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2020-05-12r-knitr : dependencies and version updated (#16579)Amjad Kotobi1-2/+3
* r-knitr : dependencies and version updated * Adding version conditions for dependencies
2020-05-12modylas: Add flag to use preprocessor when building with Fujitsu compiler. ↵Tomoki, Karatsu1-0/+2
(#16598)
2020-05-12New patch release SLEPc 3.13.2 (#16601)Jose E. Roman1-0/+1
2020-05-12py-horovod: link dependency for py-torch (#16600)Andrew W Elble1-1/+1
fix for same reasons as #16495.
2020-05-12caffe: fixed build error (#16520)Toyohisa Kameyama7-1/+362
* opencv 3.2 requires cmake 3.11 or older. caffe dependency is changed. * revert opencv variant to caffe. backport to opencv errors.
2020-05-12py-dask: new version (#16531)Sergey Kosukhin3-24/+122
* py-dask: new version * py-dask: update the constraints. * py-dask: add a list of maintainers.
2020-05-12gcc: fix several issues (#16599)Michael Kuhn2-18/+40
- GCC has moved to Git - The develop/master version requires flex - Add myself as a maintainer - Set the library path in the zstd patch
2020-05-12z3: update python dependency (#16597)Todd Gamblin1-1/+2
-[x] `z3` needs a dependency on `py-setuptools` -[x] `z3` has a run dependency on `python`, so we might as well make building with the python bindings default
2020-05-12prokka: new package at v1.14.6 (#16282)Justin S1-0/+31
2020-05-12clingo: update package (#16594)Todd Gamblin1-7/+29
`clingo` has some undocumented dependencies: - `bison`, for which the default macos version is too old - `re2c`, which isn't always available Also, the python installation was not set up properly. Clingo by default does an install in `~/.local`, so we need to disable that and add a few other options to get things right. - [x] add `bison` dependency - [x] add `re2c` dependency - [x] make `doxygen` dependency optional (and patch if needed) - [x] add options to fix `python` build - [x] make python build optional but on by default
2020-05-12xabclib: added support for Fujitsu compiler. (#16596)Tomoki, Karatsu1-0/+4
- Added Fujitsu compiler options that have the same functions as the options added for GCC - Added option to link C objects
2020-05-11Charm++: fix build prefix; add ucx/pmi support (#15666)Sajid Ali3-44/+125
* Add pmi support (required by ucx, ofi, and gni backends) * Add support for ucx backend * Add dependency on MPI for pmi=simplepmi, slurmpmi, or slurmpmi2 * Remove charmpp as an MPI provider since the changes in this PR can add MPI as a dependency (mentioned previously) * Install into transport_protocol-OS-arch subdirectory to match default charmpp installation behavior (which helps dependents find it)
2020-05-11python: add -fwrapv to cflags for python@3.8.0: %intel (#16592)Greg Becker1-0/+9
2020-05-11fio: Add 3.19 (#16571)Michael Kuhn1-0/+4
Earlier versions are not compatible with gcc@10:.
2020-05-11adios: Fix build with gcc@10: (#16569)Michael Kuhn1-0/+5
2020-05-11Add avizo version 2020.1 (#16567)asmaahassan901-2/+8
2020-05-11py-plac: remove erroneous argparse dependency (#16584)Adam J. Stewart1-1/+1
2020-05-11mpich: Fix build with gcc@10: (#16568)Michael Kuhn1-0/+4
2020-05-11Remove 'spack bootstrap' and associated docs (#15179)Massimiliano Culpo7-192/+9
fixes #15145 This commit removes the outdated `spack bootstrap` command and any reference to it in the documentation and unit tests.
2020-05-11r-rstudioapi : new version (#16574)Amjad Kotobi1-0/+1
2020-05-11r-rlang : new version (#16575)Amjad Kotobi1-0/+1
2020-05-11r-digest : version updated (#16578)Amjad Kotobi1-0/+1
2020-05-11Map the spack skylake arch to Kokkos BDW, rather than SKX (#16583)Andrew Gaspar1-1/+6
SKX includes AVX-512 extensions that consumer Skylake processors do not have. Therefore, map Skylake to the prior arch to work on these systems. Skylake-X processors will still map as the skylake_avx512 spack arch and get the correct optimzations.
