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authorJustin Lecher <jlec@gentoo.org>2013-12-02 17:20:22 +0100
committerJustin Lecher <jlec@gentoo.org>2013-12-02 17:20:22 +0100
commit3ab3adea4f5b74d90d9df714c3f76d5ed48180cb (patch)
treeccd3f23d60bfc0d72034cbb7722ec7b25a824b41
parentsci-mathematics/z3: Make build verbose; respect CXX, CXXFLAGS, LDFLAGS; use E... (diff)
parentMerge pull request #157 from jauhien/tauola (diff)
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Merge branch 'master' into zhou13-master
* master: (25 commits) xdrfile got added to gx86 hpl: fix build with MKL blas and/or lapack libraries [sci-visualization/yt] provide workaround for latest Forthon [sci-visualization/yt] fix slots in CDEPEND Tentative prefixification Version bump: mne-python 0.7 Masked live yt dev-python/Forthon: Version bump, keyworded for prefix [sci-visualization/yt] version bump sci-physics/geant-vmc: Version bump dev-python/emcee: Version bump sci-chemistry/coot: Update patch for current HEAD Update PyQtGraph to 0.9.8. Support of python 3.3 sci-physics/lammps-20131123: Version bump. sys-cluster/charm-6.6.0-rc1: Reorganized some variables. sci-physics/tauola: new ebuild added Add 1 more chunk for multifit/Makefile.am ebuild cleanup sci-misc/openfst: version bump, patch from Kaldi sci-physics/mc-tester: ebuild improvements, thanks to jlec ...
-rw-r--r--dev-python/Forthon/ChangeLog8
-rw-r--r--dev-python/Forthon/Forthon-0.8.13.ebuild (renamed from dev-python/Forthon/Forthon-0.8.12.ebuild)4
-rw-r--r--dev-python/Forthon/Manifest2
-rw-r--r--dev-python/Forthon/files/Forthon-0.8.11-fix_options_parser.patch17
-rw-r--r--dev-python/Forthon/metadata.xml11
-rw-r--r--dev-python/emcee/ChangeLog7
-rw-r--r--dev-python/emcee/Manifest1
-rw-r--r--dev-python/emcee/emcee-2.0.0.ebuild27
-rw-r--r--dev-python/emcee/metadata.xml4
-rw-r--r--dev-python/pyqtgraph/ChangeLog6
-rw-r--r--dev-python/pyqtgraph/Manifest2
-rw-r--r--dev-python/pyqtgraph/pyqtgraph-0.9.8.ebuild (renamed from dev-python/pyqtgraph/pyqtgraph-0.9.7.ebuild)2
-rw-r--r--eclass/alternatives-2.eclass2
-rw-r--r--eclass/intel-sdp.eclass497
-rw-r--r--licenses/CPC41
-rw-r--r--profiles/package.mask2
-rw-r--r--sci-biology/mne-python/Manifest1
-rw-r--r--sci-biology/mne-python/mne-python-0.7.ebuild55
-rw-r--r--sci-chemistry/coot/ChangeLog3
-rw-r--r--sci-chemistry/coot/files/9999-pc.patch43
-rw-r--r--sci-chemistry/xdrfile/ChangeLog21
-rw-r--r--sci-chemistry/xdrfile/Manifest1
-rw-r--r--sci-chemistry/xdrfile/metadata.xml9
-rw-r--r--sci-chemistry/xdrfile/xdrfile-1.1.1.ebuild23
-rw-r--r--sci-libs/gsl/files/gsl-1.16-cblas-external.patch13
-rw-r--r--sci-misc/openfst/ChangeLog6
-rw-r--r--sci-misc/openfst/Manifest2
-rw-r--r--sci-misc/openfst/files/kaldi.patch599
-rw-r--r--sci-misc/openfst/openfst-1.3.4.ebuild (renamed from sci-misc/openfst/openfst-1.3.2.ebuild)14
-rw-r--r--sci-physics/geant-vmc/ChangeLog6
-rw-r--r--sci-physics/geant-vmc/Manifest2
-rw-r--r--sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild (renamed from sci-physics/geant-vmc/geant-vmc-4.2.14a.ebuild)0
-rw-r--r--sci-physics/lammps/ChangeLog5
-rw-r--r--sci-physics/lammps/Manifest1
-rw-r--r--sci-physics/lammps/lammps-20131123.ebuild115
-rw-r--r--sci-physics/mc-tester/ChangeLog11
-rw-r--r--sci-physics/mc-tester/Manifest1
-rw-r--r--sci-physics/mc-tester/files/mc-tester-1.25.0-compare.sh.patch30
-rw-r--r--sci-physics/mc-tester/mc-tester-1.25.0.ebuild65
-rw-r--r--sci-physics/mc-tester/metadata.xml16
-rw-r--r--sci-physics/tauola/ChangeLog12
-rw-r--r--sci-physics/tauola/Manifest1
-rw-r--r--sci-physics/tauola/files/tauola-1.1.3-makefile.patch12
-rw-r--r--sci-physics/tauola/files/tauola-1.1.3-tau-spinner-makefile.patch11
-rw-r--r--sci-physics/tauola/metadata.xml17
-rw-r--r--sci-physics/tauola/tauola-1.1.3.ebuild69
-rw-r--r--sci-physics/tauola/tauola-9999.ebuild75
-rw-r--r--sci-visualization/yt/Manifest1
-rw-r--r--sci-visualization/yt/yt-2.6.ebuild51
-rw-r--r--sci-visualization/yt/yt-9999.ebuild25
-rw-r--r--sys-cluster/charm/ChangeLog13
-rw-r--r--sys-cluster/charm/charm-6.6.0_rc1.ebuild222
-rw-r--r--sys-cluster/charm/files/charm-6.6.0-static-library-fix.patch403
-rw-r--r--sys-cluster/hpl/ChangeLog16
-rw-r--r--sys-cluster/hpl/hpl-2.1.ebuild3
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}|" \