PR #13975 added makefile filtering to replace gcc/g++ with the spack
compiler. This conflicts with other filtering that is done in the package to
add paths for dependencies. The text of the dependency paths might
have 'gcc' in the path name, depending on the install_path_scheme, and
that was being replaced by the new compiler filters. That would mangle
the path to the dependecy resulting in a failed build.
This PR moves the compiler filters to be before the other filters to
make sure that the compiler is set before the dependency paths.
* Add missing dependency on setuptools to py-subprocess32
* Update package.py
* Update var/spack/repos/builtin/packages/py-subprocess32/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
PR #10589 introduced a libiconv dependency to doxygen. This causes
problems on Linux systems, since the iconv symbols are included in libc,
which causes CMake to use the external header but not the external
library. Work around this by always using the external libiconv.
The xed CLI is handy, and can be gotten by building the examples in the
intel-xed package. This PR builds the examples and installs the xed CLI.
It would also be possible to install more of the example binaries if
someone thinks they are useful.
* openmolcas: new package at 19.11
* openmolcas: fill description
* openmolcas: rewrite using CMakePackage
* openmolcas: add py-six dep
* openmolcas: use setup_build_environment, setup_run_environment
* openmolcas: remove redundant cmake dep
* openmolcas: explicitly cast Executable to str
Recent commit e9ee9eaf (#13989) fixed testing version ranges inside
patch when clauses. Previously, it was necessary to write all revs
individually for packages with multiple length version numbers (2019
and 2019.1).
This fixes the build for the old 2017.* versions.
* elpa: port to microarch
* flake8
* Update package.py
* Update var/spack/repos/builtin/packages/elpa/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Adding libid3tag package for supporting feh
* Adding libexif package for supporting feh
* Adding imlib2 package for supporting feh
* Adding the feh package
* Rewording the cleanup function for libid3tag
* Fixing some flake8 issues for imlib2 and libid3tag
* Adding sources for the patches and swapping rm for os.remove
* Flake8 fixes
* swapping md5sums for sha256sums
* CUDA HeaderList: Unit Test
* Spec Header Dirs: Only first include/
Avoid matching recurringly nested include paths that usually
refer to internally shipped libraries in packages.
Example in CUDA Toolkit, shipping a libc++ fork internally
with libcu++ since 10.2.89:
`<prefix>/include/cuda/some/more/details/include/` or
`<prefix>/include/cuda/std/detail/libcxx/include`
regex: non-greedy first match of include
Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* CUDA: Re-Enable 10.2.89 as Default
* ibm-java: add version 8.0.6.0
Add version 8.0.6.0 and remove 8.0.5.30. IBM is fairly aggressive
about removing old versions, and 8.0.5.30 is no longer available from
their download site.
* Restore version 8.0.5.30, although it is no longer available for
download from IBM.
* Addition of repository branches to maestrowf.
* Addition of 1.1.5dev pre-release.
* Correction of a merge conflict.
* Addition of Maestro release 1.1.5
* Addition of Maestro release 1.1.6 (removal of 1.1.5)
* Sets 1.1.6 to the preferred version.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Tweak to the url to point to latest.
* Fix Apex and OTF2 support
- Comment out apex as a dependncy: it is bundled with HPX.
- Apply a patch to v1.3.0 to correctly build with APEX.
- Add otf2 as a dependency when APEX is enabled.
* Remove depends_on('apex')
* augustus: Set compile commands for each compiler and Fix for using 'boost' on Spack
* fix for flake8
* delete 'string' args
* Fix args of filter_file func
* Fix args of other filter_file func
* Add patch to fix issue building current llvm develop master on power9
* Conform to proper block commenting
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add tensorflow
Change-Id: Id778c68d148cc42f0b478a9d10a8f937cb54cdc6
* make bazel and tensorflow build
Change-Id: Iae9005e8f4dcc8f1ed36ea9337d2430aeebb291f
* fix flake8
Change-Id: Ib05529dd796eab4a8855a5d7775cc4efea8e479d
* 2nd flake8 attempt
Change-Id: I46224be3a374b2a65793048b0c5178ea64adbd78
* replace md5 sums with sha256
* add version 1.13.2
* bazel() -> bazel('build',...
