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2020-02-15mafft: add 7.453 (#15006)Justin S1-0/+1
2020-02-15cloc: add version 1.84 (#15012)Matthias Diener1-0/+1
2020-02-15Add a new package: Metall (#14903)Keita Iwabuchi1-0/+22
* Add a new package: Metall * Fix errors in metall/package.py * Update var/spack/repos/builtin/packages/metall/package.py Change to https style URL Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update in metall/package.py. Change Metall to depend on Boost always * Update in metall/package.py. Change to install Boost with the default variants * Update metall/package.py. Removed a comment Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-14Buildcache creation/extraction use temp tarfile to preserve hardlinks during ↵Patrick Gartung2-26/+30
copy to/from prefix. (#15003) * Buildcache creation change the way prefix is copied to workdir. * install_tree copies hardlinked files * tarfile creates hardlinked files on extraction. * create a temporary tarfile from prefix and extract it to workdir * Use temp tarfile to move workdir to prefix to preserve hardlinks instead of copying
2020-02-14cuda: add libxml2 as a dependency for newer versions (#14758)Scott Wittenburg1-0/+8
2020-02-14docs: fix typo in arch in build settings examples (#14998)Paul1-6/+6
2020-02-14py-whichcraft: new package (#14907)Matthias Wolf1-0/+17
* py-whichcraft: new package * address comment
2020-02-13spack compiler info: quick fix for failing command (#14928)Massimiliano Culpo1-1/+1
fixes #14927
2020-02-13fix env vars before install (#14575)Sajid Ali1-0/+3
2020-02-13Updated both cub and nccl versions. Fixed a bug in the cub download (#14852)Brian Van Essen2-1/+10
url.
2020-02-13Fix shell detection: zsh5 -> zsh (#14858)Adam J. Stewart1-1/+2
2020-02-13New package: r-codex (#14869)Glenn Johnson2-0/+50
This PR adds the r-codex package. - new package: r-bsgenome-hsapiens-ucsc-hg19
2020-02-13openblas: add variant +consistentFPCSR (#14876)Kai Torben Ohlhus1-0/+6
Add the OpenBLAS variant `+consistentFPCSR`, by default `False`, which adds the compile definition `CONSISTENT_FPCSR=1` as documented in OpenBLAS `Makefile.rule`.
2020-02-13[rsync] Use popt and zlib (#14755)Dr. Christian Tacke1-0/+6
popt and zlib are available as spack packages. So use them instead of building internal ones.
2020-02-13New package: r-exomedepth (#14884)Glenn Johnson2-0/+52
This PR adds the r-exomedepth package and r-aod as a dependency.
2020-02-13New package: r-exomecopy (#14885)Glenn Johnson1-0/+24
2020-02-13New package: r-fdb-infiniummethylation-hg18 (#14890)Glenn Johnson2-0/+43
This PR adds the r-fdb-infiniummethylation-hg18 package and the needed dependency of r-txdb-hsapiens-ucsc-hg18-knowngene.
2020-02-13Update and fix the r-rhtslib package (#14863)Glenn Johnson5-1/+68
This PR adds an updated version to the r-rhtslib package as well as fix the build. - add patches to use compiler flags from R - add variables for bzip2 and xz dependencies - use the spack Makeconf file when building the in-tree htslib - make patchelf available to allow R to remove reference to temporary installation directory in htslib shared object - Add new version of r-rsamtools as the r-rsamtools and r-rhtlib packages are closely paired.
2020-02-13Patch silo for %clang@9 (#14892)Seth R. Johnson1-0/+26
2020-02-13Add missing dep to git. (#14895)Alec Thomas1-0/+1
As discussed in: https://spackpm.slack.com/archives/C5VL7V81G/p1581394270058800
2020-02-13Fix run environment (#14908)asmaahassan901-2/+2
* Fix run environment Trying to install Avizo, i get "Error: NameError: name 'run_env' is not defined". Correcting it to be just "env" * fix identation
2020-02-13intel-tbb: update to new tar file names for 2020 versions (#14924)Mark W. Krentel1-9/+16
Starting with 2020, the tar files are named v2020.0.tar.gz, v2020.1.tar.gz, etc, not 2020_U1.tar.gz. https://github.com/intel/tbb/releases The previous commit (7a10478708) fixed the checksum mismatch, but didn't update url_for_version (my bad).
