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2018-04-24petsc and slepc: add 3.9.0; hypre: add 2.14 (needed by petsc) (#7877)Denis Davydov3-2/+8
2018-04-23ARAGORN: Create new package (#7875)Eric1-0/+46
2018-04-23prinseq-lite: Create new package (#7873)Eric1-0/+60
* prinseq-lite: Create new package * prinseq-lite: set variant description and add dependency type
2018-04-237851 pmix aarch64 (#7852)Ross Miller1-0/+10
* Fix build issue with PMIx on aarch64 Work around a bug in PMIx that causes build issues on aarch64. Bug was fixed in PMIx 2.1.1, so the spack package checks both the architecture and the PMIx version. Workaround is to just not build the PMIx test and example code. * Minor code cleanups Minor corrections to make 'spack flake8' happy. * Add support for version 2.1.1
2018-04-23New colm, ragel packages (#7867)Mark Olesen2-0/+81
- Ragel is a parser and finite state machine generator that can be used as an alternative means for solving parsing problems without Flex.
2018-04-23Add a new version 5.4.1.7 for mono. (#7866)健美猫1-0/+1
2018-04-22omega-h: new package (#7861)Dan Ibanez1-0/+67
* omega-h: new package * omega-h: fix multiple package.py issues * omega-h: use tarball checksum to avoid warning * omega-h: wrap lines for flake8
2018-04-22new package: racon (bioinformatics) (#7726)Sinan1-0/+51
* new package: racon (bioinformatics) * add cmake_arg method
2018-04-21Add a new pacakage: HiC-Pro. (#7858)健美猫1-0/+80
* HiC-Pro: a new package. * Flake8. * Update. * Remove nektar.
2018-04-21A new pacakge: IMP. (#7859)健美猫1-0/+40
2018-04-21py-mg-rast-tools: Create new package and its dependencies. (#7816)lingnanyuan8-0/+316
* r-matr: Create new package. * shocklibs: Create new package. * r-biom-utils: Create new package. * r-mgraster: Create new package * py-poster: Create new package. * py-requests-toolbelt: Create new package. * perl-libwww-perl: Create new package. * py-mg-rast-tools: Create new package. * mg-rast-tools: Fix version constraints for dependencies. * Change dependency type of py-setuptools.
2018-04-21py-pymol: new package (#7823)Levi Baber1-0/+51
* py-pymol: new package * py-pymol: needs python+tk
2018-04-21add variant htmlreport to package cppcheck (#7824)healther1-0/+6
Change-Id: I31766d3ceb4fa8852b9bdc82444e36514e760f4b
2018-04-21gnuplot: add 5.2.2 (#7831)Denis Davydov1-0/+1
2018-04-21dealii: disable +slepc with ~petsc (#7832)Denis Davydov1-0/+1
2018-04-21DIAMOND: Add version 0.9.20 (#7847)Eric1-0/+2
* DIAMOND: Add version 0.9.20 * DIAMOND: add version 0.9.21
2018-04-21jellyfish: fixing url for v2 package retrieval (#7849)Levi Baber1-1/+2
2018-04-19self has no attribute named satisfies. (#7826)健美猫1-1/+1
2018-04-19openPMD-api (#7765)Axel Huebl1-0/+102
* openPMD-api Add a new package for openPMD-api. openPMD is a meta-data standard (markup, schema) for hierarchical, scientific particle and mesh based data. openPMD-api is a library wrapping the underlying backends (HDF5, ADIOS, ...) into a single, object-aware API. * Repository: https://github.com/openPMD/openPMD-api * Project: https://github.com/openPMD http://www.openPMD.org * mpi variant forwarding: fix concretization
2018-04-19libxml2: adding subdir to cpath for deps (#7819)Levi Baber1-0/+4
* libxml2: adding subdir to cpath for deps * libxml2: no join_path * libxml2: fix cpath for run_env * libxml2: typo
2018-04-19freetype: adding subdir to cpath for deps (#7818)Levi Baber1-0/+4
* freetype: adding subdir to cpath for deps * freetype: no join_path * freetype: fix cpath for run_env
2018-04-19Suite-sparse: provide patch to fix builts with clang@6.0.0. (#7811)Kelly (KT) Thompson2-0/+14
+ I am unable to build suite-sparse@5.2.0 with clang@6.0.0. The build fails with the error: ``` 2397 [ 99%] Linking C executable wildtype_demo 2398 make[4]: Leaving directory `/tmp/kellyt/spack-stage/spack-stage-w0XYhK/SuiteSparse/GraphBLAS/build' >> 2399 libgraphblas.so.2.0.1: undefined reference to `__fpclassify' >> 2400 clang-6.0: error: linker command failed with exit code 1 (use -v to see invocation) >> 2401 make[4]: *** [wildtype_demo] Error 1 ``` + This error appears because libgraphblas.so requires `-lm`, but that link dependency is not explicitly listed in GraphBLAS\CMakeLists.txt. + A patch file is provided to add this dependency. The patch is only applied when the compiler is `%clang`.
