Commit graph

4195 commits

Author SHA1 Message Date
Todd Gamblin
10bb681b57 Unbuffer so that output from packages appears when redirecting
- 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.
2017-08-20 16:51:10 -07:00
Massimiliano Culpo
99fb394ac1 Group Travis CI jobs in stages (#5104)
- 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
2017-08-19 14:52:27 -07:00
健美猫
be0e051870 Add version 1.7.1 for cub. (#5164) 2017-08-19 09:22:19 -05:00
Adam Moody
d80c70538f lbann: add depends_on hwloc (#5165) 2017-08-19 01:00:52 -05:00
Audrey Thoma
fa39afb598 cufflinks: new package (#5158) 2017-08-18 16:02:15 -05:00
Audrey Thoma
3d1c5f679f muscle: fix (#5160) 2017-08-18 16:01:30 -05:00
Kelly (KT) Thompson
c41c5bc9b8 For Tk, also provide a symlink for wishX.X. (#5161)
+ 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`
2017-08-18 16:01:02 -05:00
healther
6d155833c5 build boost with graph library even when +mpi
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.
2017-08-18 11:19:55 -07:00
Audrey Thoma
9ad8e79332 corset: new package (#5157) 2017-08-18 11:02:58 -05:00
Audrey Thoma
6abe8e7d91 parsimonator: new package (#5143)
* parsimonator: new package

* adding variant conflict
2017-08-18 09:36:35 -05:00
Audrey Thoma
5fb23b21e0 vegas2: new package (#5150)
* vegas2: new package

* small version things
2017-08-18 09:36:18 -05:00
George Hartzell
9af953a4cb Add info for nextflow@v0.25.6 (#5148) 2017-08-18 09:36:02 -05:00
Stephen McDowell
61238baf56 add man-db package and friends (#4844)
* add man-db package and friends

* fix groff, libpipeline, and man-db dependencies

* remove parallel groff altogether, build-only deps
2017-08-18 14:17:25 +02:00
zenln
6d2092e1eb Add a new package for gaussian (#5149)
* 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
2017-08-17 18:33:44 -05:00
Audrey Thoma
cf796ed595 pagit: new package (#5140)
* pagit: new package

* removed unneeded env var
2017-08-17 15:32:30 -05:00
Audrey Thoma
94af7ccb77 new package libfabric (#5146)
* pbmpi: new package

* forgot about libfabric
2017-08-17 15:31:31 -05:00
Audrey Thoma
cb4ede001c pbmpi: new package (#5144) 2017-08-17 11:59:02 -05:00
Audrey Thoma
46d8cb8913 paml: new package (#5142) 2017-08-17 11:21:56 -05:00
Audrey Thoma
aa21590099 microbiomeutil: new package (#5134)
* microbiomeutil: new package

* got rid of unnecessary self

* oops
2017-08-17 09:19:00 -05:00
Adam J. Stewart
187f4420e2 Add new package for rhash, a cmake dependency (#5120)
* Add new package for rhash, a cmake dependency

* Add missing libuv dependency to cmake
2017-08-17 08:17:45 -05:00
Audrey Thoma
3bb7767839 py-faststructure: new package (#5131) 2017-08-17 07:49:57 -05:00
healther
d65d1269b9 add libiconv dependency to libxslt (#5138)
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
2017-08-17 07:18:02 -05:00
sknigh
dd790fdaae add missing dependencies to elfutils (#5135) 2017-08-16 20:46:12 -05:00
Audrey Thoma
4c32b0ad56 tppred: new package (#5091)
* tppred: new package

* fixed url_for_version

* fixed version spec on dependency

* removing unneeded dependency
2017-08-16 17:48:50 -07:00
Audrey Thoma
d423f85fed dialign-tx: new package (#5126)
* dialign-tx: new package

