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2019-09-08py-gpaw: Fixing missing numpy include path, adding newer version of p… ↵Simo Tuomisto2-3/+28
(#12737) * py-gpaw: Fixing missing numpy include path, adding newer version of py-gpaw and fixing a bug with libxc.c in older py-gpaw * py-gpaw: Fix Python and ASE version dependencies - GPAW 19.8.1 requires Python 3.x, add dependency on python@3.5: - GPAW releases are associated with a corresponding ASE release, add matching ASE version dependencies. * py-gpaw: Enable the scalapack variant by default GPAW installation instructions say scalapack is optional but "highly recommended". Thus enable it by default.
2019-09-08py-cutadapt: Updated version checksum (#12741)Owen Solberg1-2/+7
* add new cutadapt release 2.5, and adjust dependencies conditional on version * use https, not ssh, for git url Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-08new package: py-bz2file (#12761)Owen Solberg1-0/+15
* update py-xopen (add 0.8.2 checksum) * refine version specific dependencies add py-bz2file, which needs to be created * create py-bz2file * Revert "refine version specific dependencies" This reverts commit 70649da98851fefb2f936ca99a012fe6bef07b70. * Revert "update py-xopen (add 0.8.2 checksum)" This reverts commit 7400f44caa6e98419eb4bc3107704b91e8a2018b.
2019-09-08py-xopen: update release 0.8.2 checksum (#12742)Owen Solberg1-1/+4
* update py-xopen (add 0.8.2 checksum) * refine version specific dependencies add py-bz2file, which needs to be created * py-bz2file needed when built with python 2.7 Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * space after comma
2019-09-08py-dnaio: new package need by py-cutadapt (#12743)Owen Solberg1-0/+20
* add new package py-dnaio * provide git url with https, not ssh, protocol Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-07flake8: make entire repository pass `spack flake8 -a`Todd Gamblin61-292/+300
- Fix trailing whitespace missed by the bug described in #12755. - Fix other style issues that have crept in over time (this can happen when flake8 adds new checks with new versions)
2019-09-07patch boost version 1.54-1.55 when being built with ANY gcc version after ↵Owen Solberg1-1/+1
5.0 (#12718)
2019-09-07Updating TAU package. Fixing compiler specification for OSX (#12720)Kevin Huck1-5/+13
and making Fortran an option that can be disabled. Also added support for the POSIX I/O wrapper and OMPT for OpenMP.
2019-09-07mesa: disable use of libunwind for arm arch (#12735)Howard Pritchard1-0/+3
There are problems with libunwind for arm and trying to use it with mesa. See for example: https://github.com/grate-driver/mesa/issues/6 disabling use of libunwind for arm, allows the package to be built Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2019-09-07add mpi variant to p4est package to allow turning off MPI (#12739)Jonas Lippuner1-2/+7
2019-09-07ncurses: improve build time (#12621)Axel Huebl1-1/+3
Apply configure options to skip manpage generation and test builds for both wide and non-wide builts.
2019-09-07luarocks: Use `make` command instead of `install` (#12703)Ruben Di Battista2-2/+2
This way luarocks does not attempt to pull stuff from the internet. Fix #3909
2019-09-07Add py-numpy 1.17.2 (#12753)Adam J. Stewart1-1/+2
2019-09-07Add patches to work around CMake versions (#12744)Piotr Luszczek3-0/+38
- Use of symbol testing macro requires explicit include() - CMake policies are not version-portable and the support has to queried based on CMake version
2019-09-07font-util 1.3.2 (#12728)Owen Solberg1-0/+1
2019-09-07new package: py-pygdal (#12747)Sinan1-0/+31
2019-09-07adding shadow-uidmap (#12750)Vanessasaurus1-0/+18
Signed-off-by: Vanessa Sochat <vsochat@stanford.edu>
2019-09-06upcxx: new packageMathias Jacquelin1-0/+89
Adding a UPC++ spack package pointing to the default 2019.3.2 UPC++ version, and allowing to build UPC++ with the experimental CUDA variant.
2019-09-06openspeedshop: fixed build on arm. (#11861)Toyohisa Kameyama4-0/+52
* openspeedshop: fixed build on arm. * remove patch comment.
2019-09-06libpeas@1.22.0: new package (#12385)Geoffrey Oxberry1-0/+107
* libpeas@1.22.0: new package * libpeas: note more build dependencies Build and link dependencies were obtained through a combination of examining the `config.log` file from `configure` and looking at the pkg-config files of `libpeas`. * libpeas: add search path for GIR/typelib files
2019-09-06iso-codes: new package (#12389)Geoffrey Oxberry1-0/+23
2019-09-05fftw: change default value of simd variant for other than x86_64 (#11627)Toyohisa Kameyama1-1/+38
* Use spec.architecture.target insted of platform. * remove default in simd variant value. simd variant change to archtecture independent values. * Add check simd values. * rewrite check simd values. * * flake8 * change aarch64 to arm (neon support only 32 bit arm.)
