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2017-09-26Autodock vina: spec (#5333)zenln3-0/+130
* Autodock vina: spec * Adding comment to patch. The implemnetation of boost is version dependent on older boost replacing depecrated function of boost. * Adding in boost version dependency
2017-09-26Add ability to build llvm-openmp-ompt alone, with gnu compilers and use the ↵Jim Galarowicz2-6/+38
resulting ompt interface in cbtf-krell and openspeedshop to gather openmp specific performance information. (#5288) * Update the krell institute products to use the latest features of spack for building on cluster platforms. * Address travis error messages and resubmit the pull request. * Update the contents of openspeedshop package.py so it passes the flake8 tests. * Fix flake8 error-whitespack issue in mrnet package.py file. * Add updates based on spack reviewer feedback. * More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH. * More review related changes. Update MPIOption.append lines and take out xercesc references. * Create a base options function for common openspeedshop base cmake options to reduce redundencies. * Add libxml2+python depends on to get around issues with the libxml2 package file. * Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build. * Fix bad syntax in specifying the boost version range. * Update the version numbers for the krell institute components and tools: cbtf and openspeedshop. * Do not build glib for qt3, it is not needed and causes build problems at this time anyway. * A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set. * Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH. * A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set. * Trim comments to fit more concisely. * Fix tabs versus spaces and swap if and else clause check from a negative to a positive check. * Add ability to build llvm-openmp-ompt alone, with gnu compilers and use the resulting ompt interface in cbtf-krell and openspeedshop to gather openmp specific performance information. * Fix flake8 errors. * Fix flake8 errors - stage 2. * Fixes based on reviewer suggestions and comments. * Use build_type variant to set the build type and allow changing of the type. * Fix missing comma in cmake_arg list, found on another test machine.
2017-09-26Set LANG= for _spack_fn_exists (#5475)Michael Kuhn1-1/+1
type's output can be localized, causing the grep to fail.
2017-09-26astyle: homepage dead, use mirror (#5483)Christoph Junghans1-1/+3
2017-09-26snappy: Update to 1.1.7 (#5477)Michael Kuhn1-4/+20
Convert to CMakePackage and add a pkg-config file (otherwise libmongoc's pkg-config file does not contain all required flags).
2017-09-26autoconf, automake: Add missing perl dependency (#5187)Michael Kuhn2-0/+30
* autoconf, automake: Add missing perl dependency * automake: Add 1.15.1
2017-09-26Missing perl dependencies (#5204)Michael Kuhn4-0/+29
* glib: Add missing perl dependency * shared-mime-info: Add missing perl dependency * libx11: Add missing perl dependency * likwid: Add missing perl dependency
2017-09-25r-limma: new package. (#5468)lingnanyuan1-0/+35
* r-limma: Create New Package. * pr-quantities: add version & py-numpy conflict (#5307) * r-limma: Create new package. * r-limma: Correct format. * Update package.py
2017-09-25r-affy: created new package (#5471)Yifan Zhu1-0/+44
2017-09-25r-genefilter: New package. (#5467)lingnanyuan1-0/+38
* r-genefilter: Create New Package. * r-genefilter: Create new package. * r-genefilter: Correct format. * Update package.py
2017-09-25r-xml: updated url and added version 3.98-1.9 (#5466)Yifan Zhu1-3/+4
* r-xml: updated url and added version 3.98-1.9 * Update package.py
2017-09-25r-multtest: new package. (#5469)lingnanyuan1-0/+36
* r-multtest: Create New Package. * pr-quantities: add version & py-numpy conflict (#5307) * r-multtest: Create new package. * r-multtest: Correct format.
2017-09-25r-plogr: new package. (#5443)lingnanyuan1-0/+36
* pr-quantities: add version & py-numpy conflict (#5307) * r-plogr:Create new package. * r-plogr: Correct format.
2017-09-25r-glmnet: update version. (#5470)lingnanyuan3-6/+10
* r-glmnet: Create New Package. * pr-quantities: add version & py-numpy conflict (#5307) * r-glmnet: Update version to 2.0-13 * r-matrix: Update version to 1.2-11 * r-lattice: Update version to 0.20-35.
2017-09-25r-pkgconfig: new package. (#5441)lingnanyuan1-0/+36
* pr-quantities: add version & py-numpy conflict (#5307) * r-pkgconfig: Create new package. * r-pkgconfig: Correct format. * r-pkgconfig: Correct format.
2017-09-25r-bit64: new package. (#5437)lingnanyuan1-0/+47
* pr-quantities: add version & py-numpy conflict (#5307) * r-bit64: Create new package. * r-bit64: Correct format.
2017-09-25r-annotationdbi: new package (#5408)lingnanyuan2-0/+89
* r-annotationdbi: Create New Package. * r-iranges: Create new package. * r-s4vectors: Create new package. * r-annotationdbi: Create new package. * r-s4vectors: Delete file. * r-annotationdbi: Correct format. * r-iranges: Correct format.
2017-09-25r-blob: new package. (#5438)lingnanyuan1-0/+39
* pr-quantities: add version & py-numpy conflict (#5307) * r-blob: Create new package. * r-blob: Correct format.
