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2018-06-06Add new package: rngstreams (#8395)Javier Cervantes1-0/+34
* Add new package: rngstreams * Remove unnecessary list_url
2018-06-06xsimd: test type (#8405)Axel Huebl1-1/+9
Add the new type 'test` to the `googletest` dependency of xsimd.
2018-06-06Add new package: prng (#8396)Javier Cervantes3-0/+243
* Add new package: prng * Add missing dependencies and use force_autoreconf option * Add dependency types
2018-06-06Fix ADIOS 1.13.1: Maxium SZ (#8408)Axel Huebl1-2/+2
Fix the maximum accepted SZ version for the latest ADIOS release.
2018-06-06numpy: nosetest (#8404)Axel Huebl1-3/+1
the type 'test' exists now :-)
2018-06-06ISAAC Server 1.3.3 (#8403)Axel Huebl1-0/+1
Forgot to bump this package with the library release.
2018-06-06Trilinos update (#8363)Andrey Prokopenko1-5/+75
* trilinos: add more package conflicts This was done by putting in required lib dependencies from each package's `cmake/Dependencies.cmake`. * trilinos: added few more trilinos packages * trilinos: hiccup fix
2018-06-06r-splitstackshape: Create new package. (#8370)lingnanyuan1-0/+47
* r-splitstackshape: Create new package. * r-splitstackshape: Add version constraints. * add list_url and change dependency type.
2018-06-06add 1.4.13.4 for SZ (#8375)Sheng Di1-1/+2
* add 1.4.13.4 for SZ * undo spack link (change llnl/spack to spack/spack) and change .zip to .tar.gz * revise package.py for SZ 1.4.13.4 based on Adam's comments.
2018-06-06py-mpmath: added version 1.0.0 (#8382)Massimiliano Culpo1-2/+3
* py-mpmath: added version 1.0.0 * Fixed checksum for version 0.19
2018-06-06py-scikit-learn: added version 0.19.1 and updated dependencies (#8399)Massimiliano Culpo3-0/+3
py-numpy: added version 1.14.3 py-scipy: added version 1.1.0
2018-06-06py-theano: added version 1.0.2 (#8400)Massimiliano Culpo1-0/+1
2018-06-05py-sympy: added version 1.1.1 (#8381)Massimiliano Culpo1-1/+2
2018-06-05py-cython: added version 0.28.3 (#8379)Massimiliano Culpo1-0/+1
2018-06-05Added py-pip 10.0.1 and py-setuptools 39.2.0 (#8377)Massimiliano Culpo2-0/+2
2018-06-05py-virtualenv: added version 16.0.0 (#8380)Massimiliano Culpo1-0/+1
2018-06-04added line 43 (#8369)Daniel Topa1-0/+1
version('1.4.1.2', '38c7d33210155e5796b16d536d1b5cfe') Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2018-06-04clean up version names (#8368)Daryl W. Grunau1-6/+6
2018-06-04New package: phast (#7993)Yifan Zhu1-0/+58
* adding partially completed recipe for phast. will need clapack as dependency * try to install phast * seems to still need CLAPCK * using CLAPACK instead * phast: updated * fixed flake8 error * phast cannot build with clapack built with external blas? * phast: depend on clapack built without external blas * fixed flake8 errors * phast: updated build_directory
2018-06-04New package: clapack (#7992)Yifan Zhu1-0/+63
* clapack: new package * clapack: updated edit phase and fixed flake9 errors * clapack: added description for variant * clapack: updated * removed .package.py.swo
2018-06-04pybind11: test functionality (#8304)Axel Huebl1-1/+5
* pybind11: test support Add a test functionality to pybind11. * CMake: test also on "make check" Some projects use non-CTest manual targets for tests.
2018-06-03Add branch with bugfix (#8355)Mario Melara1-0/+3
2018-06-02add 2.17.1 for git (#8316)healther1-1/+6
2018-06-02legion: version bump (#8352)Christoph Junghans1-0/+2
2018-06-02cmake: update version (#8357)Matthias Diener1-0/+1
2018-06-01Fix digest for abyss@1.5.2 (#8341)George Hartzell1-2/+2
* Fix digest for abyss@1.5.2 The digest value for v1.5.2 appears to have changed. This value works for me, today. The existing value v2.0.2 works as is. * Use "download" URL for ABYSS Following the suggestion of the project team, switch to using the release tarballs from the "download" URL instead of the automagically generated ones at the "archive" URL. Converstation here: https://github.com/bcgsc/abyss/issues/232
2018-06-01added avro and avro_json_serializer python packages (#8351)Gregory Lee2-0/+74
2018-06-01added py-cffi 1.11.5 (#8349)Gregory Lee1-0/+1
2018-06-01make provision to install version 6.4.0beta.2 (#8338)Daryl W. Grunau1-1/+2
* make provision to install version 6.4.0beta.2 * drop flang.patch for the newer version per junghans
2018-06-01gmake: fix build with glibc 2.27 (#8344)Michael Kuhn1-0/+10
Also add an nls variant for gettext support.
