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2018-07-10fetch: remove 'trying' when cloning repos (#8651)Matthias Diener2-5/+5
* fetch: remove 'trying' when cloning repos This makes it similar to what the URL strategy prints. * change svn/hg names
2018-07-10libxshmfence: Update to 1.3 (#8667)Michael Kuhn1-2/+3
libxshmfence@1.2 does not compile with recent versions of glibc.
2018-07-09charm: add possibility to run tests (#8665)Matthias Diener1-0/+6
2018-07-09libnova: new package (#8666)Levi Baber1-0/+42
* libnova: new package * libnova: flake8
2018-07-09Add ccache support (#3761)Christoph Junghans5-1/+41
If the user sets "ccache: true" in spack's config.yaml, Spack will use an available ccache executable when compiling c/c++ code. This feature is disabled by default (i.e. "ccache: false") and the documentation is updated with how to enable ccache support
2018-07-09Make 'netlib-lapack' a CMakePackage. (#8661)Sergey Kosukhin1-48/+70
* Make 'netlib-lapack' a CMakePackage. * Add a comment. * Some refactoring.
2018-07-09express: bamtools lib handling (#8552)Levi Baber1-5/+2
* express: bamtools lib handling * express: use libs property * express: remove old comment
2018-07-08trilinos: update dtk dependencies (#8660)Andrey Prokopenko1-0/+3
2018-07-08fix typo in help of `spack clone` prefix is singular (#8658)Andreas Baumbach1-1/+1
Change-Id: I3bfe5b4ba497fae57d5382502ea9a1b054688fdb
2018-07-07blasr: new package (#8367)Miles Perry1-0/+96
* blasr: new package * blasr: changed version release, created list with 9 things, seperated make into build phase. * blasr: fixed build phase by adding : * blasr: fixed syntax for configure_args * blasr: flake8 edits * blasr-libcpp: fixed configure_args syntax * blasr: fixed install issues resulting from PacBio changes * blasr: removed accidental blasr-libcpp upload * blasr: removed accidental blasr-libcpp upload * blasr: removed blasr-libcpp * blasr: edited out comment
2018-07-07ECP VELOC (#8581)Elsa Gonsiorowski, PhD7-0/+388
* kvtree package file * MPI is default on * proper mpi compiler * rankstr package * better rankstr description * typo * redset package * shuffile package * er package * axl package * proper pythor * mpi is default on * alpha releases and master versions * veloc package with boost headers dep * cmake version * added C++11 requirement * flake8 * flake8 * ecp tag * axl: better async api option handling * veloc package description * prettier args list * C++11 flag handler * v1.0 of veloc
2018-07-06Added support for uncrustify 0.67. (#8655)estebanpauli1-1/+17
* Added support for uncrustify 0.67. Since the build system changed for uncrustify at version 0.64, I had to change the package from an AutotoolsPackage to a plain Package and use @when annotations to build the packages differently. * Removed blank line at end of file * Added support for python2.6 in uncrustify configuration.
2018-07-06Fix security issue in singularity + misc cleanups (#8657)George Hartzell1-9/+15
- Versions before 2.5.2 suffer from a serious security problem (https://nvd.nist.gov/vuln/detail/CVE-2018-12021). Deleted all versions prior to v2.5.2. - Update homepage (looks like singularity's going Freemium). - Use release tarball instead of automagically generated archive tarball (digest values are more stable). - No longer need autotools for released versions, just @devel. - Install needs to be single-threaded, otherwise when installed as root the various 'chmod' operations race against the copies.
2018-07-06Fix digests for git@2.17.0 and git@2.17.1 (#8652)George Hartzell1-4/+4
The entries for git@2.17.1 and git@2.17.0 were swapped. This fixes them.
2018-07-06Update nettle package with info for v3.4 (#8653)George Hartzell1-0/+1
2018-07-06Clear up a bit of modules/dotkit confusion (#8650)George Hartzell1-5/+7
`use` is an overloaded word between dotkit, modules and spack. Add additional words to make the distinction clear in the docs.
2018-07-06Add url_for_version and list_url to Ruby package (#8216)Adam J. Stewart1-0/+6
2018-07-06precice: new package (issue #8643) (#8644)Mark Olesen2-0/+181
preCICE (Precise Code Interaction Coupling Environment) is a coupling library for partitioned multi-physics simulations. Partitioned means that preCICE couples existing programs (solvers) capable of simulating a subpart of the complete physics involved in a simulation. of-precice: new package preCICE adapter for OpenFOAM
2018-07-06switch git to kernel.org source and sha256 (#8580)Andreas Baumbach1-48/+49
* switch git to kernel.org source and sha256 Change-Id: I5fe15689adb1163e9ed2b7127b52c95bd0d48564 * fix forgotton md5s Change-Id: Ib01f21e20678d9aac3344b6ee311134a90b87bdd * remove old url Change-Id: I717a084a0357a84b83bc6c8542749aac7e04f68b
2018-07-06Glog: make is a function (#8648)Adam J. Stewart1-2/+2
2018-07-05cleverleaf: Intel compiler fails compilation without c++11 flag (#8550) (#8598)twang151-0/+6
2018-07-05Add missing dependencies and variants to wcslib (#8603)Adam J. Stewart1-2/+34
* Add missing dependencies and variants to wcslib * Add flex version requirement
2018-07-05ncbitoolkit: Create new package. (#8591)lingnanyuan1-0/+65
* ncbitoolkit: Create new package. * Fix Flake8 Error. * Add version constraints and change format. * Fix version constraints.
