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2017-08-20Unbuffer so that output from packages appears when redirectingTodd Gamblin1-0/+45
- Python I/O would not properly interleave (or appear) with output from subcommands. - Add a flusing wrapper around sys.stdout and sys.stderr when redirecting, so that Python output is synchronous with that of subcommands.
2017-08-19Group Travis CI jobs in stages (#5104)Massimiliano Culpo1-0/+2
- This should speed-up Travis CI tests and refers to #5049 - Travis uses build-stages to group tests together - The idea is to let fast tests fail first, then move to longer ones. - Added external perl to avoid download failure from CPAN and reduce build time - Disabling perl-dbi: continues to fail with (504 Gateway Time-out) on Travis - We now cover all the build systems in tests: - Add back `openblas` to Travis as a separate package. - Switched `openblas` for `astyle` to build a simpler MakefilePackage. - Added 'tut' (WafPackage) - Added 'py-setuptools' (PythonPackage) - Added 'perl-dbi' (PerlPackage) - Added 'build_systems' directory to the ones for which we get a summary - Added 'openjpeg' (CMakePackage) - Added 'r-rcpp' (RPackage) - Added comments to build tests to show the covered build system
2017-08-19Add version 1.7.1 for cub. (#5164)健美猫1-0/+1
2017-08-19lbann: add depends_on hwloc (#5165)Adam Moody1-0/+1
2017-08-18cufflinks: new package (#5158)Audrey Thoma1-0/+46
2017-08-18muscle: fix (#5160)Audrey Thoma1-0/+5
2017-08-18For Tk, also provide a symlink for wishX.X. (#5161)Kelly (KT) Thompson1-0/+5
+ gitk (and possibly other tools) expect to find the Tk executable `wish`, so add a symlink with this name that points to the the versioned filename. + Example: `wish --> wish8.6`
2017-08-18build boost with graph library even when +mpihealther1-1/+0
Previously, when +graph and +mpi were enabled, the graph library was replaced with the graph_parallel library. This alters the logic for +graph+mpi to build both libraries.
2017-08-18corset: new package (#5157)Audrey Thoma1-0/+44
2017-08-18parsimonator: new package (#5143)Audrey Thoma1-0/+65
* parsimonator: new package * adding variant conflict
2017-08-18vegas2: new package (#5150)Audrey Thoma4-1/+126
* vegas2: new package * small version things
2017-08-18Add info for nextflow@v0.25.6 (#5148)George Hartzell1-0/+2
2017-08-18add man-db package and friends (#4844)Stephen McDowell5-0/+212
* add man-db package and friends * fix groff, libpipeline, and man-db dependencies * remove parallel groff altogether, build-only deps
2017-08-17Add a new package for gaussian (#5149)zenln1-0/+71
* Gaussian: Gaussian install * Adding Patch to spack installed files * Adding extra environment variables for gaussian at run time * Adding provides linda * Adding linda as a provided package * Shortning vars and fixing flake8 indentation and spacings
2017-08-17pagit: new package (#5140)Audrey Thoma1-0/+68
* pagit: new package * removed unneeded env var
2017-08-17new package libfabric (#5146)Audrey Thoma1-0/+35
* pbmpi: new package * forgot about libfabric
2017-08-17pbmpi: new package (#5144)Audrey Thoma1-0/+48
2017-08-17paml: new package (#5142)Audrey Thoma1-0/+52
2017-08-17microbiomeutil: new package (#5134)Audrey Thoma1-0/+53
* microbiomeutil: new package * got rid of unnecessary self * oops
2017-08-17Add new package for rhash, a cmake dependency (#5120)Adam J. Stewart2-40/+120
* Add new package for rhash, a cmake dependency * Add missing libuv dependency to cmake
2017-08-17py-faststructure: new package (#5131)Audrey Thoma1-0/+39
2017-08-17add libiconv dependency to libxslt (#5138)healther1-0/+1
this is a fix to an installation that failed due to configure for some reason not finding the libiconv shipped with glibc, but still trying to link against it see http://xmlsoft.org/FAQ.html
2017-08-16add missing dependencies to elfutils (#5135)sknigh1-2/+10
2017-08-16tppred: new package (#5091)Audrey Thoma2-1/+55
* tppred: new package * fixed url_for_version * fixed version spec on dependency * removing unneeded dependency
2017-08-16dialign-tx: new package (#5126)Audrey Thoma1-0/+50
* dialign-tx: new package * utilizing build_directory variable * forgot one
2017-08-16discovar: new package (#5129)Audrey Thoma1-0/+36
2017-08-16gapcloser: new package (#5130)Audrey Thoma1-0/+39
2017-08-16py-misopy: new package (#5119)Audrey Thoma1-0/+46
* py-misopy: new package * waiting for link to be fixed * got correct url and checksum * specifying dependency version requirements
2017-08-16Add package rtags (#5111)healther2-0/+116
