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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
2020-02-13hepmc: 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 Ficarelli1-0/+159
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
2020-02-12protobuf: 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
2020-02-11r-truncdist: new package at 1.0-2codeandkey1-0/+19
2020-02-11[mono] add version 6.8.0.105Jen Herting1-0/+2
2020-02-11Fix intel-mkl package (#14856)Scott Wittenburg2-0/+20
* Add cpio package * intel-mkl: Depend on cli tool needed during build
2020-02-11Fix QT4 platform detection for linux clang (#14891)Seth R. Johnson1-3/+25
* Fix QT4 platform name for linux clang * Fix clang compiler flags on QT4
2020-02-11precice: add version 2.0.0 (#14842)Frédéric Simonis1-7/+31
Added python3 dependency Added support for new CMake variables
2020-02-11unifdef: added new package (#14880)Matthias Diener1-0/+25
2020-02-11heffte: added v0.2 (#14881)Christoph Junghans1-0/+1
2020-02-11hepmc: added versions up to v3.2.0 (#14805)darmac1-1/+7
2020-02-10Hydrogen: update dependency on aluminum (#14760)Brian Van Essen3-11/+19
* Hydrogen now depends on `aluminum +nccl` vs. `aluminum +mpi_cuda` * Hydrogen: Simplify Mac OS OpenMP-detection logic * Aluminum: Add Mac OS OpenMP-detection logic * LBANN: depend on conduit@0.4.0: instead of conduit@master
2020-02-10Spack find: fix queries that specify dependencies (#14757)Massimiliano Culpo1-0/+15
Fixes #10019 If multiple instances of a package were installed in a single instance of Spack, and they differed in terms of dependencies, then "spack find" would not distinguish specs based on their dependencies. For example if two instances of X were installed, one with Y and one with Z, then "spack find X ^Y" would display both instances of X.
2020-02-10libedit package: add version 3.1-20191231 (#14851)Peter Scheibel1-0/+1
This new version of libedit can make use of an ncurses dependency built with +termlib (which moves some symbols into a separate libtinfo).
2020-02-10Fix vim build with ^ncurses+termlibGlenn P Johnson1-1/+4
This PR will set the approriate library if ncurses is built with a separate tinfo library.
2020-02-10icedtea: added versions up to v3.9.0 (#14806)darmac1-1/+7
2020-02-10New package: r-biomartr (#14812)Glenn Johnson3-3/+77
This PR creates the r-biomartr package as well as needed new packages and updates. - new dependency: r-philentropy - update: r-curl
2020-02-10acts-core: added v0.16.0 (#14839)Hadrien G1-6/+17
* Adapt to ACTS v0.16 * ACTS uses the DD4hep XML components nowadays
2020-02-10New package: r-watermelon (#14864)Glenn Johnson8-0/+185
This PR creates the r-watermelon package, along with dependencies. - new package: r-fdb-infiniummethylation-hg19 - new package: r-illuminahumanmethylation450kanno-ilmn12-hg19 - new package: r-lumi - new package: r-methylumi - new package: r-roc - new package: r-txdb-hsapiens-ucsc-hg19-knowngene - updated package: r-matrixstats, new version needed as a dependency
2020-02-10New package: r-suppdists (#14865)Glenn Johnson1-0/+22
2020-02-10New package: r-imager (#14866)Glenn Johnson3-0/+83
This PR adds the r-imager package and dependencies. - new package: r-bmp - new package: r-readbitmap
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