" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-libs/scikits_learn[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + sci-biology/pysurfer[${PYTHON_USEDEP}] + sci-visualization/mayavi[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + cuda? ( + dev-python/pycuda[${PYTHON_USEDEP}] + dev-python/scikits-cuda[${PYTHON_USEDEP}] + ) +" + +DEPEND=" + test? ( dev-python/nose ${RDEPEND} ) +" + +S="${WORKDIR}/mne-python-${PV}" + +run_test() { + PYTHONPATH=. MNE_SKIP_SAMPLE_DATASET_TESTS=1 nosetests -v mne +} + +python_test() { + distutils_install_for_testing + esetup.py install --root="${T}/test-${EPYTHON}" --no-compile + # Link to test data that won't be included in the final installation + local TEST_DIR="${T}/test-${EPYTHON}/$(python_get_sitedir)" + cd ${S} || die + find . -type d -name data -exec ln -s ${S}/{} ${TEST_DIR}/{} \; || die + cd ${TEST_DIR} || die + VIRTUALX_COMMAND="run_test" + virtualmake +} diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog index d1c958455..9baf72666 100644 --- a/sci-chemistry/coot/ChangeLog +++ b/sci-chemistry/coot/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Nov 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch: + Update patch for current HEAD + 02 Oct 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch: Update patch for HEAD diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch index 7f8553215..32d08e119 100644 --- a/sci-chemistry/coot/files/9999-pc.patch +++ b/sci-chemistry/coot/files/9999-pc.patch @@ -262,9 +262,7 @@ index 7734f09..c58fe1d 100644 libccp4mg_utils_la_SOURCES = geomutil.cc mgtree.cc cartesian.cc \ diff --git a/ccp4mg-utils/mmut/Makefile.am b/ccp4mg-utils/mmut/Makefile.am -old mode 100755 -new mode 100644 -index d0651db..d4e0bf8 +index d0651db..d4e0bf8 100755 --- a/ccp4mg-utils/mmut/Makefile.am +++ b/ccp4mg-utils/mmut/Makefile.am @@ -70,9 +70,9 @@ INCLUDES = \ @@ -281,9 +279,7 @@ index d0651db..d4e0bf8 # $(WITH_SCRIPT_CFLAGS) diff --git a/ccp4mg-utils/pygl/Makefile.am b/ccp4mg-utils/pygl/Makefile.am -old mode 100755 -new mode 100644 -index a7e68b5..e26a6c8 +index a7e68b5..e26a6c8 100755 --- a/ccp4mg-utils/pygl/Makefile.am +++ b/ccp4mg-utils/pygl/Makefile.am @@ -108,9 +108,9 @@ INCLUDES = \ @@ -300,9 +296,7 @@ index a7e68b5..e26a6c8 # $(WITH_SCRIPT_CFLAGS) diff --git a/ccp4mg-utils/util/Makefile.am b/ccp4mg-utils/util/Makefile.am -old mode 100755 -new mode 100644 -index 399f453..3d2ff55 +index 399f453..3d2ff55 100755 --- a/ccp4mg-utils/util/Makefile.am +++ b/ccp4mg-utils/util/Makefile.am @@ -73,9 +73,9 @@ INCLUDES = \ @@ -546,10 +540,10 @@ index cf81182..3a2af5c 100644 libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \ sequence-assignment.cc diff --git a/ideal/Makefile.am b/ideal/Makefile.am -index be4dc3e..f4cc8eb 100644 +index e52c271..c5c8e6a 100644 --- a/ideal/Makefile.am +++ b/ideal/Makefile.am -@@ -32,11 +32,11 @@ pkgincludedir = $(includedir)/coot/ideal +@@ -33,11 +33,11 @@ pkgincludedir = $(includedir)/coot/ideal INCLUDES = \ -I$(top_srcdir) \ @@ -805,19 +799,20 @@ index de8ab65..4c1b418 100644 ]) diff --git a/macros/goo-canvas.m4 b/macros/goo-canvas.m4 -index e2494a5..cf96688 100644 +index e2494a5..89c908e 100644 --- a/macros/goo-canvas.m4 +++ b/macros/goo-canvas.m4 -@@ -35,7 +35,7 @@ if test x$goocanvas_prefix != x; then +@@ -35,8 +35,7 @@ if test x$goocanvas_prefix != x; then # SGI compiler CC (CXX=CC) needs -lm to link maths library, but # GCC c++ does not. # - GOOCANVAS_LDOPTS="-L$goocanvas_prefix/lib -lgoocanvas" +- + GOOCANVAS_LIBS="-L$goocanvas_prefix/lib -lgoocanvas" - else # the compiler looks in the "standard" places for GOOCANVAS. (or uses pkgconfig) -@@ -54,15 +54,15 @@ else + +@@ -54,18 +53,16 @@ else break;; esac if test -z "${PKG_CONFIG}"; then @@ -834,9 +829,23 @@ index e2494a5..cf96688 100644 -LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS" +LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS" CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS" +- +- + dnl # 20130929: why do I do this? I don't remember. Using libtool + dnl # in this way is not a good idea (configure makes libtool). + dnl # +@@ -85,18 +82,15 @@ dnl # note that we use ./libtool (running in the build dir) because $LIBTOOL + dnl CXX="libtool --mode=link $CXX" + dnl break;; + dnl esac +- +- + AC_LANG_PUSH(C++) + AC_TRY_LINK([#include "goocanvas.h"] ,[ GooCanvas *a; ], have_goocanvas=yes, have_goocanvas=no) + AC_LANG_POP +- + AC_MSG_RESULT($have_goocanvas) - -@@ -96,7 +96,7 @@ AC_MSG_RESULT($have_goocanvas) if test x$have_goocanvas = xyes; then GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS" diff --git a/sci-chemistry/xdrfile/ChangeLog b/sci-chemistry/xdrfile/ChangeLog deleted file mode 100644 index e96258494..000000000 --- a/sci-chemistry/xdrfile/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-chemistry/xdrfile -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*xdrfile-1.1.1 (30 Dec 2012) - - 30 Dec 2012; Christoph Junghans <ottxor@gentoo.org> +xdrfile-1.1.1.ebuild, - -xdrfile-1.1.ebuild: - version bump - - 09 Oct 2012; Alexey Shvetsov <alexxy@gentoo.org> xdrfile-1.1.ebuild: - [sci-chemistry/xdrfile] Add keywords - - 09 Oct 2012; Alexey Shvetsov <alexxy@gentoo.org> xdrfile-1.1.ebuild: - [sci-chemistry/xdrfile] actualy allow optional fortran - -*xdrfile-1.1 (09 Oct 2012) - - 09 Oct 2012; Alexey Shvetsov <alexxy@gentoo.org> +metadata.xml, - +xdrfile-1.1.ebuild: - [sci-chemistry/xdrfile] Add to repo diff --git a/sci-chemistry/xdrfile/Manifest b/sci-chemistry/xdrfile/Manifest deleted file mode 100644 index de3e93aad..000000000 --- a/sci-chemistry/xdrfile/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST xdrfile-1.1.1.tar.gz 378942 SHA256 4a2c8c7626dc3bdce45a6165d15d092cea85f39dfce0d176695d98ab3e6b4047 SHA512 bff06b08e547b956825f9b16a55fe93d07ff0c529426b892fd4b39be538774aa06facffc68994215e22e36edfa5642674653022da0762ca7cd1b7bc654112868 WHIRLPOOL d71a6a33334dfed2cd9e6036128cced52afbc215d608263086f50484a1dd4571568d66cd3d81e509ea5e1e55940755cb90846fc9f359035be6cfd13d46f3b8d4 diff --git a/sci-chemistry/xdrfile/metadata.xml b/sci-chemistry/xdrfile/metadata.xml deleted file mode 100644 index b2558d8c6..000000000 --- a/sci-chemistry/xdrfile/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>alexxy@gentoo.org</email> - <name>Alexey Shvetsov</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/xdrfile/xdrfile-1.1.1.ebuild b/sci-chemistry/xdrfile/xdrfile-1.1.1.ebuild deleted file mode 100644 index 9228cfae6..000000000 --- a/sci-chemistry/xdrfile/xdrfile-1.1.1.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -FORTRAN_NEEDED="fortran" - -inherit fortran-2 - -DESCRIPTION="Library to read xtc gromacs trajectory" -HOMEPAGE="http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library" -SRC_URI="ftp://ftp.gromacs.org/pub/contrib/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="fortran" - -src_configure() { - econf \ - $(use_enable fortran) -} diff --git a/sci-libs/gsl/files/gsl-1.16-cblas-external.patch b/sci-libs/gsl/files/gsl-1.16-cblas-external.patch index 7277aa42e..c29ef5294 100644 --- a/sci-libs/gsl/files/gsl-1.16-cblas-external.patch +++ b/sci-libs/gsl/files/gsl-1.16-cblas-external.patch @@ -207,6 +207,19 @@ diff -Nur gsl-1.16.orig/Makefile.am gsl-1.16/Makefile.am -e 's|@LIBS[@]|$(LIBS)|g' \ -e 's|@VERSION[@]|$(VERSION)|g' +--- gsl-1.16.orig/multifit/Makefile.am 2013-07-18 06:04:26.000000000 +1000 ++++ gsl-1.16/multifit/Makefile.am 2013-11-22 16:57:26.170330257 +1100 +@@ -13,8 +13,8 @@ + TESTS = $(check_PROGRAMS) + + test_SOURCES = test.c +-test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ++test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la + + #demo_SOURCES = demo.c +-#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ++#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la + diff -Nur gsl-1.16.orig/multimin/Makefile.am gsl-1.16/multimin/Makefile.am --- gsl-1.16.orig/multimin/Makefile.am 2013-07-17 13:04:26.000000000 -0700 +++ gsl-1.16/multimin/Makefile.am 2013-08-19 15:25:27.729497736 -0700 diff --git a/sci-misc/openfst/ChangeLog b/sci-misc/openfst/ChangeLog index b84b7dbd2..3d9cf2cd8 100644 --- a/sci-misc/openfst/ChangeLog +++ b/sci-misc/openfst/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*openfst-1.3.4 (21 Nov 2013) + + 21 Nov 2013; Pavel Denisov <pavel.a.denisov@gmail.com> +files/kaldi.patch, + +openfst-1.3.4.ebuild, -openfst-1.3.2.ebuild: + sci-misc/openfst: version bump, patch from Kaldi + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> openfst-1.2.7.ebuild, openfst-1.3.2.ebuild, metadata.xml: Add ~amd64 or ~x86 keywords for revdeps diff --git a/sci-misc/openfst/Manifest b/sci-misc/openfst/Manifest index 6c0467fd1..effcbf472 100644 --- a/sci-misc/openfst/Manifest +++ b/sci-misc/openfst/Manifest @@ -1,2 +1,2 @@ DIST openfst-1.2.7.tar.gz 668134 SHA256 a38b10a7a1b6c054fb15035f3197f566ac6b23bc2acd5958052165ae7ce5c11c SHA512 899297a12b51acef51a82148a04160acd4bb4e1925da18e20a810814401542aaa582928ae3b80b96f49890420796cae7acd7cbf1d21fb6bc6c755254f1ae2c67 WHIRLPOOL b9c1d9a7b592a43cd77aa6778451c9de8bbf135f39f1415d467b25279c6a360c9537dcdb8b9795023e482462668e61ad66de8e843f211b72a7986b448d6e200a -DIST openfst-1.3.2.tar.gz 723259 SHA256 4e1c2e4f6c54aef15cf13f4f01611ac72122a97214dfa7dab0b7d1a7e1214602 SHA512 5cbaebc3e99c2156379bdaeddef6972b37019cbdce7e2744cf5020f300e959410dce8d1fb1b354c3691975a2d1c0f40123feab46ded59919e4b13a010bbb78f0 WHIRLPOOL a0ca8e814ff1f7c09fd64687dacadf66da3945560e3b16f9afc797df391dc85b7d124314354ddd823ee142131b3d7bbd7914f5659e8c6fc49e8b0abac74be0b2 +DIST openfst-1.3.4.tar.gz 769158 SHA256 e95fa96674e1c9d6866bbf79b9cd755c5121ad165b76224c7c6bbfa139399a61 SHA512 6ed87cbb949776b8702545a51d129e03f33428369b20255d637191e054ce04e529969aef49549b098b144cfde45cd9b741e6cba6680f815c04ad5717fdb0cbd9 WHIRLPOOL 593fd22668044f9ec8df70c274ee910f9da85a48fcd33c73993e54afd21298208d69804342b4e3a5d36e59aa92e853e84d95d1623c3708e7e1fc70e42916949f diff --git a/sci-misc/openfst/files/kaldi.patch b/sci-misc/openfst/files/kaldi.patch new file mode 100644 index 000000000..3a3854eff --- /dev/null +++ b/sci-misc/openfst/files/kaldi.patch @@ -0,0 +1,599 @@ +diff -crB openfst-1.3.4.orig/src/include/fst/interval-set.h openfst-1.3.4/src/include/fst/interval-set.h +*** openfst-1.3.4.orig/src/include/fst/interval-set.h 2013-01-24 06:36:23.000000000 +0400 +--- openfst-1.3.4/src/include/fst/interval-set.h 2013-11-21 15:59:08.541136087 +0400 +*************** +*** 37,74 **** + class IntervalSet { + public: + struct Interval { +! T begin; +! T end; + +! Interval() : begin(-1), end(-1) {} + +! Interval(T b, T e) : begin(b), end(e) {} + + bool operator<(const Interval &i) const { +! return begin < i.begin || (begin == i.begin && end > i.end); + } + + bool operator==(const Interval &i) const { +! return begin == i.begin && end == i.end; + } + + bool operator!