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2020-05-13revbayes: Update checksum (#16628)Nick Booher1-1/+1
2020-05-13conda4aarch64:New Package. (#16617)Toyohisa Kameyama1-0/+24
2020-05-13ncl: Fix build with gcc@10: (#16624)Michael Kuhn1-0/+7
2020-05-13r-exactextractr: new package (#16626)Amjad Kotobi1-0/+26
2020-05-13QE Update May 2020 (#16627)Nichols A. Romero1-5/+8
* Clarify comments about QMCPACK-to-QE converter. * Allow hdf5=serial with QE 6.4.1 + qmcpack, but apply filter_file. * Ammend comments about the use of the filter_file.
2020-05-13py-pint: added versions up to v0.11 (#16537)lpritch-lanl1-3/+9
Co-authored-by: Lori Pritchett-Sheats <lpritch@pn2002926.lanl.gov>
2020-05-13parallel-netcdf: fix build with gcc@10: (#16620)Michael Kuhn1-6/+20
2020-05-13r-xml2: new version & updated dependencies (#16604)Amjad Kotobi1-1/+2
* r-xml2: new version & updated dependencies * r-xml2: updated dependencies
2020-05-13ppopen-appl-fdm: added support to Fujitsu compilers. (#16616)Tomoki, Karatsu2-1/+17
2020-05-13charmpp: support for aarch64. (#16619)Toyohisa Kameyama1-0/+2
2020-05-13tcsh: fix build with gcc@10: (#16621)Michael Kuhn1-10/+11
2020-05-13esmf: fix build with gcc@10: (#16622)Michael Kuhn1-0/+3
2020-05-12Update docs on "spack external find" (#16482)Peter Scheibel2-8/+80
This improves the documentation for `spack external find` in several ways: * Provide a code example of implementing `determine_spec_details` for a package * Explain how to define executables to look for (and also e.g. that they are treated as regular expressions and so can pull in unexpected files). * Add the "why" for a couple of constraints (i.e. explain that this logic only works for build/run deps because it examines `PATH` for executables) * Spread the docs between build customization and packaging sections * Add cross-references * Add a label so that `spack external find` is linked from the command reference.
2020-05-12Fix axom install target (#16613)Chris White1-1/+1
2020-05-12py-plotly: unfix dependency versions (fixes #16544) (#16546)Pariksheet Nanda1-3/+5
* py-plotly: unfix dependency versions (fixes #16544) * py-plotly: add missing dependencies for #16546 * py-plotly: match setup.py instead of requirements.txt for #16546
2020-05-12velvetoptimiser: new package at 2.2.6 (#16611)Justin S1-0/+22
2020-05-12r-testthat : dependencies and version updated (#16576)Amjad Kotobi1-0/+4
* r-testthat : dependencies and version updated * Adding version conditions for dependencies * r-testthat: Fix dependecies condition
2020-05-12py-scikit-learn: add new version (#16607)Adam J. Stewart1-3/+6
2020-05-12zstd: add 1.4.4 (#16608)Justin S1-0/+1
2020-05-12travis: use bionic as default for Linux (#16521)Massimiliano Culpo3-42/+66
Modifications: - [x] Travis now uses `bionic` as a default (`xenial` used for Python 3.5, `trusty` for Python 2.6) - [x] Shell unit tests have been factored into their own run - [x] `kcov` is built only for tests that upload coverage results Overall with this we shave 3-4 mins. on each run and add an additional run of about 3 min. For some reason `kcov` 38 fails forwarding output when used with Python unit tests, so I used v34 for that and v38 (latest) for shell testing. Previously we were using v25.
2020-05-12py-threadpoolctl: add new package (#16606)Adam J. Stewart1-0/+19
2020-05-12revbayes: update for 1.1.0 (#16603)Nick Booher1-8/+20
* revbayes: update for 1.1.0 * revbayes: Fix flake8
2020-05-12bugfix: reorder variants in Spec strings (#16462)Greg Becker3-18/+17
* change print order for variants to avoid zsh parsing bugs * change tests for new variant parse order
2020-05-12new version r-rcurl (#16550)Amjad Kotobi1-0/+2
* new version r-rcurl * RCurl dependency R version updated * Adding version conditions
2020-05-12new version r-cli (#16553)Amjad Kotobi1-0/+3
* new version r-cli * r-cli : dependencies updated * Adding version conditions for dependencies
2020-05-12new version r-ellipsis (#16556)Amjad Kotobi1-0/+2
* new version r-ellipsis * r-ellipsis : R dependency updated * Adding version conditions for dependencies
2020-05-12r-rematch2 : new package (#16563)Amjad Kotobi1-0/+23
* r-rematch2 : new package * Updating URL
2020-05-12r-roxygen : dependencies and version updated (#16565)Amjad Kotobi1-0/+5
* r-roxygen : dependencies and version updated * Dependencies updated for condition
2020-05-12r-purrr : dependencies and version update (#16566)Amjad Kotobi1-0/+2
* r-purrr : dependencies and version update * Dependencies updated for condition
2020-05-12r-rversions : new package (#16572)Amjad Kotobi1-0/+28
* r-rversions : new package * URL updated r-rversions
2020-05-12r-withr : dependencies and version updated (#16577)Amjad Kotobi1-0/+2
* r-withr : dependencies and version updated * Adding version conditions for dependencies
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.
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