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2018-06-13ADIOS: Revert Patch (#8463)Axel Huebl2-19/+0
That patch is only a partial solution and does not solve the issue. Revert is, unnecessary.
2018-06-13Add: MPILander (#8464)Axel Huebl1-0/+64
MPILander - There can only be one (MPI process)! The final MPI implementation.
2018-06-13gplates: new package (#8336)Michael Kuhn3-55/+148
This also adds an older 1.x version to gdal that is required by gplates.
2018-06-13openfoam-com: added submodule flag to git fetch (#8446)Simone Bnà1-1/+1
2018-06-13blasr-libcpp: new package (#8366)Miles Perry1-0/+73
* blasr-libcpp: new package * blasr-libcpp: added version #, and moved make into build phase. * blasr-libcpp: added prefix.include to PBBAM_INC, added version URL * blasr-libcpp: indented comments, made list of configure_args, and added prefix.include * blasr-libcpp: added setup_dependent_environment from blasr * blasr-libcpp: fixed syntax for configure_args * blasr-libcpp: fixed configure_args syntax * blasr-libcpp: fixed syntax * blasr-libcpp: syntaxtest * blasr-libcpp: fixed def build error * blasr-libcpp: edited dependent environment to move after install phase * blasr-libcpp: rearranged build and install * blasr-libcpp: added configure_args * blasr-libcpp: fixed syntax error * blasr-libcpp: removed .spec from INC and LIB alignment, pbdata, hdf * blasr-libcpp: seperated configure args * blasr-libcpp: edited configure and setup_dependent steps * blasr-libcpp: added CPATH arg * blasr-libcpp: C_INCLUDE_PATH * blasr-libcpp: fixed install issues resulting from PacBio change
2018-06-13trilinos: use 'branch' option to specify branches such as develop/master ↵Satish Balay1-2/+2
[they are not tags] (#8448) Fixes the following problem: ==> Installing trilinos ==> Warning: Suspicious requests to set or unset 'LD_LIBRARY_PATH' found ==> Warning: env.unset('LD_LIBRARY_PATH') at /home/balay/spack.new/lib/spack/spack/build_environment.py:269 ==> Warning: ---> env.set('%s' % key, value) at /home/balay/spack.new/lib/spack/spack/build_environment.py:292 ==> Trying to clone git repository: https://github.com/trilinos/Trilinos.git at tag develop Fetching tags only, you probably meant: git fetch --tags error: pathspec 'develop' did not match any file(s) known to git. ==> Fetching from [git] https://github.com/trilinos/Trilinos.git failed. ==> Error: FetchError: All fetchers failed for trilinos-develop-tgkpnctp6nn4imoizxlw4ymqyztcie4n
2018-06-13new package: dealii-parameter-gui (#8456)Timo Heister1-0/+40
2018-06-13petsc: 'master' is a branch - not a tag - so fix it accordingly. (#8457)Satish Balay1-1/+1
2018-06-13[GLVis] Add new version: 3.4 (#8454)Veselin Dobrev1-5/+13
* [glvis] Add new version, 3.4; update all checksums to be SHA-256. * [GLVis] Use the new bit.ly short link for v3.4.
2018-06-12new package: pdftk (#8166)Elizabeth Fischer2-0/+171
2018-06-12Package: ISAAC 1.4.0 (#8447)Axel Huebl2-2/+4
2018-06-12superlu_dist: fix 'spack install superlu-dist@develop' (#8442)Satish Balay1-0/+1
Latest superlu_dist sources now use INCLUDEDIR. This change should not affect older superlu_dist version builds
2018-06-11Fixed compilation of quantum-espresso (#8439)Massimiliano Culpo1-2/+20
The patch to select ELPA API needs to be applied to version 6.2.0 too. The link line of hdf5 is computed incorrectly from the configuration part of the build-system. To fix this the relevant file (make.inc) is patched.
2018-06-11boost: fix cxxstd=default (#8438)Denis Davydov1-1/+3
2018-06-11Add new package: unuran (#8397)Javier Cervantes1-0/+60
* Add new package: unuran * Remove list_url and prng variant due to compilation problems * Make shared library option more explicit
2018-06-10arpack-ng: add 3.6.0 (#8433)Denis Davydov1-0/+1
2018-06-10A new package: axel. (#8434)健美猞猁1-0/+42
* A new package: axel. * Remove duplicate pkgconf.