=(const Interval &i) const { +! return begin != i.begin || end != i.end; + } + + istream &Read(istream &strm) { + T n; + ReadType(strm, &n); +! begin = n; + ReadType(strm, &n); +! end = n; + return strm; + } + + ostream &Write(ostream &strm) const { +! T n = begin; + WriteType(strm, n); +! n = end; + WriteType(strm, n); + return strm; + } +--- 37,74 ---- + class IntervalSet { + public: + struct Interval { +! T begin_; +! T end_; + +! Interval() : begin_(-1), end_(-1) {} + +! Interval(T b, T e) : begin_(b), end_(e) {} + + bool operator<(const Interval &i) const { +! return begin_ < i.begin_ || (begin_ == i.begin_ && end_ > i.end_); + } + + bool operator==(const Interval &i) const { +! return begin_ == i.begin_ && end_ == i.end_; + } + + bool operator!=(const Interval &i) const { +! return begin_ != i.begin_ || end_ != i.end_; + } + + istream &Read(istream &strm) { + T n; + ReadType(strm, &n); +! begin_ = n; + ReadType(strm, &n); +! end_ = n; + return strm; + } + + ostream &Write(ostream &strm) const { +! T n = begin_; + WriteType(strm, n); +! n = end_; + WriteType(strm, n); + return strm; + } +*************** +*** 108,114 **** + lower_bound(intervals_.begin(), intervals_.end(), interval); + if (lb == intervals_.begin()) + return false; +! return (--lb)->end > value; + } + + // Requires intervals be normalized. +--- 108,114 ---- + lower_bound(intervals_.begin(), intervals_.end(), interval); + if (lb == intervals_.begin()) + return false; +! return (--lb)->end_ > value; + } + + // Requires intervals be normalized. +*************** +*** 123,129 **** + + bool Singleton() const { + return intervals_.size() == 1 && +! intervals_[0].begin + 1 == intervals_[0].end; + } + + +--- 123,129 ---- + + bool Singleton() const { + return intervals_.size() == 1 && +! intervals_[0].begin_ + 1 == intervals_[0].end_; + } + + +*************** +*** 178,194 **** + T size = 0; + for (T i = 0; i < intervals_.size(); ++i) { + Interval &inti = intervals_[i]; +! if (inti.begin == inti.end) + continue; + for (T j = i + 1; j < intervals_.size(); ++j) { + Interval &intj = intervals_[j]; +! if (intj.begin > inti.end) + break; +! if (intj.end > inti.end) +! inti.end = intj.end; + ++i; + } +! count_ += inti.end - inti.begin; + intervals_[size++] = inti; + } + intervals_.resize(size); +--- 178,194 ---- + T size = 0; + for (T i = 0; i < intervals_.size(); ++i) { + Interval &inti = intervals_[i]; +! if (inti.begin_ == inti.end_) + continue; + for (T j = i + 1; j < intervals_.size(); ++j) { + Interval &intj = intervals_[j]; +! if (intj.begin_ > inti.end_) + break; +! if (intj.end_ > inti.end_) +! inti.end_ = intj.end_; + ++i; + } +! count_ += inti.end_ - inti.begin_; + intervals_[size++] = inti; + } + intervals_.resize(size); +*************** +*** 208,224 **** + oset->count_ = 0; + + while (it1 != intervals_.end() && it2 != iintervals->end()) { +! if (it1->end <= it2->begin) { + ++it1; +! } else if (it2->end <= it1->begin) { + ++it2; + } else { + Interval interval; +! interval.begin = max(it1->begin, it2->begin); +! interval.end = min(it1->end, it2->end); + ointervals->push_back(interval); +! oset->count_ += interval.end - interval.begin; +! if (it1->end < it2->end) + ++it1; + else + ++it2; +--- 208,224 ---- + oset->count_ = 0; + + while (it1 != intervals_.end() && it2 != iintervals->end()) { +! if (it1->end_ <= it2->begin_) { + ++it1; +! } else if (it2->end_ <= it1->begin_) { + ++it2; + } else { + Interval interval; +! interval.begin_ = max(it1->begin_, it2->begin_); +! interval.end_ = min(it1->end_, it2->end_); + ointervals->push_back(interval); +! oset->count_ += interval.end_ - interval.begin_; +! if (it1->end_ < it2->end_) + ++it1; + else + ++it2; +*************** +*** 235,255 **** + oset->count_ = 0; + + Interval interval; +! interval.begin = 0; + for (typename vector<Interval>::const_iterator it = intervals_.begin(); + it != intervals_.end(); + ++it) { +! interval.end = min(it->begin, maxval); +! if (interval.begin < interval.end) { + ointervals->push_back(interval); +! oset->count_ += interval.end - interval.begin; + } +! interval.begin = it->end; + } +! interval.end = maxval; +! if (interval.begin < interval.end) { + ointervals->push_back(interval); +! oset->count_ += interval.end - interval.begin; + } + } + +--- 235,255 ---- + oset->count_ = 0; + + Interval interval; +! interval.begin_ = 0; + for (typename vector<Interval>::const_iterator it = intervals_.begin(); + it != intervals_.end(); + ++it) { +! interval.end_ = min(it->begin_, maxval); +! if (interval.begin_ < interval.end_) { + ointervals->push_back(interval); +! oset->count_ += interval.end_ - interval.begin_; + } +! interval.begin_ = it->end_; + } +! interval.end_ = maxval; +! if (interval.begin_ < interval.end_) { + ointervals->push_back(interval); +! oset->count_ += interval.end_ - interval.begin_; + } + } + +*************** +*** 263,269 **** + oset->count_ = 0; + } else { + IntervalSet<T> cset; +! iset.Complement(intervals_.back().end, &cset); + Intersect(cset, oset); + } + } +--- 263,269 ---- + oset->count_ = 0; + } else { + IntervalSet<T> cset; +! iset.Complement(intervals_.back().end_, &cset); + Intersect(cset, oset); + } + } +*************** +*** 277,285 **** + typename vector<Interval>::const_iterator it2 = intervals->begin(); + + while (it1 != intervals_.end() && it2 != intervals->end()) { +! if (it1->end <= it2->begin) { + ++it1; +! } else if (it2->end <= it1->begin) { + ++it2; + } else { + return true; +--- 277,285 ---- + typename vector<Interval>::const_iterator it2 = intervals->begin(); + + while (it1 != intervals_.end() && it2 != intervals->end()) { +! if (it1->end_ <= it2->begin_) { + ++it1; +! } else if (it2->end_ <= it1->begin_) { + ++it2; + } else { + return true; +*************** +*** 300,320 **** + bool overlap = false; // point in both intervals_ and intervals + + while (it1 != intervals_.end() && it2 != intervals->end()) { +! if (it1->end <= it2->begin) { // no overlap - it1 first + only1 = true; + ++it1; +! } else if (it2->end <= it1->begin) { // no overlap - it2 first + only2 = true; + ++it2; +! } else if (it2->begin == it1->begin && it2->end == it1->end) { // equals + overlap = true; + ++it1; + ++it2; +! } else if (it2->begin <= it1->begin && it2->end >= it1->end) { // 1 c 2 + only2 = true; + overlap = true; + ++it1; +! } else if (it1->begin <= it2->begin && it1->end >= it2->end) { // 2 c 1 + only1 = true; + overlap = true; + ++it2; +--- 300,320 ---- + bool overlap = false; // point in both intervals_ and intervals + + while (it1 != intervals_.end() && it2 != intervals->end()) { +! if (it1->end_ <= it2->begin_) { // no overlap - it1 first + only1 = true; + ++it1; +! } else if (it2->end_ <= it1->begin_) { // no overlap - it2 first + only2 = true; + ++it2; +! } else if (it2->begin_ == it1->begin_ && it2->end_ == it1->end_) { // equals + overlap = true; + ++it1; + ++it2; +! } else if (it2->begin_ <= it1->begin_ && it2->end_ >= it1->end_) { // 1 c 2 + only2 = true; + overlap = true; + ++it1; +! } else if (it1->begin_ <= it2->begin_ && it1->end_ >= it2->end_) { // 2 c 1 + only1 = true; + overlap = true; + ++it2; +*************** +*** 346,356 **** + typename vector<Interval>::const_iterator it2 = intervals->begin(); + + while (it1 != intervals_.end() && it2 != intervals->end()) { +! if (it1->end <= it2->begin) { // no overlap - it1 first + ++it1; +! } else if (it2->begin < it1->begin || it2->end > it1->end) { // no C + return false; +! } else if (it2->end == it1->end) { + ++it1; + ++it2; + } else { +--- 346,356 ---- + typename vector<Interval>::const_iterator it2 = intervals->begin(); + + while (it1 != intervals_.end() && it2 != intervals->end()) { +! if (it1->end_ <= it2->begin_) { // no overlap - it1 first + ++it1; +! } else if (it2->begin_ < it1->begin_ || it2->end_ > it1->end_) { // no C + return false; +! } else if (it2->end_ == it1->end_) { + ++it1; + ++it2; + } else { +*************** +*** 370,376 **** + ++it) { + if (it != intervals->begin()) + strm << ","; +! strm << "[" << it->begin << "," << it->end << ")"; + } + strm << "}"; + return strm; +--- 370,376 ---- + ++it) { + if (it != intervals->begin()) + strm << ","; +! strm << "[" << it->begin_ << "," << it->end_ << ")"; + } + strm << "}"; + return strm; +diff -crB openfst-1.3.4.orig/src/include/fst/minimize.h openfst-1.3.4/src/include/fst/minimize.h +*** openfst-1.3.4.orig/src/include/fst/minimize.h 