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2017-11-01r-affycoretools: Create new package and its dependency r-ff. (#6082)lingnanyuan2-0/+92
* r-ff: Create new package * r-affycoretools: Create new package. * r-ff: update url.
2017-11-01r-agimicrorna: Create new package. (#6083)lingnanyuan1-0/+41
2017-11-01r-complexheatmap: created new package (#6084)Yifan Zhu1-0/+46
2017-11-01r-shape: created new package (#6086)Yifan Zhu1-0/+36
2017-11-01r-pmcmr: new package (#6085)Yifan Zhu1-0/+47
2017-11-01Opencv eigen (#6014)Brian Van Essen1-1/+1
* Added a package for the MDAnalysis toolkit. * Changed dependency for the eigen library to not include support for multiple-precision (arbitrary-precision) floating point arithmetic, since OpenCV does not support these data types. * Fixed incorrect implementation
2017-11-01flux: update flux-core to v0.8.0 (#5914)Mark Grondona3-14/+19
* dockbook: remove update to dependent environment Remove override of setup_dependent_environment in both docbook-xml and docbook-xsl, which seems to generate a warning from spack about "Suspicious requests to set or unset 'XML_CATLOG_FILES' found." * flux: update version/dependencies to 0.8.0 Update flux-core to v0.8.0. Clean up dependencies and remove unneeded extra invocation of ./autogen.sh when building from @master. * flux: modify environment for Lua tests Modify Spack environment to add `./?.lua` to LUA_PATH so that fluxometer.lua can be found by tests during `make check` run from `spack install --tests all flux` * flux: fix broken flux version when on master When building @master with spack, the flux version test from `make check` fails because spack is using a shallow clone. Add a setup section for @master that calls git pull --depth=50 --tags to pull down tags and (hopefully) enough information for git-describe to work properly.
2017-11-01mfem does not use cmake for builds [anymore] - so remove code corresponding ↵Satish Balay1-10/+0
to this dependency. (#6073) This enables mfem build on OSX [with xcode/clang compilers]
2017-10-31MACSio and JSON-CWX packages (#6018)Elsa Gonsiorowski3-0/+167
2017-10-31Preinstall some llvm shared libraries so tblgen will work. (#5988)Patrick Gartung1-10/+17
2017-10-31r-somaticsignatures: created new package (#6065)Yifan Zhu1-0/+53
2017-10-31r-nloptr: Create new package. (#6063)lingnanyuan1-9/+13
2017-10-31r-ptw: Create new package. (#6062)lingnanyuan1-0/+46
2017-10-31r-iso: Create new package. (#6061)lingnanyuan1-0/+36
2017-10-31r-nnls: Create new package. (#6060)lingnanyuan1-0/+37
2017-10-31r-als: Create new package. (#6059)lingnanyuan1-0/+44
2017-10-31r-ggbio: new package (#6058)Yifan Zhu1-0/+69
2017-10-31Fix spack build for RAJA: master requires submodules (#6052)Bill Williams1-1/+1
* Fix spack build for RAJA: master requires submodules * Rename version: git to develop
2017-10-31Fix incorrect checksum value for adios2 tarball (#6054)Scott Wittenburg1-1/+1
2017-10-31r-gviz: Create new package. (#6043)lingnanyuan1-0/+63
2017-10-31Added fftw dependency (#6057)Brian Homerding1-0/+1
2017-10-31sw4lite: Added -lgfortran and set to serial build (#6055)Brian Homerding1-1/+7
* Added -lgfortran and set to serial build * Update package.py
2017-10-31ecp-proxy-suite: add nekbone and candle-benchmarks (#6053)Christoph Junghans1-0/+2
2017-10-31nekbone: add v17 (#5978)Christoph Junghans1-4/+5
2017-10-31candle-benchmarks: initial commit (#6020)Christoph Junghans1-0/+42
2017-10-31flang: fixed a typo (#6048)Christoph Junghans1-1/+1
2017-10-31Add v3.2 of Blaze library (#5992)Nils Deppe1-0/+1
2017-10-30Fix tarball URL's for htslib (#5993)George Hartzell1-3/+10
A recent update (#5907) to htslib added a different URL for an old version of htslib. Now the package is using that URL as the pattern for the newer versions too. I have a vague memory of running into this before, that it's a known issue. This fixes it by adding an explicit `url_for_version` routine.
2017-10-30sundials: update to v3.0.0 (#6004)David Gardner1-13/+10
2017-10-30Merging netcdf dependency lines in trilinos into one line for better ↵Jon Rood1-2/+1
coverage. (#5990)
2017-10-30superlu_dist: update to v5.2.2 (#6024)Satish Balay1-0/+1
2017-10-30r-progress: new package (#6034)Yifan Zhu1-0/+41
* r-progress: created new package * added version
2017-10-30r-prettyunits: created new package (#6033)Yifan Zhu1-0/+40
2017-10-30r-seqinr: Update version to 3.4-5 (#6032)lingnanyuan1-0/+2
2017-10-30r-ggplot2: dependecy r-scales version should be 0.4.1: (#6031)Yifan Zhu1-1/+1
2017-10-30r-scales: added dependencies and version 0.5.0. (#6030)Yifan Zhu1-1/+4
* r-scales: Update url. * r-scales: added version 0.5.0 and dependencies
2017-10-30r-segmented: Update version to 0.5-2.2 (#6029)lingnanyuan1-0/+2
2017-10-30r-ggally: new package (#6036)Yifan Zhu1-0/+47
* r-ggally: created new package * r-ggally: version modified
2017-10-30r-speedglm: Create new package. (#6035)lingnanyuan1-0/+39
2017-10-30r-alpine: Create new package. (#6037)lingnanyuan1-0/+50
2017-10-30r-ensembldb: created new package (#6038)Yifan Zhu1-0/+62
2017-10-30r-pcamethods: created new package (#6041)Yifan Zhu1-0/+48
2017-10-30r-proxy: created new package (#6039)Yifan Zhu1-0/+36
2017-10-30r-backports: Create new package. (#6040)lingnanyuan1-0/+42
2017-10-30r-biovizbase: Create new package. (#6042)lingnanyuan1-0/+58
2017-10-30ecp-proxy-apps: release number changed to 1.0 (#6049)Abhinav Bhatele1-12/+12
2017-10-30comd: update the git repo (#6027)Abhinav Bhatele1-2/+2
git repo has moved from exmatex to ECP-copa
2017-10-29Add bowtie2@2.3.0, fix dependencies and sbangs (#5834)George Hartzell2-3/+44
* Add bowtie2@2.3.0, fix dependencies and sbangs Add support for bowtie2@2.3.0 - digest - a patch for 2.3.0 that parallels the existing package. Truth be told it builds (for me) without this, but I'm assuming that they're there for a reason...). - tune up dependencies - need tbb - don't need readline or zlib Several things were installed with sbang's that use `/usr/bin/env` to fine perl or python. Fix the dependency and clean up the sbang lines. * Fix python exe name, avoid path banging I'd cut and pasted the python bit from the perl bit and missed one reference to perl. While I'm there, use the cleaner `spec['perl'].command` instead of banging together the path from its bits. * Fix up the "when" constraints on the dependencies Get the edge cases right. - 2.2.5 doesn't need tbb, 2.3.[01] do. - 2.3.1 needs readline and zlib.
2017-10-29add updated 2017 versions of Intel packages (#5957)Denis Davydov4-0/+8
2017-10-29Changed from setting C compiler to setting C++ compiler (#6011)mmwolf1-2/+2