Commit graph

8729 commits

Author SHA1 Message Date
Adam J. Stewart
0de42519cf
Add py-cachetools package (#12252) 2019-08-02 20:47:46 -05:00
Adam J. Stewart
eb528f89a7
Add py-pyasn1 0.4.6 (#12251) 2019-08-02 20:09:15 -05:00
Reinhard Prix
7845d91fda swig: add latest version, 4.0.0 (#12243) 2019-08-02 20:08:26 -05:00
Satish Balay
8010965a3d slepc: update python dependencies to be in sync with petsc (#12250) 2019-08-02 20:07:29 -05:00
Daryl W. Grunau
b4f8294408 packages/musl (#12247)
* new musl package
2019-08-02 20:06:59 -05:00
Marc-Andre Hermanns
0290170935 Set default resource manager to 'none' (#12092) 2019-08-02 19:23:14 -05:00
Toyohisa Kameyama
50b90ed2bf minimap2, py-mappy: change dependency and build on ARM (#12127)
* minimap2: remove py-mappy dependency and build on ARM
py-mappy: Change URL and new version.

* merge py-mappy to minimap2.

* 1. add type in depends_on.
2. remove unneeded which.
2019-08-02 19:21:33 -05:00
Chris Green
0c1496896d Resolves #11487. (#12136)
* Incorporate as a patch upstream commit 0c20dbf059 (diff-acb9169b4ccbac494ced5140d285a015) resolving problems with `-Wno-...` options not being understood by GCC.
* Incorporate as a patch upstream PR https://github.com/ericniebler/range-v3/pull/1202 fixing upstream issue https://github.com/ericniebler/range-v3/issues/1196.
* Compile tests only if we actually want to run them.
* Optionally compile documentation with a `+doc` variant.
* Add `+examples` and `+perf` variants to avoid unnecessary compilation of components usually not required for install.
* Add conditional build-only dependency on Boost when appropriate.
* Install docs, examples and performance tests if built (not part of upstream build instructions).
* Add @chissg as a maintainer.
2019-08-02 19:19:39 -05:00
Toyohisa Kameyama
b6789b2ba3 py-flye: change to build ARM. (#12176) 2019-08-02 19:15:49 -05:00
Todd Kordenbrock
a54687ead9 FAODEL: Add 1.1906.1 (#12180) 2019-08-02 19:14:21 -05:00
Toyohisa Kameyama
dbeee34829 vdt: add simd variant (#12188)
1. add simd variant and check target.
2. build on source directory before 0.3.8.
2019-08-02 19:10:39 -05:00
TiffanyAnn
ff15f61443 py-mpi4py: Added build argument for mpicc path (#12191)
* added build arguments to resolve error with Cray-MPICH

* fixed indentation
2019-08-02 19:09:37 -05:00
Hironori-Yamaji
53bd964a59 ermod: new package (#12192) 2019-08-02 19:08:35 -05:00
Toyohisa Kameyama
53b1a92f69 parsimonator: Enable build on non x86_64 hosts. (#12194) 2019-08-02 19:07:43 -05:00
Glenn Johnson
6278ba43e9 Update c-blosc and fix building tests with icc (#12204)
- Update c-blosc to 1.17.0
- Add patch to build test_forksafe for versions 1.15.0 through 1.17.0
  when compiled with the Intel compiler.
- Remove code that turned off building the test with the Intel compiler
2019-08-02 19:05:43 -05:00
Toyohisa Kameyama
93f6833990 raxml: compile n non-x86 hosts. (#12208)
1. xmmintrrin.h is included x86 only.
2. Add makefiles for non-x86 hosts.
3. mpicc in Makefiles is replaced spacks mpi compile command.
4. variant check is rewite with satisfies.
2019-08-02 19:04:25 -05:00
Toyohisa Kameyama
3fc5a08f5b dialign-tx: build on ARM. (#12210) 2019-08-02 19:02:36 -05:00
liuyangzhuan
474bf18853 added a package butterflypack (#12222)
* added a package butterflypack

* remove one line in the python script
2019-08-02 18:58:30 -05:00
Mark W. Krentel
45d852b87d hpcviewer: update sha sums for version 2019.07 (#12236)
We (Rice HPCToolkit) issued a re-release of hpcviewer 2019.07 due to
some serious bugs.
2019-08-02 18:55:46 -05:00
Satish Balay
4ee260d3e3 ginkgo: fix branch -> commit for @1.0.0. Also add variant: develtools (#12248)
This fixes error with multiple builds - when they use the cached tarball.
2019-08-02 18:54:15 -05:00
dbs8842
2529b753da liggghts: added version 3.8.0 (#12242) 2019-08-02 18:53:06 -05:00
Gregory Lee
214b67066e glib: fix glib dependency build fixes #9992 (#12153)
add rpaths for glib config and py-pygobject build
2019-08-02 15:18:04 -05:00
wspear
9dd61f5313 Fixed arch setting variants. Activate cray arch automatically. (#11203) 2019-08-02 15:14:43 -05:00
Chuck Atkins
0e532d324c
adios2: Fix backwards compatibility version logic for FindMPI (#12241) 2019-08-02 15:27:47 -04:00
Tamara Dahlgren
574c13837f
packages: Add autotools dependencies to bolt (#12246)
Fixes #12060 (per wspear).

This change is needed for minimal container environments.
2019-08-02 12:22:51 -07:00
Patrick Gartung
9cf6aece85
Geant4 data packages: Set the install path name explicitly. (#12244)
* Geant4 data packages: Set the install path name explicitly.

* Use the correct directory name for g4photonevaporation,g4radioactivedecay,g4realsurface
2019-08-02 13:48:35 -05:00
Chris Green
023de09134 mysql package: New versions, add conflicts, cope with use of dtrace. (#11356)
* Add versions 8.0.16, 5.7.26, and 5.6.44
* Update boost dependency for versions 8.0.16, 8.0.15, and 8.0.14
* Update dtrace script when building for versions before 8 as is done
  for the glib package
* Set perl as a build dependency for versions before 8
* cxxstd=17 conflicts with version 8 when server code is built
  (~client_only)
* Add -Wno-deprecated-declarations for cxxstd > 11
* Add -Wno-error=register for cxxstd > 14
2019-08-02 10:51:02 -07:00
Axel Huebl
46f03074ef openPMD-api: Increase ADIOS2 Minimum (#12169)
The minimum required version of ADIOS2 is v2.4.0 .
2019-08-02 15:31:29 +02:00
MikeG
d384025df7 valgrind: added version 3.15.0 (#12239) 2019-08-02 15:10:37 +02:00
Seth R. Johnson
68d78c0dbe Fix py-matplotlib build (#12230) (#12234) 2019-08-01 17:58:06 -05:00
Seth R. Johnson
46027bea13 Fix QT4 build for mac (#10944)
This updates the Spack QT package to enable building qt version 4 on
MacOS. 