2013-01-24 06:36:23.000000000 +0400 +--- openfst-1.3.4/src/include/fst/minimize.h 2013-11-21 15:59:08.539136087 +0400 +*************** +*** 134,140 **** + typedef typename A::Weight Weight; + typedef ReverseArc<A> RevA; + +! CyclicMinimizer(const ExpandedFst<A>& fst) { + Initialize(fst); + Compute(fst); + } +--- 134,147 ---- + typedef typename A::Weight Weight; + typedef ReverseArc<A> RevA; + +! CyclicMinimizer(const ExpandedFst<A>& fst): +! // tell the Partition data-member to expect multiple repeated +! // calls to SplitOn with the same element if we are non-deterministic. +! P_(fst.Properties(kIDeterministic, true) == 0) { +! if(fst.Properties(kIDeterministic, true) == 0) +! CHECK(Weight::Properties() & kIdempotent); // this minimization +! // algorithm for non-deterministic FSTs can only work with idempotent +! // semirings. + Initialize(fst); + Compute(fst); + } +*************** +*** 315,321 **** + typedef typename A::StateId ClassId; + typedef typename A::Weight Weight; + +! AcyclicMinimizer(const ExpandedFst<A>& fst) { + Initialize(fst); + Refine(fst); + } +--- 322,334 ---- + typedef typename A::StateId ClassId; + typedef typename A::Weight Weight; + +! AcyclicMinimizer(const ExpandedFst<A>& fst): +! // tell the Partition data-member to expect multiple repeated +! // calls to SplitOn with the same element if we are non-deterministic. +! partition_(fst.Properties(kIDeterministic, true) == 0) { +! if(fst.Properties(kIDeterministic, true) == 0) +! CHECK(Weight::Properties() & kIdempotent); // minimization for +! // non-deterministic FSTs can only work with idempotent semirings. + Initialize(fst); + Refine(fst); + } +*************** +*** 531,543 **** + void Minimize(MutableFst<A>* fst, + MutableFst<A>* sfst = 0, + float delta = kDelta) { +! uint64 props = fst->Properties(kAcceptor | kIDeterministic| +! kWeighted | kUnweighted, true); +! if (!(props & kIDeterministic)) { +! FSTERROR() << "FST is not deterministic"; +! fst->SetProperties(kError, kError); +! return; +! } + + if (!(props & kAcceptor)) { // weighted transducer + VectorFst< GallicArc<A, STRING_LEFT> > gfst; +--- 544,550 ---- + void Minimize(MutableFst<A>* fst, + MutableFst<A>* sfst = 0, + float delta = kDelta) { +! uint64 props = fst->Properties(kAcceptor | kWeighted | kUnweighted, true); + + if (!(props & kAcceptor)) { // weighted transducer + VectorFst< GallicArc<A, STRING_LEFT> > gfst; +diff -crB openfst-1.3.4.orig/src/include/fst/partition.h openfst-1.3.4/src/include/fst/partition.h +*** openfst-1.3.4.orig/src/include/fst/partition.h 2013-01-24 06:36:23.000000000 +0400 +--- openfst-1.3.4/src/include/fst/partition.h 2013-11-21 15:59:08.539136087 +0400 +*************** +*** 43,50 **** + friend class PartitionIterator<T>; + + struct Element { +! Element() : value(0), next(0), prev(0) {} +! Element(T v) : value(v), next(0), prev(0) {} + + T value; + Element* next; +--- 43,50 ---- + friend class PartitionIterator<T>; + + struct Element { +! Element() : value(0), next(0), prev(0) {} +! Element(T v) : value(v), next(0), prev(0) {} + + T value; + Element* next; +*************** +*** 52,60 **** + }; + + public: +! Partition() {} + +! Partition(T num_states) { + Initialize(num_states); + } + +--- 52,62 ---- + }; + + public: +! Partition(bool allow_repeated_split): +! allow_repeated_split_(allow_repeated_split) {} + +! Partition(bool allow_repeated_split, T num_states): +! allow_repeated_split_(allow_repeated_split) { + Initialize(num_states); + } + +*************** +*** 137,152 **** + if (class_size_[class_id] == 1) return; + + // first time class is split +! if (split_size_[class_id] == 0) + visited_classes_.push_back(class_id); +! + // increment size of split (set of element at head of chain) + split_size_[class_id]++; +! + // update split point +! if (class_split_[class_id] == 0) +! class_split_[class_id] = classes_[class_id]; +! if (class_split_[class_id] == elements_[element_id]) + class_split_[class_id] = elements_[element_id]->next; + + // move to head of chain in same class +--- 139,154 ---- + if (class_size_[class_id] == 1) return; + + // first time class is split +! if (split_size_[class_id] == 0) { + visited_classes_.push_back(class_id); +! class_split_[class_id] = classes_[class_id]; +! } + // increment size of split (set of element at head of chain) + split_size_[class_id]++; +! + // update split point +! if (class_split_[class_id] != 0 +! && class_split_[class_id] == elements_[element_id]) + class_split_[class_id] = elements_[element_id]->next; + + // move to head of chain in same class +*************** +*** 157,165 **** + // class indices of the newly created class. Returns the new_class id + // or -1 if no new class was created. + T SplitRefine(T class_id) { + // only split if necessary +! if (class_size_[class_id] == split_size_[class_id]) { +! class_split_[class_id] = 0; + split_size_[class_id] = 0; + return -1; + } else { +--- 159,169 ---- + // class indices of the newly created class. Returns the new_class id + // or -1 if no new class was created. + T SplitRefine(T class_id) { ++ ++ Element* split_el = class_split_[class_id]; + // only split if necessary +! //if (class_size_[class_id] == split_size_[class_id]) { +! if(split_el == NULL) { // we split on everything... + split_size_[class_id] = 0; + return -1; + } else { +*************** +*** 163,180 **** + split_size_[class_id] = 0; + return -1; + } else { +- + T new_class = AddClass(); + size_t remainder = class_size_[class_id] - split_size_[class_id]; + if (remainder < split_size_[class_id]) { // add smaller +- Element* split_el = class_split_[class_id]; + classes_[new_class] = split_el; +- class_size_[class_id] = split_size_[class_id]; +- class_size_[new_class] = remainder; + split_el->prev->next = 0; + split_el->prev = 0; + } else { +- Element* split_el = class_split_[class_id]; + classes_[new_class] = classes_[class_id]; + class_size_[class_id] = remainder; + class_size_[new_class] = split_size_[class_id]; +--- 167,189 ---- + split_size_[class_id] = 0; + return -1; + } else { + T new_class = AddClass(); ++ ++ if(allow_repeated_split_) { // split_size_ is possibly ++ // inaccurate, so work it out exactly. ++ size_t split_count; Element *e; ++ for(split_count=0,e=classes_[class_id]; ++ e != split_el; split_count++, e=e->next); ++ split_size_[class_id] = split_count; ++ } + size_t remainder = class_size_[class_id] - split_size_[class_id]; + if (remainder < split_size_[class_id]) { // add smaller + classes_[new_class] = split_el; + split_el->prev->next = 0; + split_el->prev = 0; ++ class_size_[class_id] = split_size_[class_id]; ++ class_size_[new_class] = remainder; + } else { + classes_[new_class] = classes_[class_id]; + class_size_[class_id] = remainder; + class_size_[new_class] = split_size_[class_id]; +*************** +*** 245,254 **** +--- 254,269 ---- + vector<T> class_size_; + + // size of split for each class ++ // in the nondeterministic case, split_size_ is actually an upper ++ // bound on the size of split for each class. + vector<T> split_size_; + + // set of visited classes to be used in split refine + vector<T> visited_classes_; ++ ++ // true if input fst was deterministic: we can make ++ // certain assumptions in this case that speed up the algorithm. ++ bool allow_repeated_split_; + }; + + diff --git a/sci-misc/openfst/openfst-1.3.2.ebuild b/sci-misc/openfst/openfst-1.3.4.ebuild index 7f92b1cc3..70e39d14d 100644 --- a/sci-misc/openfst/openfst-1.3.2.ebuild +++ b/sci-misc/openfst/openfst-1.3.4.ebuild @@ -2,6 +2,8 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ +EAPI="5" + inherit eutils flag-o-matic multilib DESCRIPTION="Finite State Transducer tools by Google et al." @@ -9,19 +11,11 @@ HOMEPAGE="http://www.openfst.org" SRC_URI="http://www.openfst.org/twiki/pub/FST/FstDownload/${P}.tar.gz" LICENSE="Apache-2.0" - SLOT="0" - KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" - -src_install() { - emake DESTDIR="${D}" install || die "install failed" - dodoc AUTHORS NEWS README || die "docs missing" +src_prepare() { + epatch "${FILESDIR}/kaldi.patch" } src_test() { diff --git a/sci-physics/geant-vmc/ChangeLog b/sci-physics/geant-vmc/ChangeLog index 073cddd20..f555d288f 100644 --- a/sci-physics/geant-vmc/ChangeLog +++ b/sci-physics/geant-vmc/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*geant-vmc-4.2.14b (26 Nov 2013) + + 26 Nov 2013; Sébastien Fabbro <bicatali@gentoo.org> +geant-vmc-4.2.14b.ebuild, + -geant-vmc-4.2.14a.ebuild: + sci-physics/geant-vmc: Version bump + *geant-vmc-3.1.15a (05 Jun 2013) *geant-vmc-4.2.14a (05 Jun 2013) diff --git a/sci-physics/geant-vmc/Manifest b/sci-physics/geant-vmc/Manifest index 0709d2517..ff977f576 100644 --- a/sci-physics/geant-vmc/Manifest +++ b/sci-physics/geant-vmc/Manifest @@ -1,2 +1,2 @@ DIST geant321+_vmc.1.15a.tar.gz 11301200 SHA256 bcb29719be1a6dd2842f1a2d66e50d176b1be9d9dd07e7d573db500465857922 SHA512 a5d92cbd0b4199feeedace3e0b09f7cdef6e8270bed44ae7adb024a3a8e6f0fdce51ed6ade3dd58a841594ebf1b4430c2702b71e262075b790e8a82c24c2ac0a WHIRLPOOL 98f0cf1d23bd54a58413aaa8c14cccd626654371ac43f00b7c3d8ff729db2e9f421c0251a0768ed77dadf791982c3f1853d46f44af8e34cdb3bb4eed8fa3d73c -DIST geant4_vmc.2.14a.tar.gz 19221674 SHA256 ec460c0099aab368b43dbcec94a5e535ea12044670662728acc87aedd843c7e2 SHA512 7e800afc5aa31959310b6b95cd0b6fb8db0157f0e72d4d6e039e0b8ad263759edbd83c850658523d7311bd157bc4c7ca3a96ca676de84976ab2952f85cca7952 WHIRLPOOL 7e5bd14d610d5eeb4433d4799f3344a8a50f5d1c7b4a1737891671b4f22ec2f7dd4c87bf907b52a606b10198d05cba6b00952aade896d4a98c95d0c9905ae407 +DIST geant4_vmc.2.14b.tar.gz 631633 SHA256 