2018-06-10Bump miniconda to 4.5.4. (#8435)健美猞猁2-0/+2
2018-06-09py-projectq: Added new package and fixed its dependency py-pybind11 (#8378)toffer932-0/+69
* py-pybind11: Additionally install python extensions e.g. run python setup * py-projectq: Added new package for quantum computing * py-projectq: corrected typos * edited flake8 incompatibilities * additional flake8 faults * changes according to suggestions * flake8 errors fixed * typo and missing environment variable set * py-pybind11:added setup_environemt * py-projectq:changed version according to request * flake8 correction * py-pybind11:changed to setup_py and removed noop * py-projectq:removed dependency and changed type of py-pytest dependency * py-pybind11: flake8 error corrected * py-projectq: Small error correction
2018-06-09Git's gitk needs TK's wish to be found in PATH (#8360)Kelly (KT) Thompson1-1/+13
* Git's gitk needs TK's wish to be found in PATH * Add a _runtime_ dependency on `tk` * Add an environment rule to add the path to TK's `wish` program to $PATH for the generated `git` modulefile. * Make TclTk run environment an optional variant for git. * Cleanup based on PR recommendations.
2018-06-08compiler flags: add cxx98 standard support (#7601)Chris Green2-2/+43
The following improvements are made to cxx standard support (e.g. compiler.cxxNN_flag functions) in compilers: * Add cxx98_flag property * Add support for throwing an exception when a flag is not supported (previously if a flag was not supported the application was terminated with tty.die) * The name of the flag associated with e.g. c++14 standard support changes for different compiler versions (e.g. c++1y vs c++14). This makes a few corrections on what flag to return for which version. * Added tests to confirm that versions report expected flags for various c++ standards (or raise an exception for versions that don't provide a given cxx standard) Note that if a given cxx standard is the default, the associated flag property will return ""; cxx98 is assumed to be the default standard so this is the behavior for the associated property in the base compiler class. Package changes: * Improvements to the boost spec to take advantage of the improved standard flag facility. * Update the clingo spec to catch the new exception rather than look for an empty flag to indicate non-support (which is not part of the compiler flag API)
2018-06-08r-mice: new package (#8423)Yifan Zhu1-0/+57
* r-mice: new package * flake8 fixed
2018-06-08tcl package: Install sources (#8153)Elizabeth Fischer1-0/+21
The tcl package references the original sources upon install, and the tk build requires the tcl sources. This updates the tcl package to install its sources following the example of #4102, and also updates the tclConfig.sh file to properly reference the installed sources (rather than the staging directory created by Spack).
2018-06-08new version scotch@6.0.5a (#8254)Oliver Pola2-0/+636
* new version scotch@6.0.5a * patch metis headers on scotch@6.0.4 according to https://gforge.inria.fr/tracker/?func=detail&atid=1082&aid=19521&group_id=248
2018-06-08GDL and missing dependencies (#8283)Ricardo Silva4-0/+349
* GDL and missing dependencies Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * GDL and GraphicsMagick improvements * GDL: sort variants and dependencies, add descriptions * GDL: add wx variant * GDL: make variants explicit (in cmake args) * GraphicsMagick: sort dependencies * GraphicsMagick: cleanup boilerplate comments Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * Improvements/Fixes for gdl, plplot and graphicsmagick * gdl: * variants: * openmp * be explicit about enabling/disabling x11 * dependencies: * logic for plplot with/without wx * some previously missing (where being picked up from the system) * graphicsmagick: previously missing dependencies (where being picked up from the system) * plplot: more versions + variants + dependencies Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * GDL: hdf4/5 variants * also sorted explicit enabling/disabling of cmake flags for readability Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * plplot: fix variant descriptions Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * Add tcl variant, use find_libraries for portability Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * plplot: flake8 Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>
2018-06-08go: Update to 1.10.3 (#8426)Michael Kuhn1-0/+1
2018-06-07Added elastic search (#8424)sknigh1-0/+50
2018-06-07Update intel-tbb to 2018.3 and improve version URLs, dependencies and ↵Chris Green3-47/+85
patching. (#7932) * Update to 2018.3 and improve version URLs, dependencies and patching. Improve to version -> URL translation to be algorithmic rather than manual. Make binutils build dependency explicit where appropriate because we're sensitive to the assembler used. Build's use of '-mrtm' is only patched away if it needs to be because the assembler is too old. Incorporate @adamjstewart request to convert GCC version check to a conflict. * Allow specification of C++ standard. * Improve TBB patch per PR comments. * Restrict RTM patch application to older OS only. * New version 2018_U4.
