Commit graph

8093 commits

Author SHA1 Message Date
Dustin Wheeler
c2e087c411 Fix typo in openmpi@2.1.6 libmpi.so comment. (#11529) 2019-05-22 10:37:33 -05:00
Denis Davydov
a973ab4751 dealii: add 9.1.0 (#11527) 2019-05-21 16:23:03 -05:00
Levi Baber
b13665d065 py-htseq: new version (#11525) 2019-05-21 12:08:31 -05:00
Elizabeth Fischer
a45c4ef33d Add version (#10594) 2019-05-21 10:03:50 -04:00
Michael Kuhn
1f828ce5b8 Update scorep and friends (#11523) 2019-05-21 12:28:12 +02:00
Denis Davydov
5d6461b895 dealii: fix symengine constraints (#11517)
disable symengine constraints due to limitations of Spack
2019-05-21 07:38:58 +02:00
Chuck Atkins
a34142ed30
mesa: Patch missing gl symbols in OSMesa (#11518) 2019-05-20 22:41:41 -04:00
Glenn Johnson
d1ea5ba2cd OpenMPI: update behavior for fabrics/schedulers=auto (#11431)
* When fabrics=auto or schedulers=auto, the intent is to defer to the
  OpenMPI configure and let it determine and use what it finds
  available on the system. The current behavior for 'with_or_without'
  in the case of 'auto' explicitly disables all possible values.
  This updates the logic to call 'with_or_without' only when the
  value of fabrics/schedulers is not 'auto'.
* To allow explicitly disabling all fabrics/schedulers, each of these
  variants has added support for 'none' (which is also the default
  value).
* Add a conflict for the loadleveler scheduler for openmpi-3 and
  above as it is no longer a valid configure option.
2019-05-20 17:52:17 -07:00
Andrew Gaspar
2168c08ac5 Update optional-lite and span-lite to use CMakePackage (#11407)
* Update optional-lite and span-lite to use CMakePackage

These packages only have CMake installs on their most recent versions.
Therefore, we overload all of the CMake stages to fallback to the old
versions (no-op for most, copytree for install), and use CMakePackage on
the new versions.

* Add new string-view-lite version with CMake install support

* Only override phases for old versions of *-lite packages
2019-05-20 13:04:06 -05:00
Adam J. Stewart
7fe0230492
Add py-kmodes package (#11497) 2019-05-19 14:17:30 -05:00
Adam J. Stewart
5b6445e519
Add latest version of joblib (#11495) 2019-05-19 14:17:03 -05:00
Adam J. Stewart
ac358a1b4d
Add latest version of setuptools (#11493) 2019-05-19 14:16:37 -05:00
David Beckingsale
866b9b5d13 Update Umpire package with new versions (#11441)
* Update Umpire package with new versions

* Fix version ordering
2019-05-18 23:04:12 -05:00
Denis Davydov
a66cc59bb0 trilinos: add variant to disable chaco from seacas (#11482)
* trilinos: add variant to disable chaco from seacas

keep it OFF by default due to the presence of the global symbol "divide"
that can lead to symbol clash with other libraries, for example see
https://github.com/dealii/dealii/issues/8170#issuecomment-492700787

* dealii: add conflict statement for adol-c and Trilinos SEACAS Chaco
2019-05-18 23:01:44 -05:00
Mark W. Krentel
e1bb6821aa dyninst: rework the cmake args for version 10.1 and later (#11484)
* dyninst: rework the cmake args for version 10.1 and later

Add a separate when() case for the cmake args for Dyninst 10.1.0 and
later.  The prereq args have changed enough that this makes things
easier going forward.  (My previous commit 26b9369c was inaccurate and
temporary.)

Dyninst 10.1.0 accepts boost 1.70, but earlier dyninst are restricted
to <= 1.69 (not worth back porting every boost change).

Change all the dyninst versions to 3 digits for clarity and
consistency.

* Add version 10.1.0.
2019-05-18 23:00:48 -05:00
Nichols A. Romero
6ba6c84de5 QMCPACK Update May 2019 (#11492)
* Add QMCPACK 3.7.0

* SOA is now the default.

