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2017-09-21Use trusted/historic site for texlive installer (#5347)George Hartzell1-8/+11
* Make texlive untrusted TeXLive updates their installer without changing its name. We've been playing keep-up with them, but I'm proposing it's not worth it. I seem to end up installing it '--no-checksum' anyway. This commit updates the package to make that approach official, removing the checksum, adding a note to the description and a bigger note/comment inthe package body. * Pull installer from stable source (packages are still *live*) This pulls the installer script from the "historic" repository. It appears to be stable, so that we can use a checksum with it (one hopes, time will tell). The installer still pulls the packages from the live repos so installations aren't reproducible.
2017-09-21fix install method of cereal (#5094)healther1-9/+2
* removed unnecessary install method from cereal * attempt to fix flake8 error * adjusted install method * add CMake options instead of manually patching stuff * flake8
2017-09-21r-zlibbioc: new package (#5399)Yifan Zhu1-0/+38
2017-09-21r-biocinstaller: added version 1.26.1 (#5406)Yifan Zhu1-2/+4
2017-09-21dealii: add cuda support (#5402)BenBrands1-0/+17
2017-09-20Opencv: fix dependencies and variants (#5232)Brian Van Essen1-1/+2
Fixes #5159 * Added dependency on google protobuf when using v3.3.0. * Set default for variant core to be true.
2017-09-20latte: add v1.0.1 (#5403)Christoph Junghans1-0/+1
2017-09-20r-biobase: new package (#5398)Levi Baber2-11/+43
Add r-biobase package. Remove explicit R dependency from r-biocgenerics package (since it is an instance of RPackage). Update version for r-biocgenerics and remove github versions.
2017-09-20Add info for mono@5.4.0.167 (#5405)George Hartzell1-0/+1
2017-09-20r-survival: updated to version 2.41-3 (#5409)Yifan Zhu1-1/+3
2017-09-20[WIP]: Sambamba new package (#5304)George Hartzell2-0/+63
* First draft package for sambamba Depends on the ldc package (#5279) that alalazo's working on. It requires a patch to the Makefile because one of ldc's library functions mentions dlopen. I *think* that ldc should be handling this. See the discusssion in #5279. It also requires a "static" ldc. Again, see #5279. Finally, it needs "undeaD" as a resource, but I'm guessing at the appropriate release. See https://github.com/lomereiter/sambamba/issues/312. * alalazo renamed the shared_libs variant, keep up...
2017-09-20Update recipe for cgns to avoid build warnings/errors: (#5382)Kelly (KT) Thompson1-10/+3
+ The recipe for cgns seems to be wrong. CMake complains about variables set but not used (`HDF5_NEEDS_ZLIB`, `HDF5_NEEDS_MPI` and `HDF5_NEEDS_SZIP`) and fails to find HDF5. + This change set removes these variables from the cmake configure line, replacing them with `'-DHDF5_DIR=%s' % spec['hdf5'].prefix` + cgns also has trouble with parallel make, so I set `parallel = False`.