2020-02-13unifyfs: remove numa dependency (#14925)Cameron Stanavige1-11/+5
UnifyFS no longer has an option to depend on numa. This removes the numa variant, dependency, and associated conflict. This commit also - renames the `pmpi` variant to the more appropriate `auto-mount` - changes the preferred version to the most recent release
2020-02-13charmpp: add version 6.10.0, switch to https for download (#14930)Matthias Diener1-1/+2
2020-02-13byobu: add version 5.131 (#14932)Matthias Diener1-0/+3
2020-02-13libcircle depends on pkg-config for build (#14933)eugeneswalker1-0/+1
2020-02-13Replace direct call to patchelf with get_existing_elf_rpaths which handles ↵Patrick Gartung1-9/+2
exceptions. (#14929) * Replace direct call to patchelf with get_existing_elf_rpaths which handles exceptions. * Remove unused patchelf definition. * Convert to set.
2020-02-13hepmc: fixed wrong sha256 for latest versions (#14926)Massimiliano Culpo1-4/+4
2020-02-13py-binaryornot: new package (#14906)Matthias Wolf1-0/+19
2020-02-13py-poyo: new package (#14909)Matthias Wolf1-0/+17
2020-02-13py-jinja2-time: new package (#14910)Matthias Wolf1-0/+19
2020-02-13py-elasticsearch: added v7.5.1 and v6.4.0 (#14913)Matthias Wolf1-0/+2
2020-02-13py-clustershell: new package (#14914)Matthias Wolf1-0/+20
2020-02-13py-magic: new package (#14912)Matthias Wolf1-0/+18
2020-02-13gdb: added v9.1 (#14919)Matthias Diener1-0/+1
2020-02-13hipsycl: new package and new 'sycl' virtual package (#14051)Federico Ficarelli2-0/+160
2020-02-12bmi depends on automake for buildeugeneswalker1-0/+1
2020-02-12macsio: cast JsonGetInt from int to unsigned int (#14736)noguchi-k2-0/+14
* macsio: cast from int to unsigned int * macsio: apply a patch only when version is 1.1
2020-02-12spack python: add -m option to run modules as scriptsTodd Gamblin3-2/+32
It's often useful to run a module with `python -m`, e.g.: python -m pyinstrument script.py Running a python script this way was hard, though, as `spack python` did not have a similar `-m` option. This PR adds a `-m` option to `spack python` so that we can do things like this: spack python -m pyinstrument ./test.py This makes it easy to write a script that uses a small part of Spack and then profile it. Previously thee easiest way to do this was to write a custom Spack command, which is often overkill.
2020-02-12protobuf: Fix intel compiler failures. (#14916)Chuck Atkins3-1/+59
2020-02-12Adding Intel LLVM compiler (#13618)Jon Rood1-0/+50
* Adding Intel LLVM compiler. * Fixing some minor issues. * Split build environment on run environment in intel-llvm.
2020-02-12Paraview: fix PYTHONPATH for static build. (#14648)Dan Lipsa1-5/+12
* Fix PYTHONPATH for static build. * Only for the latest version.
2020-02-12openPMD-api: Build Env Fix & Dev (#14904)Axel Huebl1-2/+2
- fix a missing `env.` prefix in the build environment. - rename development branch to same name as in git
2020-02-11WarpX: master is the new develop (#14898)Axel Huebl1-6/+2
WarpX removed the `dev` branch in favor of a simpler, `master`-centric development model. `master` is the new development branch and there is no stable branch anymore (we use tags and release branches instead).
2020-02-11New package: ReFrame (#14737)victorusu1-0/+34
2020-02-11ROOT: Add Pythia8 support (#14790)Hadrien G2-4/+5
2020-02-11OpenCV package: add versions 4.2.0, 4.1.2, and 4.1.1(#14814)darmac1-1/+4
2020-02-11[dd4hep] Make DDDigi work with current TBB releases (#14791)Hadrien G2-0/+45
Add patch for DDDigi's broken TBB support. The issue is fixed in DD4hep master so the patch is only required for 1.11.0
2020-02-11New package: libvips (#14794)Sajid Ali1-0/+45
2020-02-11libdrm: add version 2.4.100 (#14809)darmac1-7/+8
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