* Add QMCPACK converter based on QE 6.4
2019-05-18 22:57:52 -05:00
Jean-Paul Pelteret
517212b8a3 Add conflicts in deal.II package between SymEngine and Trilinos variants (#11499) 2019-05-18 22:56:56 -05:00
Owen Solberg
92604ed576 intel-tbb: fix patch for old compilers (#11371)
* added patch for intel-tbb@2019.1: with old compilers

* sparately specify when @:2018 and @2019

the reason we can't say @:2019 is that would include @2019.1 where the
patch doesn't work.

* should be possible to list when constraint as @:2019

According to my reading of ["Version ranges" in the Spack
docs](https://spack.readthedocs.io/en/latest/packaging_guide.html#version-ranges),
this should apply to up to `2019` but not `2019.1:`

* @:2019.0 appears to be necessary to specify 2019 but not 2019.1

* specifying 2019.1 2019.2 2019.3 2019.4 separately and explcitly

* flake8 fixes for long lines.

* add comments to explain why so many different patch directives

* remove blank like for flake8

* revert spec %gcc@4.8.0:4.99999 -> %gcc@4.8.0:
2019-05-18 21:00:32 -05:00
Justin S
c595883195 r-popvar: new package at 1.2.1 (#11490) 2019-05-17 14:45:21 -05:00
Justin S
cc6f822cb1 smof: new package at 2.13.1 (#11502) 2019-05-17 14:44:35 -05:00
Justin S
c7a28ec1d4 r-bglr: new package at 1.0.8 (#11489) 2019-05-17 14:35:38 -05:00
Justin S
719cd6741d r-rrblup: new package at 4.6 (#11488) 2019-05-17 14:34:33 -05:00
Justin S
8c5b41793c r-qtl: new package at 1.44-9 (#11487) 2019-05-17 14:33:42 -05:00
Justin S
c00ed0d942 py-metasv: new package at 0.5.4 (#11476) 2019-05-17 14:33:04 -05:00
Justin S
7a459857e7 py-pybedtools: new package at 0.6.9 (#11475)
* py-pybedtools: new package at 0.6.9

* py-pybedtools: add bedtools2 dep
2019-05-17 14:32:21 -05:00
Justin S
79a0da6098 repeatmodeler: new package at 1.0.11 (#11472) 2019-05-17 14:31:26 -05:00
Sriram Swaminarayan
0557d93080 added branch multisplice to the parsplice package (#11504) 2019-05-17 12:08:40 -06:00
Christoph Junghans
b7f2923607
gasnet: 2019.3.0 (#11503) 2019-05-17 12:02:43 -06:00
Christoph Junghans
2af7688c55
parsplice: needs LAMMPS_EXCEPTIONS (#11500) 2019-05-17 08:57:35 -06:00
Piotr Luszczek
900f8f0806 Add version 2.5.1-alpha1 of MAGMA (#11486) 2019-05-17 08:19:32 -05:00
Todd Gamblin
23c48d94d3
cmake: default to +ownlibs to improve build times (#11483)
- CMake is built *very* frequently, and the number of dependencies it has
  accumulated can take a very long time on some systems.

- Use +ownlibs by default to avoid the build overhead. This won't
  interfere with other packages by introducing conflicting libraries, as
  CMake is nearly always a build dependency.
2019-05-17 08:47:58 +02:00
Jim Galarowicz
c7f23dcd8d OpenSpeedShop/CBTF package updates and fixes (#11470)
This avoids using Boost 1.70.0, fixes library access in OpenSpeedShop
packages, adds new versions, and updates QT dependency constraints
in CBTF and OpenSpeedShop packages

- Constrain Boost dependency to 1.69.0 or earlier to avoid issues
  with 1.70.0 for Open|SpeedShop and CBTF packages
- Update DYNINSTAPI_RT_LIB environment variable to use single library
  from "find_libraries" (which returns a list) in OpenSpeedShop
  packages
  Fixes #11443
- Add version 1.9.3 for CBTF Argo Navis, CBTF Krell, CBTF LANL, and
  CBTF packages
- Add version 2.4.1 for OpenSpeedShop Utils and OpenSpeedShop
  packages
- Update QT dependency to 5.10.0 or greater for QtGraph and CBTF Argo
  Navis packages
2019-05-16 18:19:55 -07:00
Michael Kuhn
e90b4ce6fb CDO package: Fix build with gcc@9 (#11464)
This makes several changes to make CDO work with gcc@9:

- Add version 1.9.7rc2
- Add a patch to make version 1.9.7rc2 build with gcc@9:
- Add a conflict with GCC 9 for earlier versions of CDO

