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-rw-r--r--dev-python/astlib/ChangeLog8
-rw-r--r--dev-python/astlib/Manifest2
-rw-r--r--dev-python/astlib/astlib-0.17.1.ebuild (renamed from dev-python/astlib/astlib-0.6.1.ebuild)5
-rw-r--r--dev-python/astlib/files/astlib-0.17.1-wcstools.patch75
-rw-r--r--dev-python/astlib/files/astlib-0.6.0-wcstools.patch56
-rw-r--r--licenses/ligplot+138
-rw-r--r--metadata/layout.conf2
-rw-r--r--profiles/profiles.desc1
-rw-r--r--profiles/use.local.desc120
-rw-r--r--sci-chemistry/ligplot+/ChangeLog10
-rw-r--r--sci-chemistry/ligplot+/Manifest1
-rw-r--r--sci-chemistry/ligplot+/ligplot+-1.4.ebuild43
-rw-r--r--sci-chemistry/ligplot+/metadata.xml5
-rw-r--r--sci-chemistry/ssp/ChangeLog3
-rw-r--r--sci-chemistry/ssp/ssp-09.11.ebuild6
-rw-r--r--sci-libs/bigdft/ChangeLog11
-rw-r--r--sci-libs/bigdft/bigdft-1.6_pre1-r4.ebuild (renamed from sci-libs/bigdft/bigdft-1.6_pre1-r3.ebuild)4
-rw-r--r--sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch (renamed from sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs.patch)21
-rw-r--r--sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc-1.patch (renamed from sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc.patch)8
-rw-r--r--sci-libs/exodusii/ChangeLog7
-rw-r--r--sci-libs/exodusii/Manifest2
-rw-r--r--sci-libs/exodusii/exodusii-5.22.ebuild (renamed from sci-libs/exodusii/exodusii-4.98.ebuild)14
-rw-r--r--sci-libs/exodusii/files/exodusii-4.98-find-netcdf.patch35
-rw-r--r--sci-libs/exodusii/files/exodusii-5.22-multilib.patch20
-rw-r--r--sci-visualization/paraview/ChangeLog16
-rw-r--r--sci-visualization/paraview/files/paraview-3.14.1-gcc-4.7.patch28
-rw-r--r--sci-visualization/paraview/files/paraview-3.14.1-mpi4py.patch15
-rw-r--r--sci-visualization/paraview/files/paraview-3.14.1-python-exit.patch46
-rw-r--r--sci-visualization/paraview/files/paraview-3.14.1-removesqlite.patch526
-rw-r--r--sci-visualization/paraview/files/paraview-3.14.1-vtknetcd.patch75
-rw-r--r--sci-visualization/paraview/paraview-3.14.1-r2.ebuild (renamed from sci-visualization/paraview/paraview-3.14.1.ebuild)37
31 files changed, 1175 insertions, 165 deletions
diff --git a/dev-python/astlib/ChangeLog b/dev-python/astlib/ChangeLog
index 46252bede..7d86e5759 100644
--- a/dev-python/astlib/ChangeLog
+++ b/dev-python/astlib/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*astlib-0.17.1 (06 Sep 2012)
+
+ 06 Sep 2012; Sébastien Fabbro <bicatali@gentoo.org> +astlib-0.17.1.ebuild,
+ +files/astlib-0.17.1-wcstools.patch, -astlib-0.6.1.ebuild,
+ -files/astlib-0.6.0-wcstools.patch:
+ dev-python/astlib: Version bump
+
*astlib-0.6.1 (20 Apr 2012)
20 Apr 2012; Sébastien Fabbro <bicatali@gentoo.org> -astlib-0.6.0.ebuild,
@@ -21,4 +28,3 @@
15 Jul 2010; Sébastien Fabbro <bicatali@gentoo.org> +astlib-0.4.0.ebuild,
+files/astlib-0.4.0-wcstools.patch, +metadata.xml:
Initial import
-
diff --git a/dev-python/astlib/Manifest b/dev-python/astlib/Manifest
index b4accd423..be7b45e86 100644
--- a/dev-python/astlib/Manifest
+++ b/dev-python/astlib/Manifest
@@ -1 +1 @@
-DIST astLib-0.6.1.tar.gz 702436 SHA256 ac6ea190012058b6001b254145dbeb3a1f5e95e49754f49641265188887c10f1 SHA512 d1101c8f33d066508e04be6bc51ed689ff058fae6503d475dd161b8b1f6074ad8081d8a54b06023f30a531d1b8c08af6b04202021e106ded6d378c96c93984d1 WHIRLPOOL 039a91448c672e96d083763b3f55ef0d0abf515ba77ce250f67909ad3cfd7c9723201736f6f916a03bb311f3643265522bc939ae8320b9add80393a608fd783a
+DIST astLib-0.17.1.tar.gz 547431 SHA256 ff03cab7e9b41b3c9366c56273929b721fee08ec39ae8984606aa71bbaeeb961 SHA512 511282e0794dc72a295678b833cac634f9c3053456fa715b0e936e1de2915e675e614e74adaa68347d0952daf7da7d375deab2c05675cd375e287e1b8edcc0ba WHIRLPOOL c667fa216a50d720c8205fab7b905956c6d600affb9cbd740845f670a64fb3f4f95c858d831c44369f9878bb5e7b48f70f31799e0a1a9751be0a95803f728b44
diff --git a/dev-python/astlib/astlib-0.6.1.ebuild b/dev-python/astlib/astlib-0.17.1.ebuild
index 28a6d47f5..8d5beb6ec 100644
--- a/dev-python/astlib/astlib-0.6.1.ebuild
+++ b/dev-python/astlib/astlib-0.17.1.ebuild
@@ -4,7 +4,6 @@
EAPI=4
-PYTHON_DEPEND="2"
SUPPORT_PYTHON_ABIS="1"
RESTRICT_PYTHON_ABIS="3.*"
@@ -19,7 +18,7 @@ SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.gz"
IUSE="doc examples"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
LICENSE="BSD"
DEPEND="sci-astronomy/wcstools"
@@ -32,7 +31,7 @@ RDEPEND="${DEPEND}
S="${WORKDIR}/${MYP}"
src_prepare() {
- epatch "${FILESDIR}"/${PN}-0.6.0-wcstools.patch
+ epatch "${FILESDIR}"/${PN}-0.17.1-wcstools.patch
distutils_src_prepare
}
diff --git a/dev-python/astlib/files/astlib-0.17.1-wcstools.patch b/dev-python/astlib/files/astlib-0.17.1-wcstools.patch
new file mode 100644
index 000000000..dac0a6a02
--- /dev/null
+++ b/dev-python/astlib/files/astlib-0.17.1-wcstools.patch
@@ -0,0 +1,75 @@
+--- setup.py.orig 2012-09-06 09:40:12.270646957 -0700
++++ setup.py 2012-09-06 09:45:04.370193374 -0700
+@@ -13,23 +13,23 @@
+ exampleScripts=glob.glob("scripts"+os.path.sep+"*.py")
+
+ class build_PyWCSTools_ext(build_ext):
+-
++
+ def build_extensions(self):
+-
++
+ os.chdir(sourceDir)
+-
++
+ cc=distutils.ccompiler.new_compiler()
+-
+- WCSToolsCFiles=["actread.c", "binread.c", "ctgread.c", "catutil.c", "cel.c", "daoread.c", "dateutil.c", "distort.c", "dsspos.c",
++
++ WCSToolsCFiles=["actread.c", "binread.c", "ctgread.c", "catutil.c", "cel.c", "daoread.c", "dateutil.c", "distort.c", "dsspos.c",
+ "fileutil.c", "imutil.c", "findstar.c", "fitsfile.c", "fitswcs.c", "gscread.c", "gsc2read.c", "hget.c", "hput.c", "iget.c",
+ "imgetwcs.c", "imhfile.c", "imio.c", "imsetwcs.c", "imrotate.c", "lin.c", "matchstar.c", "platefit.c", "platepos.c",
+ "polfit.c", "proj.c", "sdssread.c", "sortstar.c", "sph.c", "tabread.c", "tmcread.c", "tnxpos.c", "ty2read.c", "uacread.c",
+ "ubcread.c", "ucacread.c", "ujcread.c", "wcs.c", "wcsinit.c", "wcscon.c", "wcslib.c", "wcstrig.c", "webread.c", "worldpos.c"]
+ cc.compile(WCSToolsCFiles)
+-
++
+ os.chdir(topDir)
+-
+- build_ext.build_extensions(self)
++
++ build_ext.build_extensions(self)
+
+ setup(name='astLib',
+ version='0.17.1',
+@@ -51,35 +51,11 @@
+ with World Coordinate System (WCS) information through PyWCSTools - a simple wrapping of WCSTools by Doug Mink.