640396025d8c6f10d78ff1442d0b73721a2809b757a712682ceb58672e790254 SHA512 01b51aafbc27b03a7aff938b27511f0fcc4b17b731d3cb770698be9216b9d22f1c9bc0c962750064167e90bb50e92920ccae31debd3fe07cd4a3feec6154dc60 WHIRLPOOL 9cdc90197e4609b79abc7a4a11762f23d9c6adff70d2404e4a6988a59c4c365fad3f1bd793bba1936f9b051c5826b985e032292e722a3df7d5a6723931675ad8 diff --git a/sci-physics/geant-vmc/geant-vmc-4.2.14a.ebuild b/sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild index 801bbb048..801bbb048 100644 --- a/sci-physics/geant-vmc/geant-vmc-4.2.14a.ebuild +++ b/sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog index 17335b174..d48b682c5 100644 --- a/sci-physics/lammps/ChangeLog +++ b/sci-physics/lammps/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*lammps-20131123 (22 Nov 2013) + + 22 Nov 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20131123.ebuild: + sci-physics/lammps-20131123: Version bump. + *lammps-20131111 (11 Nov 2013) 11 Nov 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20131111.ebuild: diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest index 9b47fffed..2cf4032d8 100644 --- a/sci-physics/lammps/Manifest +++ b/sci-physics/lammps/Manifest @@ -1,6 +1,7 @@ DIST lammps-11Nov13.tar.gz 57121119 SHA256 911035f4a428b4abfe744239fd54660a8caefcf70bc5abea820ff6c4baec9ad9 SHA512 7fa1d20834c2b58277c54ec36b286099eb29728f73a28c596285eed37c7ca0f1dfe22460eb49000d3586c88c00a0051cf73c35f718b1cd9fd1bb41aabe710021 WHIRLPOOL c79b4be1cc7dd8d038d9b4e523ec71229122de9b9d0f98d93e6255896f8f5b68dd38f5264146f22d206dee32ed5a972a881b9160f0a3b52b053613582aecf38b DIST lammps-16Aug13.tar.gz 48337879 SHA256 740d35046961df7ea2dd39e2b7a28e5ff1414f283ac9f568986bd1f2b8b036d9 SHA512 1e56751b94e2af8487c77066846cad7e3a98b7f990a90db9b57e32dc8e3c0a4b9be3431a92f393962fb703ce4957c1d2580545e27549e47a3207e88ec158aa8d WHIRLPOOL d3d442d1d7e9e0267de2a637fd44c87df6dc8eaad61de28cc1aa75d93b49b7877c1de21df251fc8d812e36391f2c5d5e7a75b4b349e6749e9efb9b5266edeb77 DIST lammps-17Sep13.tar.gz 49985563 SHA256 607f6bfadd644bfa8403af1f38d28b4b36bc8d2fe50f09514c7fa13c2d180cbb SHA512 fb303d26846ea3cf42cd6fae2a641989b1debd5c3c4482f006293cb9ace91040faf7bfdc9fbb7c99934414fbeb8b85899c7ff8ce7239a0c3d698a0e1187ae3c6 WHIRLPOOL bd1e308845880831d404447b88784a769c18c472cd22463b949e22a6444de0ffe7826ed2ffc238d909429e2b58c024d368f2c7ee870bda41172958cff840b394 +DIST lammps-23Nov13.tar.gz 57113682 SHA256 2291e26b7bc3e640f1fbd9ffebbaa2173b665fa9d3757b1eb2aa73bc7837876c SHA512 68758c58f6b8f3b554cad18e610da06875e4abfd0ddb9d85da079ccc52f8d1fce5b3447d9b7c7c607a2e887b2d71af04f221bbe96e13d4276702054338537a2a WHIRLPOOL b9aab585fd735e31beb59c5f1ce1187da8d4235aefbc1a83e89b410f79299c39f37d9157cc3549a139f9746d7b22cf2b2277609c0d675fee6cc35e67ca0c026e DIST lammps-23Sep13.tar.gz 50063308 SHA256 0d8c575dc137a67865bbfc408f60dd7d3c74371c48d5f64f884dcfa02501a6d4 SHA512 0ffa44fe9e2ad3d16b0c23699e3a9c114c7731f49b5b7b561fda2f811c57bc273ad236cb9a091eb9bcf98324ee6451689c769cfc418046af0024862f99f81e17 WHIRLPOOL aa3c23c95071594453d585596d8cac0ecd5909a342143fdee78f9d97e205c32faa0705b6341028529bf8347c55f5f5f8e74f408010545e1154e6375e4566c7f6 DIST lammps-30Aug13.tar.gz 48632345 SHA256 8d20ab00412feda5c9869de0188c52fb77f1faa51b317f09706eff35e651d961 SHA512 9722a3a4a7adc3387014650bd5a3ed18f3081065791507d0c39227a394f375f10a8ffbb5510fac24fcc6e84a40b98c0ad21d576969824284e65be94c445e5a24 WHIRLPOOL 50c6f4aed0ef21aa9078eb16ea15f6d6a89bc24316a40183ac993fbf3fecca2c55a5bcf1715cfbecff24ea07e96c55ba082679b11926c50f6ac2da2ec17547e4 DIST lammps-30Sep13.tar.gz 50062591 SHA256 a39df3b158e1cc587e5f25e2aba6c3dd4696d90a30e1067b17bf64a9ebcc5795 SHA512 f6caf05d19bff3b2bf39cda55ca85966b09cf2f0a6bdbe60c4c9daa8caf13e409270db9a37e6d28267b35b5f262cdb8ae2e36095f9c942515368d9e6d8c5020b WHIRLPOOL 60236db937618d15e9b61f7aeeeecfe8273b17ff9798c91790d9a31a7578c17bb6dfcd72bbaed861f16d7df07a18348adfadf4ac5fcb8ebe32c9fa966b6c73b1 diff --git a/sci-physics/lammps/lammps-20131123.ebuild b/sci-physics/lammps/lammps-20131123.ebuild new file mode 100644 index 000000000..9ef5cddc2 --- /dev/null +++ b/sci-physics/lammps/lammps-20131123.ebuild @@ -0,0 +1,115 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/lammps-20130526.ebuild,v 1.1 2013/06/26 23:53:11 ottxor Exp $ + +EAPI=5 + +FORTRAN_NEEDED="package-meam" + +inherit eutils fortran-2 + +convert_month() { + case $1 in + 01) echo Jan + ;; + 02) echo Feb + ;; + 03) echo Mar + ;; + 04) echo Apr + ;; + 05) echo May + ;; + 06) echo Jun + ;; + 07) echo Jul + ;; + 08) echo Aug + ;; + 09) echo Sep + ;; + 10) echo Oct + ;; + 11) echo Nov + ;; + 12) echo Dec + ;; + *) echo unknown + ;; + esac +} + +MY_P=${PN}-$((10#${PV:6:2}))$(convert_month ${PV:4:2})${PV:2:2} + +DESCRIPTION="Large-scale Atomic/Molecular Massively Parallel Simulator" +HOMEPAGE="http://lammps.sandia.gov/" +SRC_URI="http://lammps.sandia.gov/tars/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" + +DEPEND="mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MY_P}" + +lmp_emake() { + local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" + LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" + + # Note: The lammps makefile uses CC to indicate the C++ compiler. + emake \ + ARCHIVE=$(tc-getAR) \ + CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ + F90=$(usex mpi "mpif90" "$(tc-getFC)") \ + LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ + CCFLAGS="${CXXFLAGS}" \ + F90FLAGS="${FCFLAGS}" \ + LINKFLAGS="${LDFLAGS}" \ + LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ + MPI_INC=$(usex mpi '' "-I../STUBS") \ + MPI_PATH=$(usex mpi '' '-L../STUBS') \ + MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ + "$@" +} + +src_compile() { + # Compile stubs for serial version. + use mpi || lmp_emake -C src stubs + + # Build optional packages. + if use package-meam; then + lmp_emake -C src yes-meam + lmp_emake -j1 -C lib/meam -f Makefile.gfortran + fi + use package-dipole && emake -C src yes-dipole + use package-rigid && emake -C src yes-rigid + + # Compile. + lmp_emake -C src serial +} + +src_install() { + newbin "src/lmp_serial" "lmp" + + local LAMMPS_POTENTIALS="/usr/share/${PF}/potentials" + insinto "${LAMMPS_POTENTIALS}" + doins potentials/* + echo "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS}" > 99lammps + doenvd 99lammps + + if use examples; then + local LAMMPS_EXAMPLES="/usr/share/${PF}/examples" + elog "The examples can be found in ${LAMMPS_EXAMPLES}" + insinto "${LAMMPS_EXAMPLES}" + doins -r examples/* + fi + + dodoc README + if use doc; then + dodoc doc/Manual.pdf + dohtml -r doc/* + fi +} diff --git a/sci-physics/mc-tester/ChangeLog b/sci-physics/mc-tester/ChangeLog new file mode 100644 index 000000000..e93c066f9 --- /dev/null +++ b/sci-physics/mc-tester/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-physics/mc-tester +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*mc-tester-1.25.0 (20 Nov 2013) + + 20 Nov 2013; Jauhien Piatlicki (jauhien) <piatlicki@gmail.com> + +mc-tester-1.25.0.ebuild, +files/mc-tester-1.25.0-compare.sh.patch, + +metadata.xml: + Ebuild for sci-physics/mc-tester added + diff --git a/sci-physics/mc-tester/Manifest b/sci-physics/mc-tester/Manifest new file mode 100644 index 000000000..baeebc68d --- /dev/null +++ b/sci-physics/mc-tester/Manifest @@ -0,0 +1 @@ +DIST MC-TESTER-1.25.0.tar.gz 4298408 SHA256 21736b8ec317f39caa0fab2d53635a10ddafef4b675839f5d4a46eef4b9ce587 SHA512 0cd529e05ae18f7f2fe62251b11fbdc62ce7c0cbb59218b56d682f854c731713ce72b8baf5a08ca0b359dc4600e6b411f165827b2d9829b98e1d3dbace78fbb0 WHIRLPOOL 233d0e5b25cbf1527d58e95c0ed32d2fa71fcc519027f526d179e8b323d567836287574f08786836f9f1440dce70bc9a5086da8335e497687b6d685804700656 diff --git a/sci-physics/mc-tester/files/mc-tester-1.25.0-compare.sh.patch b/sci-physics/mc-tester/files/mc-tester-1.25.0-compare.sh.patch new file mode 100644 index 000000000..180dcb029 --- /dev/null +++ b/sci-physics/mc-tester/files/mc-tester-1.25.0-compare.sh.patch @@ -0,0 +1,30 @@ +--- analyze/compare.sh ++++ analyze/compare.sh +@@ -6,13 +6,14 @@ + #---------------------------------- + # Change these variables + #---------------------------------- +-FILE1=mc-tester.root #first generation step file +-FILE2=mc-tester2.root #second generation step file +-MCTESTER_DIR= #location of MC-TESTER ++FILE1="${1}" #first generation step file ++FILE2="${2}" #second generation step file ++MCTESTER_DIR=/usr #location of MC-TESTER + + #---------------------------------- + +-MCTESTER_ANALYZE_DIR=${MCTESTER_DIR}/analyze ++MCTESTER_ANALYZE_DIR=${MCTESTER_DIR}/libexec/mc-tester/analyze ++MCTESTER_DATA_DIR=${MCTESTER_DIR}/share/mc-tester + export MC_TESTER_LIBS_DIR=${MCTESTER_DIR}/lib + + WORKING_DIR=`pwd` +@@ -24,7 +25,7 @@ + cd $WORKING_DIR + + #copy base .tex file needed for booklet and create +-cp ${MCTESTER_ANALYZE_DIR}/tester.tex ./ ++cp ${MCTESTER_DATA_DIR}/tester.tex ./ + latex tester.tex + latex tester.tex + latex tester.tex diff --git a/sci-physics/mc-tester/mc-tester-1.25.0.ebuild b/sci-physics/mc-tester/mc-tester-1.25.0.ebuild new file mode 100644 index 000000000..43f835d4d --- /dev/null +++ b/sci-physics/mc-tester/mc-tester-1.25.0.ebuild @@ -0,0 +1,65 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +MYPN=MC-TESTER + +DESCRIPTION="A universal tool for comparisons of Monte Carlo predictions in High Energy Physics" +HOMEPAGE="http://mc-tester.web.cern.ch/MC-TESTER/" +SRC_URI="http://mc-tester.web.cern.ch/MC-TESTER/${MYPN}-${PV}.tar.gz" +LICENSE="CPC GPL-2+" +#HepMC interface is licensed under GPL, other code under CPC + +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples hepmc" + +RDEPEND="sci-physics/root + hepmc? ( sci-physics/hepmc ) +" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +S="${WORKDIR}/${MYPN}" + +src_prepare() { + epatch "${FILESDIR}/${P}-compare.sh.patch" +} + +src_configure() { + econf \ + --with-root="${EPREFIX}/usr" \ + --without-Pythia8 \ + $(use_with hepmc HepMC "${EPREFIX}/usr") +} + +src_compile() { + emake + use doc && cd doc && emake +} + +src_install() { + emake PREFIX="${D}/usr" install + newbin analyze/compare.sh mc-tester-compare + + insinto /usr/libexec/${PN}/analyze + doins analyze/*.C + insinto /usr/share/${PN} + doins analyze/*.tex + + if use doc; then + dohtml doc/doxygenDocs/html/* + dodoc doc/{README*,USER-TESTS,tester.ps.gz} + fi + + use examples && dodoc -r examples-* +} + +pkg_postinst() { + elog "A script to perform an analysis step is installed as /usr/bin/mc-tester-compare" + elog "it takes two root files with generation results as command line arguments" +} diff --git a/sci-physics/mc-tester/metadata.xml b/sci-physics/mc-tester/metadata.xml new file mode 100644 index 000000000..2edb7b2ba --- /dev/null +++ b/sci-physics/mc-tester/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + +<herd>sci-physics</herd> +<maintainer> + <email>piatlicki@gmail.com</email> +</maintainer> + +<longdescription> + A universal tool for comparisons of Monte Carlo predictions in High Energy Physics +</longdescription> +<use> + <flag name="hepmc">Compile <pkg>sci-physics/hepmc</pkg> interface</flag> +</use> +</pkgmetadata> diff --git a/sci-physics/tauola/ChangeLog b/sci-physics/tauola/ChangeLog new file mode 100644 index 000000000..dfcbc894f --- /dev/null +++ b/sci-physics/tauola/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-physics/tauola +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*tauola-9999 (22 Nov 2013) +*tauola-1.1.3 (22 Nov 2013) + + 22 Nov 2013; Jauhien Piatlicki <piatlicki@gmail.com> +tauola-1.1.3.ebuild, + +tauola-9999.ebuild, +files/tauola-1.1.3-makefile.patch, + +files/tauola-1.1.3-tau-spinner-makefile.patch, +metadata.xml: + ebuild added + diff --git a/sci-physics/tauola/Manifest b/sci-physics/tauola/Manifest new file mode 100644 index 000000000..c582281d2 --- /dev/null +++ b/sci-physics/tauola/Manifest @@ -0,0 +1 @@ +DIST TAUOLA.1.1.3.tar.gz 7152535 SHA256 9b9141a6460477e6cb3c53845f384740539e54540130f69373268b7c2995defc SHA512 ca0c67d61d8476715788ebd7f145bea86ffce2d2a6f5590d66dfd14551fe817d97b1527f6d160b2ea2dc195f1af478f80a5644408e4c1da5ac0ecdbaccc20624 WHIRLPOOL 1ec2b22da2e12ecc400f174ba2fe40bc2bc24e0495f0ae793b2211a5f1dcdc600f31543056a9c9900fe4d049222046604e789ec2eb809a927b26c66ff7d636da diff --git a/sci-physics/tauola/files/tauola-1.1.3-makefile.patch b/sci-physics/tauola/files/tauola-1.1.3-makefile.patch new file mode 100644 index 000000000..5d4195253 --- /dev/null +++ b/sci-physics/tauola/files/tauola-1.1.3-makefile.patch @@ -0,0 +1,12 @@ +--- Makefile ++++ Makefile +@@ -36,8 +36,7 @@ + + install: + mkdir -p $(PREFIX)/include +- mkdir -p $(PREFIX)/include/Tauola +- cp include/Tauola/* $(PREFIX)/include/Tauola/. ++ cp -r include/* $(PREFIX)/include + mkdir -p $(PREFIX)/lib + cp lib/* $(PREFIX)/lib/. + diff --git a/sci-physics/tauola/files/tauola-1.1.3-tau-spinner-makefile.patch b/sci-physics/tauola/files/tauola-1.1.3-tau-spinner-makefile.patch new file mode 100644 index 000000000..8b3474c5d --- /dev/null +++ b/sci-physics/tauola/files/tauola-1.1.3-tau-spinner-makefile.patch @@ -0,0 +1,11 @@ +--- TauSpinner/Makefile ++++ TauSpinner/Makefile +@@ -30,7 +30,7 @@ + + %.o: %.cxx + $(CC) $(CFLAGS) -c $< -o $@ -Iinclude \ +- -I$(PREFIX)/include \ ++ -I../include \ + -I$(LHAPDFLOCATION)/include + + %.o: %.f diff --git a/sci-physics/tauola/metadata.xml b/sci-physics/tauola/metadata.xml new file mode 100644 index 000000000..b4f9e77e4 --- /dev/null +++ b/sci-physics/tauola/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + +<herd>sci-physics</herd> +<maintainer> + <email>piatlicki@gmail.com</email> +</maintainer> + +<longdescription> + tau decay Monte Carlo generator +</longdescription> +<use> + <flag name="hepmc">Compile <pkg>sci-physics/hepmc</pkg> interface</flag> + <flag name="tau-spinner">Compile with TauSpinner library</flag> +</use> +</pkgmetadata> diff --git a/sci-physics/tauola/tauola-1.1.3.ebuild b/sci-physics/tauola/tauola-1.1.3.ebuild new file mode 100644 index 000000000..1abb1a44d --- /dev/null +++ b/sci-physics/tauola/tauola-1.1.3.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +MYPN=TAUOLA + +DESCRIPTION="tau decay Monte Carlo generator" +HOMEPAGE="http://tauolapp.web.cern.ch/tauolapp/" +SRC_URI="http://tauolapp.web.cern.ch/tauolapp/resources/${MYPN}.${PV}/${MYPN}.${PV}.tar.gz" +LICENSE="CPC GPL-2+" +#HepMC interface is licensed under GPL, other code under CPC + +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples hepmc tau-spinner" + +RDEPEND="hepmc? ( sci-physics/hepmc ) + tau-spinner? ( sci-physics/lhapdf ) +" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen + app-text/ghostscript-gpl + app-text/texlive ) +" + +S="${WORKDIR}/${MYPN}" + +src_prepare() { + epatch "${FILESDIR}/${P}-makefile.patch" "${FILESDIR}/${P}-tau-spinner-makefile.patch" +} + +src_configure() { + econf \ + --without-mc-tester \ + --without-pythia8 \ + $(use_with hepmc hepmc "${EPREFIX}/usr") \ + $(use_with tau-spinner) \ + $(use_with tau-spinner lhapdf "${EPREFIX}/usr") +} + +src_compile() { + emake + if use doc; + then + cd "${S}/documentation/doxy_documentation" || die + emake + cd "${S}/documentation/latex_documentation" || die + emake + fi +} + +src_install() { + emake PREFIX="${D}/usr" install + + if use doc; then + dohtml documentation/doxy_documentation/html/* + dodoc documentation/latex_documentation/Tauola_interface_design.pdf + fi + + if use examples; + then + dodoc -r examples + use tau-spinner && docinto tau-spinner && dodoc -r TauSpinner/examples + fi +} diff --git a/sci-physics/tauola/tauola-9999.ebuild b/sci-physics/tauola/tauola-9999.ebuild new file mode 100644 index 000000000..67bc2b686 --- /dev/null +++ b/sci-physics/tauola/tauola-9999.ebuild @@ -0,0 +1,75 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +MYPN=TAUOLA + +DESCRIPTION="tau decay Monte Carlo generator" +HOMEPAGE="http://tauolapp.web.cern.ch/tauolapp/" +SRC_URI="" +LICENSE="CPC GPL-2+" +#HepMC interface is licensed under GPL, other code under CPC + +SLOT="0" +IUSE="doc examples hepmc tau-spinner" + +RDEPEND="hepmc? ( sci-physics/hepmc ) + tau-spinner? ( sci-physics/lhapdf ) +" +DEPEND="${RDEPEND} + net-misc/wget + doc? ( app-doc/doxygen + app-text/ghostscript-gpl + app-text/texlive ) +" + +S="${WORKDIR}/${MYPN}" + +src_unpack() { + #there is no public svn, just generated tarball, so fetch it + wget "http://tauolapp.web.cern.ch/tauolapp/resources/${MYPN}.development.version/${MYPN}.development.version.tar.gz" || die + unpack "./${MYPN}.development.version.tar.gz" +} + +src_prepare() { + epatch "${FILESDIR}/${PN}-1.1.3-makefile.patch" "${FILESDIR}/${PN}-1.1.3-tau-spinner-makefile.patch" +} + +src_configure() { + econf \ + --without-mc-tester \ + --without-pythia8 \ + $(use_with hepmc hepmc "${EPREFIX}/usr") \ + $(use_with tau-spinner) \ + $(use_with tau-spinner lhapdf "${EPREFIX}/usr") +} + +src_compile() { + emake + if use doc; + then + cd "${S}/documentation/doxy_documentation" || die + emake + cd "${S}/documentation/latex_documentation" || die + emake + fi +} + +src_install() { + emake PREFIX="${D}/usr" install + + if use doc; then + dohtml documentation/doxy_documentation/html/* + dodoc documentation/latex_documentation/Tauola_interface_design.pdf + fi + + if use examples; + then + dodoc -r examples + use tau-spinner && docinto tau-spinner && dodoc -r TauSpinner/examples + fi +} diff --git a/sci-visualization/yt/Manifest b/sci-visualization/yt/Manifest new file mode 100644 index 000000000..0e4b9dda4 --- /dev/null +++ b/sci-visualization/yt/Manifest @@ -0,0 +1 @@ +DIST yt-2.6.tar.gz 2327271 SHA256 5dce4c865c4e390ed1b7e6e3bf89a8d89014f32eb5669a219d7d468c58c04459 SHA512 cbd20db03b1cd5fe8fff3b24d51de13ef620add8f0808a50e45efe9568efba008c23625f1cd8edb3adc5315bc2ebc2898032bdf9f9611df1148569975c9fdf1c WHIRLPOOL 41be52855ae6f915aac2393a02cc014fc7023222b82c7a68365a32780509968ec817f55600dbc6608f51f068d3a70bc488310c7716d38bb5d9388d8b1c49c95f diff --git a/sci-visualization/yt/yt-2.6.ebuild b/sci-visualization/yt/yt-2.6.ebuild new file mode 100644 index 000000000..8484302c8 --- /dev/null +++ b/sci-visualization/yt/yt-2.6.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +PYTHON_COMPAT=( python2_7 ) +DISTUTILS_IN_SOURCE_BUILD=1 + +inherit distutils-r1 flag-o-matic + +DESCRIPTION="Astrophysical Simulation Analysis and Vizualization package" +HOMEPAGE="http://yt-project.org/" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +CDEPEND="media-libs/freetype:2 + media-libs/libpng:0= + sci-libs/hdf5:=" +RDEPEND="${CDEPEND} + dev-python/ipython[notebook,${PYTHON_USEDEP}] + dev-python/pyx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/sympy[${PYTHON_USEDEP}]" +DEPEND="${CDEPEND} + dev-python/Forthon[${PYTHON_USEDEP}] + >=dev-python/cython-0.19[${PYTHON_USEDEP}] + >=dev-python/setuptools-0.7[${PYTHON_USEDEP}] + test? ( ${RDEPEND} + dev-python/nose[${PYTHON_USEDEP}] + )" + +python_prepare_all() { + append-flags -fno-strict-aliasing + sed -i setup.py \ + -e 's:build/lib:../../../&:' || die + sed -i yt/utilities/setup.py \ + -e "s:/usr:${EPREFIX}/usr:g" || die + mv yt/utilities/kdtree/fKD.