It also adds a pkgconfig build dependency as configure checks for it.
2019-05-16 17:53:38 -07:00
Andrew Gaspar
8675f44d45 Kokkos package: add debug variant (#11469) 2019-05-16 17:35:23 -07:00
Chris Green
f90507a227 numpy: new version 1.16.3; update historical versions. (#11364) 2019-05-16 11:44:43 -05:00
Chuck Atkins
c2d6095cf3
paraview: fix several dependency issues (#11432)
* Use externally provided mpi4py
* Make mpi4py and numpy both build deps instead of only run deps
* libxt is only on ~osmesa platform=linux
2019-05-16 09:04:44 -04:00
David Beckingsale
5ccc695bfb Fix CMake versions dependencies in RAJA package (#11440) 2019-05-16 13:54:52 +02:00
Thomas Gruber
0337170d34 Likwid: added versions 4.3.3 and 4.3.4 (#11479) 2019-05-16 13:35:25 +02:00
Denis Davydov
38a59e6e37 symengine: add 0.4.0, fix dependency in dealii (#11473) 2019-05-16 12:23:21 +02:00
ktsai7
f68f5e3014 Update flecsi package.py (#11442)
* Update flecsi package.py

* Update package.py

* Update package.py

* Update package.py
2019-05-15 15:29:08 -06:00
Justin S
bfb0f57492 r-geonames: new package at 0.999 (#11455) 2019-05-15 16:04:50 -05:00
Justin S
11bd795ca8 repeatscout: new package at 1.0.5 (#11409)
* repeatscout: new package at 1.0.5

* repeatscout: add trf runtime dependency

* repeatscout: add nseg runtime dependency
2019-05-15 16:04:17 -05:00
Justin S
19355cafae r-phylostratr: new package (#11053) 2019-05-15 16:03:36 -05:00
Justin S
5f5616d6a2 r-taxizedb: new package at 0.1.4 (#11052) 2019-05-15 16:02:54 -05:00
Justin S
b19429159f r-rmysql: add 0.10.17, mariadb-connector-c dependency (#11044)
* r-rmysql: add 0.10.17, mariadb-connector-c dependency

* r-rmysql: add dbi, mariadb version constraints
2019-05-15 15:58:15 -05:00
Justin S
62fa813678 recon: new package at 1.08 (#11408)
* recon: new package at 1.08

* recon: add period

* recon: use proper decorators, better documentation

* recon: fix incorrect os import

* recon: add repeatmasker patch as variant
2019-05-15 15:55:10 -05:00
Justin S
80d7573df8 r-rnoaa: new package at 0.8.4 (#11461) 2019-05-15 15:52:17 -05:00
Justin S
a99454ec6d r-isdparser: new package at 0.3.0 (#11460) 2019-05-15 15:51:50 -05:00
Justin S
cdd8da7251 r-crul: new package at 0.7.4 (#11459) 2019-05-15 15:51:11 -05:00
Justin S
cfad3cd06c r-httpcode: new package at 0.2.0 (#11454) 2019-05-15 15:50:32 -05:00
Justin S
f3dd933e3f r-urltools: new package at 1.7.3 (#11458) 2019-05-15 15:48:54 -05:00
Justin S
c49017a4c5 r-triebeard: new package at 0.3.0 (#11457) 2019-05-15 15:48:17 -05:00
Justin S
230db7c880 r-curl: add 3.3 (#11456) 2019-05-15 15:47:45 -05:00
Denis Davydov
9d34326992 fix suite-sparse built with tbb from intel-parallel-studio (#11134)
* fix suite-sparse built with tbb from intel-parallel-studio

* intel: add tbb_headers, strip newline from cxx_lib

* use property
2019-05-15 11:03:19 -07:00
Justin S
5c021f5416 New package: NSEG (starting at version 1.0) (#11410)
The source is managed as a set of files in an FTP URL. Since there
are no FetchStrategy's implemented for this setup, the files are
managed as a set of Resource's
2019-05-15 10:35:38 -07:00
Leonhard Reichenbach
eae9b0908a CMake package: add dependencies (#11257)
Add dependencies to CMake and GnuTLS which would otherwise be
picked up from the system