2017-09-25patch py-mccabe and py-flake8 to not require pytest-runner for install (#5427)Todd Gamblin2-0/+8
- Filter the pytest-runner dependency out of setup.py in py-mccabe and py-flake8
2017-09-25update for conduit 0.3.0 release (#5421)Cyrus Harrison1-14/+32
* update for conduit 0.3.0 release * use mpicxx * Update package.py
2017-09-25Fix Protobuf URLs (#5373)Axel Huebl1-3/+15
The default implementation of Package.fetch_remote_versions will take a URL like https://github.com/google/protobuf/archive/ and automatically search https://github.com/google/protobuf/releases/ for new package versions. In the case of protobuf the release/ path contains release artifacts for a version and the archive/ path contains the desired source. Since both are associated with the version, and Package.fetch_remote_versions only stores one URL for a given version, the two paths are in conflict; previously the URL returned for a given version was arbitrarily chosen between the two paths. This updates the definition for the Protobuf package to always search for URLs in https://github.com/google/protobuf/archive/
2017-09-25module files: system paths are excluded from path inspection (#5460)Massimiliano Culpo4-11/+72
closes #5201 Currently, if a user sets an external package to have a prefix that is one of the system paths (like '/usr') the module files that are generated will prepend '/usr/bin' to 'PATH', etc. This is particularly nasty at the time when a module file is unloaded, and e.g. paths like '/usr/bin' will be discarded from PATH. This PR solves the issue skipping system paths when a prefix inspection is made to generate module files.
2017-09-25lammps: add support of latte package (#5446)Christoph Junghans2-1/+35
2017-09-25Add info for lmod@7.7 and lmod@7.6.14 (#5450)George Hartzell1-0/+2
Lightly tested on CentOS 7
2017-09-25add assimp package. link against it in dealii (#5463)Denis Davydov2-0/+56
2017-09-24New version for mosh1.3.2 (#5448)George Hartzell2-1/+2
Required an update to the protobuf digest value, which seems to be amongst the set creamed by GitHub's change.
2017-09-24llvm: patch lldb for gcc-7 (#5239)Andrey Prokopenko2-0/+13
2017-09-23hdf5: fix macOS build by not using numactl (#5458)Denis Davydov1-1/+4
2017-09-23parsplice: add version 1.1 (#5461)Christoph Junghans1-1/+2
2017-09-23blas_lapack: add multithreading variant consistent in all implementations. ↵Denis Davydov5-22/+67
(#5340) * blas_lapack: add multithreading variant * elemental: update * intel-mkl: extend to macOS * rename multithreading to threads * intel-mkl: avoid long lines * intel-mkl: make one install error a conflict * openblas: fix a minor bug in the test
2017-09-23r-rsqlite: Update version to 2.0. (#5444)lingnanyuan1-3/+10
* pr-quantities: add version & py-numpy conflict (#5307) * r-rsqlite: Update version to 2.0
2017-09-23r-bh: update version. (#5442)lingnanyuan1-2/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-bh: Update version to 1.65.0-1
2017-09-23r-memoise: update version. (#5440)lingnanyuan1-2/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-memoise: Update version to 1.1.0
2017-09-23r-tibble: update version. (#5439)lingnanyuan1-3/+4
* pr-quantities: add version & py-numpy conflict (#5307) * r-tibble: Update version to 1.3.4
2017-09-23r-bit: new package. (#5436)lingnanyuan1-0/+34
* pr-quantities: add version & py-numpy conflict (#5307) * r-bit: Create new package.
2017-09-23r-assertthat: update version to 0.2.0 (#5435)lingnanyuan1-1/+2
* pr-quantities: add version & py-numpy conflict (#5307) * r-assertthat: Update version to 0.2.0
2017-09-23r-preprocesscore: created new package (#5434)Yifan Zhu1-0/+35
2017-09-23r-affyio: created new package (#5433)Yifan Zhu1-0/+37
2017-09-23r-xvector: created new package (#5432)Yifan Zhu1-0/+41
2017-09-23superlu-dist: fix has after 09/17/2017 update (#5457)Denis Davydov1-2/+2
2017-09-22tmux: add version 2.5 (#5449)George Hartzell1-0/+1
2017-09-22Ack: add version 2.18 (#5445)George Hartzell1-0/+1
2017-09-23Add info for httpie@0.9.9 (#5451)George Hartzell1-0/+1
Lightly tested on CentOS 7.
2017-09-23Add info for lftp@4.8.1 (#5452)George Hartzell1-0/+1
Lightly tested on CentOS 7.
2017-09-22Update git to @2.14.1, requires pcre+jit variant (#5430)George Hartzell2-1/+13
Update the git package to git@2.14.1. This requires a pcre that has been built with `--enable-jit`, so this adds a variant to pcre to support that and arranges so that git versions before 2.14 depend on pcre and git 2.14 and after depend on pcre+jit.
2017-09-22git-lfs: add 2.2.1 and 2.3.0 (#5429)George Hartzell1-0/+2
2017-09-22emacs: add version 25.3 (security update) (#5447)George Hartzell1-0/+1
25.3 is a security update. Info here: https://lists.gnu.org/archive/html/info-gnu/2017-09/msg00006.html Build both +X and ~X on CentOS 7 and lightly tested.
2017-09-22plumed: fixed possible linking issue (#5425)Massimiliano Culpo1-1/+6
Due to the logic in configure.ac, we may be using both the system linker (LD_RO='ld -r -o') and the linker tied to the compiler (LD=$CXX). This may produce weird link-time errors when the two executables are not the same. The PR works around the issue disabling 'ld -r'
2017-09-22PMIx: add PMIx package to Spack (#5426)Howard Pritchard1-0/+71
Open MPI has been relying on versions of PMIx since the 2.0.0 release. Although the embedded version can be used, it makes more sense long term for Spack to know about the PMIx package, and to build Open MPI against PMIx as an external package. There are other software components that may eventually be reliant on PMIx including MPICH, GASNet, the OpenSHMEM reference implementation, etc. This is also partly motivated by the desire to have ECP ST projects to be released through Spack. Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2017-09-22Version fixes for py-csvkit (#5393)sknigh4-3/+7
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