2018-04-19add variants and conflicts for curl (#7804)healther2-7/+61
* add variants and conflicts for curl * darwinssl - Apple's SSL/TLS implementation * libssh - use libssh implementation * add darwin conflict for libssh{,2} * add linux conflict for darwinssl * remove openssl when +darwinssl * Update package.py * Update package.py * Update package.py * Update package.py
2018-04-18freeglut: new package (#7820)Levi Baber1-0/+43
2018-04-18glew: adding gl dependency (#7817)Levi Baber1-0/+1
2018-04-18Add -d option to diy to specify source path move -j to common args (#5963)Matthew Scott Krafczyk3-4/+20
2018-04-18Fix bug/oversight in formatting error message. (#7810)Elizabeth Fischer1-1/+1
2018-04-18Simple updates to the Krell Institute OpenSpeedShop and CBTF components ↵Jim Galarowicz5-8/+10
build package files. (#7812)
2018-04-18xrandr: needs randrproto (#7814)Levi Baber1-0/+1
* xrandr: needs xrandrproto * xrandr: fix typo
2018-04-18ADIOS 1.13.1 & SZ 1.4.12.3 (#7808)Axel Huebl2-1/+4
* ADIOS 1.13.1 ADIOS 1.13.1 fixes several issues with zero-sized block reading and writing when compression transports are used. * SZ 1.4.12.3 Add the lastest SZ release used in ADIOS1.
2018-04-18bcl2fastq2: package update (#7794)Matteo Guglielmi1-9/+10
* bcl2fastq2: package update * package/bcl2fastq2: homepage fix * package/bcl2fastq2: glob fix * package/bcl2fastq2: code clean up * package/bcl2fastq2: code clean up #2
2018-04-18Add grackle 3.1 (#7805)Loic Hausammann1-2/+3
2018-04-17cmake: update version (#7802)Matthias Diener1-0/+1
2018-04-17DIAMOND: add zlib dependency (#7801)Eric1-0/+2
2018-04-17Add latest version of cURL (#7800)Adam J. Stewart1-1/+2
2018-04-17bismark: Create new package (#7795)Eric1-0/+54
* bismark: Create new package * bismark: fix dependency types
2018-04-17psmc: new package (#7773)Yifan Zhu1-0/+45
* psmc: new package * psmc: changed version number * psmc: overwrite build phase
2018-04-17perl-statistics-pca: Create new package (#7796)Eric1-0/+39
* perl-statistics-pca: Create new package * perl-statistics-pca: fix dependency types
2018-04-17r-biomart: package update (#7787)Matteo Guglielmi1-1/+5
2018-04-17r-delayedarray: package update (#7788)Matteo Guglielmi1-2/+5
2018-04-17DIAMOND: add versions 0.9.19, 0.8.38, 0.8.26 (#7789)Eric1-0/+3
2018-04-17r-summarizedexperiment: package update (#7790)Matteo Guglielmi1-3/+6
2018-04-17r-genomicalignments: package update (#7791)Matteo Guglielmi1-9/+13
2018-04-17r-bsgenome: package update (#7792)Matteo Guglielmi1-8/+12
2018-04-17r-topgo: package update (#7793)Matteo Guglielmi1-6/+7
2018-04-17r-s4vectors: package update (#7779)Matteo Guglielmi1-2/+4
* r-s4vectors: package update * r-s4vectors: dependencies fix
2018-04-17r-biobase: package update (#7785)Matteo Guglielmi1-2/+3
2018-04-17Package/r-iranges (#7780)Matteo Guglielmi1-3/+7
* r-iranges: package update * r-iranges: package update * r-iranges: dependencies fix
2018-04-17r-genomicranges: package update (#7782)Matteo Guglielmi1-5/+8
* r-genomicranges: package update * r-genomicranges: dependencies fix
2018-04-17Autocomplete spack providers (#7783)Adam J. Stewart1-2/+5
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