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2019-11-27BLD: enforce C++11 std for boost + xl_r (#13829)Tyler Reddy1-0/+6
* BLD: enforce C++11 std for boost + xl_r * the spack `cxxstd` variant is not sufficient to enforce `-std=c++11` usage in boost compile lines when `xl_r` compiler spec is in use; while it would be nice if this were fixed in a boost config file somewhere, for now this patch allows boost to build on POWER9 with an %xl_r compiler spec if the user specifies i.e.,: `spack install boost@1.70.0+mpi cxxstd=11 %xl_r@16.1.1.5` * Update var/spack/repos/builtin/packages/boost/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-27Build R without recommended packages (#12015)Glenn Johnson1-0/+1
The documentation states that Spack builds R without the recommmened packages, with Spack handling the build of those packages to satisfy dependencies. From the docs: > Spack explicitly adds the --without-recommended-packages flag to > prevent the installation of these packages. Due to the way Spack > handles package activation (symlinking packages to the R installation > directory), pre-existing recommended packages will cause conflicts for > already-existing files. We could either not include these recommended > packages in Spack and require them to be installed through > --with-recommended-packages, or we could not install them with R and > let users choose the version of the package they want to install. We > chose the latter. However, this is not what Spack is actually doing. The `--without-recommended` configure option is not passed to R and therefore those packages are built. This prevents R extension activation from working as files in the recommended packages installed with R will block linking of file from the respective `r-` packages. This PR adds the `--without-recommended` flag to the configure options of the R package. This will then have the Spack R build match what is documented.
2019-11-27Replace git-based Bioconductor R packages (#12005)Justin S186-1326/+3320
* Replace git-based Bioconductor R packages The current collection of bioconductor packages tend to have scattered dependencies and missing versions. This commit replaces git-based packages with tool-generated Spack package recipes with correct dependencies and descriptions in place. * Fix some broken package names, add periods to title docstrings * r-clue: new package at 0.3-57 * r-genomeinfodbdata: add 1.2.1 * r-gofuncr: new package at 1.4.0 * r-pfam-db: add 3.8.2 * Add missed package r-genelendatabase * update r-goseq package * update r-glimma package * update r-rots package * r-org-hs-eg-db: add 3.8.2 * r-vgam: fix incorrect R version * r-rnaseqmap: new package at 2.42.0 * r-rhdf5lib: new package at 1.6.0 * r-scrime: new package at 1.3.5 * r-delayedmatrixstats: new package at 1.6.0 * r-hdf5array: new package at 1.12.1 * r-biocfilecache: new package at 1.8.0 * r-ctc: add new versions, dependencies * r-genemeta: new package at 1.56.0 * r-scrime: fix flake8 * r-ensembldb: add missing dependencies * Added missing dependencies to packages with certain DESCRIPTIONS * r-mapplots: new package at 1.5.1 * r-beachmat: new package at 2.0.0 * r-beeswarm: new package at 0.2.3 * r-biocneighbors: new package at 1.2.0 * r-biocsingular: new package at 1.0.0 * r-ecp: new package at 3.1.1 * r-enrichplot: new package at 1.4.0 * r-europepmc: new package at 0.3 * r-ggbeeswarm: new package at 0.6.0 * r-ggplotify: new package at 0.0.3 * r-ggraph: new package at 1.0.2 * r-gridgraphics: new package at 0.4-1 * r-rcppannoy: new package at 0.0.12 * r-rcpphnsw: new package at 0.1.0 * r-rsvd: new package at 1.0.1 * r-scater: new package at 1.12.2 * r-singlecellexperiment: new package at 1.6.0 * r-tximport: new package at 1.12.3 * r-upsetr: new package at 1.4.0 * r-vioplot: new package at 0.3.2 * r-readr: add 1.3.1 * r-matrixstats: add 0.54.0 * r-ecp: flake8 fix * r-biocmanager: new package at 1.30.4 * update bioconductor packages requiring BiocManager, new versions * r-lambda-r: add 1.2.3 * r-vegan: add 2.5-5 * r-cner, r-rcppannoy, r-reportingtools, r-rsvd: add missing newlines at EOF * r-chemometrics: flake8 fixes * r-vgam: flake8 fixes * CRAN packages: use cloud.r-project.org * Use DESCRIPTION for R version constraints over bioconductor releases * Update missed packages ABAData, acde, affydata * Update remaining missed packages * bio: Drop 'when' clause from first checksummed versions * bio: improve package description generation logic * r-genomeinfodbdata: use explicit sha256 sums * r-pfam-db: update dependencies, add 3.10.0 * update r-org-hs-eg-db * r-dirichletmultinomial: re-add gsl * r-polyclip: new package at 1.10-0 * r-farver: new package at 1.1.0 * r-tweenr: new package at 1.0.1 * r-ggforce: new package at 0.3.1 * r-ggforce: remove redundant dep * r-ggraph: add missing deps * r-rcpphnsw: remove redundant depends_on * r-reportingtools: re-add r-r-utils dep * r-rhdf5: add gmake dep * r-rhtslib: add system dependencies * r-rsamtools: add gmake dep * r-farver: remove redundant dep * r-tweenr: remove redundant dep * r-variantannotation: add gmake dep * r-rgraphviz: add graphviz dep * r-vsn: correct r-hexbin constraint * r-scater: fix obsolete deps * r-variantannotation: fix gmake dep type * r-scater: tighten R version constraints * r-rsamtools: fix gmake dep type * r-rhtslib: fix gmake dep type * r-rhtslib: use xz over lzma * r-rhdf5: fix gmake dep type * r-farver: replace with newer recipe for 2.0.1 * r-mzr: remove old dependency * r-reportingtools: remove builtin dependency * r-mzr: add gmake dep * r-rhtslib: make system libraries link deps * r-genomeinfodbdata: fix R version constraints * r-geoquery: remove old deps from new versions * r-genomicfeatures: tighten r-rmysql dep * r-ensembldb: tighten r-annotationhub dep * r-complexheatmap: fix r-dendextend dep * r-cner: fix utils dep name * r-clusterprofiler: fix r-gosemsim version req * r-biostrings: fix r-iranges version reqs * r-rhdf5lib: add gmake dep * r-oligoclasses: fix r-biocinstaller dep range * r-organismdbi: fix r-biocinstaller dep range * r-hdf5array: add gmake dep * r-gtrellis: tighten r-circlize version req * r-gostats: fix r-graph version req * r-glimma: fix old dependency ranges * r-biostrings: syntax fix * r-organismdbi: syntax fix * r-dose: fix r-igraph dep * r-dose: fix r-scales, r-rvcheck deps * r-affy: fix r-biocinstaller dep * r-ampliqueso: fix homepage * r-aneufinder: fix r-biocgenerics dep * r-beachmat: fix changed deps * r-biocneighbors: fix old R constraint * r-biocmanager: rewrite recipe for 1.30.10 * Update var/spack/repos/builtin/packages/r-biocinstaller/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/r-oligoclasses/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-27Add version 2.1.0 to 'aspect' package (#13830)Rene Gassmoeller1-3/+4
2019-11-27Update cartopy version and fix recipe (#13898)iarspider1-7/+19
* Update cartopy version and fix recipe Cartopy 0.17.0 works fine with proj 6 * Update cartopy version and fix recipe Cartopy 0.17.0 works fine with proj 6 * Set ACCEPT_USE_OF_DEPRECATED_PROJ_API_H flag when building extension * Add variants to py-cartopy recipe as suggested * Fix proj dependency * Split dependency * Fix PEP-8; remove extra dependency
2019-11-27QMCPACK Update Nov2019 (#13832)Nichols A. Romero1-31/+34
* Bump up QE version number to 6.4.1. * Fix QMCPACK conflicts. * HDF5 dependencies where over specified which could cause unnecessary installs of HDF5. * Update QMCPACK testing option. * Remove support for serial QE 6.4.1 converter. Add support for parallel QE 6.4.1. converter with serial HDF5. * Switch to setup_run_environment. * Fix setup_run_environment call arguements. * Fix typo. * switch run_env to env
2019-11-27mpich: Add ucx dependency (#13921)Ken Raffenetti1-2/+7
2019-11-27cuda: add polymorphic package versions (#13912)Federico Ficarelli1-24/+41
2019-11-27scm-git-archive python package (#13915)Marc Mengel1-0/+24
* scm-git-archive python package * flake8 * per comments
2019-11-27New package: py-cheroot (#13583)Marc Mengel1-0/+25
* package py-cheroot * package py-cheroot * autopep8, docutils cleanup * Update var/spack/repos/builtin/packages/py-cheroot/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * missing deps * flake8 * license bits * Update var/spack/repos/builtin/packages/py-cheroot/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-cheroot/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-cheroot/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-cheroot/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * python dep * flake8
2019-11-27openmpi: add 3.1.5 and 3.0.5 (#13918)Howard Pritchard1-0/+2
Note to spack people: these are expected to be end of line releases for both the 3.1.5 an 3.0.5 releases Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2019-11-27json-fortran: get unit tests working (#13919)Adam J. Stewart1-0/+8
2019-11-27Fix py-pyarrow recipe (#13914)iarspider1-1/+1
Fix name of one dependency
2019-11-27accfft: fix narrowing error. (#13909)t-karatsu2-0/+14
2019-11-27Bump intel compiler suite to 2019u5. (#13835)健美猞猁4-0/+7
* Bump intel compiler suite to 2019u5. * Remove a duplicate line.