{f,F}90 || die # Forthon-0.8.13 + distutils-r1_python_prepare_all +} + +# TODO +#python_test() { +# nosetests || die +#} diff --git a/sci-visualization/yt/yt-9999.ebuild b/sci-visualization/yt/yt-9999.ebuild index 39886ced3..16ef051ce 100644 --- a/sci-visualization/yt/yt-9999.ebuild +++ b/sci-visualization/yt/yt-9999.ebuild @@ -1,10 +1,11 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 PYTHON_COMPAT=( python2_7 ) +DISTUTILS_IN_SOURCE_BUILD=1 EHG_REPO_URI="https://bitbucket.org/yt_analysis/yt" EHG_REVISION="yt" @@ -14,14 +15,14 @@ DESCRIPTION="Astrophysical Simulation Analysis and Vizualization package" HOMEPAGE="http://yt-project.org/" SRC_URI="" -LICENSE="GPL-3" +LICENSE="BSD" SLOT="0" KEYWORDS="" IUSE="test" -CDEPEND="media-libs/freetype - media-libs/libpng - sci-libs/hdf5" +CDEPEND="media-libs/freetype:2 + media-libs/libpng:0= + sci-libs/hdf5:=" RDEPEND="${CDEPEND} dev-python/ipython[notebook,${PYTHON_USEDEP}] dev-python/pyx[${PYTHON_USEDEP}] @@ -30,12 +31,22 @@ RDEPEND="${CDEPEND} dev-python/matplotlib[${PYTHON_USEDEP}] dev-python/sympy[${PYTHON_USEDEP}]" DEPEND="${CDEPEND} - dev-python/Forthon[${PYTHON_USEDEP}] + dev-python/Forthon[${PYTHON_USEDEP}] >=dev-python/cython-0.19[${PYTHON_USEDEP}] >=dev-python/setuptools-0.7[${PYTHON_USEDEP}] test? ( ${RDEPEND} dev-python/nose[${PYTHON_USEDEP}] - )" + )" + +python_prepare_all() { + append-flags -fno-strict-aliasing + sed -i setup.py \ + -e 's:build/lib:../../../&:' || die + sed -i yt/utilities/setup.py \ + -e "s:/usr:${EPREFIX}/usr:g" || die + mv yt/utilities/kdtree/fKD.{f,F}90 || die # Forthon-0.8.13 + distutils-r1_python_prepare_all +} # TODO #python_test() { diff --git a/sys-cluster/charm/ChangeLog b/sys-cluster/charm/ChangeLog index cab86a4e6..833fa0760 100644 --- a/sys-cluster/charm/ChangeLog +++ b/sys-cluster/charm/ChangeLog @@ -2,6 +2,19 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 22 Nov 2013; Nicolas Bock <nicolasbock@gmail.com> charm-6.6.0_rc1.ebuild: + sys-cluster/charm-6.6.0-rc1: Reorganized some variables. + + 20 Nov 2013; Nicolas Bock <nicolasbock@gmail.com> + +files/charm-6.6.0-static-library-fix.patch, charm-6.6.0_rc1.ebuild: + sys-cluster/charm-6.6.0_rc1: Rewrote patch to enable shared mode. The patch + is targeted now for v6.7.0 by upstream. + +*charm-6.6.0_rc1 (20 Nov 2013) + + 20 Nov 2013; Nicolas Bock <nicolasbock@gmail.com> +charm-6.6.0_rc1.ebuild: + sys-cluster/charm-6.6.0_rc1: Version bump. + *charm-6.5.1-r3 (08 Nov 2013) 08 Nov 2013; Nicolas Bock <nicolasbock@gmail.com> +charm-6.5.1-r3.ebuild, diff --git a/sys-cluster/charm/charm-6.6.0_rc1.ebuild b/sys-cluster/charm/charm-6.6.0_rc1.ebuild new file mode 100644 index 000000000..7823e50e0 --- /dev/null +++ b/sys-cluster/charm/charm-6.6.0_rc1.ebuild @@ -0,0 +1,222 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sys-cluster/charm/charm-6.5.0.ebuild,v 1.1 2013/06/26 23:58:38 ottxor Exp $ + +EAPI=5 + +FORTRAN_STANDARD="90" +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit eutils flag-o-matic fortran-2 git-r3 multilib python-any-r1 toolchain-funcs + +DESCRIPTION="Message-passing parallel language and runtime system" +HOMEPAGE="http://charm.cs.uiuc.edu/" +SRC_URI="" + +EGIT_REPO_URI="http://charm.cs.uiuc.edu/gerrit/charm" +EGIT_BRANCH="charm" +EGIT_COMMIT="57051a8f07496b9f8f696f59fad477c8a2bc3e4d" + +LICENSE="charm" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="charmdebug charmtracing charmproduction cmkopt doc examples mlogft mpi numa smp static-libs syncft tcp" + +RDEPEND="mpi? ( virtual/mpi )" +DEPEND=" + ${RDEPEND} + doc? ( + >=app-text/poppler-0.12.3-r3[utils] + dev-tex/latex2html + virtual/tex-base + >=dev-python/beautifulsoup-4 + dev-python/lxml + media-libs/netpbm + ${PYTHON_DEPS} + )" + +REQUIRED_USE=" + doc? ( ${PYTHON_REQ_USE} ) + cmkopt? ( !charmdebug !charmtracing ) + charmproduction? ( !charmdebug !charmtracing )" + +get_opts() { + local CHARM_OPTS + + # TCP instead of default UDP for socket comunication + # protocol + CHARM_OPTS+="$(usex tcp ' tcp' '')" + + # enable direct SMP support using shared memory + CHARM_OPTS+="$(usex smp ' smp' '')" + + CHARM_OPTS+="$(usex mlogft ' mlogft' '')" + CHARM_OPTS+="$(usex syncft ' syncft' '')" + + # Build shared libraries by default. + CHARM_OPTS+=" --build-shared" + + if use charmproduction; then + CHARM_OPTS+=" --with-production" + else + if use charmdebug; then + CHARM_OPTS+=" --enable-charmdebug" + fi + + if use charmtracing; then + CHARM_OPTS+=" --enable-tracing --enable-tracing-commthread" + fi + fi + + CHARM_OPTS+="$(usex numa ' --with-numa' '')" + + echo $CHARM_OPTS +} + +src_prepare() { + sed \ + -e "/CMK_CF77/s:[fg]77:$(usex mpi "mpif90" "$(tc-getF77)"):g" \ + -e "/CMK_CF90/s:f95:$(usex mpi "mpif90" "$(tc-getFC)"):g" \ + -e "/CMK_CF90/s:\`which f90.*$::g" \ + -e "/CMK_CXX/s:g++:$(usex mpi "mpic++" "$(tc-getCXX)"):g" \ + -e "/CMK_CC/s:gcc:$(usex mpi "mpicc" "$(tc-getCC)"):g" \ + -e '/CMK_F90_MODINC/s:-p:-I:g' \ + -e "/CMK_LD/s:\"$: ${LDFLAGS} \":g" \ + -i src/arch/$(usex mpi "mpi" "net")*-linux*/*sh || die + sed \ + -e "/CMK_CF90/s:gfortran:$(usex mpi "mpif90" "$(tc-getFC)"):g" \ + -e "/F90DIR/s:gfortran:$(usex mpi "mpif90" "$(tc-getFC)"):g" \ + -e "/f95target/s:gfortran:$(usex mpi "mpif90" "$(tc-getFC)"):g" \ + -e "/f95version/s:gfortran:$(usex mpi "mpif90" "$(tc-getFC)"):g" \ + -i src/arch/common/*.sh || die + + sed \ + -e "s:-o conv-cpm:${LDFLAGS} &:g" \ + -e "s:-o charmxi:${LDFLAGS} &:g" \ + -e "s:-o charmrun-silent:${LDFLAGS} &:g" \ + -e "s:-o charmrun-notify:${LDFLAGS} &:g" \ + -e "s:-o charmrun:${LDFLAGS} &:g" \ + -e "s:-o charmd_faceless:${LDFLAGS} &:g" \ + -e "s:-o charmd:${LDFLAGS} &:g" \ + -i \ + src/scripts/Makefile \ + src/util/charmrun-src/Makefile || die + + # CMK optimization + use cmkopt && append-cppflags -DCMK_OPTIMIZE=1 + + # Fix QA notice. Filed report with upstream. + append-cflags -DALLOCA_H + + #epatch "${FILESDIR}/charm-6.5.1-cleanup-config.patch" + #epatch "${FILESDIR}/charm-6.5.1-CkReductionMgr.patch" + #epatch "${FILESDIR}/charm-6.5.1-fix-string-parsing.patch" + epatch "${FILESDIR}/charm-6.5.1-fix-navmenuGenerator.patch" + epatch "${FILESDIR}/charm-6.5.1-fix-markupSanitizer.patch" + epatch "${FILESDIR}/charm-6.6.0-static-library-fix.patch" +} + +src_compile() { + local build_version="$(usex mpi "mpi" "net")-linux$(usex amd64 "-amd64" '')" + local build_options="$(get_opts)" + local build_charmc_options="${MAKEOPTS} -j1" + local build_commandline="${build_version} ${build_options} ${build_charmc_options}" + + # Build charmm++ first. + einfo "running ./build charm++ ${build_commandline}" + ./build charm++ ${build_commandline} || die "Failed to build charm++" + + # make pdf/html docs + if use doc; then + emake -j1 -C doc/charm++ + fi +} + +src_test() { + make -C tests/charm++ test TESTOPTS="++local" || die +} + +src_install() { + # Make charmc play well with gentoo before we move it into /usr/bin. This + # patch cannot be applied during src_prepare() because the charmc wrapper + # is used during building. + epatch "${FILESDIR}/charm-6.5.1-charmc-gentoo.patch" + + sed -e "s|gentoo-include|${P}|" \ + -e "s|gentoo-libdir|$(get_libdir)|g" \ + -e "s|VERSION|${P}/VERSION|" \ + -i ./src/scripts/charmc || die "failed patching charmc script" + + # In the following, some of the files are symlinks to ../tmp which we need + # to dereference first (see bug 432834). + + local i + + # Install binaries. + for i in bin/*; do + if [[ -L ${i} ]]; then + i=$(readlink -e "${i}") || die + fi + dobin "${i}" + done + + # Install headers. + insinto /usr/include/${P} + for i in include/*; do + if [[ -L ${i} ]]; then + i=$(readlink -e "${i}") || die + fi + doins "${i}" + done + + # Install static libs. Charm has a lot of .o "libs" that it requires at + # runtime. + if use static-libs; then + for i in lib/*.{a,o}; do + if [[ -L ${i} ]]; then + i=$(readlink -e "${i}") || die + fi + dolib "${i}" + done + fi + + # Install shared libs. + for i in lib_so/*; do + if [[ -L ${i} ]]; then + i=$(readlink -e "${i}") || die + fi + dolib.so "${i}" + done + + # Basic docs. + dodoc CHANGES README + + # Install examples. + if use examples; then + find examples/ -name 'Makefile' | xargs sed \ + -r "s:(../)+bin/charmc:/usr/bin/charmc:" -i || \ + die "Failed to fix examples" + find examples/ -name 'Makefile' | xargs sed \ + -r "s:./charmrun:./charmrun ++local:" -i || \ + die "Failed to fix examples" + insinto /usr/share/doc/${PF}/examples + doins -r examples/charm++/* + fi + + # Install pdf/html docs + if use doc; then + cd "${S}/doc/charm++" + # Install pdfs. + insinto /usr/share/doc/${PF}/pdf + doins *.pdf + # Install html. + docinto html + dohtml -r manual/* + fi +} + +pkg_postinst() { + einfo "Please test your charm installation by copying the" + einfo "content of /usr/share/doc/${PF}/examples to a" + einfo "temporary location and run 'make test'." +} diff --git a/sys-cluster/charm/files/charm-6.6.0-static-library-fix.patch b/sys-cluster/charm/files/charm-6.6.0-static-library-fix.patch new file mode 100644 index 000000000..1281a6515 --- /dev/null +++ b/sys-cluster/charm/files/charm-6.6.0-static-library-fix.patch @@ -0,0 +1,403 @@ +From 5885fa33575116c8d5c8e6e2e4beb007279a7fdb Mon Sep 17 00:00:00 2001 +From: Nicolas Bock <nicolasbock@gmail.com> +Date: Mon, 14 Oct 2013 07:15:14 -0600 +Subject: [PATCH] Some libraries are only built statically, + +preventing a Charm++ installation with only dynamic libraries. + +On a typical Linux system only shared libraries are installed, because of the +usual security and bloat arguments. However, if I build charm with +--build-shared, and then install only what is in lib_so, the charmc script +breaks because some Converse libraries are built purely as .o and don't end up +in lib_so. One example is seed based load balancing, e.g. libldb-rand.o. As +far as I can