2020-05-11stata: add new libpng dependency (#16582)Justin S1-2/+2
2020-05-11netcdf-fortran: Fix build with gcc@10: (#16573)Michael Kuhn1-0/+5
2020-05-11New package: py-mmcv (#16536)Jen Herting1-0/+24
* [py-mmcv] Created template * [py-mmcv] added description and homepage * [py-mmcv] requires python 3.6+ * [py-mmcv] added dependencies * [py-mmcv] depends on opencv * [py-mmcv] cleaned up fixmes * [py-mmcv] requires numpy >= 1.11.1
2020-05-11gcc: added v10.1.0 (#16525)Michael Kuhn2-3/+37
2020-05-11py-configobj: remove url function (#16522)Sinan1-10/+0
It seems the pypi version of the package somehow compiles just fine Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-05-11py-jupyterlab: added package at v2.1.0 (#16562)takanori-ihara1-0/+30
2020-05-10Add new package:py-jupyterlab-server (#16561)takanori-ihara1-0/+25
2020-05-10PyTorch: fix master and mkldnn builds (#16560)Adam J. Stewart1-3/+4
2020-05-10new version r-rcpp (#16549)Amjad Kotobi1-0/+1
2020-05-10new version r-glue (#16558)Amjad Kotobi1-0/+1
2020-05-10new version r-pkgbuild (#16559)Amjad Kotobi1-0/+1
2020-05-10new version r-jsonlite (#16557)Amjad Kotobi1-0/+1
2020-05-10new version r-dt (#16555)Amjad Kotobi1-0/+1
2020-05-10new version r-covr (#16554)Amjad Kotobi1-0/+1
2020-05-10new version r-callr (#16552)Amjad Kotobi1-0/+1
2020-05-10DGL: add new version (#16547)Adam J. Stewart1-3/+10
2020-05-09Fix MacOS tests on developMassimiliano Culpo1-1/+1
The -u option allows to update the current head, so tests won't fail if we are on develop
2020-05-09macOS nightly: +1hr py-jupyterAxel Huebl1-1/+1
check if failures ares actually a real timeout or an error that just causes a hang.
2020-05-09macOS nightly: two coresAxel Huebl1-0/+1
All GitHub actions provide two cores. Just make sure this does not get oversubscribed with potentially visible additional physical cores.
2020-05-09Add unit test on MacOS using Github Actions (#14220)Massimiliano Culpo4-22/+50
- Remove macos tests from travis - Add macos tests in github actions.
2020-05-09[dd4hep] variant and run env updates (#16524)vvolkl1-2/+8
* [dd4hep] variant and run env updates * address comments from #16524
2020-05-09Add maintainers and variants for building with default earlier api versions. ↵Larry Knox1-0/+12
(#16534) * Add maintainers. Add variants for building with default earlier api versions. * Update var/spack/repos/builtin/packages/hdf5/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-09New package: py-addict (#16535)Jen Herting1-0/+19
* [py-addict] created template * [py-addict] added homepage and description * [py-addict] cleaned up fixmes * [py-addict] depends on py-setuptools
2020-05-09QMCPACK Update May 2020 (#16542)Nichols A. Romero1-23/+2
* Add naromero77 as a maintainer for QMCPACK Spack package. * Add QMCPACK 3.9.2 * Remove QE-to-QMCPACK wave function converter from QMCPACK Spack package. Already been moved to QE Spack package.
2020-05-09Fix dependency of geant4 (amends #16497) (#16504)iarspider3-10/+14
* Fix dependency of geant4 (amends #16497) * Update geant4-data dependencies * Reviewer comments (part 1/2) * Reviewer comments (part 2/2) * Update var/spack/repos/builtin/packages/geant4-data/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-09Increase coverage of spack.relocate (#16475)Massimiliano Culpo3-120/+286
- add docstrings and make parameter names consistent in `relocate.py` - Make `replace_prefix_*` and other functions private (as they are implementation details) - remove unused function _replace_prefix_nullterm() - Add unit tests for `relocate.py` functions - add patchelf to Travis and use it during tests - add hello_world fixture with a compiled binary, so we can test relocation
2020-05-09update visit package with 3.1.1 release and add comments (#16498)Cyrus Harrison3-7/+154
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