This includes the following changes to the qt package:

* add version 4.8.7
* add option to build with or without shared libs
* add options to disable tools, ssl, sql, and freetype support
* add qt4-tools patch when building qt@4+tools
* add option to build as a framework (only available on MacOS)
* replace qt4-el-capitan patch with qt4-mac patch (which includes the
  edits from qt4-el-capitan)
* apply qt4-pcre-include-conflict.patch only for version 4.8.6
  (rather than all 4.x versions)
* apply qt4-gcc-and-webkit.patch for 4.x versions before 4.8.7 and
  create a separate qt4-gcc-and-webkit-487.patch for version 4.8.7
* update patch function for qt@4 on MacOS to update configure
  variables relevant to Spack (e.g. PREFIX)
* add option to build freetype with Spack, as a vendored dependency
  of QT, or not at all (default is to build with Spack)

This includes the following edits outside of the qt package:

* Update MacOS version utility function to return all parts of the
  Mac version (rather than just the first two)
* gettext package: implement "libs"
* python package: add gettext as a dependency
2019-08-01 10:22:35 -07:00
Ben Bergen
8922c1f666 Add HDF5 variant to Legion package (#12221) 2019-08-01 10:33:29 -06:00
Sajid Ali
e21e10837f modified: var/spack/repos/builtin/packages/blis/package.py (#12225) 2019-08-01 09:37:23 -05:00
Sajid Ali
f30b717744 Add libflame (#12193)
* Add libflame

	new file:   var/spack/repos/builtin/packages/libflame/Makefile_5.1.0.patch
	new file:   var/spack/repos/builtin/packages/libflame/package.py

* 	modified:   var/spack/repos/builtin/packages/libflame/package.py
2019-08-01 09:33:24 -05:00
Adam J. Stewart
61b824580e py-pyqt5: add missing py-enum34 dependency (#12224) 2019-08-01 13:30:35 +02:00
t-karatsu
9b03ab43ed bdw-gc: add variant for Multithreading (#12223) 2019-08-01 13:29:41 +02:00
Mark W. Krentel
e628f1b4eb unzip: fix build for cray back-end
Fixes #12007.

The Cray cc wrappers don't handle the -s flag (strip) cleanly, It's
not essential to strip the binary, so just remove the flag on Cray.

Note: the default build on Cray is for the back end and the unzip
binary won't run on the front end.  To build for FE, use something
like arch=cray-fe-x86_64.
2019-07-31 20:44:40 -07:00
Gregory Lee
2c2abb454c fix mpa package build error with a patch (#12217) 2019-07-31 16:48:06 -05:00
Gregory Lee
162f1338d9 patch launchmon to fix char * conversion error (#12219) 2019-07-31 16:47:35 -05:00
Rémi Lacroix
5c970613b6 Magma: fix prefix (#12220)
`prefix` is not available in `cmake_args` method, use `self.prefix`.
Fixes #12214.
2019-07-31 16:43:47 -05:00
Adam J. Stewart
f7d1df4d3a
Update Package Creation Tutorial for PEARC19 (#12209)
* Update Package Creation Tutorial for PEARC19

* A few remaining fixes

* Fix section link
2019-07-31 12:54:09 -05:00
Matthieu Dorier
65a1db87f8 Preventing jsoncpp from building tests (#11948)
* Preventing jsoncpp from building tests
jsoncpp: making -DJSONCPP_WITH_TESTS=OFF conditioned by self.run_tests
2019-07-31 12:18:25 -05:00
Ondřej Čertík
7e61527f9e F18: Fix the location to the f18 binary (#12186) 2019-07-31 15:43:08 +02:00
jthies
ae1524821e phist: added version 1.8.0 (#12201) 2019-07-31 15:35:59 +02:00
t-karatsu
b744accaf6 igvtools: fixed query on jdk instead of java (#12195) 2019-07-31 14:49:51 +02:00
Ryan S. Elliott
86ff5baed7 kim-api: added version 2.1.2 (#12189) 2019-07-31 09:13:13 +02:00
t-karatsu
268c806111 genomefinisher: fixed query on jdk instead of java (#12196) 2019-07-31 08:55:56 +02:00
Adam J. Stewart
db2bbbcecf
Add pandas 0.25.0 (#12173) 2019-07-30 17:16:32 -05:00
Adam J. Stewart
59e9541386
Add tables 3.5.2 (#12172) 2019-07-30 17:16:15 -05:00
Adam J. Stewart
60da9303c6
Update numexpr dependency version (#12168) 2019-07-30 17:15:38 -05:00
Adam J. Stewart
70512b8ba2
Add py-matplotlib 3.1.1 (#12164) 2019-07-30 17:15:20 -05:00
Adam J. Stewart
482152e092
Add py-wxpython package (#12163) 2019-07-30 17:13:32 -05:00
Adam J. Stewart
c1c5f58d12
Add py-cairocffi package (#12161) 2019-07-30 17:13:02 -05:00
Adam J. Stewart
b34da4e108
Add SIPPackage base class (#12157) 2019-07-30 17:12:48 -05:00
Adam J. Stewart
f487f87e3e
Add Magics 4.1.0 (#12078) 2019-07-30 17:11:47 -05:00
Adam J. Stewart
e728883c71
Add eccodes 2.13.0 (#12077) 2019-07-30 17:11:29 -05:00
Adam J. Stewart
354ef2f9ca
Allow bsseeker to build with Python 3 (#12075) 2019-07-30 17:11:14 -05:00
Adam J. Stewart
e13bc0212c
Add py-pipits 2.4 (#12074)
* Add py-pipits 2.4

* Flake8 fix
2019-07-30 17:10:57 -05:00
Justin S
175abecc0b mii: new package at 1.0.2 (#12184)
* mii: new package at 1.0.2

