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2020-01-08Remove extensions from view in the correct order (#12961)Jeffrey Salmond2-17/+39
When removing packages from a view, extensions were being deactivated in an arbitrary order. Extensions must be deactivated in preorder traversal (dependents before dependencies), so when this order was violated the view update would fail. This commit ensures that views deactivate extensions based on a preorder traversal and adds a test for it.
2020-01-08fix build for qt5 and the Intel compiler (#14387)Glenn Johnson3-3/+35
* Set conflicts for qt5 and the Intel compiler This PR sets a `conflicts` statement for QT5 and the Intel compiler. * New patches for intel compiles This commit adds two patches to get QT5 to compile with the intel compilers. The two patches are very similar but the file being patched was changed substantially between qt-5.11 and qt-5.12. The patch checks versions of both GCC and Intel compilers to know when to use overflow builtis. Essentially, GCC must be >= 5 and Intel must be >= 18. The sqlite dependency needs the `+column_metadata` variant when the Intel compiler is used. That is made conditional on the compiler but it might make sense to make that the default for the sqlite dependency. Some other changes were made based on testing builds of various QT5 versions with several Intel compilers. - The libxext dependency is still needed for QT5 - A dependency on libxrender is needed - The gtk option format needs to be constrained at the qt@5.7 level, not qt@5.8. - An extra configure option is needed for the sql plugins RPATH
2020-01-08lrslib: fix return value (#14422)noguchi-k2-0/+40
2020-01-08cmake: Create an optimized release build (#14414)Chuck Atkins1-1/+8
2020-01-08Adding a new package, scikit-build, which is useful for building Python ↵Corey adams1-0/+27
Extensions (#14417) * Adding a new package, scikit-build, which is very useful for building python extensions * Update package.py * Update package.py Trying to address flake8 corrections * Update var/spack/repos/builtin/packages/py-scikit-build/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-scikit-build/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-08spack.compilers.clang: add new version check (#14365)Tim Haines2-1/+11
2020-01-07hpcviewer: add version 2019.12 (#14419)Mark W. Krentel1-0/+9
Add conflicts for aarch64 and darwin.
2020-01-07Record a new ROOT/GCC incompatibility (#14371)Hadrien G1-0/+4
2020-01-07py-rapidjson: new package at 0.9.1 (#14280)Justin S1-0/+18
* py-rapidjson: new package at 0.9.1 * py-rapidjson: rename to py-python-rapidjson, use PyPI mirror * py-python-rapidjson: add missing deps * python-rapidjson: use short PyPI url * py-python-rapidjson: remove extra dependencies
2020-01-07r-ldheatmap: new package at 0.99-7 (#14405)Justin S1-0/+22
2020-01-07NumPy 1.18.1 requires Cython 0.29.14 (#14418)Adam J. Stewart2-2/+5
2020-01-07Package/opencv: cudacodec fix (#14409)Sinan1-0/+8
* create new variant, fix build error * flake8 * add conflict, re-arrange config arg for cudacodec
2020-01-07bugfix: Issue #14346, buildcache create s3 push fails when package w same ↵eugeneswalker1-1/+1
DAG hash already exists at mirror (#14412)
2020-01-07gdb: add version 8.3.1 (#14413)Matthias Diener1-0/+1
2020-01-07ncl: Add missing fontconfig dependency (#14411)Michael Kuhn1-1/+3
Moreover, cairo needs to have its freetype variant enabled.
2020-01-07gdal: Fix libgeotiff dependency (#14410)Michael Kuhn1-1/+1
gdal@2.4.3 is missing the libgeotiff dependency.
2020-01-07Spack can automatically remove unused specs (#13534)Massimiliano Culpo7-7/+193
* Spack can uninstall unused specs fixes #4382 Added an option to spack uninstall that removes all unused specs i.e. build dependencies or transitive dependencies that are left in the store after the specs that pulled them in have been removed. * Moved the functionality to its own command The command has been named 'spack autoremove' to follow the naming used for the same functionality by other widely known package managers i.e. yum and apt. * Speed-up autoremoving specs by not locking and re-reading the scratch DB * Make autoremove work directly on Spack's store * Added unit tests for the new command * Display a terser output to the user * Renamed the "autoremove" command "gc" Following discussion there's more consensus around the latter name. * Preserve root specs in env contexts * Instead of preserving specs, restrict gc to the active environment * Added docs * Added a unit test for gc within an environment * Updated copyright to 2020 * Updated documentation according to review Rephrased a couple of sentences, added references to `spack find` and dependency types. * Updated function naming and docstrings * Simplified computation of unused specs Since the new approach uses private attributes of the DB it has been coded as a method of that class rather than a freestanding function.