+ PyWCSTools is distributed (and developed) as part of astLib.""",
+ packages=['astLib', 'PyWCSTools'],
+- cmdclass={"build_ext": build_PyWCSTools_ext},
+ scripts=exampleScripts,
+ ext_modules=[
+- Extension('PyWCSTools._wcscon', [sourceDir+"wcscon_wrap.c"],
+- extra_objects=[sourceDir+"actread.o", sourceDir+"binread.o", sourceDir+"ctgread.o", sourceDir+"catutil.o",
+- sourceDir+"cel.o", sourceDir+"daoread.o", sourceDir+"dateutil.o", sourceDir+"distort.o",
+- sourceDir+"dsspos.o", sourceDir+"fileutil.o", sourceDir+"imutil.o", sourceDir+"findstar.o",
+- sourceDir+"fitsfile.o", sourceDir+"fitswcs.o", sourceDir+"gscread.o", sourceDir+"gsc2read.o",
+- sourceDir+"hget.o", sourceDir+"hput.o", sourceDir+"iget.o", sourceDir+"imgetwcs.o",
+- sourceDir+"imhfile.o", sourceDir+"imio.o", sourceDir+"imsetwcs.o", sourceDir+"imrotate.o",
+- sourceDir+"lin.o", sourceDir+"matchstar.o", sourceDir+"platefit.o",
+- sourceDir+"platepos.o", sourceDir+"polfit.o", sourceDir+"proj.o", sourceDir+"sdssread.o",
+- sourceDir+"sortstar.o", sourceDir+"sph.o", sourceDir+"tabread.o", sourceDir+"tmcread.o",
+- sourceDir+"tnxpos.o", sourceDir+"ty2read.o", sourceDir+"uacread.o", sourceDir+"ubcread.o",
+- sourceDir+"ucacread.o", sourceDir+"ujcread.o", sourceDir+"wcs.o", sourceDir+"wcsinit.o",
+- sourceDir+"wcscon.o", sourceDir+"wcslib.o", sourceDir+"wcstrig.o", sourceDir+"webread.o",
+- sourceDir+"worldpos.o"]),
+- Extension('PyWCSTools._wcs', [sourceDir+"wcs_wrap.c"],
+- extra_objects=[sourceDir+"actread.o", sourceDir+"binread.o", sourceDir+"ctgread.o", sourceDir+"catutil.o",
+- sourceDir+"cel.o", sourceDir+"daoread.o", sourceDir+"dateutil.o", sourceDir+"distort.o",
+- sourceDir+"dsspos.o", sourceDir+"fileutil.o", sourceDir+"imutil.o", sourceDir+"findstar.o",
+- sourceDir+"fitsfile.o", sourceDir+"fitswcs.o", sourceDir+"gscread.o", sourceDir+"gsc2read.o",
+- sourceDir+"hget.o", sourceDir+"hput.o", sourceDir+"iget.o", sourceDir+"imgetwcs.o",
+- sourceDir+"imhfile.o", sourceDir+"imio.o", sourceDir+"imsetwcs.o", sourceDir+"imrotate.o",
+- sourceDir+"lin.o", sourceDir+"matchstar.o", sourceDir+"platefit.o",
+- sourceDir+"platepos.o", sourceDir+"polfit.o", sourceDir+"proj.o", sourceDir+"sdssread.o",
+- sourceDir+"sortstar.o", sourceDir+"sph.o", sourceDir+"tabread.o", sourceDir+"tmcread.o",
+- sourceDir+"tnxpos.o", sourceDir+"ty2read.o", sourceDir+"uacread.o", sourceDir+"ubcread.o",
+- sourceDir+"ucacread.o", sourceDir+"ujcread.o", sourceDir+"wcs.o", sourceDir+"wcsinit.o",
+- sourceDir+"wcscon.o", sourceDir+"wcslib.o", sourceDir+"wcstrig.o", sourceDir+"webread.o",
+- sourceDir+"worldpos.o"])]
++ Extension('PyWCSTools._wcscon', [sourceDir+"wcscon_wrap.c"],
++ libraries=['wcstools']),
++ Extension('PyWCSTools._wcs', [sourceDir+"wcs_wrap.c"],
++ libraries=['wcstools'])]
++
+ )
diff --git a/dev-python/astlib/files/astlib-0.6.0-wcstools.patch b/dev-python/astlib/files/astlib-0.6.0-wcstools.patch
deleted file mode 100644
index adf468db4..000000000
--- a/dev-python/astlib/files/astlib-0.6.0-wcstools.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-Debundle wcstools
-
---- a/setup.py
-+++ b/setup.py
-@@ -13,36 +13,8 @@
- topDir=os.getcwd()
- sourceDir="PyWCSTools"+os.path.sep+"wcssubs-3.8.4"+os.path.sep
-
--#oFiles=glob.glob(sourceDir+"*.o")
--#print oFiles
--oFiles=['PyWCSTools/wcssubs-3.8.4/cel.o', 'PyWCSTools/wcssubs-3.8.4/wcs.o', 'PyWCSTools/wcssubs-3.8.4/proj.o', 'PyWCSTools/wcssubs-3.8.4/distort.o', 'PyWCSTools/wcssubs-3.8.4/wcsinit.o', 'PyWCSTools/wcssubs-3.8.4/wcslib.o', 'PyWCSTools/wcssubs-3.8.4/poly.o', 'PyWCSTools/wcssubs-3.8.4/platepos.o', 'PyWCSTools/wcssubs-3.8.4/zpxpos.o', 'PyWCSTools/wcssubs-3.8.4/iget.o', 'PyWCSTools/wcssubs-3.8.4/imio.o', 'PyWCSTools/wcssubs-3.8.4/dsspos.o', 'PyWCSTools/wcssubs-3.8.4/tnxpos.o', 'PyWCSTools/wcssubs-3.8.4/wcscon.o', 'PyWCSTools/wcssubs-3.8.4/fitsfile.o', 'PyWCSTools/wcssubs-3.8.4/dateutil.o', 'PyWCSTools/wcssubs-3.8.4/imhfile.o', 'PyWCSTools/wcssubs-3.8.4/lin.o', 'PyWCSTools/wcssubs-3.8.4/fileutil.o', 'PyWCSTools/wcssubs-3.8.4/wcstrig.o', 'PyWCSTools/wcssubs-3.8.4/slasubs.o', 'PyWCSTools/wcssubs-3.8.4/sph.o', 'PyWCSTools/wcssubs-3.8.4/worldpos.o', 'PyWCSTools/wcssubs-3.8.4/hget.o', 'PyWCSTools/wcssubs-3.8.4/hput.o']
--
- exampleScripts=glob.glob("scripts"+os.path.sep+"*.py")
-
--class build_PyWCSTools_ext(build_ext):
--
-- def build_extensions(self):
--
-- os.chdir(sourceDir)
--
-- cc=distutils.ccompiler.new_compiler(distutils.ccompiler.get_default_compiler())
-- distutils.command.config.customize_compiler(cc)
--
-- # Suppress warnings from compiling WCSTools wcssubs-3.8.4
-- if "-Wstrict-prototypes" in cc.compiler_so:
-- cc.compiler_so.pop(cc.compiler_so.index("-Wstrict-prototypes"))
-- if "-Wall" in cc.compiler_so:
-- cc.compiler_so.pop(cc.compiler_so.index("-Wall"))
--
-- WCSToolsCFiles=glob.glob("*.c")
-- WCSToolsCFiles.pop(WCSToolsCFiles.index("wcs_wrap.c"))
-- WCSToolsCFiles.pop(WCSToolsCFiles.index("wcscon_wrap.c"))
-- cc.compile(WCSToolsCFiles)
--
-- os.chdir(topDir)
--
-- build_ext.build_extensions(self)
--
- setup(name='astLib',
- version='0.6.0',
- url='http://astlib.sourceforge.net',
-@@ -65,12 +37,11 @@
- PyWCSTools is distributed (and developed) as part of astLib.""",
- packages=['astLib', 'PyWCSTools'],
- package_data={'astLib': ['data/*']},
-- cmdclass={"build_ext": build_PyWCSTools_ext},
- scripts=exampleScripts,
- ext_modules=[
- Extension('PyWCSTools._wcscon', [sourceDir+"wcscon_wrap.c"],
-- extra_objects=oFiles),
-+ libraries=['wcstools']),
- Extension('PyWCSTools._wcs', [sourceDir+"wcs_wrap.c"],
-- extra_objects=oFiles)
-+ libraries=['wcstools'])
- ]
- )
diff --git a/licenses/ligplot+ b/licenses/ligplot+
new file mode 100644
index 000000000..7457f6622
--- /dev/null
+++ b/licenses/ligplot+
@@ -0,0 +1,138 @@
+LIGPLOT - Automated representation of protein-ligand interactions
+ ----------------------------------------------------------------
+
+ CONFIDENTIALITY AGREEMENT
+ -------------------------
+
+
+
+In regard to the LIGPLOT , specified in the Appendix herewith
+(the Software) supplied to us, the copyright and other
+intellectual property rights to which belong to the authors, we
+
+
+ __________________________________________________________________
+
+undertake to the authors that we shall be bound by the following terms
+and conditions:-
+
+1. We will receive the Software and any related documentation in
+confidence and will not use the same except for the purpose of the
+department's own research. The Software will be used only by such of
+our officers or employees to whom it must reasonably be communicated
+to enable us to undertake our research and who agree to be bound by
+the same confidence. The department shall procure and enforce such
+agreement from its staff for the benefit of the authors.
+
+2. The publication of research using the Software must reference
+"Wallace A C, Laskowski R A, Thornton J M (1995). LIGPLOT: A program
+to generate schematic diagrams of protein-ligand interactions. Protein
+Engineering, 8, 127-134."
+
+3. Research shall take place solely at the department's premises at
+
+
+ __________________________________________________________________
+
+4. All forms of the Software will be kept in a reasonably secure place
+ to prevent unauthorised access.
+
+5. Each copy of the Software or, if not practicable then, any package
+associated therewith shall be suitably marked (and such marking
+maintained) with the following copyright notice: " Copyright 1994
+A C Wallace, R A Laskowski, & J M Thornton All Rights Reserved".
+
+6. The Software may be modified but any changes made shall be made
+available to the authors.
+
+7. The Software shall be used exclusively for academic teaching and
+research. The Software will not be used for any commercial research or
+research associated with an industrial company.
+
+8. The confidentiality obligation in paragraph one shall not apply:
+
+ (i) to information and data known to the department at the time of
+ receipt hereunder (as evidenced by its written records);
+
+ (ii) to information and data which was at the time of receipt in the
+ public domain or thereafter becomes so through no wrongful act of
+ the department;
+
+ (iii) to information and data which the department receives from a third
+ party not in breach of any obligation of confidentiality owed to
+ the authors.
+
+Please sign this Undertaking and return a copy of it to indicate that you
+have read, understood and accepted the above terms.
+
+
+
+ For and on behalf of _____________________________
+
+ _________________________________________________
+
+ ..................................................
+
+ Dated ............................................
+
+
+
+e-mail address ___________________________
+
+
+
+Please complete the above form, sign it, and then send it, or fax it, to:-
+
+
+Roman Laskowski
+European Bioinformatics Institute,
+Wellcome Trust Genome Campus,
+Hinxton,
+Cambridge, CB10 1SD,
+United Kingdom
+
+Fax:- +44 (0)1223 494 468
+
+roman@ebi.ac.uk
+
+
+If you have any problems either installing the software or running it,
+please e-mail your problems to:-
+
+ roman@ebi.ac.uk
+
+
+APPENDIX - Files supplied as part of the LIGPLOT program
+--------------------------------------------------------
+
+Source program files:-
+1. ligplot.c
+2. ligplot.h
+3. hbadd.c
+4. hbadd.h
+5. dimer.c
+6. dimer.h
+
+Script files:-
+1. ligplot.scr
+2. ligonly.scr
+3. dimplot.scr
+4. dimonly.scr
+
+Parameter file:-
+1. ligplot.prm
+
+Installation instructions:-
+1. install.doc
+
+Documentation:-
+1. manual.tar.Z
+2. README
+
+Confidentiality Agreement:-
+1. confid.txt
+
+
+
+ v.4.4.2 - 7 Mar 2003
+
diff --git a/metadata/layout.conf b/metadata/layout.conf
index 46ccb35e9..081a32668 100644
--- a/metadata/layout.conf
+++ b/metadata/layout.conf
@@ -14,7 +14,7 @@ thin-manifests = true
sign-manifests = false
# sign commits using git mechanisms
-sign-commits = false
+sign-commits = true
# Make egencache generate newer (more reliable)
# md5-dict cache format (see bug #409445).
diff --git a/profiles/profiles.desc b/profiles/profiles.desc
index e69de29bb..8b1378917 100644
--- a/profiles/profiles.desc
+++ b/profiles/profiles.desc
@@ -0,0 +1 @@
+
diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 597e7df73..3193225dc 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -2,25 +2,48 @@
# your descriptions to your package's metadata.xml ONLY.
# * generated automatically using egencache *
+dev-cpp/eigen:adolc - Enable use for automatic differentiation using sci-libs/adolc
+dev-cpp/eigen:sparse - Enable use for extra sparse matrix with sci-libs/umfpack, sci-libs/cholmod, sci-libs/superlu and dev-cpp/sparsehash
dev-java/hdf-java:hdf - Add support for the Hierarchical Data Format v.4 (sci-libs/hdf)
+dev-java/hdf-java:hdfview - Build a GUI viewer for all files supported in dev-java/hdf-java
+dev-java/jogl:cg - Enable NVidia Cg binding.
dev-lang/icc:eclipse - Install the dev-util/eclipse-sdk plugins
dev-lang/idb:eclipse - Install the dev-util/eclipse-sdk plugins
-dev-lang/path64:debugger - Build PathDB
+dev-lang/path64:assembler - Build PathAS assembler
+dev-lang/path64:debugger - Build PathDB debugger
dev-lang/path64:native - Use EKOPath/Path64 for bootstraping
+dev-lang/path64:valgrind - Support compiler debugging with dev-util/valgrind
dev-libs/intel-common:compiler - Install the libraries needed for the icc and ifort compilers
dev-ml/mlgmpidl:mpfr - add support for mpfr, the library for multiple-precision floating-point computations with exact rounding
-dev-python/cvxopt:glpk - Use GNU Linear Programming Kit
+dev-ml/zarith:mpir - Use mpir library instead of gmp
dev-python/ffnet:matplotlib - Use matplotlib for drawing
+dev-python/pyhdf:szip - Allow to use sci-libs/szip for SZIP compression method in SDsetcompress()
+dev-util/nvidia-cuda-sdk:cuda - Build CUDA binaries
+dev-util/nvidia-cuda-sdk:opencl - Build OpenCL binaries
+dev-util/nvidia-cuda-toolkit:debugger - Installs the NVIDIA CUDA debugger
+dev-util/nvidia-cuda-toolkit:profiler - Installs the NVIDIA CUDA visual profiler
media-gfx/brlcad:benchmarks - Run benchmarks during test phase (need test option enabled)
+net-fs/cvmfs:client - Install the cvmfs client programs and init script
+net-fs/cvmfs:server - Install the cvmfsd program and init script
net-misc/dhcp:client - Install the dhclient program
-net-misc/dhcp:infiniband - Enable ipoib support
net-misc/dhcp:server - Install the dhcpd and dhcrelay programs
sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
-sci-biology/estscan:intel - Use intel compiler
+sci-astronomy/scamp:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
+sci-astronomy/sextractor:modelfit - Enable profile model fitting, needs sci-libs/atlas and sci-libs/fftw
+sci-astronomy/zpeg:gdl - Install GDL/IDL plotting routines
sci-chemistry/avogadro:glsl - Enable glsl features via GLEW.