* mii: fix improper formatting in description

* mii: add 1.0.3
2019-07-30 16:16:41 -05:00
健美猞猁
544914f34b gromacs: added version 4.5.5 (#12197) 2019-07-30 16:07:07 +02:00
Ben Bergen
73a9d6556e New package: cgdb (#12154) 2019-07-29 17:19:53 -07:00
Hans Pabst
6db873532c LIBXSMM package: add version 1.13 and optional shared libs (#11998)
* Add +shared variant, which builds shared library in addition to the
  static library.
* Install libraries even when specifying the header-only option
  (header-only is just about installing an additional folder).
* An additional make call is not required to build generator
  executables (they are built by default).
* Streamlined help-line of each variant.
2019-07-29 17:14:41 -07:00
Toyohisa Kameyama
5f716b7ffa hpgmp package: Don't add cpu=native on ARM when using gcc 5.x or before (#12034) 2019-07-29 16:53:59 -07:00
Adam J. Stewart
b8b2fa226e CMOR package: add version 3.4.0 (Python3-compatible) (#12076) 2019-07-29 16:12:37 -07:00
Nick Forrington
6e9f51d1d2 Quantum Espresso package: Specify F90 compiler (#12119) 2019-07-29 15:53:39 -07:00
Adam J. Stewart
c9e5de85fd SimulationIO package: add version 9.0.1 (#12079) 2019-07-29 15:40:57 -07:00
Chuck Atkins
f18c9e0ba5 catalyst package: Fix paths used for intermediate code generation (#12082)
Fixes #12065
2019-07-29 15:31:07 -07:00
Adam J. Stewart
f88636b090 PISM package: add version 1.1.4 (#12083) 2019-07-29 15:26:03 -07:00
Adam J. Stewart
9af155f0f6 Fix some Mac constraint checks (#12138)
* Fix Mac platform check for dependency in py-ipython package: 'when'
  constraints in Spack directives must be Specs (either a Spec
  object or a Spec in string format)
* Fix Mac version check in py-numpy: platform.mac_ver() returns a
  3-part string as its first tuple item so the check as written would
  never pass; use Spack Version object to simplify check.
* Fix Mac version check in qt package (the check was incorrectly
  comparing ints and strings) and use Spack version object to
  simplify check.
2019-07-29 15:05:02 -07:00
Glenn P Johnson
e7d9a6f426 Add conflicts statement for Python-3.6.7+ and Intel compiler
Python-3.6.7 and up do not build with the Intel compiler

- https://bugs.python.org/issue35473
- https://bugs.python.org/issue37415
2019-07-29 14:38:05 -07:00
Federico Ficarelli
dbd294c204 zeromq package: choose URL based on version; add versions (#12149)
* Add versions 4.3.0, 4.3.1, and 4.3.2
* The URL format changed after 4.1.4, so this adds a url_for_version
  function to choose the URL format based on the version
2019-07-29 14:36:33 -07:00
Hironori-Yamaji
43dd6b3418 Gromacs package: add openmp, mdrun_only, double_precision options (#12150) 2019-07-29 14:29:04 -07:00
Adam J. Stewart
c3dc63ce8f New package: py-pytest-isort (#12160) 2019-07-29 14:02:06 -07:00
Jon Rood
3e02dc258b LLVM package: add optional libomp_tsan support (#11793)
This is only available for LLVM version 6 or greater. So this also
adds a conflict statement for earlier versions of LLVM.
2019-07-29 12:23:15 -07:00
Owen Solberg
ee1c36a2b0 update cmake 3.15.1 checksum (#12182) 2019-07-29 15:13:52 -04:00
Adam J. Stewart
0d0a02b230 OpenGL package: always provides gl (#12158)
With this PR, a user can designate older versions of OpenGL as an
external Spack package, and dependents can use that installation
as long as they do not have version requirements.

MacOS currently comes with OpenGL 2.1; there is currently no
'provides' directive in the OpenGL Spack package which specifies a
gl version provided for versions earlier than OpenGL 3.3, so earlier
versions of OpenGL are not considered to provide any version of gl.
This PR records that any version of OpenGL provides 'gl' (which is
sufficient for any package that does not require a specific version
of gl).
2019-07-29 12:11:53 -07:00
Adam J. Stewart
d1752d8640 py-scipy package: add version 1.3.0 (#12171)
* Version 1.3.0 requires python 3.5 or later (no Python 2 support)
* Remove test of scipy.weave import (not available since 1.0)
* Add more-sensitive py-numpy constraints based on py-scipy version
* Replace py-nose dependency with py-pytest
* Add adamjstewart as maintainer
2019-07-29 11:57:59 -07:00
Adam J. Stewart
249f571556 New package: py-torchvision (#12175) 2019-07-29 11:42:08 -07:00
Adam J. Stewart
18bd189876 PyTorch package: add version 1.1.0 (#12174)
* Rename py-pytorch to py-torch
* Add versions 1.1.0 and 1.0.1
* Define modules to test import of after installation (import_modules)
* py-typing dependency is only needed for older versions of Python
  (3.4 or before)
* Newer versions of py-torch depend on newer versions of CUDA
* Add adamjstewart as maintainer
2019-07-29 11:39:05 -07:00
Seth R. Johnson
3d0b5bd541 Change dependencies to use virtual jpeg package (#12179)
This prevents conflicts between descendents that depend on an unintentional
arbitrary jpeg implementation.
2019-07-29 12:08:55 -05:00
Kelly (KT) Thompson
a3f6f52622 Add a new version (7.2) of draco. (#11852)
This change also
+ Makes the `build_type` user settable and
+ Adds support for running tests.
+ Provide depends_on('cmake') for versions prior to 7.0.
2019-07-28 22:15:21 -05:00
Jeongseok Lee
e23d613ee6 Update checksum of fmt 5.3.0 (#12037) 2019-07-28 22:07:51 -05:00
Seth R. Johnson
95985e0798 Prevent conflicts between libuuid and Apple Cocoa Framework on Mac (#12166)
* Remove libuuid dependency for python on Darwin

Python 2.7 includes Carbon, which requires a proprietary typedef defined in
the system `/usr/include/uuid/uuid.h`:
```
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Python/mactoolboxglue.c:27:
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Include/pymactoolbox.h:10:
In file included from /System/Library/Frameworks/Carbon.framework/Headers/Carbon.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:23:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
```

