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2017-09-28r-gdata: Update version to 2.18.0 (#5495)lingnanyuan1-1/+3
2017-09-28fixing tag name for development branch (#5496)Mark C. Miller1-1/+1
2017-09-28r-biostrings: created new package (#5498)Yifan Zhu1-0/+41
2017-09-28r-gcrma: created new package (#5500)Yifan Zhu1-0/+42
2017-09-28r-yaqcaffy: created new package (#5538)Yifan Zhu1-0/+38
2017-09-28Add metaphysicl package (#5539)Jon Rood1-0/+38
* Adding package Metaphysicl. * Removing list_url from metaphysical package.
2017-09-28Adding masa package. (#5541)Jon Rood1-0/+65
2017-09-28r-rlang: created new package (#5535)Yifan Zhu1-0/+36
2017-09-28tycho2: initial commit (#5196)Christoph Junghans1-0/+56
2017-09-28Restrict openfoam to using openmpi+thread_multiple (partially resolves ↵Mark Olesen1-0/+4
#5428) (#5479) - latest version requires openmpi+thread_multiple for collated output.
2017-09-28snappy: Build shared library by default (#5534)Michael Kuhn1-0/+14
2017-09-28r-ggvis: Update version to 0.4.3 (#5532)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-ggvis: Update version to 0.4.3 * Update package.py * Update package.py
2017-09-28r-dplyr: Update version to 0.7.3 (#5531)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-dplyr: Update version to 0.7.3 * Update package.py * Update package.py
2017-09-28ncl: Add tcsh dependency (#5195)Michael Kuhn1-0/+19
All ncl scripts hardcode /bin/csh, so fix them up.
2017-09-28tcsh: New package (#5194)Michael Kuhn1-0/+65
The patches are taken from the Fedora package.
2017-09-28r-annaffy: new package. (#5414)lingnanyuan3-0/+116
* r-annaffy: Create New Package. * r-annaffy: Create new package. * r-go-db: Create new package. * r-kegg-db: Create new package. * r-annaffy: Correct indentation. * r-go-db: Correct indentation. * r-kegg-db: Correct format. * r-kegg-db: Correct format. * r-go-db: Correct format. * r-annaffy: Correct format.
2017-09-28fastq-screen: new package (#5431)Audrey Thoma6-0/+228
* fastq-screen: new package * fixing descriptions and previously made packages' old copyright date * added wrong perl package after change
2017-09-28Added hacckernels package (#5533)Brian Homerding1-0/+46
2017-09-28r-r6: Update version to 2.2.2 (#5529)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-r6: Update version to 2.2.2
2017-09-28r-shiny: update version to 1.0.5 (#5530)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-shiny: Update version to 1.0.5
2017-09-28r-htmltools: Update version to 0.3.6 (#5528)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-htmltools: Update version to 0.3.6
2017-09-28r-httpuv: Update version to 1.3.5 (#5527)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-httpuv: Update version to 1.3.5
2017-09-28r-rcpp: Update version to 0.12.13 (#5526)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-rcpp: Update version to 0.12.13 * r-rcpp: Correct url.
2017-09-28Provide a new Perl package 'cloc'. (#5525)Kelly (KT) Thompson1-0/+50
+ Count, or compute differences of, physical lines of source code in the given files (may be archives such as compressed tarballs or zip files) and/or recursively below the given directories.
2017-09-28r-jsonlite: Update version to 1.5 (#5524)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-jsonlite: Update version to 1.5
2017-09-28r-rda: new package. (#5523)lingnanyuan1-0/+35
* pr-quantities: add version & py-numpy conflict (#5307) * r-rda: Create new package.
2017-09-27- build paraview without qt when osmesa is specified. (#5480)Mark Olesen1-0/+4
- new paraview version (5.4.1 from August)
2017-09-27r-sfsmisc: new package. (#5516)lingnanyuan1-0/+36
* pr-quantities: add version & py-numpy conflict (#5307) * r-sfsmisc: Create new package. * r-sfsmisc: Correct format.
2017-09-27Added spackage for branson (#5520)Robert Pavel1-0/+61
Added spackage for branson proxy for monte carlo
2017-09-27added qt creator version 4.4.0 (#5518)Gregory Lee1-0/+1
2017-09-27r-varselrf: new package. (#5515)lingnanyuan1-0/+41
* pr-quantities: add version & py-numpy conflict (#5307) * r-varselrf: Create new package.
2017-09-27r-pamr: new package (#5514)lingnanyuan1-0/+34
* pr-quantities: add version & py-numpy conflict (#5307) * r-pamr: Create new package.
2017-09-27r-rocr: new package. (#5513)lingnanyuan1-0/+49
* pr-quantities: add version & py-numpy conflict (#5307) * r-rocr: Create new package.
2017-09-27r-a4core: new package. (#5512)lingnanyuan1-0/+37
* pr-quantities: add version & py-numpy conflict (#5307) * r-a4core: Create new package. * r-a4core: Correct format.
2017-09-27r-simpleaffy: created new package (#5510)Yifan Zhu1-0/+44
2017-09-27ExaMPM (#5509)Robert Pavel1-0/+37
* Added ExaMPM Spackage * Removed template text
2017-09-27Added Support for BML 1.2.2 (#5502)Robert Pavel1-2/+3
* Added Support for BML 1.2.2 * Added checksums * Update package.py
2017-09-27Added shards and intrepid(2) to trilinos (#5481)Robert Pavel1-0/+12
Added support for shards, intrepid, and intrepid2 variants to trilinos spackage
2017-09-27Added CoEVP Spackage (#5485)Robert Pavel1-0/+89
* Added CoEVP Spackage Added spackage for baseline (mpi, no other dependencies) CoEVP * coevp: add more variants * tag as proxy-app
2017-09-27SZ: add version 1.4.11 (#5517)Sheng Di1-2/+4
2017-09-27flann: fix build for 1.8.1 (#5508)Christoph Junghans1-3/+11
* Update url_for_version for versions 1.8.1 and earlier * Add python dependency when +python is enabled
2017-09-27lammps: add user-omp package (#5486)Christoph Junghans1-23/+17
* Simplify cmake arg generation * Set -DFFT when kspace variant is enabled
2017-09-27Additional MPICH configs (#5259)Ken Raffenetti1-1/+59
* Add support for building develop version from git * Add device and netmod variants
2017-09-27r-gplots: Create New Package. (#5494)lingnanyuan1-0/+40
* r-gplots: Create New Package. * r-gplots: Correct format.
2017-09-27libbson, libmongoc: Update to 1.8.0 (#5478)Michael Kuhn2-0/+2
2017-09-26r-rcurl: created new package (#5492)Yifan Zhu1-0/+62
2017-09-26r-annotate: new package. (#5490)lingnanyuan1-0/+39
* pr-quantities: add version & py-numpy conflict (#5307) * r-annotate: Create new package. * r-annotate: Create new package.
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.
2017-09-26astyle: homepage dead, use mirror (#5483)Christoph Junghans1-1/+3
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