tell, this is not too hard to fix. In the main makefile, the +targets libldb-*.o are renamed to libldb-*.a, and the charmc script now tests +both .a and .so when linking the seed based load balancing code. +--- + src/scripts/Makefile | 136 +++++++++++++++++++++++++-------------------------- + src/scripts/charmc | 39 +++++++++------ + 2 files changed, 92 insertions(+), 83 deletions(-) + +diff --git a/src/scripts/Makefile b/src/scripts/Makefile +index a52b801..d0e5a03 100644 +--- a/src/scripts/Makefile ++++ b/src/scripts/Makefile +@@ -358,7 +358,7 @@ dirs+sources: + # Converse Libraries + # + ############################################################################### +-CLBLIBS=$(L)/libldb-rand.o $(L)/libldb-spray.o $(L)/libldb-workstealing.o $(L)/libldb-neighbor.o $(L)/libldb-none.o $(L)/libldb-test.o $(L)/libldb-bluegene.o ++CLBLIBS=$(L)/libldb-rand.a $(L)/libldb-spray.a $(L)/libldb-workstealing.a $(L)/libldb-neighbor.a $(L)/libldb-none.a $(L)/libldb-test.a $(L)/libldb-bluegene.a + + TRACELIBS = $(L)/libtrace-converse.a $(L)/libtracef_f.a + +@@ -372,32 +372,32 @@ TRACELIBS += $(L)/libtrace-projections.a $(L)/libtrace-summary.a \ + $(L)/libtrace-memory.a $(L)/libtrace-autoPerf.a + endif + +-MEMLIBS=$(L)/libmemory-default.o $(L)/libmemory-os.o $(L)/libmemory-gnu.o \ +- $(L)/libmemory-gnuold.o $(L)/libmemory-verbose.o \ +- $(L)/libmemory-paranoid.o \ +- $(L)/libmemory-leak.o $(L)/libmemory-isomalloc.o \ +- $(L)/libmemory-os-verbose.o $(L)/libmemory-os-isomalloc.o \ +- $(L)/libmemory-os-leak.o $(L)/libmemory-os-paranoid.o \ +- $(L)/libmemory-os-lock.o $(L)/libmemory-os-wrapper.o ++MEMLIBS=$(L)/libmemory-default.a $(L)/libmemory-os.a $(L)/libmemory-gnu.a \ ++ $(L)/libmemory-gnuold.a $(L)/libmemory-verbose.a \ ++ $(L)/libmemory-paranoid.a \ ++ $(L)/libmemory-leak.a $(L)/libmemory-isomalloc.a \ ++ $(L)/libmemory-os-verbose.a $(L)/libmemory-os-isomalloc.a \ ++ $(L)/libmemory-os-leak.a $(L)/libmemory-os-paranoid.a \ ++ $(L)/libmemory-os-lock.a $(L)/libmemory-os-wrapper.a + + BUILD_CHARMDEBUG=$(shell CHARMINC=.; if test -f ./conv-config.sh; then . ./conv-config.sh; echo $$CMK_CHARMDEBUG; fi ) + + ifneq "$(BUILD_CHARMDEBUG)" "0" +-MEMLIBS += $(L)/libmemory-charmdebug.o $(L)/libmemory-charmdebug-mmap.o \ +- $(L)/libmemory-charmdebug-slot.o \ +- $(L)/libmemory-charmdebug-mmap-slot.o \ +- $(L)/libmemory-os-charmdebug.o $(L)/libmemory-hooks-charmdebug.o ++MEMLIBS += $(L)/libmemory-charmdebug.a $(L)/libmemory-charmdebug-mmap.a \ ++ $(L)/libmemory-charmdebug-slot.a \ ++ $(L)/libmemory-charmdebug-mmap-slot.a \ ++ $(L)/libmemory-os-charmdebug.a $(L)/libmemory-hooks-charmdebug.a + endif + +-THREADLIBS=$(L)/libthreads-default.o $(L)/libthreads-default-tls.o \ +- $(L)/libthreads-qt.o $(L)/libthreads-qt-tls.o \ +- $(L)/libthreads-context.o $(L)/libthreads-context-tls.o \ +- $(L)/libthreads-uJcontext.o $(L)/libthreads-uJcontext-tls.o \ +- $(L)/libthreads-pthreads.o $(L)/libthreads-fibers.o \ +- $(L)/libthreads-stackcopy.o $(L)/libthreads-memoryalias.o \ +- $(L)/libthreads-qt-memoryalias.o \ +- $(L)/libthreads-context-memoryalias.o \ +- $(L)/libthreads-uJcontext-memoryalias.o ++THREADLIBS=$(L)/libthreads-default.a $(L)/libthreads-default-tls.a \ ++ $(L)/libthreads-qt.a $(L)/libthreads-qt-tls.a \ ++ $(L)/libthreads-context.a $(L)/libthreads-context-tls.a \ ++ $(L)/libthreads-uJcontext.a $(L)/libthreads-uJcontext-tls.a \ ++ $(L)/libthreads-pthreads.a $(L)/libthreads-fibers.a \ ++ $(L)/libthreads-stackcopy.a $(L)/libthreads-memoryalias.a \ ++ $(L)/libthreads-qt-memoryalias.a \ ++ $(L)/libthreads-context-memoryalias.a \ ++ $(L)/libthreads-uJcontext-memoryalias.a + + CVLIBS=$(L)/libconv-core.a \ + $(L)/libconv-cplus-y.a $(L)/libconv-cplus-n.a \ +@@ -494,19 +494,19 @@ pup_f.o: pup_f.f90 $(CVHEADERS) + -$(CHARMC) -c pup_f.f90 && $(CHARMC) -cpmod ../include pupmod.M || touch pup_f.o + + ## Converse load balancers (seed balancers, -balance) +-$(L)/libldb-none.o: cldb.none.c $(CVHEADERS) ++$(L)/libldb-none.a: cldb.none.c $(CVHEADERS) + $(CHARMC) -o $@ cldb.none.c + +-$(L)/libldb-rand.o: cldb.rand.c cldb.h $(CVHEADERS) ++$(L)/libldb-rand.a: cldb.rand.c cldb.h $(CVHEADERS) + $(CHARMC) -o $@ cldb.rand.c + +-$(L)/libldb-neighbor.o: cldb.neighbor.c cldb.neighbor.h graph.h $(CVHEADERS) ++$(L)/libldb-neighbor.a: cldb.neighbor.c cldb.neighbor.h graph.h $(CVHEADERS) + $(CHARMC) -o $@ cldb.neighbor.c + +-$(L)/libldb-workstealing.o: cldb.workstealing.c cldb.workstealing.h graph.h $(CVHEADERS) ++$(L)/libldb-workstealing.a: cldb.workstealing.c cldb.workstealing.h graph.h $(CVHEADERS) + $(CHARMC) -o $@ cldb.workstealing.c + +-$(L)/libldb-spray.o: cldb.spray.c $(CVHEADERS) ++$(L)/libldb-spray.a: cldb.spray.c $(CVHEADERS) + $(CHARMC) -o $@ cldb.spray.c + + +@@ -516,138 +516,138 @@ $(L)/libldb-spray.o: cldb.spray.c $(CVHEADERS) + #//$(L)/libldb-prioritycentralizedopt.o: cldb.prioritycentralizedopt.c cldb.prioritycentralizedopt.h $(CVHEADERS) + #// $(CHARMC) -o $@ cldb.prioritycentralizedopt.c + +-$(L)/libldb-test.o: cldb.test.c $(CVHEADERS) ++$(L)/libldb-test.a: cldb.test.c $(CVHEADERS) + $(CHARMC) -o $@ cldb.test.c + +-$(L)/libldb-bluegene.o: cldb.bluegene.c $(CVHEADERS) ++$(L)/libldb-bluegene.a: cldb.bluegene.c $(CVHEADERS) + $(CHARMC) -o $@ cldb.bluegene.c + + ## Memory allocation libraries (-memory) + MEM_DEPS=memory.c memory-gnu.c memory-gnuold.c converse.h conv-mach.h $(CVHEADERS) +-$(L)/libmemory-default.o: $(MEM_DEPS) ++$(L)/libmemory-default.a: $(MEM_DEPS) + $(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_DEFAULT memory.c + +-$(L)/libmemory-os.o: $(MEM_DEPS) ++$(L)/libmemory-os.a: $(MEM_DEPS) + $(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_OS memory.c + +-$(L)/libmemory-os-verbose.o: memory-verbose.c $(MEM_DEPS) ++$(L)/libmemory-os-verbose.a: memory-verbose.c $(MEM_DEPS) + -$(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_OS_WRAPPED -DCMK_MEMORY_BUILD_VERBOSE memory.c || touch $@ + +-$(L)/libmemory-os-paranoid.o: memory-paranoid.c $(MEM_DEPS) ++$(L)/libmemory-os-paranoid.a: memory-paranoid.c $(MEM_DEPS) + -$(CHARMC) -o $@ -DCMK_MEMORY_BUILD_OS_WRAPPED -DCMK_MEMORY_BUILD_PARANOID memory.c || touch $@ + +-$(L)/libmemory-os-leak.o: $(MEM_DEPS) ++$(L)/libmemory-os-leak.a: $(MEM_DEPS) + -$(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_OS_WRAPPED -DCMK_MEMORY_BUILD_LEAK memory.c || touch $@ + +-$(L)/libmemory-os-isomalloc.o: memory-isomalloc.c $(MEM_DEPS) ++$(L)/libmemory-os-isomalloc.a: memory-isomalloc.c $(MEM_DEPS) + -$(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_OS_WRAPPED -DCMK_MEMORY_BUILD_ISOMALLOC memory.c || touch $@ + +-$(L)/libmemory-os-lock.o: memory-lock.c $(MEM_DEPS) ++$(L)/libmemory-os-lock.a: memory-lock.c $(MEM_DEPS) + -$(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_OS_WRAPPED -DCMK_MEMORY_BUILD_LOCK memory.c || touch $@ + +-$(L)/libmemory-os-charmdebug.o: memory-charmdebug.c $(MEM_DEPS) ++$(L)/libmemory-os-charmdebug.a: memory-charmdebug.c $(MEM_DEPS) + -$(CHARMC) -o $@ -DCMK_MEMORY_BUILD_OS_WRAPPED -DCMK_MEMORY_BUILD_CHARMDEBUG memory.c || touch $@ + +-$(L)/libmemory-os-wrapper.o: memory-os-wrapper.C $(MEM_DEPS) ++$(L)/libmemory-os-wrapper.a: memory-os-wrapper.C $(MEM_DEPS) + -$(CHARMC) -o $@ memory-os-wrapper.C || touch $@ + +-$(L)/libmemory-hooks-charmdebug.o: memory-charmdebug.c $(MEM_DEPS) ++$(L)/libmemory-hooks-charmdebug.a: memory-charmdebug.c $(MEM_DEPS) + -$(CHARMC) -o $@ -DCMK_MEMORY_BUILD_GNU_HOOKS -DCMK_MEMORY_BUILD_CHARMDEBUG memory.c || touch $@ + + # If the system doesn't have sbrk, these compilations may fail. + # This is OK, but then we can't use "-memory gnu" or friends. +-$(L)/libmemory-gnu.o: $(MEM_DEPS) ++$(L)/libmemory-gnu.a: $(MEM_DEPS) + -$(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_GNU memory.c || touch $@ + +-$(L)/libmemory-gnuold.o: $(MEM_DEPS) ++$(L)/libmemory-gnuold.a: $(MEM_DEPS) + -$(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_GNUOLD memory.c || touch $@ + +-$(L)/libmemory-verbose.o: memory-verbose.c $(MEM_DEPS) ++$(L)/libmemory-verbose.a: memory-verbose.c $(MEM_DEPS) + -$(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_VERBOSE memory.c || touch $@ + +-$(L)/libmemory-paranoid.o: memory-paranoid.c $(MEM_DEPS) ++$(L)/libmemory-paranoid.a: memory-paranoid.c $(MEM_DEPS) + -$(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_PARANOID memory.c || touch $@ + +-$(L)/libmemory-leak.o: memory-leak.c $(MEM_DEPS) ++$(L)/libmemory-leak.a: memory-leak.c $(MEM_DEPS) + -$(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_LEAK memory.c || touch $@ + +-$(L)/libmemory-cache.o: memory-cache.c $(MEM_DEPS) ++$(L)/libmemory-cache.a: memory-cache.c $(MEM_DEPS) + -$(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_CACHE memory.c || touch $@ + +-$(L)/libmemory-isomalloc.o: memory-isomalloc.c $(MEM_DEPS) ++$(L)/libmemory-isomalloc.a: memory-isomalloc.c $(MEM_DEPS) + -$(CHARMC) -I. -o $@ -DCMK_MEMORY_BUILD_ISOMALLOC memory.c || touch $@ + +-$(L)/libmemory-charmdebug.o: memory-charmdebug.c $(MEM_DEPS) ++$(L)/libmemory-charmdebug.a: memory-charmdebug.c $(MEM_DEPS) + -$(CHARMC) -I. -optimize -o $@ -DCMK_MEMORY_BUILD_CHARMDEBUG memory.c || touch $@ + +-$(L)/libmemory-charmdebug-slot.o: memory-charmdebug.c $(MEM_DEPS) ++$(L)/libmemory-charmdebug-slot.a: memory-charmdebug.c $(MEM_DEPS) + -$(CHARMC) -I. -optimize -o $@ -DCMK_MEMORY_BUILD_CHARMDEBUG -DCMK_SEPARATE_SLOT memory.c || touch $@ + +-$(L)/libmemory-charmdebug-mmap.o: memory-charmdebug.c $(MEM_DEPS) ++$(L)/libmemory-charmdebug-mmap.a: memory-charmdebug.c $(MEM_DEPS) + -$(CHARMC) -I. -optimize -o $@ -DCMK_MEMORY_BUILD_CHARMDEBUG -DCPD_USE_MMAP memory.c || touch $@ + +-$(L)/libmemory-charmdebug-mmap-slot.o: memory-charmdebug.c $(MEM_DEPS) ++$(L)/libmemory-charmdebug-mmap-slot.a: memory-charmdebug.c $(MEM_DEPS) + -$(CHARMC) -I. -optimize -o $@ -DCMK_MEMORY_BUILD_CHARMDEBUG -DCPD_USE_MMAP -DCMK_SEPARATE_SLOT memory.c || touch $@ + + ## Thread libraries (-thread) + + LIBTHREADSDEPS = threads.c $(CVHEADERS) QUICK_THREADS + +-$(L)/libthreads-default.