+sci-chemistry/ball:cuda - Include cuda support
+sci-chemistry/ball:sql - Include SQL database support
+sci-chemistry/ball:webkit - Uses x11-libs/qt-webkit for drawing
+sci-chemistry/gromacs:avx128fma - Enable 128bit avx with fma (e.g. AMD BullDozer)
+sci-chemistry/gromacs:avx256 - Enable 256bit avx (e.g. Intel Sandy Bridge)
+sci-chemistry/gromacs:cuda - Enable cuda non-bonded kernels
sci-chemistry/gromacs:double-precision - More precise calculations at the expense of speed
sci-chemistry/gromacs:fkernels - Enable building of Fortran Kernels for platforms that dont have assembly loops
+sci-chemistry/gromacs:hybrid - Enable hybrid acceleration kernels
+sci-chemistry/gromacs:power6 - Enable Power6 optimizations
sci-chemistry/gromacs:single-precision - Single precision version of gromacs (default)
+sci-chemistry/gromacs:sse41 - Enable sse4.1 acceleration
sci-chemistry/jmol:client-only - Install the viewer only, no applet files for httpd
sci-chemistry/pymol:apbs - Pymol supprt for sci-chemistry/apbs
sci-chemistry/pymol:numpy - Enable numpy support for Pymol
@@ -28,8 +51,7 @@ sci-chemistry/pymol:vmd - Builds molfile plugin support
sci-chemistry/pymol:web - Install Pymodule needed for web app support
sci-chemistry/rosetta:boinc - compile rosetta as a rosetta@home client
sci-chemistry/rosetta:boost - compile rosetta with boost supported code
-sci-chemistry/votca-csg:boost - Compile against external boost headers from dev-libs/boost
-sci-chemistry/votca-csg:extras - Pull in extra applications from dev-libs/boost
+sci-chemistry/votca-csg:extras - Pull in extra applications from sci-chemistry/votca-csg-apps
sci-chemistry/votca-csg:gromacs - Add support for gromacs file formats through sci-chemistry/gromacs
sci-electronics/player:boost - Automatically generated description for boost
sci-electronics/player:festival - Automatically generated description for festival
@@ -38,15 +60,30 @@ sci-electronics/player:sphinx2 - Automatically generated description for sphinx2
sci-geosciences/libtcd:non-commercial - Allows the use of a tide constituent database that is available for non-commercial use only.
sci-geosciences/qgis:grass - Add support for sci-geosciences/grass
sci-geosciences/xtide:non-commercial - Allows the use of a tide constituent database that is available for non-commercial use only.
-sci-libs/atlas:xblas - Build LAPACK with extra precision (needs sci-libs/xblas)
+sci-libs/acml:gfortran - Fetch and install acml compiled with GNU FORTRAN compiler
+sci-libs/acml:ifort - Fetch and install acml compiled with the Intel FORTRAN compiler
+sci-libs/acml:int64 - Install the 64 bits integer library
+sci-libs/acml:nag - Fetch and install acml compiled with the NAG FORTRAN compiler
+sci-libs/acml:open64 - Fetch and install acml compiled with the Open64 FORTRAN Compiler
+sci-libs/acml:pgi - Fetch and install acml compiled with the Portland Group FORTRAN compiler
+sci-libs/armadillo:atlas - Link with ATLAS libraries for cblas and clapack (needs sci-libs/lapack-atlas)
+sci-libs/atlas:generic - Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)
sci-libs/bigdft:cuda - Add cuda support
sci-libs/calculix-ccx:arpack - Add sparse eigen value support via sci-libs/arpack
+sci-libs/coinor-clp:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
+sci-libs/coinor-clp:metis - Enable partitioning with sci-libs/metis
+sci-libs/coinor-clp:mumps - Enable sci-libs/mumps support
+sci-libs/coinor-clp:sparse - Enable support for sparse matrix with sci-libs/cholmod
+sci-libs/coinor-osi:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
+sci-libs/coinor-symphony:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
+sci-libs/coinor-utils:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
sci-libs/factory:singular - Enable support for sci-mathematics/singular
-sci-libs/fox:dom - Automatically generated description for dom
-sci-libs/fox:fast - Automatically generated description for fast
-sci-libs/fox:sax - Automatically generated description for sax
-sci-libs/fox:wcml - Automatically generated description for wcml
-sci-libs/fox:wxml - Automatically generated description for wxml
+sci-libs/fox:dom - Compile the W3C document object model module
+sci-libs/fox:fast - Compile with best known optimization flags
+sci-libs/fox:sax - Compile the streaming, validating parser based on java's Simple API for XML
+sci-libs/fox:wcml - Compile the module for a subset of the Chemical Markup Language
+sci-libs/fox:wkml - Compile the module for the creation of KML documents used by applications such as Google Earth
+sci-libs/fox:wxml - Compile the XML writer used to sequentially create arbitrary XML documents quickly with minimal memory requirements
sci-libs/gmsh:cgns - Enables cgns output support
sci-libs/gmsh:chaco - Enables chaco partitioner support
sci-libs/gmsh:med - Enables med support
@@ -56,19 +93,27 @@ sci-libs/gmsh:opencascade - Enable OpenCASCADE support
sci-libs/gmsh:petsc - Enable sci-mathematics/petsc support
sci-libs/gmsh:taucs - Enable sci-libs/taucs support
sci-libs/gmsh:tetgen - Enable 3D delauny triangulation using tetgen lib
-sci-libs/libcmatrix:atlas - Use of atlas blas implementation
+sci-libs/gotoblas2:dynamic - Build dynamic architecture detection at run time (for multi targets)
+sci-libs/gotoblas2:incblas - Build the CBLAS interface
+sci-libs/gotoblas2:int64 - Build the 64 bits integer library
+sci-libs/ipopt:mumps - Enable sci-libs/mumps support
+sci-libs/lapack-reference:xblas - Build LAPACK with extra precision (needs sci-libs/xblas)
+sci-libs/lapacke-reference:xblas - Build LAPACKE with extra precision (needs sci-libs/xblas)
+sci-libs/levmar:plasma - Use the multi-threaded sci-libs/plasma library for linear algebra
sci-libs/libfac:singular - Automatically generated description for singular
sci-libs/lwpr:octave - Add sci-mathematics/octave support
+sci-libs/magma:fermi - Compile for GPU NVIDIA Fermi family (2.x cards)
+sci-libs/magma:tesla - Compile for GPU NVIDIA Tesla family (1.x cards)>
+sci-libs/mumps:metis - Enable ordering with METIS (sci-libs/metis, sci-libs/parmetis)
+sci-libs/mumps:scotch - Enable ordering with sci-libs/scotch
sci-libs/oasa:cairo - Add support for Cairo graphics library using dev-python/pycairo
sci-libs/openblas:dynamic - Build dynamic architecture detection at run time (for multi targets)
sci-libs/openblas:incblas - Build the CBLAS interface
sci-libs/openblas:int64 - Build the 64 bits integer library
-sci-libs/openmm:cuda - Build Cuda lib
-sci-libs/openmm:opencl - Build OpenCL lib
sci-libs/pagmo:kepler - Automatically generated description for kepler
sci-libs/pagmo:nlopt - Automatically generated description for nlopt
-sci-libs/votca-tools:boost - Compile against external boost headers (dev-libs/boost)
-sci-libs/xdrfile:dmalloc - Enable use of Debug Malloc
+sci-libs/parmetis:double-precision - Floating-point operation done as double precision
+sci-libs/parmetis:int64 - Build the 64 bits integer library (needed for > 2^31 vertices)
sci-mathematics/Macaulay2:optimization - Accept upstream's choices for -O option, i.e. -O3 almost everywhere.
sci-mathematics/algae:intel - Use icc as c compiler
sci-mathematics/apron:ppl - Enable optional interface to the Parma Polyhedra Library
@@ -83,11 +128,20 @@ sci-mathematics/frama-c:why - ?why?
sci-mathematics/gambit:X - Enable gui support using wxWidgets.
sci-mathematics/gap:xtom - Automatically generated description for xtom
sci-mathematics/giac:fltk - ?fltk?
+sci-mathematics/htk:hdecode - Install HDecode, a large vocabulary word recogniser
+sci-mathematics/htk:hlmtools - Install the tools for manipulation of language models
+sci-mathematics/htk:hslab - Install HSLab a label editor for speech label manipulation
+sci-mathematics/htk:htkbook - Build the HTK documentation (HTK Book)
sci-mathematics/netgen:opencascade - Enable OpenCASCADE support
+sci-mathematics/petsc:afterimage - Use Afterstep image library (media-libs/libafterimage)
sci-mathematics/petsc:complex-scalars - Make scalars complex
-sci-mathematics/petsc:hypre - Use HYPRE (sci-mathematics/hypre) for preconditioning
+sci-mathematics/petsc:hypre - Use HYPRE (sci-mathematics/hypre) and for preconditioning
sci-mathematics/petsc:metis - Use METIS (sci-libs/parmetis) for partitioning
-sci-mathematics/polybori:sage - Replace the standard python interface by sage's python interface for easy integration in sage.
+sci-mathematics/petsc:sparse - Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization
+sci-mathematics/petsc:superlu - Use superlu (sci-libs/superlu) for preconditioning
+sci-mathematics/polymake:libpolymake - Build the polymake library to build applications using the C++ interface.
+sci-mathematics/rstudio:desktop - Build the QT4 desktop interface
+sci-mathematics/rstudio:server - Build and install the RStudio server
sci-mathematics/scilab:gui - Build the Java base graphical interface
sci-mathematics/scilab:matio - Enable support for MATLAB file through sci-libs/matio
sci-mathematics/scilab:umfpack - Adds support for sparse solving with sci-libs/umfpack
@@ -98,37 +152,42 @@ sci-mathematics/why:gappa - ?gappa?
sci-mathematics/why:gtk - ?gtk?
sci-mathematics/why:jessie - ?jessie?
sci-mathematics/why:pff - ?pff?
+sci-misc/hfst:foma - Add optional support for foma backend library (sci-misc/foma)
+sci-misc/hfst:glib - Parse UTF-8 and collate unicode using glib instead of homebrewn methods
sci-misc/hfst:openfst - Add optional support for openfst backend library (sci-misc/openfst)
sci-misc/hfst:sfst - Add optional support for sfst backend library (sci-misc/sfst)
-sci-misc/nco:ncap2 - Build next generation netcdf arithmetic processor (needs dev-java/antlr)
-sci-misc/nco:udunits - Add sci-libs/udunits files support
+sci-misc/hfst:xml - Include parsers for grammars and formats that require XML support
sci-misc/opennlp-tools:models - Automatically generated description for models
sci-misc/salome-kernel:numpy - Enable support for dev-python/numpy
sci-misc/salome-med:metis - Add support for metis
sci-misc/salome-med:scotch - Add support for scotch
sci-physics/abinit:cuda - Enable support for nVidia CUDA
+sci-physics/abinit:cuda-double - Enable support for double precision nVidia CUDA
+sci-physics/abinit:fftw-threads - Use the threaded version of sci-libs/fftw
sci-physics/abinit:fox - Enable support for FoX Fortran XML library
+sci-physics/abinit:gui - Build the abinit GUI (requires java)
+sci-physics/abinit:libabinit - Build the libabinit used by sci-libs/bigdft (usage not tested yet, circular dependency not resolved)
sci-physics/abinit:vdwxc - Activate van der Waals exchange-correlation
sci-physics/atompaw:libxc - Use libxc for something
sci-physics/elk:libxc - Use sci-libs/libxc library of exchange-correlation functionals by ETSF.
sci-physics/espresso:examples - Installs the examples
sci-physics/espresso:packages - Installs extra subpackages
-sci-physics/fastjet:allcxxplugins - Build all C++ plugins.