* Add package rtags * fixed license * transform to cmakepackage and add dependencies * add dependencies and patch for rtags * flake8 fix * clean up dependencies
2017-08-16Adding Thrift versions 0.10.0 and 0.9.3 (#5117)Cesare Cugnasco1-0/+2
* Adding Thrift version 0.10.0 and 0.9.3 Hi, I've added the versions 0.10.0 and 0.9.3 * fixed flake8 errors
2017-08-16phylip: new package (#5121)Audrey Thoma1-0/+45
2017-08-16preseq: new package (#5122)Audrey Thoma1-0/+44
2017-08-16Add better generator support to CMakePackage (#4988)Adam J. Stewart2-23/+6
* Add better generator support to CMakePackage * List valid CMake generators on error
2017-08-16Refactor IntelInstaller into IntelPackage base class (#4300)Adam J. Stewart7-499/+584
* Refactor IntelInstaller into IntelPackage base class * Move license attributes from __init__ to class-level * Flake8 fixes: remove unused imports * Fix logic that writes the silent.cfg file * More specific version numbers for Intel MPI * Rework logic that selects components to install * Final changes necessary to get intel package working * Various updates to intel-parallel-studio * Add latest version of every Intel package * Add environment variables for Intel packages * Update env vars for intel package * Finalize components for intel-parallel-studio package Adds a +tbb variant to intel-parallel-studio. The tbb package was renamed to intel-tbb. Now both intel-tbb and intel-parallel-studio+tbb provide tbb. * Overhaul environment variables set by intel-parallel-studio * Point dependent packages to the correct MPI wrappers * Never default to intel-parallel-studio * Gather env vars by sourcing setup scripts * Use mpiicc instead of mpicc when using Intel compiler * Undo change to ARCH * Add changes from intel-mpi to intel-parallel-studio * Add comment explaining mpicc vs mpiicc * Prepend env vars containing 'PATH' or separators * Flake8 fix * Fix bugs in from_sourcing_file * Indentation fix * Prepend, not set if contains separator * Fix license symlinking broken by changes to intel-parallel-studio * Use comments instead of docstrings to document attributes * Flake8 fixes * Use a set instead of a list to prevent duplicate components * Fix MKL and MPI library linking directories * Remove +all variant from intel-parallel-studio * It is not possible to build with MKL, GCC, and OpenMP at this time * Found a workaround for locating GCC libraries * Typos and variable names * Fix initialization of empty LibraryList
2017-08-16mpiblast: new package (#5106)Audrey Thoma2-0/+233
2017-08-16scorep: Fix build with GCC 7 (#5107)Michael Kuhn2-0/+44
2017-08-16otf2: Add 2.1 (#5108)Michael Kuhn1-0/+1
2017-08-16Fix future import in hdf5-blosc (#5010)Adam J. Stewart1-1/+0
2017-08-16Add package rr (#5105)healther1-0/+66
* Add package rr * Flake8 fixes * fix flake8 no2 * add future dependency stub, add hw dependency and clean up * add missing self
2017-08-16Add package PyPytestXdist and dependencies (#5095)healther3-0/+114
* Add py-pytest-xdist * fixed licenses * attempt to fix flake8 * added missing build dependency
2017-08-16Add package py-pybind11 (#5096)healther1-0/+51
* py-pybind11 package was missing * fixed license file * attempt to fix flake8 * use python3 compatible python detection
2017-08-16cdhit: new package (#5085)Audrey Thoma1-0/+49
2017-08-15fix reference to spec in apex package (#5076)Gregory Lee2-2/+3
* fix reference to spec in apex package * fixed md5 sums for ompt-openmp and apex packages
2017-08-15Openblas clang fix (#5065)Brian Van Essen1-6/+9
* Added a package for the MDAnalysis toolkit. * Openblas now builds with clang when using 0.2.20 * Fixed flake8 error * Added a guard to fail for openblas+openmp when on OSX systems * Changed the guard to look for Apple's build of clang and to improve the error messages. * Removed blank line.
2017-08-15Fix ffmpeg (add missing yasm dependency) (#5087)healther1-0/+2
2017-08-15nco: Add patch to fix invalid conversion from char to char* (#5102)Michael Kuhn2-0/+54
This patch is needed to be able to build nco with GCC 7.
2017-08-15ncview: Fix download URL (#5103)Michael Kuhn1-1/+1
2017-08-15add version 0.2.10 to py-lazyarray (#5093)healther1-1/+2
2017-08-15gcc: Add 7.2.0 (#5098)Michael Kuhn1-3/+4
2017-08-15Use correct variant syntax to build zfp (#5099)Mark C. Miller1-2/+1
`h5z-zfp` now builds zfp with correct bit stream word size; the syntax of the variant declaration did not work in previous versions of spack but does now
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