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-default.a: $(LIBTHREADSDEPS) + $(CHARMC) -o $@ -DCMK_THREADS_BUILD_DEFAULT=1 -IQuickThreads -I. threads.c + +-$(L)/libthreads-default-tls.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-default-tls.a: $(LIBTHREADSDEPS) + -$(CHARMC) -o $@ -DCMK_THREADS_BUILD_DEFAULT=1 -DCMK_THREADS_BUILD_TLS=1 -IQuickThreads -I. threads.c 2> /dev/null || touch $@ + +-$(L)/libthreads-qt.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-qt.a: $(LIBTHREADSDEPS) + $(CHARMC) -o $@ -DCMK_THREADS_BUILD_QT=1 -IQuickThreads threads.c + +-$(L)/libthreads-qt-tls.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-qt-tls.a: $(LIBTHREADSDEPS) + -$(CHARMC) -o $@ -DCMK_THREADS_BUILD_QT=1 -DCMK_THREADS_BUILD_TLS=1 -IQuickThreads threads.c 2> /dev/null || touch $@ + +-$(L)/libthreads-context.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-context.a: $(LIBTHREADSDEPS) + -$(CHARMC) -o $@ -DCMK_THREADS_BUILD_CONTEXT=1 -IQuickThreads threads.c || touch $@ + +-$(L)/libthreads-context-tls.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-context-tls.a: $(LIBTHREADSDEPS) + -$(CHARMC) -o $@ -DCMK_THREADS_BUILD_CONTEXT=1 -DCMK_THREADS_BUILD_TLS=1 -IQuickThreads threads.c 2> /dev/null || touch $@ + +-$(L)/libthreads-uJcontext.o: $(LIBTHREADSDEPS) uJcontext.c ++$(L)/libthreads-uJcontext.a: $(LIBTHREADSDEPS) uJcontext.c + -$(CHARMC) -o $@ -DCMK_THREADS_BUILD_JCONTEXT=1 -IQuickThreads -I. threads.c || touch $@ + +-$(L)/libthreads-uJcontext-tls.o: $(LIBTHREADSDEPS) uJcontext.c ++$(L)/libthreads-uJcontext-tls.a: $(LIBTHREADSDEPS) uJcontext.c + -$(CHARMC) -o $@ -DCMK_THREADS_BUILD_JCONTEXT=1 -DCMK_THREADS_BUILD_TLS=1 -IQuickThreads -I. threads.c || touch $@ + +-$(L)/libthreads-pthreads.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-pthreads.a: $(LIBTHREADSDEPS) + -$(CHARMC) -o $@ -DCMK_THREADS_BUILD_PTHREADS=1 -IQuickThreads threads.c || touch $@ + +-$(L)/libthreads-fibers.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-fibers.a: $(LIBTHREADSDEPS) + -$(CHARMC) -o $@ -DCMK_THREADS_BUILD_FIBERS=1 -IQuickThreads threads.c 2> /dev/null || touch $@ + +-$(L)/libthreads-stackcopy.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-stackcopy.a: $(LIBTHREADSDEPS) + -$(CHARMC) -o $@ -DCMK_THREADS_BUILD_STACKCOPY=1 -IQuickThreads threads.c || touch $@ + +-$(L)/libthreads-memoryalias.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-memoryalias.a: $(LIBTHREADSDEPS) + -$(CHARMC) -o $@ -DCMK_THREADS_ALIAS_STACK=1 -DCMK_THREADS_BUILD_DEFAULT=1 -IQuickThreads threads.c || touch $@ + +-$(L)/libthreads-qt-memoryalias.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-qt-memoryalias.a: $(LIBTHREADSDEPS) + -$(CHARMC) -o $@ -DCMK_THREADS_ALIAS_STACK=1 -DCMK_THREADS_BUILD_QT=1 -IQuickThreads threads.c || touch $@ + +-$(L)/libthreads-context-memoryalias.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-context-memoryalias.a: $(LIBTHREADSDEPS) + -$(CHARMC) -o $@ -DCMK_THREADS_ALIAS_STACK=1 -DCMK_THREADS_BUILD_CONTEXT=1 -IQuickThreads threads.c || touch $@ + +-$(L)/libthreads-uJcontext-memoryalias.o: $(LIBTHREADSDEPS) ++$(L)/libthreads-uJcontext-memoryalias.a: $(LIBTHREADSDEPS) + -$(CHARMC) -o $@ -DCMK_THREADS_ALIAS_STACK=1 -DCMK_THREADS_BUILD_JCONTEXT=1 -IQuickThreads -I. threads.c || touch $@ + + ## Global swapping (-swapglobal) +-swapglobal-target: $(L)/libglobal-swap.o $(L)/libglobal-copy.o $(L)/loadsym.o ++swapglobal-target: $(L)/libglobal-swap.a $(L)/libglobal-copy.a $(L)/loadsym.a + +-$(L)/libglobal-swap.o: global-elfgot.C $(CVHEADERS) ++$(L)/libglobal-swap.a: global-elfgot.C $(CVHEADERS) + -$(CHARMC) -c global-elfgot.C -o $@ || touch $@ + +-$(L)/libglobal-copy.o: global-elfcopy.C $(CVHEADERS) ++$(L)/libglobal-copy.a: global-elfcopy.C $(CVHEADERS) + -$(CHARMC) -c global-elfcopy.C -o $@ || touch $@ + +-$(L)/loadsym.o: loadsym.c $(CVHEADERS) ++$(L)/loadsym.a: loadsym.c $(CVHEADERS) + -$(CHARMC) -c loadsym.c -o $@ || touch $@ + + ############################################################################### +diff --git a/src/scripts/charmc b/src/scripts/charmc +index 0502c27..a984b18 100755 +--- a/src/scripts/charmc ++++ b/src/scripts/charmc +@@ -346,6 +346,14 @@ printVersion() + echo Charm++ Version $version + } + ++getLibraryObject() ++{ ++ if [[ -f "${CHARMLIB}/$1-$2.a" ]]; then ++ echo "${CHARMLIB}/$1-$2.a" ++ else ++ echo "${CHARMLIBSO}/$1-$2.so" ++ fi ++} + + ############################################################################## + # +@@ -1697,13 +1705,12 @@ then + fi + + BAL_EXT=`getExtention $BALANCE` +-if [ -z "$BAL_EXT" ] +-then +-# Balance has no extention-- is a library reference +- BAL_OBJ="$CHARMLIB/libldb-$BALANCE.o" ++if [[ -z "$BAL_EXT" ]]; then ++ # Balance has no extension-- is a library reference ++ BAL_OBJ=$(getLibraryObject "libldb" ${BALANCE}) + else +-# Balance has some extention-- must be a .o or .a file +- BAL_OBJ="$BALANCE" ++ # Balance has some extension-- must be a .o or .a file ++ BAL_OBJ="$BALANCE" + fi + + Debug "Finished with BAL_OBJ=$BAL_OBJ, TRACEMODE=$TRACEMODE..." +@@ -1719,10 +1726,11 @@ then + fi + fi + ++Debug "Finished with BAL_OBJ=$BAL_OBJ, TRACEMODE=$TRACEMODE..." + + # Check for valid choice of MEMORY + +-MEM_OBJ="$CHARMLIB/libmemory-$MEMORY.o" ++MEM_OBJ=$(getLibraryObject "libmemory" ${MEMORY}) + + if [ ! -r $MEM_OBJ -o ! -s $MEM_OBJ ] + then +@@ -1733,7 +1741,7 @@ fi + # For memory wrapping around the OS allocator, need to add also the wrapper object + case $MEMORY in + os-*) +- MEM_OBJ=$MEM_OBJ" $CHARMLIB/libmemory-os-wrapper.o" ++ MEM_OBJ="${MEM_OBJ} $(getLibraryObject 'libmemory' 'os-wrapper')" + ;; + esac + +@@ -1751,7 +1759,8 @@ then + THREAD=${THREAD}-tls + fi + fi +-THREAD_OBJ="$CHARMLIB/libthreads-$THREAD.o" ++ ++THREAD_OBJ=$(getLibraryObject "libthreads" ${THREAD}) + + if [ ! -r $THREAD_OBJ -o ! -s $THREAD_OBJ ] + then +@@ -1931,7 +1940,7 @@ esac + + if [ "$BUILD_SHARE" = "0" ] + then +- MIDDLE_LIBS="$MEM_OBJ $THREAD_OBJ $MIDDLE_LIBS" ++ MIDDLE_LIBS="$MIDDLE_LIBS $MEM_OBJ $THREAD_OBJ" + fi + + if [ "$CHARM_SHARED" = "1" ] +@@ -1943,23 +1952,23 @@ then + then + LANG_LIBS="-L$CHARMLIBSO $OBJECTFILES $PRE_LIBRARIES" + else +- LANG_LIBS="-L$CHARMLIBSO $BAL_OBJ $OBJECTFILES $modInitObj $PRE_LIBRARIES" ++ LANG_LIBS="-L$CHARMLIBSO $OBJECTFILES $modInitObj $PRE_LIBRARIES" + fi + else + # if interoperate, need a lib with moduleinit + if [ "$MPI_INTEROPERATE" != "" ] + then +- LANG_LIBS="-L$CHARMLIB -I$CHARMINC $CMK_SYSINC $BAL_OBJ $PRE_LIBRARIES" ++ LANG_LIBS="-L$CHARMLIB -I$CHARMINC $CMK_SYSINC $PRE_LIBRARIES" + else +- LANG_LIBS="-L$CHARMLIB -I$CHARMINC $CMK_SYSINC $BAL_OBJ $OBJECTFILES $modInitObj $PRE_LIBRARIES" ++ LANG_LIBS="-L$CHARMLIB -I$CHARMINC $CMK_SYSINC $OBJECTFILES $modInitObj $PRE_LIBRARIES" + fi + fi + if [ "$TRACE_WITH_TAU" = 1 ] + then + echo "Linking with the TAU libraries: $TAU_LIBS" +- ALL_LIBS="$LANG_LIBS $MIDDLE_LIBS $CMK_LIBS $POST_LIBRARIES $CMK_SYSLIBS $TAU_LIBS" ++ ALL_LIBS="$LANG_LIBS $MIDDLE_LIBS $BAL_OBJ $CMK_LIBS $POST_LIBRARIES $CMK_SYSLIBS $TAU_LIBS" + else +- ALL_LIBS="$LANG_LIBS $MIDDLE_LIBS $CMK_LIBS $POST_LIBRARIES $CMK_SYSLIBS" ++ ALL_LIBS="$LANG_LIBS $MIDDLE_LIBS $BAL_OBJ $CMK_LIBS $POST_LIBRARIES $CMK_SYSLIBS" + fi + Debugf "All libraries are: $ALL_LIBS" + +-- +1.8.3.2 + diff --git a/sys-cluster/hpl/ChangeLog b/sys-cluster/hpl/ChangeLog index 9a1784a3b..2c18ce848 100644 --- a/sys-cluster/hpl/ChangeLog +++ b/sys-cluster/hpl/ChangeLog @@ -2,6 +2,22 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 27 Nov 2013; Andrew Savchenko <bircoph@gmail.com> hpl-2.1.ebuild: + Fix build failure with MKL used for blas and lapack + + Ebuild stripped -L$path and -l from pkg-config output for blas and + lapack. This works fine for atlas, gotoblas2, openblas, eigen or reference + implementations — for all those installing libraries directly to + /usr/lib/. But MKL is different and is installed to /opt/... + outside of gcc default library path. That's why build with MKL + failed and is fixed now. (I also checked that other implementations + build fine.) + + I have no idea why -L$path and -l were stripped originally, + probably because they may contain coma symbols which will broke + original sed script. This is fixed by switching to another sed + delimiter sign. + *hpl-2.1 (29 Jun 2013) 29 Jun 2013; Andrew Savchenko <bircoph@gmail.com> +hpl-2.1.ebuild: diff --git a/sys-cluster/hpl/hpl-2.1.ebuild b/sys-cluster/hpl/hpl-2.1.ebuild index ac066244b..65c09f16a 100644 --- a/sys-cluster/hpl/hpl-2.1.ebuild +++ b/sys-cluster/hpl/hpl-2.1.ebuild @@ -26,7 +26,6 @@ src_prepare() { local mpicc_path="$(mpi_pkg_cc)" local a="" local locallib="${EPREFIX}/usr/$(get_libdir)/lib" - local localblas="$(for i in $($(tc-getPKG_CONFIG) --libs-only-l blas lapack);do a="${a} ${i/-l/${locallib}}.so "; done; echo ${a})" cp setup/Make.Linux_PII_FBLAS Make.gentoo_hpl_fblas_x86 || die sed -i \ @@ -35,7 +34,7 @@ src_prepare() { -e '/^ARCH\>/s,= .*,= gentoo_hpl_fblas_x86,' \ -e '/^MPdir\>/s,= .*,=,' \ -e '/^MPlib\>/s,= .*,=,' \ - -e "/^LAlib\>/s,= .*,= ${localblas}," \ + -e "/^LAlib\>/s%= .*%= $($(tc-getPKG_CONFIG) --libs blas lapack)%" \ -e "/^LINKER\>/s,= .*,= ${mpicc_path}," \ -e "/^CC\>/s,= .*,= ${mpicc_path}," \ -e "/^CCFLAGS\>/s|= .*|= \$(HPL_DEFS) ${CFLAGS}|" \ |