2018-06-01Adding nektar++ package (#8167)Mayeul d'Avezac1-0/+75
* Adding nektar++ package * - -> ~ and add explicit conflict with metis * Add messages explaing nektar's conflicts
2018-06-01subread: use compiler wrappers when compiling (#8328)Massimiliano Culpo1-0/+5
2018-05-31Added dependency for hdf5 version number (known incompatibility with 1.10). ↵Nate Roberts1-0/+1
(#8337)
2018-05-31Use GitHub URL for pigz, supports > 1 release (#8339)George Hartzell1-2/+3
The URL that we were using for pigz only provides the current version. When the author released v2.4 the package became uninstallable (unless you have the tarball cached). It turns out that their are tarballs of the tagged source tree available on GitHub and they're sufficient to build things (no additional bits needed). This commit switches the URL to the GitHub archive URL. Sadly, this changes the v2.3.4 digest, but that version was no longer available/install-able anyway, so "net-net we're still in positive territory".
2018-05-31Add missing expand=False for v2.18.3 (#8342)George Hartzell1-1/+1
Installing the current version of Picard fails with: ``` ==> Error: Unable to parse extension from https://github.com/broadinstitute/picard/releases/download/2.18.3/picard.jar. If this URL is for a tarball but does not include the file extension in the name, you can explicitly declare it with the following syntax: version('1.2.3', 'hash', extension='tar.gz') If this URL is for a download like a .jar or .whl that does not need to be expanded, or an uncompressed installation script, you can tell Spack not to expand it with the following syntax: version('1.2.3', 'hash', expand=False) ``` Fix it, but adding `expand=False`, like the other versions.
2018-05-31fix missing -lrt for Centos6, issue: #7552 (#7597)Sinan1-1/+4
* fix missing -lrt for Centos6, issue: #7552 * fix missing -lrt for Centos6, issue: #7552 * fix using make() as opposed to patching * remove patch, as the fix is provided withing package.py instead * make flake8 happy
2018-05-31latte: specify blas and lapack explicitly (#8327)Massimiliano Culpo1-0/+5
2018-05-30trimgalore: Use perl from env (#8318)Eric1-0/+2
2018-05-30fastqc: Add version 0.11.7 (#8319)Eric1-0/+1
2018-05-30Update package: add info for emacs@26.1 (#8302)George Hartzell1-2/+7
* Update package: add info for emacs@26.1 In addition to the digest, it needs gnutls (perhaps there's a way to turn it off, but it seems like a Good Thing to encourage, so...). * Clean up tls variant handling - Don't to specify the dependency for @26.1:, just need to fix what's already there. - Don't assume that configure will DTRT w.r.t. gnutls when it's discovered in the environmnet, use explicit configure switches. - Clean up some unnecessary dependencies when +tls. Why would you need libxpm when building +tls? Will ask the original author about this. * Use append when adding configure switches * Add dependency on pcre When one builds +X, Spack's pcre is pulled into the build via the X dependencies. When one builds without it, the build discovers and links against the system library. We might as well just depend on it and have a consistent outcome.
2018-05-30paraview: set PARAVIEW_VTK_DIR in spack_env and run_env (#8308)Daryl W. Grunau1-0/+11
2018-05-29Add info for bedops@v2.4.35 (#8310)George Hartzell1-0/+1
2018-05-29new version: Phist 1.6.0 (#8312)jthies1-0/+1
* gmp: add oldish version 5.1.3 with checksum * new version phist 1.6.0
2018-05-29Add umpire package (#8229)David Beckingsale1-0/+61
* Add umpire package * Style fixes * Add package URL
2018-05-29perl: Fix build on Fedora 28 (#8305)Michael Kuhn1-0/+4
2018-05-29python: Update to 2.7.15 (#8306)Michael Kuhn1-1/+2
2.7.14 does not compile with GCC 8, see https://bugs.python.org/issue33374.
2018-05-29nasm: Fix compilation with GCC 8 (#8307)Michael Kuhn1-0/+4
2018-05-29Quantum espresso (#8183)nvarini3-9/+20
Changed the name from espresso to more appropriate quantum-espresso. Added github mirror.
2018-05-28py-pillow : update version and fix jpeg dependency (#8300)Sajid Ali1-14/+6
* modified: package.py * as requested.
2018-05-28Add far variant to openfst package (#8299)Jimmy Tang1-0/+11
* Add far variant * Append instead of extend