* utilizing build_directory variable

* forgot one
2017-08-16 17:36:29 -07:00
Audrey Thoma
3a55d45497 discovar: new package (#5129) 2017-08-16 17:35:04 -07:00
Audrey Thoma
6a2cfedc7a gapcloser: new package (#5130) 2017-08-16 17:34:43 -07:00
Audrey Thoma
dc3526c7f1 py-misopy: new package (#5119)
* py-misopy: new package

* waiting for link to be fixed

* got correct url and checksum

* specifying dependency version requirements
2017-08-16 14:53:43 -05:00
healther
b547e6a273 Add package rtags (#5111)
* Add package rtags

* fixed license

* transform to cmakepackage and add dependencies

* add dependencies and patch for rtags

* flake8 fix

* clean up dependencies
2017-08-16 13:14:54 -05:00
Cesare Cugnasco
ffaa0b7eee Adding Thrift versions 0.10.0 and 0.9.3 (#5117)
* 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
2017-08-16 13:14:37 -05:00
Audrey Thoma
b12fd4e831 phylip: new package (#5121) 2017-08-16 13:13:38 -05:00
Audrey Thoma
7aa81afa68 preseq: new package (#5122) 2017-08-16 13:13:18 -05:00
Adam J. Stewart
11b3ce27b7 Add better generator support to CMakePackage (#4988)
* Add better generator support to CMakePackage

* List valid CMake generators on error
2017-08-16 12:25:37 -05:00
Adam J. Stewart
db657d938d Refactor IntelInstaller into IntelPackage base class (#4300)
* 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
2017-08-16 12:21:07 -05:00
Audrey Thoma
ad8c60239f mpiblast: new package (#5106) 2017-08-16 10:48:39 -05:00
Michael Kuhn
3a0e9f29e6 scorep: Fix build with GCC 7 (#5107) 2017-08-16 10:48:20 -05:00
Michael Kuhn
95915b81d0 otf2: Add 2.1 (#5108) 2017-08-16 10:48:02 -05:00
Adam J. Stewart
2f9b0f6dd6 Fix future import in hdf5-blosc (#5010) 2017-08-16 10:34:52 -05:00
healther
f6a452d3ad Add package rr (#5105)
* Add package rr

* Flake8 fixes

* fix flake8 no2

* add future dependency stub, add hw dependency and clean up

* add missing self
2017-08-16 10:29:02 -05:00
healther
dbdf38f617 Add package PyPytestXdist and dependencies (#5095)
* Add py-pytest-xdist

* fixed licenses

* attempt to fix flake8

* added missing build dependency
2017-08-16 10:26:39 -05:00
healther
480764de5c Add package py-pybind11 (#5096)
* py-pybind11 package was missing

* fixed license file

* attempt to fix flake8

* use python3 compatible python detection
2017-08-16 08:29:54 -05:00
Audrey Thoma
619e298b8d cdhit: new package (#5085) 2017-08-16 07:05:16 +02:00
Gregory Lee
450b19b6e0 fix reference to spec in apex package (#5076)
* fix reference to spec in apex package

* fixed md5 sums for ompt-openmp and apex packages
2017-08-15 17:17:02 -05:00
Brian Van Essen
7b51791625 Openblas clang fix (#5065)
* 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.
2017-08-15 16:57:11 -05:00
healther
8df9f9e1f4 Fix ffmpeg (add missing yasm dependency) (#5087) 2017-08-15 16:54:39 -05:00
Michael Kuhn
256cd68b27 nco: Add patch to fix invalid conversion from char to char* (#5102)
This patch is needed to be able to build nco with GCC 7.
2017-08-15 16:53:22 -05:00
Michael Kuhn
8d4dec7430 ncview: Fix download URL (#5103) 2017-08-15 16:52:34 -05:00
healther
b52e549758 add version 0.2.10 to py-lazyarray (#5093) 2017-08-15 12:15:00 +02:00
Michael Kuhn
43a634ca80 gcc: Add 7.2.0 (#5098) 2017-08-15 12:14:07 +02:00
Mark C. Miller
5712fbfeb0 Use correct variant syntax to build zfp (#5099)
`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
2017-08-15 12:10:09 +02:00