2017-09-20Rm arpack parpack (#5391)Mark C. Miller3-144/+1
* fixes #967 * Version bump to 0.9.1 - Bugfixes for spack find - 0.9.1 can read specs from current develop. * Don't assume spack is in the path when building docs. * fixing build issues for gcc on osx * reverting inadvertent change on develop * fixing typesetting of bsws description * very minor update to RTD docs footer to ref github contributors * Revert "very minor update to RTD docs footer to ref github contributors" This reverts commit c40d75da7f3b918350a263e7a9ef34df56b7fb01. * switch fastmath to depend_on arpack_ng; remove arpack/parpack
2017-09-20added Intel 2018 tools (#5404)Gregory Lee2-0/+8
2017-09-20mirdeep: new package (#5302)Audrey Thoma10-0/+387
2017-09-20orthomcl: new package (#5345)Audrey Thoma2-2/+51
Add orthocml package and fix mariadb url
2017-09-20tmhmm: new package (#5335)Audrey Thoma1-0/+56
2017-09-20bbmap: new package (#5396)Audrey Thoma1-0/+39
2017-09-19targetp: new package (#5334)Audrey Thoma1-0/+67
2017-09-19added p7zip package (#5394)sknigh1-0/+41
2017-09-19pr-quantities: add version & py-numpy conflict (#5307)healther1-2/+6
2017-09-19Modulefiles generated with a template engine (#3183)Massimiliano Culpo4-2/+85
* Module files now are generated using a template engine refers #2902 #3173 jinja2 has been hooked into Spack. The python module `modules.py` has been splitted into several modules under the python package `spack/modules`. Unit tests stressing module file generation have been refactored accordingly. The module file generator for Lmod has been extended to multi-providers and deeper hierarchies. * Improved the support for templates in module files. Added an entry in `config.yaml` (`template_dirs`) to list all the directories where Spack could find templates for `jinja2`. Module file generators have a simple override mechanism to override template selection ('modules.yaml' beats 'package.py' beats 'default'). * Added jinja2 and MarkupSafe to vendored packages. * Spec.concretize() sets mutual spec-package references The correct place to set the mutual references between spec and package objects at the end of concretization. After a call to concretize we should now be ensured that spec is the same object as spec.package.spec. Code in `build_environment.py` that was performing the same operation has been turned into an assertion to be defensive on the new behavior. * Improved code and data layout for modules and related tests. Common fixtures related to module file generation have been extracted in `conftest.py`. All the mock configurations for module files have been extracted from python code and have been put into their own yaml file. Added a `context_property` decorator for the template engine, to make it easy to define dictionaries out of properties. The default for `verbose` in `modules.yaml` is now False instead of True. * Extendable module file contexts + short description from docstring The contexts that are used in conjunction with `jinja2` templates to generate module files can now be extended from package.py and modules.yaml. Module files generators now infer the short description from package.py docstring (and as you may expect it's the first paragraph) * 'module refresh' regenerates all modules by default `module refresh` without `--module-type` specified tries to regenerate all known module types. The same holds true for `module rm` Configure options used at build time are extracted and written into the module files where possible. * Fixed python3 compatibility, tests for Lmod and Tcl. Added test for exceptional paths of execution when generating Lmod module files. Fixed a few compatibility issues with python3. Fixed a bug in Tcl with naming_scheme and autoload + unit tests * Updated module file tutorial docs. Fixed a few typos in docstrings. The reference section for module files has been reorganized. The idea is to have only three topics at the highest level: - shell support + spack load/unload use/unuse - module file generation (a.k.a. APIs + modules.yaml) - module file maintenance (spack module refresh/rm) Module file generation will cover the entries in modules.yaml Also: - Licenses have been updated to include NOTICE and extended to 2017 - docstrings have been reformatted according to Google style * Removed redundant arguments to RPackage and WafPackage. All the callbacks in `RPackage` and `WafPackage` that are not build phases have been modified not to accept a `spec` and a `prefix` argument. This permits to leverage the common `configure_args` signature to insert by default the configuration arguments into the generated module files. I think it's preferable to handling those packages differently than `AutotoolsPackage`. Besides only one package seems to override one of these methods. * Fixed broken indentation + improved resiliency of refresh Fixed broken indentation in `spack module refresh` (probably a rebase gone silently wrong?). Filter the writers for blacklisted specs before searching for name clashes. An error with a single writer will not stop regeneration, but instead will print a warning and continue the command.