-sci-physics/fastjet:allplugins - Build all standard plugins.
-sci-physics/fastjet:cgal - Use sci-mathematics/cgal instead of bundled algorithms.
-sci-physics/root:clarens - Buld the Clarens and PEAC plug-ins, to use in a GRID enabled analysis.
+sci-physics/root:c++0x - Build ROOT using the C++11 standard. Not supported, requires sys-devel/gcc>=4.7.0
sci-physics/root:fits - Support for images and data from FITS files with sci-libs/cfitsio
+sci-physics/root:geocad - Enable ROOT-CAD interface using sci-libs/opencascade
+sci-physics/root:htmldoc - Generate html documentation
sci-physics/root:llvm - Build the new cling interactive interpreter based on sys-devel/llvm
sci-physics/root:math - Build all math related libraries plugins, needs sci-libs/gsl
-sci-physics/root:pythia6 - Builds the interface to Pythia-6 (sci-physics/pythia) high energy physics generation events library
-sci-physics/root:pythia8 - Builds the interface to Pythia-8 (sci-physics/pythia) high energy physics generation events library
-sci-physics/root:reflex - Builds the reflection database for the C++ interpretor
-sci-physics/root:xrootd - Build the xrootd low latency file server
+sci-physics/root:pythia6 - Build the interface for sci-physics/pythia version 6.x
+sci-physics/root:pythia8 - Build the interface for sci-physics/pythia version 8.x
+sci-physics/root:reflex - Build the reflection database for the C++ interpreter
+sci-physics/root:xrootd - Build the interface for net-libs/xrootd
+sci-visualization/gnuplot:bitmap - Enable dot-matrix printers and pbm terminal
sci-visualization/gnuplot:gd - Add support for media-libs/gd. Needed for GIF, JPEG, and PNG image output.
-sci-visualization/gnuplot:qt4 - Build Qt4 terminal
sci-visualization/gnuplot:thin-splines - Enable thin plate splines
sci-visualization/nodemon:pbs - Enable support for the Portable Batch System.
sci-visualization/paraview:adaptive - Enable the adaptive paraview application
+sci-visualization/paraview:boost - Add support for boost
sci-visualization/paraview:cg - Add support for nvidia's cg shaders
sci-visualization/paraview:coprocessing - Enable the coprocessing infrastructure which is mainly useful in the context of clusters
sci-visualization/paraview:gui - Build paraview's gui not just the server
@@ -156,5 +215,4 @@ sys-cluster/openmpi:mpi-threads - Enable MPI_THREAD_MULTIPLE
sys-cluster/openmpi:pbs - Add support for the Portable Batch System (PBS)
sys-cluster/openmpi:romio - Build the ROMIO MPI-IO component
sys-cluster/openmpi:vt - Enable bundled VampirTrace support
-sys-fs/ocfs2-tools:external - Enable external locking
virtual/mpi:romio - Enable romio, a high-performance portable MPI-IO
diff --git a/sci-chemistry/ligplot+/ChangeLog b/sci-chemistry/ligplot+/ChangeLog
new file mode 100644
index 000000000..b1240fa83
--- /dev/null
+++ b/sci-chemistry/ligplot+/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/ligplot+
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ligplot+-1.4 (30 Aug 2012)
+
+ 30 Aug 2012; Justin Lecher <jlec@gentoo.org> +ligplot+-1.4.ebuild,
+ +metadata.xml:
+ New addition
+
diff --git a/sci-chemistry/ligplot+/Manifest b/sci-chemistry/ligplot+/Manifest
new file mode 100644
index 000000000..996b438bb
--- /dev/null
+++ b/sci-chemistry/ligplot+/Manifest
@@ -0,0 +1 @@
+DIST LigPlus.zip 1937904 SHA256 5d47af05f1fb48b4c0a6dee4d8eacb0d2ffe90966b0419d954c9d0f7a6580b49 SHA512 fee1c9b54c895d26ebd81f283ab942b199db87d189a01f22aebf26d6ed90e801f53b64cf9abf870721a4b478e68bf390b0e1c9eb9b02a692a1011271611f7afd WHIRLPOOL d86822b5e4cd0bd429df912f3b60de11094a2e549841f59343c0435a329a5c1181e543e06af9eb760d3bbbc6a12414fc5477c87f192deb40304d7ce619b65f28
diff --git a/sci-chemistry/ligplot+/ligplot+-1.4.ebuild b/sci-chemistry/ligplot+/ligplot+-1.4.ebuild
new file mode 100644
index 000000000..94aefcc98
--- /dev/null
+++ b/sci-chemistry/ligplot+/ligplot+-1.4.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit java-pkg-2
+
+DESCRIPTION="GUI-based version of LIGPLOT"
+HOMEPAGE="http://www.ebi.ac.uk/thornton-srv/software/LigPlus/"
+SRC_URI="LigPlus.zip"
+
+SLOT="0"
+LICENSE="ligplot+"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="virtual/jre"
+DEPEND=""
+
+RESTRICT="fetch"
+
+S="${WORKDIR}"/LigPlus
+
+QA_PREBUILT="opt/${PN}/.*"
+
+pkg_nofetch() {
+ einfo "Please visit"
+ einfo "http://www.ebi.ac.uk/thornton-srv/software/LigPlus/applicence.html"
+ einfo "download ${A}"
+ einfo "and save in ${DISTDIR}"
+}
+
+src_prepare() {
+ rm -rf lib/*{win,mac} || die
+}
+
+src_install() {
+ insinto /opt/${PN}
+ doins -r lib LigPlus.jar
+
+ make_wrapper ${PN} "java -jar \"${EPREFIX}/opt/${PN}/LigPlus.jar\""
+}
diff --git a/sci-chemistry/ligplot+/metadata.xml b/sci-chemistry/ligplot+/metadata.xml
new file mode 100644
index 000000000..d369d068f
--- /dev/null
+++ b/sci-chemistry/ligplot+/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/ssp/ChangeLog b/sci-chemistry/ssp/ChangeLog
index c2cb33298..87325180c 100644
--- a/sci-chemistry/ssp/ChangeLog
+++ b/sci-chemistry/ssp/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 30 Aug 2012; Justin Lecher <jlec@gentoo.org> ssp-09.11.ebuild:
+ Fix offset of reference CS DB
+
*ssp-09.11 (29 Aug 2012)
29 Aug 2012; Justin Lecher <jlec@gentoo.org> +ssp-09.11.ebuild,
diff --git a/sci-chemistry/ssp/ssp-09.11.ebuild b/sci-chemistry/ssp/ssp-09.11.ebuild
index d788a74e5..59061425e 100644
--- a/sci-chemistry/ssp/ssp-09.11.ebuild
+++ b/sci-chemistry/ssp/ssp-09.11.ebuild
@@ -18,6 +18,12 @@ DEPEND=""
S="${WORKDIR}"/${PN}
+src_prepare() {
+ sed \
+ -e "s:\(REF\/\):${EPREFIX}/usr/share/${PN}/\1:g" \
+ -i ${PN} || die
+}
+
src_install() {
dobin reref ${PN}
dodoc README
diff --git a/sci-libs/bigdft/ChangeLog b/sci-libs/bigdft/ChangeLog
index dad986751..1f24f098c 100644
--- a/sci-libs/bigdft/ChangeLog
+++ b/sci-libs/bigdft/ChangeLog
@@ -4,6 +4,17 @@
<<<<<<< HEAD
+*bigdft-1.6_pre1-r4 (01 Sep 2012)
+
+ 01 Sep 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+ -bigdft-1.6_pre1-r3.ebuild, +bigdft-1.6_pre1-r4.ebuild,
+ -files/bigdft-1.6-tuto.1-GPUlibs.patch,
+ +files/bigdft-1.6-tuto.1-GPUlibs-1.patch,
+ -files/bigdft-1.6-tuto.1-bigdft.pc.patch,
+ +files/bigdft-1.6-tuto.1-bigdft.pc-1.patch:
+ Patches to install GPU support corrected not to break linking against the
+ compiled libraries
+
10 Jul 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
files/bigdft-1.6-tuto.1-GPUlibs.patch:
bigdft-1.6-tuto.1-GPUlibs.patch updated not to forget the pkg-config file
diff --git a/sci-libs/bigdft/bigdft-1.6_pre1-r3.ebuild b/sci-libs/bigdft/bigdft-1.6_pre1-r4.ebuild
index a2cef02de..95bbebf41 100644
--- a/sci-libs/bigdft/bigdft-1.6_pre1-r3.ebuild
+++ b/sci-libs/bigdft/bigdft-1.6_pre1-r4.ebuild
@@ -64,9 +64,9 @@ pkg_setup() {
src_prepare() {
epatch \
"${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch \
- "${FILESDIR}"/"${REAL_P}"-bigdft.pc.patch \
+ "${FILESDIR}"/"${REAL_P}"-bigdft.pc-1.patch \
"${FILESDIR}"/"${REAL_P}"-gcc-4.6.patch \
- "${FILESDIR}"/"${REAL_P}"-GPUlibs.patch
+ "${FILESDIR}"/"${REAL_P}"-GPUlibs-1.patch
sed -i -e's/capitalize_module_ext/ax_fc_mod_ext/g' "${S}"/configure || die
sed -i -e's/capitalize_module_ext/ax_fc_mod_ext/g' "${S}"/configure.ac || die
eautoreconf
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch
index 507966518..386e39dc7 100644
--- a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs.patch
+++ b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch
@@ -1,24 +1,3 @@
-diff -Naur orig/bigdft-1.6-tuto.1.orig/configure.ac patched/bigdft-1.6-tuto.1/configure.ac
---- bigdft-1.6-tuto.1.orig/configure.ac 2012-07-10 08:50:27.000000000 +0000
-+++ bigdft-1.6-tuto.1/configure.ac 2012-07-10 09:03:46.303491671 +0000
-@@ -295,7 +295,7 @@ if test x"$ac_use_cuda_gpu" = "xyes" ; t
- fi
- fi
- AC_SUBST(NVCC_FLAGS)
-- LIBCUDA_LIBS="-L$ac_cuda_lib_path -lcudart -lcublas"
-+ LIBCUDA_LIBS="-L$ac_cuda_lib_path -lGPU -lcudart -lcublas"
- fi
-
- dnl Use the OpenCL support
-@@ -332,7 +332,7 @@ if test x"$ac_use_ocl" = "xyes" ; then
- ac_use_ocl="no"
- else
- dnl LIBOCL_LIBS="-L$ac_ocl_path/lib -lOpenCL -lm -lrt -lstdc++"
-- LIBOCL_LIBS="-L$ac_ocl_path/lib -lOpenCL -lm"
-+ LIBOCL_LIBS="-L$ac_ocl_path/lib -lOCL -lOpenCL -lm"
- fi
- LIBS=$LIBS_OLD
- fi
diff -Naur orig/bigdft-1.6-tuto.1.orig/src/CUDA/Makefile.am patched/bigdft-1.6-tuto.1/src/CUDA/Makefile.am
--- bigdft-1.6-tuto.1.orig/src/CUDA/Makefile.am 2011-09-27 12:43:06.000000000 +0000
+++ bigdft-1.6-tuto.1/src/CUDA/Makefile.am 2012-07-04 12:08:27.000000000 +0000
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc-1.patch
index 3ddde7014..7c3380a9b 100644
--- a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc.patch
+++ b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc-1.patch
@@ -158,7 +158,11 @@ diff -Naur bigdft-1.6-tuto_orig/Makefile.in bigdft-1.6-tuto/Makefile.in
diff -Naur bigdft-1.6-tuto_orig/bigdft.pc.in bigdft-1.6-tuto/bigdft.pc.in
--- bigdft.pc.in 1970-01-01 00:00:00.000000000 +0000
+++ bigdft.pc.in 2012-02-01 09:43:59.000000000 +0000
-@@ -0,0 +1,11 @@
+@@ -0,0 +1,15 @@
++@USE_CUDA_GPU_FALSE@libs_cuda=
++@USE_CUDA_GPU_TRUE@libs_cuda=$(top_builddir)/src/CUDA/libGPU.a
++@USE_OCL_FALSE@libs_ocl=
++@USE_OCL_TRUE@libs_ocl=$(top_builddir)/src/OpenCL/libOCL.a -lstdc++
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
@@ -168,7 +172,7 @@ diff -Naur bigdft-1.6-tuto_orig/bigdft.pc.in bigdft-1.6-tuto/bigdft.pc.in
+Description: Library for DFT calculation over wavelets.