2019-09-05FIX Catalyst: corrected catalyst package for aarch64 targets (#12707)Matthieu Dorier1-0/+5
* corrected catalyst package for aarch64 targets * corrected syntax * corrected undefined variable
2019-09-05Add pixz package (#12698)Ruben Di Battista1-0/+18
2019-09-05[jemalloc] added version 5.2.1 (#12706)Jennifer Herting1-0/+1
2019-09-05textparser: new package (#12713)Hironori-Yamaji2-0/+112
* textparser: new package * textparser: use 'parallel = False'
2019-09-05mariadb: Add missing dependencies (#12715)Michael Kuhn1-0/+7
Found while building mariadb in a minimal build environment.
2019-09-05py-ase: New version 3.18 (#12697)Janne Blomqvist1-1/+7
* py-ase: New version 3.18 Add ASE version 3.18. ASE 3.18 has dropped support for python 2.x, hence add a dependency on python@3.5: for it. * Add more ASE dependencies Address review comments, add dependencies on py-scipy, py-matplotlib, py-flask, and also add type=('build', 'run') dependency specifiers.
2019-09-04cctools: fixed to build on ARM. (#11862)Toyohisa Kameyama2-0/+29
2019-09-04Add Go 1.13Paul Bryant1-0/+1
2019-09-04openblas: Add route to f_check for Fujitsu compiler. (#11804)t-karatsu2-0/+17
2019-09-04Add gams recipe (#12700)asmaahassan901-0/+37
* Add gams recipe * Break down lines to pass lint
2019-09-04boost: add -c option to C/C++ compile commands for clang. (#12694)t-karatsu3-0/+44
2019-09-04cppflags point to ncurses headers (#12691)Mario Melara1-0/+5
While debugging this package on our Cray machine, tmux was throwing an error involving the ncurses headers. Tmux would look for headers in system locations rather than where spack installed ncurses. Tested only on a Cray.
2019-09-04Add tecplot recipe (#12688)asmaahassan901-0/+30
* Add tecplot recipe * break down description to pass lint * fix format to match python 2.6 requiremnets * importing os
2019-09-04Boost: fixed problem when requesting ~signals for boost >= 1.69 (#12627)Matthieu Dorier1-7/+7
* fixed problem when requesting ~signals for boost >= 1.69 * added checks for all libs in with_libs
2019-09-04new package: liblas (#12619)Sinan1-0/+54
* new package: liblas * explicitly disable build options * fix indentation
2019-09-03py-chardet package: add py-pytest-runner dependency (#12692)Peter Scheibel1-0/+1
This required dependency was missing
2019-09-03new package: protobuf-c (#12634)Sinan1-0/+20
* new package: protobuf-c * Update var/spack/repos/builtin/packages/protobuf-c/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-03Boost/Change the method for analysis version (#12676)t-karatsu2-0/+14
* boost:Change the method for analysis version when using Fujitsu compiler. * Change version to apply patch for Fujitsu. * fix typo
2019-09-03pmlib: new package (#12625)Hironori-Yamaji2-0/+132
* pmlib: new package * pmlib: fix options and add patch * pmlib: fix the patch file
2019-09-03ccs-qcd: new package (#12681)Hironori-Yamaji1-0/+68
* ccs-qcd: new package * ccs-qcd: fix variant and replacement string
2019-09-02tests: add tests for `spack extensions` commandTodd Gamblin3-20/+4
- add tests for `spack extensions` - refactor `test_activations` test to use real extensions.
2019-09-02esmf: Fix build with gcc@8: (#12678)Michael Kuhn3-12/+161
2019-09-02Add XSSP recipe (#12679)asmaahassan901-0/+41
2019-09-02icu4c: Add missing python dependency (#12683)Michael Kuhn1-0/+7
2019-09-02Add fpocket (#12675)asmaahassan901-0/+26
* Add fpocket * fix recipe break down the description to pass lint * update license * make changes as per maintainer's review
2019-09-01Install the newest version of ncbi-rmblastn (#12580)asmaahassan902-3/+251
* Install the newest version of ncbi-rmblastn Version ncbi-rmblastn 2.2.28 coonfiguration fails for gcc compiler on ubuntu 16.04 due to some compatibility issues that requires manual intervention to keep the installation going. However you still stumble upon other issues while compiling it. Using Intel compiler passes the configuration step but fails for the compilation process as well. Here I'm using the latest version and patch, and the recommended configuration option as mention in http://www.repeatmasker.org/RMBlast.html * uploading ncbi-blast patch
2019-09-01IDBA: package does not need conflicts with other compilers (#12674)Kevin Manalo1-8/+0
2019-09-01Add Vesta recipe (#12581)asmaahassan901-0/+29
* Add Vesta recipe * Break down description to pass lint * Make changes as maintainers' review * remove whitespaces
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