* Add gnutls as explicit dependency of CMake
* Add new package libidn2 as explicit dependency for gnutls
2019-05-15 10:07:31 -07:00
Christoph Junghans
0226a95232
parsplice: fix build (#11462) 2019-05-15 08:18:35 -06:00
Brian Van Essen
821b7d3b93 Added setuptools to receipe (#11463) 2019-05-15 12:19:04 +02:00
Michael Kuhn
58c5442d62 kitty: Fix pkgconfig dependency (#11465)
pkgconfig is the correct virtual dependency while pkg-config is a
specific implementation.
2019-05-15 12:18:16 +02:00
Sinan
54d56db1f1 New package: py-pyrosar (#11428) 2019-05-15 10:53:30 +09:00
Sinan
733c2a2554 New package: py-spatialist (#11427) 2019-05-15 10:52:31 +09:00
Sinan
63af41c0c6 New package: py-tblib (#11425) 2019-05-15 10:51:37 +09:00
Sinan
e2ce4386e2 New package: py-scoop (#11423) 2019-05-15 10:50:41 +09:00
Sinan
249845e80b New package: py-progressbar2 (#11421) 2019-05-15 10:49:28 +09:00
Sinan
544cf085b4 New package: py-python-utils (#11422) 2019-05-15 10:47:28 +09:00
Christoph Junghans
6083de3baa
nut: add v0.1.1 (#11444) 2019-05-14 16:36:31 -06:00
Justin S
723eea00f3 r-construct: new package at 1.0.3 (#11452) 2019-05-14 16:24:01 -05:00
Justin S
1ceeac8603 r-rstan: add 2.18.2 (#11447) 2019-05-14 16:23:14 -05:00
Justin S
fc890c80fb r-loo: new package at 2.1.0 (#11448) 2019-05-14 16:22:29 -05:00
Brian Van Essen
92040a475f LBANN: add support for new python front end (#11395)
* LBANN: add python dependency and required python library dependencies
* LBANN: add version 0.99 as alias for develop branch
* LBANN: build Conduit library by default
* LBANN: CUB is included with Hydrogen for later versions
* New package: py-graphviz (dependency for LBANN)
* New package: py-texttable (dependency for LBANN)
* New package: py-onnx (dependency for LBANN)
* New package: py-typing-extensions (dependency for py-onnx)
* Conduit: add version 0.4.0
* NCCL: Add versions 2.4.6-1 and 2.4.2-1
* Protobuf: Add versions 3.7.1 and 3.7.0
* py-protobuf: add version 3.7.1
* py-typing: add version 3.6.4
* cuDNN: add versions. The source differs depending on the
  architecture, so the versions include a suffix to encode this.
  For example this adds 7.5.1-10.1-x86_64 as well as
  7.5.1-10.1-ppc64le
* cuDNN: Newer versions require newer versions of CUDA
* Hydrogen: add configure options for CUB and Aluminum
2019-05-15 06:20:00 +09:00
Justin S
7ff4105ab5 gmap-gsnap: add 2019-05-12 (#11453) 2019-05-14 15:58:48 -05:00
Justin S
f726e14a0a r-rstantools: new package at 1.5.1 (#11451) 2019-05-14 15:57:54 -05:00
Justin S
ea49b64c44 r-caroline: new package at 0.7.6 (#11450) 2019-05-14 15:57:33 -05:00
Justin S
a4ceffa4ff r-stanheaders: add 2.18.1 (#11446) 2019-05-14 15:18:03 -05:00
Justin S
4f1717998a r-withr: add 2.1.2 (#11445) 2019-05-14 15:17:25 -05:00
Justin S
c6d34076dc repeatmasker: add 4.0.9, refactor interactive config (#11385) 2019-05-14 15:16:32 -05:00
Jon Rood
5cd593743e PNetCDF package: enable option required by NetCDF (#11420)
The --enable-relax-coord-bound option was added in 1.8.0. NetCDF
4.6.3 enabled relax coords by default and required it from PNetCDF.
PNetCDF 1.10.0 enabled it by default but for versions between 1.8.0
and 1.10.0 it should be enabled explicitly.
2019-05-15 05:15:38 +09:00
Peter Scheibel
c54f23d405
CUDA package: exclude compat libs (#11449)
CUDA 10.0 provides Compatability libraries for running newer versions
of CUDA with older drivers. These do not work with newer drivers.
2019-05-15 04:59:12 +09:00
Justin S
a5cf50df2e megadock: new package at 4.0.3 (#10537)
* megadock: new package at 4.0.3