2020-01-06Fix outdated bash tab completion (#14392)Adam J. Stewart1-201/+321
2020-01-06Add py-numpy 1.18.1 (#14406)Adam J. Stewart1-1/+2
2020-01-06r-snpstats: new package at 1.34.0 (#14404)Justin S1-0/+29
2020-01-06r-genetics: new package at 1.3.8.1.2 (#14403)Justin S1-0/+22
2020-01-06Add updated kaldi and openfst (#14398)Thom Troy2-0/+3
* add openfst v1.6.7 and kaldi from 2019-09-29 * revert openfst package version in url
2020-01-06Add singularity@3.5.2 (#14401)George Hartzell1-0/+1
2020-01-06Fastdfs (#14378)darmac1-0/+35
* add new package : fastdfs * refine install() * remove redundant fastdfs/fastdfs/package.py * fix install() error
2020-01-06py-ujson: new package at 1.35 (#14279)Justin S1-0/+18
* py-ujson: new package at 1.35 * py-ujson: use PyPI mirror, add missing deps * py-ujson: use short PyPI url
2020-01-06Fix QT on Linux+clang (#13684)Seth R. Johnson1-33/+56
* Add platform flag to QT for linux+clang * Extend QT platform support to more compilers and systems * Unify QT5 configure options * fixup! Unify QT5 configure options * fixup! Unify QT5 configure options * fixup! Unify QT5 configure options * Fix newer flake8 and mac qt5 configure
2020-01-06Nsimd: New package (#14226)Erik Schnetter1-0/+65
* Nsimd: New package * Various cleanups as suggested during review
2020-01-06Reference `spack help --spec` in `spack spec --help`Adam J. Stewart1-0/+4
2020-01-05Add py-thirdorder recipe (#12791)asmaahassan901-0/+37
* Add Thirdorder recipe * Remove white spaces * Converting recipe to a PythonPackage base class * remove trailing spaces * remove line at end of file * enhance recipe as per reviewer * fix post_install as requested by reviewer * rename dir to py-thirderorder * change checksum to sha256
2020-01-04Overhaul py-pillow package (#14385)Adam J. Stewart1-51/+54
* Overhaul py-pillow package * Fix bug where zlib and jpeg were always disabled
2020-01-04libwebp: CMakePackage -> AutotoolsPackage (#14384)Adam J. Stewart1-7/+49
2020-01-04Adjust constraints of gcc-5 (#14388)Glenn Johnson1-1/+2
This PR adjusts the constraints on isl with GCC-5. GCC-5.1 and GCC-5.2 need isl-0.14, not isl-0.15.
2020-01-04Add libs property to openjpeg package (#14383)Adam J. Stewart1-0/+5
2020-01-04Add libs property to lcms package (#14382)Adam J. Stewart1-0/+4
2020-01-04py-torchvision 0.4.X does not support py-pillow 7.X.Y (#14381)Adam J. Stewart1-1/+3
2020-01-04environment-modules: add version 4.4.1 (#14379)Xavier Delaruelle1-1/+2
2020-01-04add new package : lucene (#14316)darmac1-0/+28
* add new package : lucene * update lucene version url
2020-01-04add new package : kafka (#14315)darmac1-0/+35
* add new package : kafka * move url_for_version after depens_on() * refine list_depth for kafka
2020-01-04add new package : tajo (#14314)darmac1-0/+36
* add new package : tajo * refine list_depth for tajo
2020-01-03py-intervaltree: new package at 3.0.2 (#14277)Justin S1-0/+19
* py-intervaltree: new package at 3.0.2 * py-intervaltree: fix checksum * py-intervaltree: add py-setuptools dep * py-intervaltree: use inclusive ranges * py-intervaltree: change py-test dep type
2020-01-03petsc: add version 3.12.3 (#14374)Satish Balay1-0/+1
2020-01-03new package: bref3 (#14256)xfzhao2-0/+50
2020-01-02Get py-numpy > 1.16 to build with Intel compiler (#14360)Glenn Johnson1-0/+23
Beginning with numpy > 1.16 when using older versions of gcc the `std=c99` flag must be used. The Intel compiler depends on gcc for its language extensions so the version of gcc is important. If the version of gcc used by the Intel compiler is one that requires the `-std=c99` flag then that flag will have to be used for a build with the Intel compiler as well. This PR tests the version of gcc used by the Intel compiler and will abort the build if the gcc version is < 4.8 and inject the `-std=c99` flag if >= 4.8 and < 5.1. This will cover the system gcc compiler and any gcc environment module loaded at build time.
2020-01-02package/opencv fix mistake in conflict statement involving gcc (#13959)Sinan1-4/+1
* fix mistake in conflict * extend CudaPackage to resolve cuda-gcc conflicts
2020-01-02Updated version to include v3.0.1 (#14353)Jonathan R. Madsen1-0/+2
* Updated version to include v3.0.1 - this patch has a rather critical MT fix * Update package.py - Moved 3.0.1 above 3.0.0
2020-01-02fix url for mantevo packages (#14366)Christoph Junghans9-9/+9
2020-01-02RHEL8 bugfix for module_cmd (#14349)Sajid Ali1-1/+2
2020-01-02Set preferred version of perl-bioperl (#14354)Glenn Johnson1-1/+3
Due to formatting differences, the older version of perl-bioperl was getting picked up as the preferred version. This PR explicitly sets the newer version to be preferred.
2020-01-02added verbose variant to mercury package (#14355)Matthieu Dorier1-0/+3
2020-01-02gromacs: depend on hwloc v1 (#14343)Gilles Gouaillardet1-1/+3
Because of a bug in the current concretizer, spack install gromacs fails because gromacs depends on hwloc (default is v2), and Open MPI (the default MPI library) depends on hwloc v1. As discussed in https://github.com/spack/spack/issues/14339, this workaround should be removed once the concretizer is fixed Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
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