Similarly, even with Python 3, having Spack's libuuid in the toolchain
causes matplotlib to fail to build downstream because its `osx` backend
links against Carbon:
```
building 'matplotlib.backends._macosx' extension
/rnsdhpc/code/spack/lib/spack/env/clang/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/local/include -I/usr/X11/include -I/opt/X11/include -I. -I/rnsdhpc/code/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.2-bipx24oyxqxowqc75o5vfih7dljiaohz/include/python3.7m -c src/_macosx.m -o build/temp.macosx-10.14.5-x86_64-3.7/src/_macosx.o
In file included from src/_macosx.m:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
        uuid_string_t   ext_jnl_uuid;
        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char                    io_string_t[512];
```

MacOS version 10.14.5
Xcode 10.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)

* Mark libuuid as conflicting with Darwin due to framework

If Spack's libuuid is included by any other package that tests for or
requires the Cocoa or Carbon frameworks, the build will *fail* becuse it
appears that Apple's libraries require a special version of libuuid and
uuid.h.

```
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
        uuid_string_t   ext_jnl_uuid;
        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char                    io_string_t[512];
```

* Revert "Mark libuuid as conflicting with Darwin due to framework"

This reverts commit 9a68b75202005fc265abe2033e4ad36312a9a34d.

* Document libuuid exception in python package
2019-07-28 14:58:09 -05:00
Sajid Ali
9afd5113bc Bump version for BLIS (#12162)
modified:   var/spack/repos/builtin/packages/blis/package.py
2019-07-27 18:32:06 -05:00
Chuck Atkins
8d0c3e482f cmake: Bump to 3.15.1 (#12151) 2019-07-27 12:21:03 -05:00
Xavier Delaruelle
398c53eaa2 environment-modules package: add version 4.3.0 (#12155) 2019-07-27 12:20:39 -05:00
Chuck Atkins
18e41f9959 adios2: Patch findmpi for downstream issues. (#12152) 2019-07-26 13:17:31 -07:00
Sinan
511f84dd8c kealib: fix incorrect md5sum for v1.4.11 (#12126)
* fix incorrect md5sum for v1.4.11

* fix url and replace md5 with sha256

* add mainter
2019-07-26 15:14:46 -05:00
Ryan S. Elliott
12055acccc update to kim-api-2.1.1 and openkim-models-2019-07-25 (#12137)
* update to kim-api-2.1.1 and openkim-models-2019-07-25

* openkim-models provide needed dependency constraints and settings

* add maintainers and fixup flake8 errors
2019-07-26 13:06:10 -05:00
Adam J. Stewart
fbb04ece43
Add flake8 3.7.8 (#12141) 2019-07-26 12:11:07 -05:00
t-karatsu
21daa41dd6 libxc: Make configure recognize Fujitsu compiler (#12147) 2019-07-26 12:09:52 -05:00
Justin S
e2d16429ae py-pyomo: new package at 5.6.6 (#12134)
* py-pyomo: new package at 5.6.6

* py-pyomo: add missing deps, python constraint
2019-07-26 10:38:25 -05:00
Rémi Lacroix
9caba3e072 Small fixes for font-util package (#12148)
* font-util: Remove duplicated dependencies.

* font-util: Fix path handling for font resources.

The "join_path" call made no sense but still managed to work somehow most of the times.
2019-07-26 10:32:39 -05:00
Adam J. Stewart
0babdab8f0 Add GDAL 3.0.1 (#12140) 2019-07-26 09:25:35 +02:00
Adam J. Stewart
07fefea52d Add Python 3.7.4 (#12142) 2019-07-26 09:18:46 +02:00
Oliver Breitwieser
867ba9d7fe googletest: Fix reversed +pthreads option (#12128)
If +pthreads is specified, googletest actually gets build without
pthreads support and vice versa.

If pthreads is not available, googletest should detect it itself which
is why "enabling" pthreads in case of ~pthreads does not seem to cause
any error.

Change-Id: I29de8c4a23dc3901124b27a1ead3354949b7e65b
2019-07-25 19:50:23 -05:00
Justin S
94af6cad5f interproscan: new package at 5.36-75.0 (#12130) 2019-07-25 19:49:42 -05:00
Matthias Diener
7cc1292202 git-lfs: add version 2.8.0 (#12131) 2019-07-25 19:46:03 -05:00
Glenn Johnson
7ad8061cbb Patches for graphviz (#12133)
- patch to build with qt5, enabling gvedit to build
- two patches to compile graphviz with icc
2019-07-25 19:45:10 -05:00
Satish Balay
7bd3b66f6e
xsdk: phist has a conflict with gcc version <= gcc-4.9.1 (#11946)
* xsdk: phist has a conflict with gcc version <= gcc-4.9.1 - so add a variant to disable it on older compiler builds

This is triggered by #11677

* fix typo
2019-07-25 14:01:00 -05:00
Chuck Atkins
e614d4b481 cmake: Add a patch to revert a findmpi regression (#12129) 2019-07-25 10:23:01 -07:00
Chris Green
c20c153d16
catch: more versions, new and older. (#12123)
New versions 2.9.0, 2.9.1, older versions 2.2.2, 2.2.3, 2.4.1, 2.4.2, 2.7.0, 2.7.1, 2.7.2.
2019-07-25 11:33:03 -05:00
simo-tuomisto
4c7ee8b7c8 lame & libmad: Added two new packages for sox mp3 support. (#11964)
* Added a new package for LAME and a variant in sox for it.

* Fixed download url for LAME

* libmad: Added new package libmad for mp3 decoding. Changed sox variant from lame to mp3.

* libmad: Added m4 as a requirement

* libmad: Added comment on patch origins

* libmad: Added a list_url for alternate download location

* libmad: Fixing libmad download url
2019-07-25 10:40:50 -05:00
Sinan
9ace419aa5 gdal: added versions 2.4.2 and 3.0.1 (#12125) 2019-07-25 17:14:37 +02:00
Chris Green
4190f302e5 geant4: improvements with respect to building against CLHEP. (#12124) 2019-07-25 08:58:13 -05:00
Todd Gamblin
b0abbfecb8 new command: spack maintainers queries package maintainers
- We don't currently make enough use of the maintainers field on
  packages, though we could use it to assign reviews.