2019-11-27Fix py-line-profiler incompatible decorators (#13911)Oliver Breitwieser1-1/+4
`@run_after` and `@when` are incompatible, issue #12736.
2019-11-27ACTS: added version v0.11.1 (#13910)Hadrien G1-0/+1
2019-11-26Add version check when building intel-tbb with clang (#13893)Tim Haines1-0/+10
* Add version check when building with clang * Update for flake8 formatting
2019-11-26votca: help concretizer (#13906)Christoph Junghans3-6/+5
* votca: help concretizer * flake8
2019-11-26add new package : sysstat (#13907)darmac1-0/+21
2019-11-26use semicolons instead of newlines in module/python command (#13904)Greg Becker1-1/+1
2019-11-26IntelPackage: setup_env -> setup_build_env (#13888)Adam J. Stewart3-49/+26
2019-11-26buildcache list: do not display duplicate specs (#13758)Massimiliano Culpo2-6/+25
fixes #13757
2019-11-26metabat: add versions 2.14 and 2.13 (#13369)Eric Martin1-2/+4
* metabat: add versions 2.14 and 2.13 * update build environment * Update var/spack/repos/builtin/packages/metabat/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/metabat/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-26MPark.Variant: Patch NVCC C++14 Build (#13901)Axel Huebl2-0/+30
Fix an issue with NVCC when building with C++14.
2019-11-26update py-nbconvert (#13422)Andreas Baumbach1-5/+20
* update py-nbconvert * add setuptools dependency, like all the other jupyter packages it seems to be using setuptools for some commands all the time but requires it for the newest version * added dependencies, not necessarily only needed for the latest one * depends on new packages (defusedxml, pandocfilters, testpath) * should also be moved to pypi sources? * '@5:@5:' is a valid spec -> intended? * make dependencies optional * Update dependencies and add description * relax py-mistune dependency restriction * Update var/spack/repos/builtin/packages/py-nbconvert/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-26new package: py-arrow (#13575)Andreas Baumbach1-0/+28
* new package: py-arrow * actually use dependencies from 0.14.7 not from current HEAD * drop dependencies that dont appear in the source * readd sphinx as doc dependency * update dependencies * drop doc-only dependencies
2019-11-26Update Mathematica recipe (#13679)Roman Briskine1-1/+15
* Add licensing; replace url with url_for_version; create .spack dir during installation; symlink wolframscript; generate spec.yaml if missing * Reverted url change, .spack directory creation, and spec.yaml generation * Fix formatting issues
2019-11-26ocaml: fix url (#13749)noguchi-k1-1/+1
2019-11-26Days since OpenMPI+UCX trashed my cluster: 0 (#13818)sknigh2-0/+255
2019-11-26silence vtkm logging until it does not report false positives to std::cerr ↵Matt Larsen1-1/+1
(#13845)
2019-11-26add new package : busybox@1.31.1 (#13871)darmac1-0/+28
* add new package : busybox@1.31.1 * 1. add some other version for busybox 2. change Busybox class to MakefilePackage 3. move make('defconfig') and make() to build() function 4. change install_tree('', prefix) to install_tree('.', prefix)
2019-11-26add new package : blktrace (#13872)darmac1-0/+31
* add new package : blktrace * modify install_tree('', prefix) to install_tree('.', prefix)
2019-11-26lsof: fix url and checksum (#13801)noguchi-k1-2/+5
* lsof: fix url and checksum * lsof: change the download url, add list url and version 4.91, 4.90
2019-11-26Remove warning from the "Custom Extensions" section of the docs (#13804)Massimiliano Culpo1-6/+0
Extensions have been available for a while and the overall design seems solid enough to be feasible for extensions without losing backward compatibility.