* specify versions of bazel dependency
* build with CUDA
* add TODOs
* add more todo"s
* improve enum34 dependency
* py-future is a dependency as of v1.14
* Update var/spack/repos/builtin/packages/tensorflow/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/tensorflow/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/tensorflow/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/tensorflow/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* enable nccl, cuda by default
* explain patches
* add todo
* remove unnecessary copt_flag
* use join
* join argument must be an iterable
* split long line; use same opts for non-cuda build
* without opt flags, configure hangs
* introduce build phases; re-arrange
* undo mistake
* restore unset tmp_path
* as of v1.14, nccl_install_path is parsed correctly, hence change ...prefix.lib to ...prefix
* now, version 1.14 compiles successfully with cuda
* add version 2.1.0
* specify bazel dependency for version 2.1.0-rc0
* account for deprecated bazel opts for v2.1.0-rc0
* disable mkldnn contraction kernel
* Flake8 fixes
* md5 -> sha256
* Fix TF and TF-estimator version deps
* Don't just comment out patch
* Add myself as a maintainer
* Patch py-astor to support newer py-setuptools
* Add more versions and bazel version constraints
* Add a build phase
* Add note about configure interactivity
* dev-build -> build-env
* Disable iOS build
* Use correct optimization flags
* Add variants for all possible features
* nccl isn't always a dependency
* Specify correct dependency versions for each release
* Libs may not be in lib or lib64
* Add py-opt-einsum package
* Add newer version of py-protobuf
* Add newer version of py-wrapt
* Fix Python 2.6 syntax error
* Code review
* Set more env vars for older versions
* Add more env vars, fix bazel versions, add conflicts
* Fix config options
* Specify version that support --config args
* Add py-future dependency for Python 2
* Fix cuda config flag and compute capabilities
* Fix installation on macOS, add unit tests
* Override cuda variant default to True on non-macOS
* Rename tensorflow to py-tensorflow
* Has to extend something
* Fix os.symlink call
* convert cuda_arc values to capabilities
* restore nccl prefix path for v1.13.1
* Revert to v2
* Remove extraneous period
* Add new version of jdk/openjdk
* More stable cuda_arch formatting
* Fix bazel unit tests
* Fix symlinking
* Fix unit tests
* +gcp by default until build error figured out
* apply strict constraint checks for patches, otherwise Spack may incorrectly treat a version range constraint as satisfied when mixing x.y and x.y.z versions
* add mixed version checks to version comparison tests
* package for Simmetrix SimModSuite
* simmodsuite: passes flake8
* simmetrix: add version, set cmake prefix path
A given install will either use the libs built on rhel7 or rhel6.
For now, I'm sticking with the non-spack install convention of
placing the libraries into sub-directories named according to their
build process (os + compiler).
* simmetrix: add older version
* simmetrix: set build env paths
easier to build pumi using CMAKE_PREFIX_PATH
* simmetrix: address review comments
* simmetrix: add new version and remove old one
* simmetrix: flake8 fixes
* simmodsuite: oslib var is in self
* simmodsuite: update version and checksum
* simodsuite: set LD_LIBRARY_PATH for cad kernels
* update license
* update setup_environment calls
* increase indentation for flake8
* python3.8 flake8 fixes
* use spack consistent naming
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* sha256 required, update versions and hashes
* Added build dependency on gawk
* Use virtual depdendency
* Added patch to prepare libgpg-error for use with gawk@5
* Added reasoning with link for need for patch
* Add a transaction around repeated calls to `spec.prefix` in the activation process
* cache the computation of home in the python package to speed up setting deps
* ensure that module-scope variables are only set *once* per module
* amber: Improved package.py and added version 18
- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()
* dealii: Added 'threads' variant that controls the TBB dependency (#13931)
* dealii: Added 'threads' variant that controls the DEAL_II_WITH_THREADS cmake option and the dependency on Intel TBB
* Update var/spack/repos/builtin/packages/dealii/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* amber: Improved package.py and added version 18
- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()
* amber: Adding missing flex and bison dependencies
* Removed cray variant; flex and bison now build only
* amber: Improved package.py and added version 18
- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()
* amber: Adding missing flex and bison dependencies
* Removed cray variant; flex and bison now build only
* dealii: Fixed flake8 issues
* amber: corrected typo
* amber: Removed unused variant python
* dealii: Added 'threads' variant that controls the DEAL_II_WITH_THREADS cmake option and the dependency on Intel TBB
* Update var/spack/repos/builtin/packages/dealii/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Created an initial recipe for Sensei
* Cleanup syntax
* Small fixes for the Sensei recipe
* Cosmetic fixes to comply with PEP8
* More cosmetic fixes before PR
* Added more documentation before PR
* Fixed flake8 errors
* Fixes following PR review
* Fixes to pass Flake8 passes
* Some changes following PR review and support for SENSEI 3
* Update var/spack/repos/builtin/packages/sensei/package.py
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Fixed Flake8 errors
Commit 78724357 added versions 2019.5 to 2019.8 but failed to update
the patches for these versions.
1. gcc_generic-pedantic patch -- include this up through 2019.5. This
was fixed in the TBB source tree in 2019.6.
2. tbb_cmakeConfig patch -- this needs to be modified (different file)
for 2019.5 and later.
3. tbb_gcc_rtm_key patch -- replace this with filter_file. This is
simpler and eliminates the need to update the patch whenever the
surrounding context changes.
* dont add perl bin directory to PATH when setting up env (this is already handled by spack core in a way that omits system dirs); also consolidate repeated logic between build/run env setup.
* the bin/ dir of each dependency is already added to PATH in Spack core, so there is no need to do this in the Perl package
* 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>
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.
* 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>
* 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