- add a command that allows maintainers to be queried
  - can ask who is maintaining a package or packages
  - can ask what packages users are maintaining
  - can list all maintained or unmaintained packages

- add tests for the command
2019-07-24 14:10:08 -07:00
Glenn Johnson
8bb745325d Add py-setuptools as a build dependency for py-absl-py (#12109)
I needed to add py-setuptools to get py-absl-py to build.
2019-07-24 12:33:45 -05:00
Glenn Johnson
642d3345f6 Add conflicts statement to freetype for icc (#12111)
Freetype-2.8 and above use __builtin_shuffle which is not supported by
icc.
2019-07-24 12:33:24 -05:00
t-karatsu
0f98cf0398 Perl take in flags (#12112)
* perl: perl package takes in spack cflags.

* fix for flake8 test.
2019-07-24 12:32:49 -05:00
Toyohisa Kameyama
bbc689ae38 nnvm: cmake bug is fixed. (#12113) 2019-07-24 12:31:49 -05:00
Toyohisa Kameyama
cb62b1ff85 rapidjson: Don't add -march=native on ARM and gcc 5.x or before. (#12117) 2019-07-24 12:30:32 -05:00
Nichols A. Romero
63813fa9c0 QMCPACK Update July 2019 (#12097)
* Add QMCPACK v. 3.8.0

* Remove QE variant conflict for serial QMCPACK installations.

* Add support for QE 6.4.1 converter.

* FindLibxml2QMC patch function only needed prior to QMCPACK 3.8.0
2019-07-24 12:28:35 -05:00
Glenn Johnson
42c3782f7e Do not build c-blosc test if intel in spec (#12110)
While the c-blosc library compiles with icc some of the c-blosc tests do
not. Disable the tests so that the spack build can continue.
2019-07-24 11:17:11 -05:00
t-karatsu
0d690edfb2 cmake: fix cxx98flag's name (#12114) 2019-07-24 11:28:22 -04:00
Toyohisa Kameyama
a8b12f0cb6 rocksdb: Don't add -march=native on ARM and gcc 5.x or before. (#12108) 2019-07-23 22:33:05 -05:00
Douglas Duckworth
ec29461632 added relion 3.0.7 - removed deprecated versions (#12101)
* relion - added v 3.0.7 and removed deprecated versions that have inferior performance

* relion 3.0.7 does require cuda 9 or above
2019-07-23 18:13:00 -05:00
Toyohisa Kameyama
6b07407cd0 isaac-server: Don't add -march=native on ARM and gcc 5.x or before. (#12042) 2019-07-23 16:48:25 -05:00
Toyohisa Kameyama
39139b9db8 nanoflann: Don't add -mtune=native on ARM and gcc 5.x (#12093) 2019-07-23 16:47:28 -05:00
Nichols A. Romero
2b35ad7b22 Quantum Espresso Update 2019 (#12098)
* Add support for QE 6.4.1

* QE 6.3. backports branch no longer relevant.

* List QE develop first.
2019-07-23 16:44:08 -05:00
Jimmie Lin
8095e26ffa Add EFA fabric to libfabric 2019-07-23 12:08:33 -07:00
Pariksheet Nanda
5878b418c5 ioapi: add version 3.2 (#12088)
* ioapi: add version 3.2

* ioapi: unwrap version checksum; it's exempt from line length QA

* ioapi: drop overridden build(); it's the same as the default
2019-07-23 12:10:01 -05:00
Greg Becker
4ff2773704
ncurses: remove TERMINFO from build env (#12086) 2019-07-23 10:13:41 -05:00
Marco Comparato
7ea4e50587 font-util: add missing autoconf automake dependencies (#12053) 2019-07-23 09:41:04 -05:00
Daniel Topa
07f3921838 Add UCX 1.6.0 (#12089)
https://github.com/openucx/ucx/releases/tag/v1.6.0
Released 2019-07-17

Verification builds on LANL Darwin x86_64 and Power9:

dantopa@cn2037:pr-update-ucx.spack $ date
Mon Jul 22 17:04:14 MDT 2019

dantopa@cn2037:pr-update-ucx.spack $ pwd
/scratch/users/dantopa/repos/spack/pr-update-ucx.spack

dantopa@cn2037:pr-update-ucx.spack $ spack find -ldf ucx

==> 2 installed packages
-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
w7fp4n6    ucx@1.6.0%gcc
tt2hkol        ^numactl@2.0.12%gcc
srhy7ry        ^rdma-core@20%gcc
kvgvhpv            ^libnl@3.3.0%gcc

-- linux-rhel7-ppc64le / gcc@4.8.5 ------------------------------
cji3ce7    ucx@1.6.0%gcc
pmgndwh        ^numactl@2.0.12%gcc
qymrwx6        ^rdma-core@20%gcc
2263pm5            ^libnl@3.3.0%gcc

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-07-22 21:43:35 -05:00
Matthias Diener
19968a0035 scons: add version 3.1.0 (#12084) 2019-07-22 17:35:40 -05:00
Chuck Atkins
69c302f455 cmake: Move cxx11 flags for fujitsu into the flag_handler method (#12056)
* cmake: Move cxx11 flags for fujitsu into the flag_handler method

* cmake: sanitization and error checking in flag_handler

* cmake: Fix fujitsu flag check from 'fc' to 'fj'
2019-07-22 17:33:40 -05:00
Denis Davydov
8cef81363c gcc: support without command line tools (#11040) 2019-07-22 16:53:50 -05:00
zschulte
db7127c56d openjdk (#10446)
* openjdk

* Removing preferred from latest and adding a few lines for readability.

* Remove bad whitesapce

* removing formatting changes

* stable url for openjdk 1.8

* remove extra blank line

* actual binary
2019-07-22 13:11:45 -05:00
Toyohisa Kameyama
58c84423b1 tealeaf: Don't add -march=native on ARM and gcc 5.x or before. (#12080) 2019-07-22 13:03:43 -05:00
Hironori-Yamaji
8e92409263 jdk: Add JDK 12.0.2_10 (#12081) 2019-07-22 12:40:11 -05:00
Mark W. Krentel
6111758b48 hpctoolkit: add version gpu and variant cuda (#12068)
Add version for 'gpu' and variant for 'cuda'.  These are currently available from the 'master-gpu' branch.