2019-11-26Package Index: Build in Dockerhub (#13810)Axel Huebl9-87/+75
* Package Index: Build in Dockerhub Prepare to build the package index service, packages.spack.io, on Dockerhub. Local build (in spack root dir): ``` docker build -t spack/packages.spack.io:latest -f share/spack/docker/package-index/Dockerfile . ``` Local test: ``` docker run -p 8080:80 spack/packages.spack.io:latest ``` * Travis-CI: Remove Docker Remove leftover docker stages from Travis-CI. * Simplify Split Call
2019-11-26Bump miniconda2 miniconda3 to 4.7.12.1 . (#13897)健美猞猁2-0/+2
2019-11-26Variant for enabling tests, versions, cleanup (#13882)Rao Garimella1-33/+52
* add variant for enabling testing * enable tests and clean up other options * add numbered versions * updates to avoid enable_tests variant; correct versioning * fixes for style * appropriate partitioners are enabled if 'all' is specified - so no need to check in spec * define url so spack knows how to fetch the tar.gz files for different versions
2019-11-26Updating package for SOLLVE (#12607)Vivek Kale1-0/+274
* Add SOLLVE package with Shintaro's help on rebasing. Co-authored-by: Vivek Kale <vivek.lkale@gmail.com> * sollve: reflect suggestions by @adamjstewart * sollve: update target detection Copied from llvm/package.py. * sollve: fix a few things - url -> git - remove git in version() - explicit cmake options in else clauses - add newlines for better readability
2019-11-26Py-pymol package has been updated to the latest version (#13764)Hector Martinez-Seara2-13/+31
* Added new package libmmtf-cpp required by py-pymol * Added SPDX-License-Identifier to MIT * Updated py-pymol to version 2.3.0 * py-pymol: Added mising py-pmw dependency * py-pymol: flake8 minor change * py-pymol: Added patch for apbstools_tcltk8.6 This patch is borrowed from archlinux https://bugs.archlinux.org/task/39526 * libmmtf-cpp: flake8 compliance * libmmtf-cpp: flake8 compliance * libmmtf-cpp: change license to (Apache-2.0 OR MIT) when refering to the MIT license * libmmtf-cpp: Added header text about license as in examples * py-pymol: removed unnecesary dependency mesa-glu * py-pymol: removed unnecesary patch * py-pymol: Removed empty line at the end of the file to comply with flake8.
2019-11-26cmake: add support for xlf and ninja (#13796)Christoph Junghans1-0/+4
2019-11-26httperf: added new package (#13875)darmac1-0/+26
2019-11-25Add the py-coloredlogs package (#13852)Joe Koning1-0/+18
* Add the py-coloredlogs package * Remove extraneous line. * Remove dashed line. * Add version for humanfriendly dep and build to type. * Change source url to use pypi.
2019-11-25Forgot a trailing _PLUGIN (#13884)Hadrien G1-1/+1
2019-11-25add new versions to py-mistune (#13887)Andreas Baumbach1-0/+8
2019-11-25Add intel-tbb versions 2019.5 to 2019.8 (#13891)Tim Haines1-0/+4
2019-11-25Improved library access for lm-sensors and implemented use in papi. (#13885)G-Ragghianti2-4/+11
* Improved library access for lm-sensors and implemented use in papi. * Fixed comment formatting * Removed explicit "None" from return of libs(). * Added two new software release versions.
2019-11-25add package cuda@10.2.89 (#13819)René Widera2-5/+16
* add package cuda@10.2.89 add CUDA 10.2 support * CudaPackage: Add 10.2 Conflicts * CUDA: Modernize Run Environment See #11115
2019-11-25Updated LAMMPS package to use gpu and kokkos options. (#13886)David M. Rogers1-2/+25
2019-11-25Fix ROOT dependencies (for +r variant) (#13839)iarspider1-2/+2
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