+Requires:
+Version: @VERSION@
-+Libs: -L${libdir} -lbigdft -lpoissonsolver @LIBS@ @FCLIBS@
++Libs: -L${libdir} -lbigdft -lpoissonsolver ${libs_cuda} ${libs_ocl} @LIBS@ @FCLIBS@
+Cflags: -I${includedir}
diff -Naur bigdft-1.6-tuto_orig/configure bigdft-1.6-tuto/configure
--- configure 2012-03-21 10:03:26.000000000 +0000
diff --git a/sci-libs/exodusii/ChangeLog b/sci-libs/exodusii/ChangeLog
index 12d8e144d..907c612b5 100644
--- a/sci-libs/exodusii/ChangeLog
+++ b/sci-libs/exodusii/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*exodusii-5.22 (04 Sep 2012)
+
+ 04 Sep 2012; Justin Lecher <jlec@gentoo.org> -exodusii-4.98.ebuild,
+ -files/exodusii-4.98-find-netcdf.patch, +exodusii-5.22.ebuild,
+ +files/exodusii-5.22-multilib.patch:
+ Version Bump
+
22 May 2012; Justin Lecher <jlec@gentoo.org> exodusii-4.98.ebuild,
metadata.xml:
Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
diff --git a/sci-libs/exodusii/Manifest b/sci-libs/exodusii/Manifest
index 7b78f6524..09bdd0499 100644
--- a/sci-libs/exodusii/Manifest
+++ b/sci-libs/exodusii/Manifest
@@ -1 +1 @@
-DIST exodusii-4.98.tar.gz 446400 RMD160 c2da5e46ac361c22cebc9e307afa8c4d7ec7a10e SHA1 da9bede1a564346800789d999dd7baacc9f95603 SHA256 24b4e20368e4ef1d51913c742c571101eb26487ffdc2eeaf94779d20a8fa4058
+DIST exodus-5.22.tar.bz2 4225991 SHA256 f95a9c5e5970b7c6a522374d72a040c0b5f6c98f15a03a16b02a3b8d891d237a SHA512 de9929e8cf2d1945633d4033d49f1f6d649ab19ab91ac8f00e562b1789a6b90b4b07491276ac015657159159b755bb503155667ff33fa05d0c287b6b8d715c46 WHIRLPOOL 0d08c7406c3433b88a0f291873dd2acb84ecd04af55aaf7eabdceaf55d14cb190f6c5109e3c7aa174019f62a12e68edeff9475b85580cee42d64401173c6d7cb
diff --git a/sci-libs/exodusii/exodusii-4.98.ebuild b/sci-libs/exodusii/exodusii-5.22.ebuild
index 90a7abc8c..784d5190b 100644
--- a/sci-libs/exodusii/exodusii-4.98.ebuild
+++ b/sci-libs/exodusii/exodusii-5.22.ebuild
@@ -4,11 +4,11 @@
EAPI=4
-inherit cmake-utils eutils
+inherit cmake-utils multilib
DESCRIPTION="Model developed to store and retrieve transient data for finite element analyses"
HOMEPAGE="http://sourceforge.net/projects/exodusii/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+SRC_URI="mirror://sourceforge/${PN}/${P/ii/}.tar.bz2"
LICENSE="BSD"
SLOT="0"
@@ -18,12 +18,14 @@ IUSE="static-libs test"
DEPEND=">=sci-libs/netcdf-3.6.0"
RDEPEND="${DEPEND}"
-src_prepare() {
- epatch "${FILESDIR}"/${P}-find-netcdf.patch
-}
+S="${WORKDIR}"/${P/ii/}/${PN/ii/}
+
+PATCHES=( "${FILESDIR}"/${P}-multilib.patch )
-pkg_setup() {
+src_configure() {
mycmakeargs="${mycmakeargs}
+ -DLIB_INSTALL_DIR=$(get_libdir)
$(cmake-utils_use !static-libs BUILD_SHARED_LIBS)
$(cmake-utils_use test BUILD_TESTING)"
+ cmake-utils_src_configure
}
diff --git a/sci-libs/exodusii/files/exodusii-4.98-find-netcdf.patch b/sci-libs/exodusii/files/exodusii-4.98-find-netcdf.patch
deleted file mode 100644
index 8dbcb53b2..000000000
--- a/sci-libs/exodusii/files/exodusii-4.98-find-netcdf.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-diff -Naur exodusii-4.98/cbind/CMakeLists.txt source/cbind/CMakeLists.txt
---- exodusii-4.98/cbind/CMakeLists.txt 2010-10-04 08:12:11.000000000 -0600
-+++ source/cbind/CMakeLists.txt 2010-11-03 18:23:07.910378566 -0600
-@@ -1,14 +1,14 @@
--
- find_path( NETCDF_INCLUDE_DIR netcdf.h
- $ENV{ACCESS}/inc
- $ENV{NETCDF_DIR}/inc
- $ENV{NETCDF_DIR}/libsrc
--)
-+)
-
--find_path( NETCDF_LIBRARY libnetcdf.a
-- $ENV{ACCESS}/lib
-- $ENV{NETCDF_DIR}/lib
-- $ENV{NETCDF_DIR}/libsrc/.libs
-+find_library( NETCDF_LIBRARY
-+ NAMES netcdf
-+ $ENV{ACCESS}/lib
-+ $ENV{NETCDF_DIR}/lib
-+ $ENV{NETCDF_DIR}/libsrc/.libs
- )
-
- find_program (NETCDF_NCDUMP ncdump
-@@ -224,7 +224,9 @@
-
- ADD_LIBRARY(exoIIv2c ${cbind_SRCS})
-
--TARGET_LINK_LIBRARIES(exoIIv2c ${NETCDF_LIBRARY}/libnetcdf.a)
-+TARGET_LINK_LIBRARIES( exoIIv2c
-+ ${NETCDF_LIBRARY}
-+ )
-
- IF(VTK_LIBRARY_PROPERTIES)
- SET_TARGET_PROPERTIES(exoIIv2c PROPERTIES ${VTK_LIBRARY_PROPERTIES})
diff --git a/sci-libs/exodusii/files/exodusii-5.22-multilib.patch b/sci-libs/exodusii/files/exodusii-5.22-multilib.patch
new file mode 100644
index 000000000..f14cec0ef
--- /dev/null
+++ b/sci-libs/exodusii/files/exodusii-5.22-multilib.patch
@@ -0,0 +1,20 @@
+ exodus/cbind/CMakeLists.txt | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/exodus/cbind/CMakeLists.txt b/exodus/cbind/CMakeLists.txt
+index 7038c0f..7c0d229 100644
+--- a/exodus/cbind/CMakeLists.txt
++++ b/exodus/cbind/CMakeLists.txt
+@@ -295,9 +295,9 @@ ENDIF(EXODUS_LIBRARY_PROPERTIES)
+
+ IF(NOT EXODUS_INSTALL_NO_LIBRARIES)
+ INSTALL(TARGETS exoIIv2c
+- RUNTIME DESTINATION lib COMPONENT Runtime
+- LIBRARY DESTINATION lib COMPONENT Runtime
+- ARCHIVE DESTINATION lib COMPONENT Development)
++ RUNTIME DESTINATION ${LIB_INSTALL_DIR} COMPONENT Runtime
++ LIBRARY DESTINATION ${LIB_INSTALL_DIR} COMPONENT Runtime
++ ARCHIVE DESTINATION ${LIB_INSTALL_DIR} COMPONENT Development)
+ INSTALL(FILES ${cbind_HEADERS} DESTINATION include COMPONENT Development)
+ ENDIF(NOT EXODUS_INSTALL_NO_LIBRARIES)
+
diff --git a/sci-visualization/paraview/ChangeLog b/sci-visualization/paraview/ChangeLog
index 4db958d38..67889a1d4 100644
--- a/sci-visualization/paraview/ChangeLog
+++ b/sci-visualization/paraview/ChangeLog
@@ -2,6 +2,22 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*paraview-3.14.1-r2 (31 Aug 2012)
+
+ 31 Aug 2012; François Bissey <francois.bissey@canterbury.ac.nz>
+ -paraview-3.14.1-r1.ebuild, +paraview-3.14.1-r2.ebuild,
+ +files/paraview-3.14.1-vtknetcd.patch:
+ netcdf dealt with
+
+*paraview-3.14.1-r1 (30 Aug 2012)
+
+ 30 Aug 2012; François Bissey <francois.bissey@canterbury.ac.nz>
+ -paraview-3.14.1.ebuild, +paraview-3.14.1-r1.ebuild,
+ +files/paraview-3.14.1-gcc-4.7.patch, +files/paraview-3.14.1-mpi4py.patch,
+ +files/paraview-3.14.1-python-exit.patch,
+ +files/paraview-3.14.1-removesqlite.patch:
+ fix a number of things
+
*paraview-3.14.1 (28 Aug 2012)
28 Aug 2012; François Bissey <francois.bissey@canterbury.ac.nz>
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-gcc-4.7.patch b/sci-visualization/paraview/files/paraview-3.14.1-gcc-4.7.patch
new file mode 100644
index 000000000..0da9aab78
--- /dev/null
+++ b/sci-visualization/paraview/files/paraview-3.14.1-gcc-4.7.patch
@@ -0,0 +1,28 @@
+Description: fix FTBFS with gcc-4.7
+Author: Mathieu Malaterre <malat@debian.org>
+Origin: http://anonscm.debian.org/gitweb/?p=collab-maint/vtk.git;a=commitdiff;h=428e763c995bb303805e07da70c1a34fc103d208
+Reviewed-by: Anton Gladky <gladky.anton@gmail.com>
+Last-Update: 2012-05-08
+
+--- a/VTK/Rendering/vtkFreeTypeTools.cxx
++++ b/VTK/Rendering/vtkFreeTypeTools.cxx
+@@ -35,6 +35,8 @@
+ using namespace ftgl;
+ #endif
+
++#include <stdint.h>
++
+ // Print debug info
+ #define VTK_FTFC_DEBUG 0
+ #define VTK_FTFC_DEBUG_CD 0
+--- a/VTK/Rendering/vtkFreeTypeUtilities.cxx
++++ b/VTK/Rendering/vtkFreeTypeUtilities.cxx
+@@ -36,6 +36,8 @@
+ using namespace ftgl;
+ #endif
+
++#include <stdint.h>
++
+ // Print debug info
+
+ #define VTK_FTFC_DEBUG 0
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-mpi4py.patch b/sci-visualization/paraview/files/paraview-3.14.1-mpi4py.patch
new file mode 100644
index 000000000..95a0d7ac8
--- /dev/null
+++ b/sci-visualization/paraview/files/paraview-3.14.1-mpi4py.patch
@@ -0,0 +1,15 @@
+--- CMake/ParaViewCommon.cmake.orig 2012-08-29 13:38:19.392381797 +1200
++++ CMake/ParaViewCommon.cmake 2012-08-29 13:38:47.271407061 +1200
+@@ -497,9 +497,9 @@
+
+ #########################################################################
+ # Configure mpi4py
+-IF(PARAVIEW_ENABLE_PYTHON AND PARAVIEW_USE_MPI)
+- ADD_SUBDIRECTORY(Utilities/mpi4py)
+-ENDIF(PARAVIEW_ENABLE_PYTHON AND PARAVIEW_USE_MPI)
++#IF(PARAVIEW_ENABLE_PYTHON AND PARAVIEW_USE_MPI)
++# ADD_SUBDIRECTORY(Utilities/mpi4py)
++#ENDIF(PARAVIEW_ENABLE_PYTHON AND PARAVIEW_USE_MPI)
+
+
+
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-python-exit.patch b/sci-visualization/paraview/files/paraview-3.14.1-python-exit.patch
new file mode 100644
index 000000000..03ae27ae5
--- /dev/null
+++ b/sci-visualization/paraview/files/paraview-3.14.1-python-exit.patch
@@ -0,0 +1,46 @@
+--- ParaViewCore/ClientServerCore/vtkPythonProgrammableFilter.cxx.orig 2012-08-28 15:42:34.410099857 +1200
++++ ParaViewCore/ClientServerCore/vtkPythonProgrammableFilter.cxx 2012-08-28 15:45:25.731279418 +1200
+@@ -80,6 +80,16 @@
+ }
+
+ //----------------------------------------------------------------------------
++void vtkPythonProgrammableFilter::DeleteGlobalPythonInterpretor()
++{
++ if(GlobalPipelineInterpretor)
++ {
++ GlobalPipelineInterpretor->Delete();
++ GlobalPipelineInterpretor = 0;
++ }
++}
++
++//----------------------------------------------------------------------------
+ vtkPythonProgrammableFilter::vtkPythonProgrammableFilter() :
+ Implementation(new vtkPythonProgrammableFilterImplementation())
+ {
+--- ParaViewCore/ClientServerCore/vtkPythonProgrammableFilter.h.orig 2012-08-28 15:42:45.892355278 +1200
++++ ParaViewCore/ClientServerCore/vtkPythonProgrammableFilter.h 2012-08-28 15:45:54.883213682 +1200
+@@ -102,6 +102,7 @@
+ //BTX
+ static vtkPVPythonInterpretor* GetGlobalPipelineInterpretor();
+ //ETX
++static void DeleteGlobalPythonInterpretor();
+ protected:
+ vtkPythonProgrammableFilter();
+ ~vtkPythonProgrammableFilter();
+--- Utilities/VTKPythonWrapping/paraview/servermanager.py.orig 2012-08-28 15:47:14.611830975 +1200
++++ Utilities/VTKPythonWrapping/paraview/servermanager.py 2012-08-28 15:48:11.995520340 +1200
+@@ -40,7 +40,7 @@
+ # PURPOSE. See the above copyright notice for more information.