2018-06-07pbbam: new package (#8365)Miles Perry1-0/+62
* pbbam: new package * pbbam: updated version * pbbam: added option tests handling * pbbam: flake8 edits
2018-06-07Fix hydrogen@develop build (#8262)Corey McNeish3-69/+13
* Delete support for old versions of Elemental in Hydrogen * Fix cmake_args versions in lbann * Remove unused import (again) * Revert elemental to pre-llnl fork * Strip tailing whitespace from libgfortran.so * Fix flake8 * Remove debug print * * Add back elemental@develop * Prohibit installation of hydrogen previous to 0.99 * Fix flake8 * Change cmake_args error to a conflicts for old versions of Hydrogen * Use ~ not -
2018-06-07Fermi Science Tools: New package (#8126)Yifan Zhu1-0/+45
* fermisciencetools: new package * fermisciencetools: new package * added comments about the error in building the source distribution; fixed flake8 errors
2018-06-07add sqlitebrowser (#8418)healther2-0/+68
* add sqlitebrowser Change-Id: I20cac709509e82d348cebc11b0d584b53b2ad3d4 * add message and clean up unnecessary code Change-Id: Ib9d2229ee25d751274680d06824891ee78fa5970 * and make flake8 happy Change-Id: I814eb89eefe1767af4d8043b08b61991750516df * make gcc-independence great again Change-Id: I75f7271757782a6735eb7f03c0551d190722974d * remove explicit import of dso_suffix Change-Id: I626c6391b22524895199db5508606c4cf22bf9b5
2018-06-07fix qt@5.8: build on systems without wayland (#8417)healther1-0/+6
* fix qt@5.8: build on systems without wayland Change-Id: I56b83208edd46f50e003d82c071e296e905bfb15 * add links Change-Id: Ia16fc20632690340f33df77fbdcb1a166d49cedc * move 5.8 comparison into 5.7 configure block Change-Id: I7dc606beeb5b5bf4e8263bc50d28de6591633c99
2018-06-07googletest: add a shared variant for all supported versions (#8373)Daryl W. Grunau1-2/+10
* add a shared variant for all supported versions * address comment from @citibeth about MacOS lib installs * address additional comments from @citibeth about MacOS lib installs * set +shared variant to be default behavior
2018-06-07add commented test dependencies (#8407)healther25-68/+41
* add commented test dependencies Change-Id: I38ffd3caa77a59f2a0a7ae92a9c8e8215cf5b4d6 * readd make('test') to openssl Change-Id: Ia3733a3848a2a26729b4050c7d4439ea9de17b1a
2018-06-07 modified: var/spack/repos/builtin/packages/py-psutil/package.py (#8420)Sajid Ali1-1/+2
2018-06-07Add new package: ftgl (#8416)Javier Cervantes1-0/+57
* Add new package: ftgl * Check version using decorator
2018-06-07openPMD-api: Update Dependencies (#8330)Axel Huebl1-9/+6
We need a newer version of HDF5 and dropped the boost dependency. Modernize the test variant to the spack test functionality.
2018-06-07add package py-cartopy and dependencies (#8406)healther5-0/+224
* add package py-cartopy Change-Id: Ifbe541e852921c384a381594a2c1110814556311 * fix comments and flake8 Change-Id: I8d5e994580e8252e00654e68ad79d74e06089939 * remove pip dependency... not sure why added in the first place Change-Id: Ie2a788887dac30778cc43931a0732980a347514d * move build, link, run to default dependencies Change-Id: I1ec0cb7dc4a697c4ca9e68a0cc0d8694cc21c100
2018-06-06Add new package: davix (#8376)Javier Cervantes2-0/+109
* Add new package: davix * Add list_url * Remove extra spaces, add list_depth and specify dependency type
2018-06-06remove pwrType from the interface SZ_compress_args() (#8414)Sheng Di1-1/+2
2018-06-06r-mitml: new package and its dependencies r-jomo and r-pan (#8412)Yifan Zhu3-0/+120
2018-06-06libjpeg-turbo: updated checksums and added autoreconf for older versions (#8411)ynanyam1-4/+8
2018-06-06ADIOS: Serial API with Parallel Lib (#8409)Axel Huebl2-0/+19
Provides a patch for the fix in https://github.com/ornladios/ADIOS/pull/182 Installed ADIOS MPI-enabled libraries are with that able to also perform serial I/O without the need to start the whole app via `mpiexec`.
2018-06-06Add new package: rngstreams (#8395)Javier Cervantes1-0/+34
* Add new package: rngstreams * Remove unnecessary list_url
2018-06-06xsimd: test type (#8405)Axel Huebl1-1/+9
Add the new type 'test` to the `googletest` dependency of xsimd.
2018-06-06Add new package: prng (#8396)Javier Cervantes3-0/+243
* Add new package: prng * Add missing dependencies and use force_autoreconf option * Add dependency types
2018-06-06Fix ADIOS 1.13.1: Maxium SZ (#8408)Axel Huebl1-2/+2
Fix the maximum accepted SZ version for the latest ADIOS release.
2018-06-06numpy: nosetest (#8404)Axel Huebl1-3/+1
the type 'test' exists now :-)
2018-06-06ISAAC Server 1.3.3 (#8403)Axel Huebl1-0/+1
Forgot to bump this package with the library release.
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