* megadock: remove CudaPackage redundancies

* megadock: move env vars to build targets, use cuda_arch variant

* megadock: flake8 fixes, more flexible mathlib
2019-05-14 14:47:19 -05:00
Jon Rood
f7a778af3c Fix py-yt for Python 2 by requesting older py-ipython version (#11416)
* Fix py-yt for Python 2 by requesting older py-ipython version.
* Add conflicts statement to py-ipython because version 7: is not
  compatible with python@2.7
2019-05-15 04:24:52 +09:00
william-dawson
76dd7a92e1 New Package: NTPoly (#11412) 2019-05-15 04:06:10 +09:00
Jon Rood
4a013adc3e Add new versions of metaphysicl and change masa to use branch instead of tag. (#11436) 2019-05-14 08:56:52 +09:00
Justin S
4fcd70cc29 r-bh: add 1.69.0-1 (#11435) 2019-05-14 08:56:14 +09:00
Levi Baber
71d8b8a9b6 rename py-pauvr to py-pauvre (#11437)
* rename py-pauvr to py-pauvre
2019-05-14 08:55:53 +09:00
George Zagaris
a27f2978b9 m4 package: fix OS version check (#11290)
f242f5f removed spec.architecture.platform_os, which was used to test
an option in the 'm4' package. The attribute is now accessed as
'spec.architecture.os'.
2019-05-14 04:53:23 +09:00
Adam J. Stewart
f283487670 Add master branch of leveldb (#11405) 2019-05-13 14:35:15 -04:00
Shane R. Spencer
dcbe798ca7 New package: py-pycares (starting at 3.0.0) (#11340) 2019-05-11 03:48:37 +09:00
Chuck Atkins
418d9f07dc mesa: Add 19.0.4 (#11415) 2019-05-10 13:25:26 -05:00
Hans Pabst
8f0fe5939f LIBXSMM 1.12 (#11414) 2019-05-10 13:11:47 -05:00
Jon Rood
feac68d248 Add new version of PGI compiler. (#11417) 2019-05-10 13:11:23 -05:00
Chris Green
7467a46c2c sqlite: add versions; restore old versions; variant resolves security issues. (#11336)
* Add versions 3.27.{0,1,2} and 3.28.0
* Add url_for_version: the URL format includes the year so this
  function maps version ranges to years
* Restore patches for versions removed in 84c547c: this commit
  removed versions before 3.26.0 due to a security issue with FTS
  support. Add a +fts variant (default true) that enables FTS
  support along with a conflict for +fts with earlier versions.
2019-05-11 02:58:23 +09:00
Chuck Atkins
85fa2dbe36
paraview: Fix OpenGL search to ignore glvnd (#11400) 2019-05-10 09:47:20 -04:00
xfzhao
d0bfe753be py-pauvr:new package (#11292)
* py-pauvr:new package

* py-pauvr: using url and Releases

* py-pauvr: remove extra comments
2019-05-10 08:29:45 -05:00
Peter Josef Scheibel
7e94774214 update aom package license 2019-05-10 04:37:56 +09:00
Peter Josef Scheibel
57a65acedc update license date range for simgrid 2019-05-10 04:37:56 +09:00
Mark W. Krentel
26b9369c57 dyninst: update cmake args and boost dependency (#11378)
* Starting with the upcoming 10.1 release, Dyninst changed the names of
  some cmake args to camel case: LIBELF_* to LibElf_* and LIBDWARF_* to
  LibDwarf_*.  This change is needed now for @develop and will be used
  for 10.1 when it is released.
* New versions of Dyninst now requires cmake version 3.4.0 or later.
* Restrict boost dependency version to < 1.70.0 to avoid build error
2019-05-10 03:58:41 +09:00
David Gardner
ac3cbfd69a update to texlive 2019 (#11365) 2019-05-09 13:47:43 -05:00
Tiziano Müller
92c4567404 elpa: override headers prop for common include-dir localization
... and apply this in SIRIUS, CP2K & QE.

Thanks to @scheibelp for the idea.
2019-05-10 03:43:02 +09:00
Tiziano Müller
f87722b74d packages/cp2k: require libxsmm 1.11+ 2019-05-10 03:43:02 +09:00
Tiziano Müller
4b3e43cc64 packages/cp2k: build with -ggdb with GNU for backtraces 2019-05-10 03:43:02 +09:00