+ #
+ #==============================================================================
+-import paraview, re, os, os.path, new, sys, vtk
++import paraview, re, os, os.path, new, sys, atexit, vtk
+
+ if not paraview.compatibility.minor:
+ paraview.compatibility.major = 3
+@@ -3027,3 +3027,5 @@
+
+ def GetNumberOfConnections():
+ return len(MultiServerConnections)
++
++atexit.register(vtkPythonProgrammableFilter.DeleteGlobalPythonInterpretor)
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-removesqlite.patch b/sci-visualization/paraview/files/paraview-3.14.1-removesqlite.patch
new file mode 100644
index 000000000..3467fa965
--- /dev/null
+++ b/sci-visualization/paraview/files/paraview-3.14.1-removesqlite.patch
@@ -0,0 +1,526 @@
+Description: Import patch from VTK to remove sqlite
+Author: Mathieu Malaterre <mathieu.malaterre@gmail.com>
+Last-Update: 2011-09-07
+
+--- a/VTK/IO/vtkSQLiteDatabase.cxx
++++ b/VTK/IO/vtkSQLiteDatabase.cxx
+@@ -29,7 +29,7 @@
+ #include <vtksys/ios/fstream>
+ #include <vtksys/ios/sstream>
+
+-#include <vtksqlite/vtk_sqlite3.h>
++#include <sqlite3.h>
+
+ vtkStandardNewMacro(vtkSQLiteDatabase);
+
+@@ -307,15 +307,15 @@
+ }
+ }
+
+- int result = vtk_sqlite3_open(this->DatabaseFileName, & (this->SQLiteInstance));
++ int result = sqlite3_open(this->DatabaseFileName, & (this->SQLiteInstance));
+
+- if (result != VTK_SQLITE_OK)
++ if (result != SQLITE_OK)
+ {
+ vtkDebugMacro(<<"SQLite open() failed. Error code is "
+ << result << " and message is "
+- << vtk_sqlite3_errmsg(this->SQLiteInstance) );
++ << sqlite3_errmsg(this->SQLiteInstance) );
+
+- vtk_sqlite3_close(this->SQLiteInstance);
++ sqlite3_close(this->SQLiteInstance);
+ return false;
+ }
+ else
+@@ -334,8 +334,8 @@
+ }
+ else
+ {
+- int result = vtk_sqlite3_close(this->SQLiteInstance);
+- if (result != VTK_SQLITE_OK)
++ int result = sqlite3_close(this->SQLiteInstance);
++ if (result != SQLITE_OK)
+ {
+ vtkWarningMacro(<< "Close(): SQLite returned result code " << result);
+ }
+@@ -374,7 +374,7 @@
+ if (!status)
+ {
+ vtkErrorMacro(<< "GetTables(): Database returned error: "
+- << vtk_sqlite3_errmsg(this->SQLiteInstance) );
++ << sqlite3_errmsg(this->SQLiteInstance) );
+ query->Delete();
+ return this->Tables;
+ }
+@@ -403,7 +403,7 @@
+ if (!status)
+ {
+ vtkErrorMacro(<< "GetRecord(" << table << "): Database returned error: "
+- << vtk_sqlite3_errmsg(this->SQLiteInstance) );
++ << sqlite3_errmsg(this->SQLiteInstance) );
+ query->Delete();
+ return NULL;
+ }
+@@ -467,10 +467,10 @@
+ // ----------------------------------------------------------------------
+ bool vtkSQLiteDatabase::HasError()
+ {
+- return (vtk_sqlite3_errcode(this->SQLiteInstance)!=VTK_SQLITE_OK);
++ return (sqlite3_errcode(this->SQLiteInstance)!=SQLITE_OK);
+ }
+
+ const char* vtkSQLiteDatabase::GetLastErrorText()
+ {
+- return vtk_sqlite3_errmsg(this->SQLiteInstance);
++ return sqlite3_errmsg(this->SQLiteInstance);
+ }
+--- a/VTK/IO/vtkSQLiteQuery.cxx
++++ b/VTK/IO/vtkSQLiteQuery.cxx
+@@ -25,7 +25,7 @@
+ #include "vtkVariant.h"
+ #include "vtkVariantArray.h"
+
+-#include <vtksqlite/vtk_sqlite3.h>
++#include <sqlite3.h>
+
+ #include <assert.h>
+
+@@ -43,7 +43,7 @@
+ {
+ this->Statement = NULL;
+ this->InitialFetch = true;
+- this->InitialFetchResult=VTK_SQLITE_DONE;
++ this->InitialFetchResult=SQLITE_DONE;
+ this->LastErrorText = NULL;
+ this->TransactionInProgress = false;
+ }
+@@ -61,7 +61,7 @@
+ {
+ if (this->Database != NULL)
+ {
+- vtk_sqlite3_finalize(this->Statement);
++ sqlite3_finalize(this->Statement);
+ this->Statement = NULL;
+ }
+ }
+@@ -131,8 +131,8 @@
+ if (this->Statement)
+ {
+ vtkDebugMacro(<<"Finalizing old statement");
+- int finalizeStatus = vtk_sqlite3_finalize(this->Statement);
+- if (finalizeStatus != VTK_SQLITE_OK)
++ int finalizeStatus = sqlite3_finalize(this->Statement);
++ if (finalizeStatus != SQLITE_OK)
+ {
+ vtkWarningMacro(<<"SetQuery(): Finalize returned unexpected code "
+ << finalizeStatus);
+@@ -151,19 +151,19 @@
+ return false;
+ }
+
+- vtk_sqlite3 *db = dbContainer->SQLiteInstance;
++ sqlite3 *db = dbContainer->SQLiteInstance;
+ const char *unused_statement;
+
+- int prepareStatus = vtk_sqlite3_prepare_v2(db,
++ int prepareStatus = sqlite3_prepare_v2(db,
+ this->Query,
+ static_cast<int>(strlen(this->Query)),
+ &this->Statement,
+ &unused_statement);
+
+- if (prepareStatus != VTK_SQLITE_OK)
++ if (prepareStatus != SQLITE_OK)
+ {
+- this->SetLastErrorText(vtk_sqlite3_errmsg(db));
+- vtkWarningMacro(<<"SetQuery(): vtk_sqlite3_prepare_v2() failed with error message "
++ this->SetLastErrorText(sqlite3_errmsg(db));
++ vtkWarningMacro(<<"SetQuery(): sqlite3_prepare_v2() failed with error message "
+ << this->GetLastErrorText()
+ << " on statement: '"
+ << this->Query << "'");
+@@ -194,31 +194,31 @@
+ }
+ else
+ {
+- vtk_sqlite3_reset(this->Statement);
++ sqlite3_reset(this->Statement);
+ }
+
+ vtkDebugMacro(<<"Execute(): Query ready to execute.");
+
+ this->InitialFetch = true;
+- int result = vtk_sqlite3_step(this->Statement);
++ int result = sqlite3_step(this->Statement);
+ this->InitialFetchResult = result;
+
+- if (result == VTK_SQLITE_DONE)
++ if (result == SQLITE_DONE)
+ {
+ this->SetLastErrorText(NULL);
+ this->Active = true;
+ return true;
+ }
+- else if (result != VTK_SQLITE_ROW)
++ else if (result != SQLITE_ROW)
+ {
+ vtkSQLiteDatabase *dbContainer =
+ vtkSQLiteDatabase::SafeDownCast(this->Database);
+ assert(dbContainer != NULL);
+
+- vtk_sqlite3 *db = dbContainer->SQLiteInstance;
++ sqlite3 *db = dbContainer->SQLiteInstance;
+
+- this->SetLastErrorText(vtk_sqlite3_errmsg(db));
+- vtkDebugMacro(<< "Execute(): vtk_sqlite3_step() returned error message "
++ this->SetLastErrorText(sqlite3_errmsg(db));
++ vtkDebugMacro(<< "Execute(): sqlite3_step() returned error message "
+ << this->GetLastErrorText());
+ this->Active = false;
+ return false;
+@@ -239,7 +239,7 @@
+ }
+ else
+ {
+- return vtk_sqlite3_column_count(this->Statement);
++ return sqlite3_column_count(this->Statement);
+ }
+ }
+
+@@ -259,7 +259,7 @@
+ }
+ else
+ {
+- return vtk_sqlite3_column_name(this->Statement, column);
++ return sqlite3_column_name(this->Statement, column);
+ }
+ }
+
+@@ -279,22 +279,22 @@
+ }
+ else
+ {
+- switch (vtk_sqlite3_column_type(this->Statement, column))
++ switch (sqlite3_column_type(this->Statement, column))
+ {
+- case VTK_SQLITE_INTEGER:
++ case SQLITE_INTEGER:
+ return VTK_INT;
+- case VTK_SQLITE_FLOAT:
++ case SQLITE_FLOAT:
+ return VTK_FLOAT;
+- case VTK_SQLITE_TEXT:
++ case SQLITE_TEXT:
+ return VTK_STRING;
+- case VTK_SQLITE_BLOB:
++ case SQLITE_BLOB:
+ return VTK_STRING; // until we have a BLOB type of our own
+- case VTK_SQLITE_NULL:
++ case SQLITE_NULL:
+ return VTK_VOID; // ??? what makes sense here?