2017-09-19adios: fixed conditional dependencies on libevpath and dataspaces (#5392)Massimiliano Culpo1-5/+3
fixes #5379
2017-09-18added python version 2.7.14 and 3.6.2 packages (#5389)Gregory Lee1-1/+3
2017-09-18HDF5: Fortran MPI needs Numactl (#5372)Axel Huebl1-0/+1
2017-09-18add variant gmock to googletest (#5278)healther1-1/+8
2017-09-18latte: fix url and add shared variant (#5358)Christoph Junghans1-4/+20
2017-09-18qmd-progress: add shared variant (#5381)Christoph Junghans1-0/+5
2017-09-18bml: add shared variant (#5380)Christoph Junghans1-0/+8
2017-09-18lammps: fix checksum (#5342)Christoph Junghans1-3/+7
2017-09-18Improve scorep package with different compilers and mpi providers (#5386)Pramod S Kumbhar1-3/+17
* Add --with-mpi=spec['mpi'].name at configure step to avoid error when finding 2 MPI implementations * Improve scorep package with different compilers and mpi providers
2017-09-18mesa: merge multiple branches into one (#5170)Milton Woods1-34/+102
Merge work from multiple contributors on the mesa package. This includes the following changes and decisions: * Added in mesa +hwrender support * make +swrender the default selection since this represents a very common usage case (ie, cluster usage) * leave ~llvm as the default, since inadvertently building this package could take a very long time. May need to revisit this assumption in the future since the performance difference can be quite substantial. * build libGLESv1+2 and libGL for all variants * avoid dependence on dri/libdrm when ~hwrender * disable gallium drivers if none are requested
2017-09-17Fix log error parsing bug introduced in c830eda0e (#5387)Todd Gamblin1-0/+49
- '\b' in regular expression needs to be in a raw string (r'\b') - Regression test that would've caught this was unintentionally disabled - This fixes the string and the test
2017-09-17tbb: add 2018 (#5359)Denis Davydov1-1/+2
2017-09-16Open MPI: add Open MPI 3.0.0 (#5360)Howard Pritchard1-1/+2
Open MPI 3.0.0 is released! Add to spack. Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2017-09-16trilinos: update md5 for 12.10.1 (#5362)Denis Davydov1-1/+1
2017-09-16New Pcakage: numactl (#5371)Axel Huebl1-0/+39
Adds the numactl tools and libnuma.
2017-09-16Feature/methycode (#5374)ynanyam3-0/+123
* methylcode: added package * pyfasta: added package * py-bsddb3: added package * py-bsddb3: added package * Update package.py * Update package.py * Update package.py * removed fixme comments * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py
2017-09-16Cntk: fixed dependency on protobuf fixes #5266 (#5267)Pramod S Kumbhar1-1/+1
As protobuf has been converted to CMakePackage, it doesn't have a 'shared' variant anymore.
2017-09-16augustus: url fix (#5311)Audrey Thoma1-2/+3
2017-09-16add Intel 2018 libraries (#5354)Denis Davydov4-0/+8
2017-09-16Bioawk: added new package (#5375)zenln1-0/+51
2017-09-16gromacs: added 2016.4 (#5376)Christoph Junghans1-0/+1
2017-09-15Update hpctoolkit and externals to latest releasePramod S Kumbhar2-8/+8
2017-09-15add new version to package py-pybind11healther1-0/+1
2017-09-15ncl: Fix buffer overflow in ymake-filter (#5357)Michael Kuhn2-0/+35
Fixes a problem in ymake-filter: The line buffer is currently hardcoded to be 2048 bytes large but some Makefiles contain lines longer than that. This caused the Makefiles to sometimes not be generated, consequently failing parts of the build.
2017-09-14Fix checksum of Intel TBB package (#5349)Pramod S Kumbhar1-1/+1
2017-09-14Added Support for NOX Package to Trilinos Spackage (#5366)Robert Pavel1-0/+4
Added support for building NOX package to Trilinis Spackage
2017-09-14ADIOS: Fix Build (Autotools) (#5363)Axel Huebl1-11/+23
This fixes the build of the ADIOS package. The `with_or_without` interface of the Autotools builds seems to have changed, this fixes it.
2017-09-14libsodium: update URLs (#5355)Axel Huebl1-1/+5
* libsodium: update URLs updates the URLs for libsodium releases. Fixes broken builds (404). * libsodium: add new version