* hpctoolkit: add version gpu and variant cuda
* The gcc >= 4.8.x requirement only applies for dyninst >= 10.x.
2019-07-21 22:29:08 -07:00
Toyohisa Kameyama
8ca90e26d9 libsharp: Don't add -march=native on ARM (#12064)
* libsharp: Don't add -march=native on ARM

* Add preferred=True to version 1.0.0.
2019-07-21 21:56:14 -05:00
Mark W. Krentel
930011c124 hpcviewer: add version 2019.07 (#12067)
ibm-java: fix the URL to only use a machine type that ibm-java
supports so that 'spack info' doesn't report a non-existent URL on
platforms that it doesn't support.
2019-07-20 10:07:15 -07:00
Greg Becker
4f9131fdc2 Package inheritance: Find patch files defined in parent classes using MRO (#12051)
Fixes #8908, 11844

Use Python MRO to find patch files from parent classes.
2019-07-19 18:08:05 -07:00
Peter Scheibel
4b6de78062
font-util package: add autoconf/automake build deps (#12071)
Fixes #12026

These are required on some systems
2019-07-19 17:45:22 -07:00
Michael Kuhn
cadff917c7 leveldb: add 1.22 (#12044) 2019-07-19 09:26:09 -05:00
Chris Green
9b763980b6
libxpm: cope with system gettext if configured. (#10881)
* If gettext is installed in the system it won't be in the spec tree.
2019-07-19 08:36:58 -05:00
Gregory Becker
cebf1fd668 stacks: update view management for multiple/combinatorial views
This adds notion of a default view, other views in environments
2019-07-18 19:28:50 -07:00
Matthias Diener
5be1ff83d1 cmake: add version 3.15.0 (#12058) 2019-07-18 18:28:21 -05:00
Adam J. Stewart
032075af74
Add master version to sklearn (#12057) 2019-07-18 15:56:48 -05:00
Matthieu Dorier
6eba9febaa pkg PRRTE: added version 1.0.0 (#12054) 2019-07-18 13:59:39 -05:00
Matthieu Dorier
3120e06359 added version 3.1.3 of PMIx (#12055) 2019-07-18 13:59:02 -05:00
Adam J. Stewart
c96d687c7c
Workaround for #9149 (#12050) 2019-07-18 13:57:37 -05:00
Justin S
620d728aa5 py-mlxtend: new package at 0.16.0 (#12039)
* py-mlxtend: new package at 0.16.0

* py-mlxtend: fix dependencies
2019-07-18 12:25:41 -05:00
Phil Carns
7428fc66f7 update web site and git url for BMI package (#12036) 2019-07-17 21:28:39 -05:00
Jordan Ogas
ada50b968a add charliecloud v0.10 (#12046) 2019-07-17 21:28:02 -05:00
Adam J. Stewart
5d1f965e59
Fix scikit-learn build with Apple clang (#11496)
* Fix scikit-learn build with Apple clang

* Update compiler unit tests

* Fix unit tests

* Fix OpenMP dep

* recursive=True no longer necessary

* Add myself as a maintainer

* Specify which versions require OpenMP

* Typo fixes

* LLVM-OpenMP is the correct dependency, no OMPT

* Flake8 fix

* Undo Apple Clang OpenMP flag change, split into a separate PR
2019-07-17 21:27:16 -05:00
t-karatsu
1269256e25 libjpeg-turbo: set compiler flags with CMake args (#11938)
Later versions of libjpeg-turbo build with CMake; to build with
user-specified cflags, the user must supply these to CMake as
-DCMAKE_C_FLAGS (Spack's typical approach of injecting these flags
into the compiler wrapper invocation is insufficient in this case).

Currently libjpeg-turbo cannot be implemented as a CMakePackage
(and thereby take advantage of the flag_handler implementation it
provides) because not all versions of libjpeg-turbo use CMake, so
this adds a custom implementation of flag_handler and
flags_to_build_system_args to libjpeg-turbo.
2019-07-17 15:37:18 -07:00
Adam J. Stewart
7f3048c8af
Add support for .txz and .tbz2 file extensions (#12048) 2019-07-17 16:23:23 -05:00
Ryan S. Elliott
c9b6c78d3a kim-api 2.1.0 (#12041) 2019-07-17 12:11:34 -05:00
brietzke
0c5ed467ce package opencoarrays: add new version: 2.7.1 (#12043) 2019-07-17 12:11:02 -05:00
t-karatsu
5d9e67d953 Cmake/add option for fujitsu compiler (#11839)
* cmake: change c++ spec when building with Fujitsu compiler.

* cmake: define cxxflags using a Fujitsu compiler's method.

* cmake: Add condition of whether to add cxx11 option.
2019-07-17 12:49:36 -04:00
Shane R. Spencer
1b16be538e Added url_for_version to python/package.py (#12040) 2019-07-16 20:50:43 -05:00
Justin S
267d07e4b9 py-pandas: add 0.24.2 (#12038) 2019-07-16 20:46:17 -05:00
Hironori-Yamaji
c44afdcc80 r: set FPICFLAGS for compilers except 'gcc' (#12033) 2019-07-16 11:56:34 -05:00
brietzke
29d968bd84 package mutationpp: add new version: 1.0.0 (#12035) 2019-07-16 11:55:53 -05:00
Michael Kuhn
ce88cc75ef qt: fix patch checksum (#12024)
It seems that GitHub's output changed slightly for this patch (one more
letter for both short hashes on the index line), probably due to the
number of objects in the repository.
2019-07-15 23:43:02 -05:00
Brian Homerding
36919ba859 binutils: Adding Clang to narrowing conversion error workaround (#12029) 2019-07-15 23:42:02 -05:00
Marc-Andre Hermanns
2cfbde1737 Add JUBE package definition (#12023)
* Add JUBE package definition

* Fixing flake8 errors
2019-07-15 20:58:57 -05:00
Severin Strobl
0ed7204c74 Added HPX version 1.3.0. (#12025) 2019-07-15 20:54:54 -05:00
t-karatsu
e3b513874b boost: use clang toolset when building with Fujitsu compiler. (#11827) 2019-07-15 15:13:04 -07:00
Glenn Johnson
3f83a2a7d8 Add auto-dispatch specification to Intel packages (#11697)
This PR adds the ability to specify the auto-dispatch targets that can
be used by the Intel compilers. The `-ax` flag will be written to the
respective compiler configuration files. This ability is very handy when
wanting to build optimized builds for various architectures. This PR
does not set any optimization flags, however.
2019-07-15 11:37:54 -07:00
Hironori-Yamaji
68ad4caf30 binutils: added '-Wno-narrowing' to CXXFLAGS when using fj compiler via flag_handler (#11922)
FJ compiler fails for older versions w/o '-Wno-narrowing' flag.
2019-07-15 08:50:26 -07:00
Todd Gamblin
a3caf52cac packages: computation.llnl.gov is now computing.llnl.gov (#12013) 2019-07-15 07:32:51 -07:00
Milton Woods
af74c291ed py-basemap: install without egg (#11961)
* py-basemap: avoid creating egg during build, for compatibility with mpl_toolkits

