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authorJustin Lecher <jlec@gentoo.org>2012-09-10 08:30:35 +0200
committerJustin Lecher <jlec@gentoo.org>2012-09-10 08:30:35 +0200
commit9affb083e1b9c52e1be44e934567150e229b60a2 (patch)
treef9607e59fa63e7fdb24cf81535097cf0bef52404
parentdummy files added to make pcheck happy (diff)
parentdev-python/astlib: Version bump (diff)
downloadsci-9affb083e1b9c52e1be44e934567150e229b60a2.tar.gz
sci-9affb083e1b9c52e1be44e934567150e229b60a2.tar.bz2
sci-9affb083e1b9c52e1be44e934567150e229b60a2.zip
Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci: dev-python/astlib: Version bump sci-libs/exodusii: Version Bump Patches for sci-libs/bigdft to install GPU support corrected not to break linking against the compiled libraries unbundle netcdf from paraview update descriptions Bunch of fix and ubundling for paraview 3.14.1 enabled commit signing add empty files for pcheck sci-chemistry/ligplot+: New addition a license is a license not an eclass add license sci-chemistry/ssp: Fix offset of reference CS DB
-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
}