2018-07-05added rpy2 2.9.4 and added py-jinja2 dependency (#8645)Gregory Lee1-3/+14
2018-07-04gcc: Fix build of older versions with recent versions of glibc (#8510)Michael Kuhn6-0/+455
2018-07-04Parquet: new packages (#8601)Matthias Wolf6-0/+184
* parquet: new package Includes the following dependencies: * arrow * flatbuffers Changes for compilation: * snappy * thrift * zstd * parquet: improve recipes (including dependencies) * arrow: remove unused import in recipe * parquet: fix line length for flake8/py27 * parquet, arrow: fix py26 format strings * Address review comments. * arrow: simplify recipe
2018-07-03disable openblas intel openmp patch for versions > 0.2.20, fixed upstream ↵becker331-1/+1
(#8638)
2018-07-03Add new versions for log4cplus. (#8621)健美猞猁1-1/+3
* Add new versions for log4cplus. * Update log4cplus versions. * Add urls. * Add url_for_version. * Remove url_for_version.
2018-07-03Bump sbt to 1.1.6. (#8634)健美猞猁1-2/+1
2018-07-02Fix base class for py-pyserial (#8633)Adam J. Stewart1-1/+1
2018-07-02Pxz: new package (#8631)Matthias Diener1-0/+43
2018-07-02screen: update package (#8630)Matthias Diener1-0/+1
2018-07-02petsc: add in latest release 3.9.3. (#8627)Satish Balay2-62/+1
xl related fixes are 3.9.3 so remove xlc-test-3.9.0.diff
2018-07-02byobu: update package (#8628)Matthias Diener1-0/+1
2018-07-02Bump gradle to 4.8.1. (#8625)健美猞猁1-0/+1
2018-07-02Add Amrvis package (#8590)Jon Rood1-0/+188
* First draft of amrvis package file. * More additions to amrvis. * Formatting. * Forcing compiler environment variables to point to spack mpi compilers when using mpi. * Disabling intel compiler for amrvis. * Comments. * Refining amrvis package file. * Moving library and include locations variables to be inserted at the first lines of the makefile. * Globbing amrvis binary instead of constructing its name. * Making env variable setting consistent and fixing globbing of executable. * Using iglob instead of glob. * Turning MPI on by default for Amrvis.
2018-07-02ENH: Building OpenFOAM sub-packages (issue #8579) (#8592)Mark Olesen4-55/+156
* ENH: Building OpenFOAM sub-packages (issue #8579) * Some support for packages building with OpenFOAM - Adjust the wrappers calling the OpenFOAM Allwmake script. Have them look for a Allwmake-spack file first, which is assumed to contain special adjustments for compiling with spack. This file could be delivered as part of a tarball (which is unlikely) or generated on the fly by the spack sub-package as part of its patch or configure stage. CONFIG: change the default paraview variant for openfoam to be False - the different combinations of paraview backends, off-screen etc make it difficult to suggest that building with paraview as a standard dependency makes much sense. Additionally, building paraview with qt can become quite an issue. So it makes much more sense to only enable that upon request. ENH: add a +vtk variant. - for VTK with off-screen rendering to be used by the runTimePostProcessing function object, which is a fairly simple framework for generating images of some OpenFOAM derived objects (eg, sampling planes). SPACK spec problem: - reflect the flex restriction impose by the scotch dependency within the openfoam spec as well, as partial workaround for buggy or annoying spec resolution. OTHER: - updated the backstop foamEtcFile file to include args handling as per the OpenFOAM-v1806 updates. * new version: OpenFOAM-v1806 - https://www.openfoam.com/releases/openfoam-v1806/
2018-07-02A new package: xhmm. (#8620)健美猞猁1-0/+51
* A new package: xhmm. * Flake8. * Support general BLAS.
2018-06-29Add Python 3.7.0 (#8619)Adam J. Stewart1-0/+1
2018-06-29Update py-libensemble package (#8617)Stephen Hudson1-1/+2
2018-06-29numactl: fix build with glibc-2.26 (#8615)Christoph Junghans2-0/+43
2018-06-29latte: version bump (#8611)Christoph Junghans3-2/+6
2018-06-29Removed duplicate word (#8609)Paul Chelarescu1-1/+1
2018-06-28r-aer: a new package. (#8567)健美猞猁1-0/+46
* r-aer: a new package. * Flake8. * Add list_url and dependency versions.
2018-06-28Added nmap version 7.70 (#8606)Ian Lee1-1/+2
2018-06-28Add CFITSIO 3.450 (#8602)Adam J. Stewart1-1/+2
2018-06-28Add kealib 1.4.9 (#8597)Adam J. Stewart1-7/+22
2018-06-27Add Caliper 1.7.0 and Gotcha 1.0.2 (#8572)David Böhme2-1/+12
* Update Gotcha and Caliper versions * caliper: Use spack-built gotcha * caliper: Enable sampling support on Linux * More robust check for Linux
2018-06-27New version mesa-18.1.2 (#8589)Mark Olesen1-0/+1
- compiles with newer LLVM. The older mesa-17 versions balk at the changes in the llvm::FastMath class, where a member function has been removed.
2018-06-27Provide new version of sbt (simple build tool) (#8576)Andreas Baumbach1-1/+4
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