+ default:
+ {
+ vtkErrorMacro(<<"GetFieldType(): Unknown data type "
+- << vtk_sqlite3_column_type(this->Statement, column)
++ << sqlite3_column_type(this->Statement, column)
+ <<" from SQLite.");
+ return VTK_VOID;
+ }
+@@ -315,7 +315,7 @@
+ {
+ vtkDebugMacro(<<"NextRow(): Initial fetch being handled.");
+ this->InitialFetch = false;
+- if (this->InitialFetchResult == VTK_SQLITE_DONE)
++ if (this->InitialFetchResult == SQLITE_DONE)
+ {
+ return false;
+ }
+@@ -326,12 +326,12 @@
+ }
+ else
+ {
+- int result = vtk_sqlite3_step(this->Statement);
+- if (result == VTK_SQLITE_DONE)
++ int result = sqlite3_step(this->Statement);
++ if (result == SQLITE_DONE)
+ {
+ return false;
+ }
+- else if (result == VTK_SQLITE_ROW)
++ else if (result == SQLITE_ROW)
+ {
+ return true;
+ }
+@@ -339,8 +339,8 @@
+ {
+ vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
+ assert(dbContainer != NULL);
+- vtk_sqlite3 *db = dbContainer->SQLiteInstance;
+- this->SetLastErrorText(vtk_sqlite3_errmsg(db));
++ sqlite3 *db = dbContainer->SQLiteInstance;
++ this->SetLastErrorText(sqlite3_errmsg(db));
+ vtkErrorMacro(<<"NextRow(): Database returned error code "
+ << result << " with the following message: "
+ << this->GetLastErrorText());
+@@ -366,33 +366,33 @@
+ }
+ else
+ {
+- switch (vtk_sqlite3_column_type(this->Statement, column))
++ switch (sqlite3_column_type(this->Statement, column))
+ {
+- case VTK_SQLITE_INTEGER:
+- return vtkVariant(vtk_sqlite3_column_int(this->Statement, column));
++ case SQLITE_INTEGER:
++ return vtkVariant(sqlite3_column_int(this->Statement, column));
+
+- case VTK_SQLITE_FLOAT:
+- return vtkVariant(vtk_sqlite3_column_double(this->Statement, column));
++ case SQLITE_FLOAT:
++ return vtkVariant(sqlite3_column_double(this->Statement, column));
+
+- case VTK_SQLITE_TEXT:
++ case SQLITE_TEXT:
+ {
+ vtksys_ios::ostringstream str;
+- str << vtk_sqlite3_column_text(this->Statement, column);
++ str << sqlite3_column_text(this->Statement, column);
+ return vtkVariant(vtkStdString(str.str()));
+ }
+
+- case VTK_SQLITE_BLOB:
++ case SQLITE_BLOB:
+ {
+ // This is a hack ... by passing the BLOB to vtkStdString with an explicit
+ // byte count, we ensure that the string will store all of the BLOB's bytes,
+ // even if there are NULL values.
+
+ return vtkVariant(vtkStdString(
+- static_cast<const char*>(vtk_sqlite3_column_blob(this->Statement, column)),
+- vtk_sqlite3_column_bytes(this->Statement, column)));
++ static_cast<const char*>(sqlite3_column_blob(this->Statement, column)),
++ sqlite3_column_bytes(this->Statement, column)));
+ }
+
+- case VTK_SQLITE_NULL:
++ case SQLITE_NULL:
+ default:
+ return vtkVariant();
+ }
+@@ -423,11 +423,11 @@
+ vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
+ assert(dbContainer != NULL);
+
+- vtk_sqlite3 *db = dbContainer->SQLiteInstance;
++ sqlite3 *db = dbContainer->SQLiteInstance;
+ char *errorMessage = NULL;
+- int result = vtk_sqlite3_exec(db, BEGIN_TRANSACTION, NULL, NULL, &errorMessage);
++ int result = sqlite3_exec(db, BEGIN_TRANSACTION, NULL, NULL, &errorMessage);
+
+- if (result == VTK_SQLITE_OK)
++ if (result == SQLITE_OK)
+ {
+ this->TransactionInProgress = true;
+ this->SetLastErrorText(NULL);
+@@ -451,7 +451,7 @@
+ {
+ if (this->Statement)
+ {
+- vtk_sqlite3_finalize(this->Statement);
++ sqlite3_finalize(this->Statement);
+ this->Statement = NULL;
+ }
+
+@@ -463,11 +463,11 @@
+
+ vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
+ assert(dbContainer != NULL);
+- vtk_sqlite3 *db = dbContainer->SQLiteInstance;
++ sqlite3 *db = dbContainer->SQLiteInstance;
+ char *errorMessage = NULL;
+- int result = vtk_sqlite3_exec(db, COMMIT_TRANSACTION, NULL, NULL, &errorMessage);
++ int result = sqlite3_exec(db, COMMIT_TRANSACTION, NULL, NULL, &errorMessage);
+
+- if (result == VTK_SQLITE_OK)
++ if (result == SQLITE_OK)
+ {
+ this->TransactionInProgress = false;
+ this->SetLastErrorText(NULL);
+@@ -499,11 +499,11 @@
+
+ vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
+ assert(dbContainer != NULL);
+- vtk_sqlite3 *db = dbContainer->SQLiteInstance;
++ sqlite3 *db = dbContainer->SQLiteInstance;
+ char *errorMessage = NULL;
+- int result = vtk_sqlite3_exec(db, ROLLBACK_TRANSACTION, NULL, NULL, &errorMessage);
++ int result = sqlite3_exec(db, ROLLBACK_TRANSACTION, NULL, NULL, &errorMessage);
+
+- if (result == VTK_SQLITE_OK)
++ if (result == SQLITE_OK)
+ {
+ this->TransactionInProgress = false;
+ this->SetLastErrorText(NULL);
+@@ -647,11 +647,11 @@
+ if (this->Active)
+ {
+ this->Active = false;
+- vtk_sqlite3_reset(this->Statement);
++ sqlite3_reset(this->Statement);
+ }
+- int status = vtk_sqlite3_bind_int(this->Statement, index+1, value);
++ int status = sqlite3_bind_int(this->Statement, index+1, value);
+
+- if (status != VTK_SQLITE_OK)
++ if (status != SQLITE_OK)
+ {
+ vtksys_ios::ostringstream errormessage;
+ errormessage << "sqlite_bind_int returned error: " << status;
+@@ -676,11 +676,11 @@
+ if (this->Active)
+ {
+ this->Active = false;
+- vtk_sqlite3_reset(this->Statement);
++ sqlite3_reset(this->Statement);
+ }
+- int status = vtk_sqlite3_bind_int(this->Statement, index+1, static_cast<vtk_sqlite_int64>(value));
++ int status = sqlite3_bind_int(this->Statement, index+1, static_cast<sqlite_int64>(value));
+
+- if (status != VTK_SQLITE_OK)
++ if (status != SQLITE_OK)
+ {
+ vtksys_ios::ostringstream errormessage;
+ errormessage << "sqlite_bind_int64 returned error: " << status;
+@@ -705,12 +705,12 @@
+ if (this->Active)
+ {
+ this->Active = false;
+- vtk_sqlite3_reset(this->Statement);
++ sqlite3_reset(this->Statement);
+ }
+
+- int status = vtk_sqlite3_bind_double(this->Statement, index+1, value);
++ int status = sqlite3_bind_double(this->Statement, index+1, value);
+
+- if (status != VTK_SQLITE_OK)
++ if (status != SQLITE_OK)
+ {
+ vtksys_ios::ostringstream errormessage;
+ errormessage << "sqlite_bind_double returned error: " << status;
+@@ -734,12 +734,12 @@
+ if (this->Active)
+ {
+ this->Active = false;
+- vtk_sqlite3_reset(this->Statement);
++ sqlite3_reset(this->Statement);
+ }
+
+- int status = vtk_sqlite3_bind_text(this->Statement, index+1, value, length, VTK_SQLITE_TRANSIENT);
++ int status = sqlite3_bind_text(this->Statement, index+1, value, length, SQLITE_TRANSIENT);
+
+- if (status != VTK_SQLITE_OK)
++ if (status != SQLITE_OK)
+ {
+ vtksys_ios::ostringstream errormessage;
+ errormessage << "sqlite_bind_text returned error: " << status;
+@@ -763,17 +763,17 @@
+ if (this->Active)
+ {
+ this->Active = false;
+- vtk_sqlite3_reset(this->Statement);
++ sqlite3_reset(this->Statement);
+ }
+
+ int status =
+- vtk_sqlite3_bind_blob(this->Statement,
++ sqlite3_bind_blob(this->Statement,
+ index+1,
+ data,
+ length,
+- VTK_SQLITE_TRANSIENT);
++ SQLITE_TRANSIENT);
+
+- if (status != VTK_SQLITE_OK)
++ if (status != SQLITE_OK)
+ {
+ vtksys_ios::ostringstream errormessage;
+ errormessage << "sqlite_bind_blob returned error: " << status;
+@@ -797,12 +797,12 @@
+ if (this->Active)
+ {
+ this->Active = false;
+- vtk_sqlite3_reset(this->Statement);
++ sqlite3_reset(this->Statement);
+ }
+
+- int status = vtk_sqlite3_clear_bindings(this->Statement);
++ int status = sqlite3_clear_bindings(this->Statement);
+
+- if (status != VTK_SQLITE_OK)
++ if (status != SQLITE_OK)
+ {
+ vtksys_ios::ostringstream errormessage;
+ errormessage << "sqlite_clear_bindings returned error: " << status;
+--- a/VTK/IO/vtkSQLiteDatabase.h
++++ b/VTK/IO/vtkSQLiteDatabase.h
+@@ -48,7 +48,7 @@
+ class vtkSQLQuery;
+ class vtkSQLiteQuery;
+ class vtkStringArray;
+-struct vtk_sqlite3;
++struct sqlite3;
+
+ class VTK_IO_EXPORT vtkSQLiteDatabase : public vtkSQLDatabase
+ {
+@@ -146,7 +146,7 @@
+ virtual bool ParseURL(const char* url);
+
+ private:
+- vtk_sqlite3 *SQLiteInstance;
++ sqlite3 *SQLiteInstance;
+
+ // We want this to be private, a user of this class
+ // should not be setting this for any reason
+--- a/VTK/IO/vtkSQLiteQuery.h
++++ b/VTK/IO/vtkSQLiteQuery.h
+@@ -46,7 +46,7 @@
+ class vtkSQLiteDatabase;
+ class vtkVariant;
+ class vtkVariantArray;
+-struct vtk_sqlite3_stmt;
++struct sqlite3_stmt;
+
+ class VTK_IO_EXPORT vtkSQLiteQuery : public vtkSQLQuery
+ {
+@@ -154,7 +154,7 @@
+ vtkSQLiteQuery(const vtkSQLiteQuery &); // Not implemented.
+ void operator=(const vtkSQLiteQuery &); // Not implemented.