* py-basemap: not ready for py-pyproj@2 onwards
2019-07-15 10:26:13 -04:00
Matthias Diener
9be127890f gdb: add version 8.3 (#12018) 2019-07-14 16:45:55 -05:00
Reinhard Prix
9e7eae0e2f make cfitsio explicitly depend on curl (#12016)
- currently would revert to using system-curl instead, pulling in
  unwanted system dependencies and lib-paths
2019-07-14 14:40:09 -05:00
Michael Kuhn
d7b76df5ac bzip2: Add 1.0.8 (#12017)
Update URLs to official ones.
2019-07-14 14:25:20 -05:00
Adam J. Stewart
0bff0c2d0d
Make JDK version more specific (#12008) 2019-07-13 09:05:48 -05:00
Adam J. Stewart
452021398a
Add py-jsonschema 2.6.0 (#12009) 2019-07-13 09:05:17 -05:00
Tim Fuller
5bc15b2d9a find_libraries searches lib and lib64 before prefix (#11958)
The default library search for a package checks the lib/ and lib64/
directories for libraries before the root prefix, in order to save
time when searching for libraries provided by externals (which e.g.
may have '/usr/' as their root).

This moves that logic into the "find_libraries" utility method so
packages implementing their own custom library search logic can
benefit from it.

This also updates packages which appear to be replicating this logic
exactly, replacing it with a single call to "find_libraries".
2019-07-12 17:46:47 -07:00
xfzhao
f1ce1dd163 New package: Nim (#11649) 2019-07-12 17:03:26 -07:00
Justin S
9b361bea5a r package: add rmath variant for standalone rmath library (#11693) 2019-07-12 16:50:04 -07:00
egreen77
d01d79eb5d new package: umap (#12000) 2019-07-12 15:26:24 -05:00
Hironori-Yamaji
505ad8960e jdk: Add the 'provides' call (#11997) 2019-07-12 09:45:19 -07:00
Stephen Hudson
cdc72963d1 Update libensemble (#11990) 2019-07-12 10:36:44 -05:00
Phil Tooley
52e0f47a3f update scalasca to latest version, simplify recipe (#11999)
add list_url for use with spack checksum
2019-07-12 10:30:07 -05:00
Glenn Johnson
42c7d24075 Modifications to r package (#11957)
This PR has several modifications for the r package.

- The tk package is always depended on but this pulls in X11, making the
  'X' variant non-functional. This PR sets a dependency of tk on '+X'.
- There is a missing dependency on libxmu when '+X' is set.
- The libraries for R wind up in a non-standard location and are thus
  left out of the RPATH settings. This PR adds that directory to RPATH.
- The MKL integer interface for gfortran is not in the BLAS libs. This
  PR replaces the intel interface with the gfortran interface if needed.
- Use the `LibraryList` `ld_flags` method for blas as that is more in
  line with th R Installation and Administration manual.

Note that this PR depends on PR #11956. This PR closes #8642.
2019-07-11 22:22:37 -05:00
Glenn Johnson
909c5f5019 Add variants for tk package (#11956)
TK can be built with support for libXft and X Screensaver. Both of these
are turned on in the Tk configure script. That means the system
libraries will get picked up if they are on the system and nothing is
specified in the package. Since the default for both of them is 'True' I
set the default value for the variants to 'True'.
2019-07-11 22:21:17 -05:00
Toyohisa Kameyama
4288dac35b bowtie2: Add version 2.5.3.1 and fix to build on ARM (#11974)
* bowtie2: Add version 2.5.3.1 and fix to build on ARM

1. Add version 2.5.3.1.
2. Add simde for ARM.
3. Disable -fopenmp-simd when gcc 4.8.X or before for ARM.
4. Add Makefile option POPCNT_CAPABILITY=0 for ARM.

* flake8.
2019-07-11 22:04:22 -05:00
Toyohisa Kameyama
ea9ac3ee52 velvet: remove -m64 on aarch64. (#11984) 2019-07-11 21:59:24 -05:00
Nick Forrington
ff728bd06c Boost: Compile with toolset=clang for Arm compiler (#11992)
Bootstraps with gcc, but compiles with clang
2019-07-11 21:53:54 -05:00
Toyohisa Kameyama
0dfa5a467c megahit package: add patch to build on ARM. (#11963) 2019-07-11 17:40:00 -07:00
Phil Tooley
14271331f9 New package: dimemas (#11979) 2019-07-11 13:55:43 -07:00
Mark Olesen
138226e038 OpenFOAM package: update download url (#11973) 2019-07-11 13:45:38 -07:00
Phil Carns
3a4d37d6d6 libfabric package: add support for tcp provider (#11965) 2019-07-11 13:43:38 -07:00
Toyohisa Kameyama
6a731b4d8f luit package: use autotools. (#11962) 2019-07-11 13:34:50 -07:00
Tamara Dahlgren
e3299e6923 Rename build logs and make names consistent (#11806)
Fixes #11781

* Rename build log to spack-build-log.txt
* Rename environment variables file to spack-build-env.txt
* The name of the log and env files is now the same during the build
  and after the build completes
* Update packages which referred to the build log/env files
* For packages installed before this commit using older names for the
  build and env files, search for the older names
2019-07-11 13:32:06 -07:00
Michael Kuhn
d3be42fcca mpich: Add 3.3.1 (#11976) 2019-07-10 20:41:23 -05:00
Michael Kuhn
975b9a611a bzip2: Add 1.0.7 (#11975) 2019-07-10 18:37:16 -05:00
Reinhard
ea431be4b0 py-astropy: added latest version 3.2.1 (#11967)
- correctly installs under python@3.5:3.7.3
- (partially) fixes https://github.com/spack/spack/issues/11966
2019-07-09 21:19:38 -04:00
Carson Woods
2838aa772d package: Add powerapi package (#11845)
* Add powerapi package