+
+- vtk_sqlite3_stmt *Statement;
++ sqlite3_stmt *Statement;
+ bool InitialFetch;
+ int InitialFetchResult;
+ char *LastErrorText;
+--- a/VTK/Utilities/CMakeLists.txt
++++ b/VTK/Utilities/CMakeLists.txt
+@@ -55,7 +55,7 @@
+ SET_PROPERTY(GLOBAL APPEND PROPERTY VTK_TARGETS vtkmetaio)
+ ENDIF(NOT VTK_INSTALL_NO_LIBRARIES)
+ ENDIF(VTK_USE_METAIO)
+-ADD_SUBDIRECTORY(vtksqlite)
++#ADD_SUBDIRECTORY(vtksqlite)
+
+ IF(VTK_HAS_EXODUS)
+ ADD_SUBDIRECTORY(vtkexodus2)
+--- a/VTK/IO/CMakeLists.txt
++++ b/VTK/IO/CMakeLists.txt
+@@ -19,7 +19,7 @@
+ SET(KIT_JAVA_LIBS vtkFilteringJava)
+ SET(KIT_INTERFACE_LIBRARIES vtkFiltering)
+ SET(KIT_LIBS vtkDICOMParser vtkNetCDF vtkNetCDF_cxx LSDyna
+- ${_VTK_METAIO_LIB} vtksqlite
++ ${_VTK_METAIO_LIB} sqlite3
+ ${VTK_PNG_LIBRARIES} ${VTK_ZLIB_LIBRARIES} ${VTK_JPEG_LIBRARIES}
+ ${VTK_TIFF_LIBRARIES} ${VTK_EXPAT_LIBRARIES} ${VTK_OGGTHEORA_LIBRARIES}
+ ${KWSYS_NAMESPACE})
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-vtknetcd.patch b/sci-visualization/paraview/files/paraview-3.14.1-vtknetcd.patch
new file mode 100644
index 000000000..eb4046669
--- /dev/null
+++ b/sci-visualization/paraview/files/paraview-3.14.1-vtknetcd.patch
@@ -0,0 +1,75 @@
+--- Utilities/CMakeLists.txt.orig 2012-08-31 13:55:56.616827748 +1200
++++ Utilities/CMakeLists.txt 2012-08-31 13:56:43.487830247 +1200
+@@ -47,7 +47,7 @@
+ SET( verdict_INSTALL_LIB_DIR ${VTK_INSTALL_LIB_DIR_CM24})
+ ADD_SUBDIRECTORY(verdict)
+
+-ADD_SUBDIRECTORY(vtknetcdf)
++#ADD_SUBDIRECTORY(vtknetcdf)
+ IF(VTK_USE_METAIO)
+ SET(METAIO_FOR_VTK 1)
+ ADD_SUBDIRECTORY(vtkmetaio)
+--- Utilities/vtk_netcdf.h.orig 2012-08-31 13:57:25.704832693 +1200
++++ Utilities/vtk_netcdf.h 2012-08-31 13:57:59.823834877 +1200
+@@ -16,6 +16,6 @@
+ #define __vtk_netcdf_h
+
+ /* Use the netcdf library configured for VTK. */
+-#include <vtknetcdf/include/netcdf.h>
++#include <netcdf.h>
+
+ #endif
+--- Utilities/vtk_netcdfcpp.h.orig 2012-08-31 13:58:48.800838210 +1200
++++ Utilities/vtk_netcdfcpp.h 2012-08-31 13:59:31.223841343 +1200
+@@ -16,6 +16,6 @@
+ #define __vtk_netcdfcpp_h
+
+ /* Use the netcdf library configured for VTK. */
+-#include <vtknetcdf/cxx/netcdfcpp.h>
++#include <netcdfcpp.h>
+
+ #endif
+--- Utilities/vtkexodus2/CMakeLists.txt.orig 2012-08-31 14:01:26.536856845 +1200
++++ Utilities/vtkexodus2/CMakeLists.txt 2012-08-31 14:02:11.503872711 +1200
+@@ -241,7 +241,7 @@
+
+
+ VTK_ADD_LIBRARY(vtkexoIIc ${cbind_SRCS})
+-TARGET_LINK_LIBRARIES(vtkexoIIc vtkNetCDF)
++TARGET_LINK_LIBRARIES(vtkexoIIc netcdf)
+
+ # Apply user-defined properties to the library target.
+ IF(VTK_LIBRARY_PROPERTIES)
+--- Utilities/vtkexodus2/test/CMakeLists.txt.orig 2012-08-31 14:02:39.696882673 +1200
++++ Utilities/vtkexodus2/test/CMakeLists.txt 2012-08-31 14:02:59.743889790 +1200
+@@ -21,7 +21,7 @@
+ )
+
+ ADD_EXECUTABLE( ExoIICTests ${ExoIICTests} )
+-TARGET_LINK_LIBRARIES( ExoIICTests vtkCommon vtkexoIIc vtkNetCDF )
++TARGET_LINK_LIBRARIES( ExoIICTests vtkCommon vtkexoIIc netcdf )
+
+ SET( TestsToRun ${ExoIICTests} )
+ REMOVE( TestsToRun ExoIICTests.cxx )
+--- IO/CMakeLists.txt.orig 2012-08-31 14:05:00.657933170 +1200
++++ IO/CMakeLists.txt 2012-08-31 14:06:18.024961299 +1200
+@@ -18,7 +18,7 @@
+ SET(KIT_PYTHON_LIBS vtkFilteringPythonD)
+ SET(KIT_JAVA_LIBS vtkFilteringJava)
+ SET(KIT_INTERFACE_LIBRARIES vtkFiltering)
+-SET(KIT_LIBS vtkDICOMParser vtkNetCDF vtkNetCDF_cxx LSDyna
++SET(KIT_LIBS vtkDICOMParser netcdf netcdf_c++ LSDyna
+ ${_VTK_METAIO_LIB} sqlite3
+ ${VTK_PNG_LIBRARIES} ${VTK_ZLIB_LIBRARIES} ${VTK_JPEG_LIBRARIES}
+ ${VTK_TIFF_LIBRARIES} ${VTK_EXPAT_LIBRARIES} ${VTK_OGGTHEORA_LIBRARIES}
+--- vtkIncludeDirectories.cmake.orig 2012-08-31 15:36:06.599955661 +1200
++++ vtkIncludeDirectories.cmake 2012-08-31 15:37:35.759045094 +1200
+@@ -193,7 +193,7 @@
+ VTK_THIRD_PARTY_INCLUDE2(TIFF)
+ VTK_THIRD_PARTY_INCLUDE2(EXPAT)
+ VTK_THIRD_PARTY_INCLUDE2(LIBXML2)
+-VTK_THIRD_PARTY_INCLUDE(NETCDF vtknetcdf/include)
++#VTK_THIRD_PARTY_INCLUDE(NETCDF vtknetcdf/include)
+ VTK_THIRD_PARTY_INCLUDE2(Exodus2)
+ IF(VTK_USE_GL2PS)
+ VTK_THIRD_PARTY_INCLUDE2(GL2PS)
diff --git a/sci-visualization/paraview/paraview-3.14.1.ebuild b/sci-visualization/paraview/paraview-3.14.1-r2.ebuild
index 3afa0f379..30bbe3333 100644
--- a/sci-visualization/paraview/paraview-3.14.1.ebuild
+++ b/sci-visualization/paraview/paraview-3.14.1-r2.ebuild
@@ -23,6 +23,7 @@ SLOT="0"
IUSE="boost cg -coprocessing doc examples +gui mpi mysql nvcontrol +plugins +python webkit ffmpeg theora"
RDEPEND="
+ ~sci-libs/netcdf-4.1.3[cxx,hdf5]
sci-libs/hdf5[mpi=]
mpi? ( virtual/mpi[cxx,romio] )
gui? (
@@ -39,10 +40,13 @@ RDEPEND="
python? (
dev-python/sip
gui? ( dev-python/PyQt4 )
- dev-python/numpy )
+ dev-python/numpy
+ mpi? ( dev-python/mpi4py )
+ )
ffmpeg? ( virtual/ffmpeg )
theora? ( media-libs/libtheora )
dev-libs/libxml2:2
+ dev-db/sqlite:3
media-libs/libpng
virtual/jpeg
media-libs/tiff
@@ -75,6 +79,17 @@ src_prepare() {
epatch "${FILESDIR}"/${PN}-3.14.1-ffmpeg-noinstall.patch
# patch from debian for some underlinking in xdmf
epatch "${FILESDIR}"/${PN}-3.14.1-xdmf-linking.patch
+ # upstream http://paraview.org/Bug/view.php?id=13222 and
+ # commit https://github.com/Kitware/ParaView/commit/559af72e540f418310b6425055348336a48ad557
+ epatch "${FILESDIR}"/${PN}-3.14.1-python-exit.patch
+ # disable internal mpi4py copy
+ epatch "${FILESDIR}"/${PN}-3.14.1-mpi4py.patch
+ # remove the internal copy of sqlite (vtksqlite)
+ # http://patch-tracker.debian.org/patch/series/view/paraview/3.14.1-7/removesqlite.patch
+ epatch "${FILESDIR}"/${PN}-3.14.1-removesqlite.patch
+ # gcc 4.7 fix
+ # http://patch-tracker.debian.org/patch/series/view/paraview/3.14.1-7/fix_FTBFS_gcc-4.7.patch
+ epatch "${FILESDIR}"/${PN}-3.14.1-gcc-4.7.patch
# lib64 fixes
sed -i "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
@@ -82,7 +97,8 @@ src_prepare() {
sed -i "s:\/lib\/python:\/$(get_libdir)\/python:g" \
Utilities/Xdmf2/CMake/setup_install_paths.py || die
- # Install internal vtk binaries inside /usr/${PVLIBDIR}
+ # Install internal vtk binaries to PV_INSTALL_LIB_DIR as noted in the comment in the cmake file.
+ # upstream doesn't even do what they say they do.
sed -e 's:VTK_INSTALL_BIN_DIR \"/${PV_INSTALL_BIN_DIR}\":VTK_INSTALL_BIN_DIR \"/${PV_INSTALL_LIB_DIR}\":' \
-i CMake/ParaViewCommon.cmake || die "failed to patch vtk install location"
@@ -93,6 +109,8 @@ src_prepare() {
epatch "${FILESDIR}"/vtk-5.6.1-libav-0.8.patch
# debian patch for recent boost should work with 1.48 too
epatch "${FILESDIR}"/vtk-boost1.49.patch
+ # adapted from debian patch need to be applied after paraview-3.14.1-removesqlite.patch
+ epatch "${FILESDIR}"/${PN}-3.14.1-vtknetcd.patch
}
src_configure() {
@@ -114,12 +132,12 @@ src_configure() {
-DVTK_USE_SYSTEM_ZLIB=ON
-DVTK_USE_SYSTEM_EXPAT=ON
-DPARAVIEW_USE_SYSTEM_HDF5=ON
+ -DVTK_USE_SYSTEM_HDF5=ON
-DCMAKE_VERBOSE_MAKEFILE=ON
-DCMAKE_COLOR_MAKEFILE=TRUE
-DVTK_USE_SYSTEM_LIBXML2=ON
-DVTK_USE_OFFSCREEN=TRUE
-DCMAKE_USE_PTHREADS=ON
- -DBUILD_TESTING=OFF
-DVTK_USE_FFMPEG_ENCODER=OFF
-DPARAVIEW_INSTALL_THIRD_PARTY_LIBRARIES=OFF
-DPROTOC_LOCATION=$(which protoc))
@@ -147,8 +165,14 @@ src_configure() {
$(cmake-utils_use theora VTK_USE_THEORA_ENCODER)
$(cmake-utils_use theora VTK_USE_SYSTEM_OGGTHEORA))
+ # testing, disabling vtk testing as vtkpython is tested and will fail.
+ mycmakeargs+=(
+ $(cmake-utils_use test BUILD_TESTING)
+ $(cmake-utils_use test PARAVIEW_DISABLE_VTK_TESTING))
+
if ( use gui ); then
- mycmakeargs+=(-DVTK_INSTALL_QT_DIR=/${PVLIBDIR}/plugins/designer
+ mycmakeargs+=(
+ -DVTK_INSTALL_QT_DIR=/${PVLIBDIR}/plugins/designer
$(cmake-utils_use webkit VTK_QT_USE_WEBKIT))
if use python ; then
# paraview cannot guess sip directory right probably because a path is not propagated properly
@@ -177,7 +201,8 @@ src_configure() {
$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_VisTrailPlugin))
if use python; then
- mycmakeargs+=($(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_pvblot))
+ mycmakeargs+=(
+ $(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_pvblot))
fi
if use coprocessing; then
@@ -214,6 +239,8 @@ pkg_postinst() {
elog "If you experience data corruption during parsing of"
elog "data files with paraview please try setting your"
elog "locale to LC_ALL=C."
+ elog "If you plan to use paraview component from an existing shell"
+ elog "you should run env-update and . /etc/profile first"
echo
}