* Fix flake8 formatting

* Fix download URL

* Update powerapi version line

* Fix how configure arguments are selected to improve readability

* Bug Fixes

* Fix trailing whitespace

* Bug fixes

* Remove incorrect configure flag
2019-07-09 09:57:53 -04:00
Milton Woods
d0b2c77cd1 Ferret: add version 7.2 and adjust dependencies (#11921)
* ferret: use libx11 from spack

* ferret: use mpi library with or without fortran support

* ferret: add version 7.2

* ferret: no need to specify ~mpi

* ferret: creating symlinks may fail for external packages; set include/lib paths instead
2019-07-09 09:33:07 -04:00
Toyohisa Kameyama
dab3026f2f diffsplice package: remove -m64 on ARM. (#11899) 2019-07-08 17:13:49 -07:00
Toyohisa Kameyama
a718d8af08 zoltan: use autotools for new architecture host (#11924)
* use autoreconf to regenerate configure script and config.guess for
  newer architectures
* Add perl build dependency for older versions. The required perl
  version is constrained because the perl script uses syntax that
  is deprecated in older versions
2019-07-08 16:57:17 -07:00
Hironori-Yamaji
68dd327d62 motif package: fix the download url (#11939) 2019-07-08 16:20:01 -07:00
Frédéric Simonis
1fe3d6367e preCICE package: add version 1.5.2 (#11949) 2019-07-08 13:59:08 -07:00
Xavier Delaruelle
a9067821b3 environment-modules package: add version 4.2.5 (#11953) 2019-07-08 13:58:38 -07:00
Justin S
36ee7ef456 New package: r-grbase (starting at 1.8-3.4) (#11937) 2019-07-08 12:01:58 -07:00
Justin S
897cd340d8 r-graph: update R constraint to reflect DESCRIPTION (#11934) 2019-07-08 12:01:17 -07:00
Justin S
60a827daff r-rbgl: add 1.60.0 (#11936) 2019-07-08 12:00:16 -07:00
Justin S
242bdef6e8 r-biocgenerics: add 0.30.0 (#11935) 2019-07-08 11:59:54 -07:00
Kevin Huck
f21073d231 tau: add conflicts for libelf/libdwarf variants (#11944)
Declare a conflict for TAU versions older than 2.28.1, that they
can't depend on libelf or libdwarf.  The user can still install it
by specifying tau@2.24~libelf~libdwarf.
2019-07-05 19:08:43 -07:00
Christoph Junghans
e392bf0412 cmake: add v3.14.5 2019-07-05 17:02:34 -07:00
Milton Woods
a7da5dcb19 py-stratify: vertical interpolation/stratification of atmos/ocean data (#11911)
* py-stratify: vertical interpolation/stratification of atmos/ocean data

* py-stratify: download from pypi.io
2019-07-04 10:38:48 -04:00
Milton Woods
d88c657f79 py-scikit-image: include more dependencies (#11912)
* py-scikit-image: include more dependencies

* py-scikit-image: limit some dependencies to recent versions
2019-07-04 10:38:02 -04:00
Hironori-Yamaji
cd18dadf92 jdk: Add JDK 12.0.1 (#11903) 2019-07-04 10:36:21 -04:00
Paul
1ce6490132 Added latest version, 0.7.1 (#11927) 2019-07-04 10:26:59 -04:00
Milton Woods
e7a3f703be py-antlr4-python3-runtime: new package (#11890)
* py-antlr4-python3-runtime: new package

* py-antlr4-python3-runtime: fix for flake8

* py-antlr4-python3-runtime: indent docstring

* py-antlr4-python3-runtime: clarify role of this package vs ANTLR in docstring

* py-antlr4-python3-runtime: remove whitespace at end of line
2019-07-04 10:12:54 -04:00
Glenn Johnson
54e87c8da0 Set ignore files for py-reportlab (#11928)
The py-reportlab package includes binaries for easy_install and pip.
That blocks activation if py-setuptools and/or py-pip are installed.
This PR block the binaries from py-reportlab as easy_install and pip
should be installed with their respective packages.
2019-07-03 19:15:01 -07:00
t-karatsu
adffb2bff4 libtool: execute autoreconf at ver.2.4.2 (#11913)
Version 2.4.6 did not require running autoreconf, so this only does
autoreconf for 2.4.2
2019-07-03 18:04:29 -07:00
shanedsnyder
902dcfd194 libfabric package: add version 1.8.0 (#11918) 2019-07-03 17:30:25 -07:00
Milton Woods
fae14bff21 py-cf-units: new package (#11891)
* py-cf-units: new package

* py-cf-units: download from pypi.io

* py-cf-units: include py-pytest-runner as build dep

* py-cf-units: remove empty build_args function

* py-cf-units: fix for flake8

* py-cf-units: indent docstring

* py-cf-units: remove excess spaces

* py-cf-units: list master branch ahead of numeric versions

* py-cf-units: remove extension keyword from version
2019-07-03 19:20:34 -04:00
Alberto Chiusole
f3bf89ebfe OpenMPI: add support for pbs/tm at configure. (#10620) 2019-07-03 14:07:51 -07:00
Justin M Wozniak
28949787e9 turbine: Better auto-detection of R location (#11711)
If R is provided by the system with a module (i.e. registered in
packages.yaml with a "module" entry) and has no discernible prefix,
this allows turbine to still make use of R.
2019-07-03 11:24:20 -07:00
Milton Woods
ea1df6a9b4 py-pyke: new package (#11894)
* py-pyke: automatic python program generator

* py-pyke: expand the package docstring
2019-07-02 15:58:14 -04:00
Milton Woods
48bfece55e py-pyugrid: unstructured grids in netcdf files (#11900) 2019-07-02 15:56:18 -04:00
ktsai7
229ba28ad5 Add llvm as deps when static analyzer is enabled (#11888)
* dep llvm if static analyzer
dep caliper if caliper

* fix typo

* adding variants for toggles
2019-07-02 11:45:13 -06:00
Toyohisa Kameyama
f1592e339d portcullis package: remove -m64 on aarch64. (#11905)
GCC on aarch64 dose not support -m64. This patch removes the -m64
flag if target is aarch64.
2019-07-02 10:42:06 -07:00
Phil Carns
2709f948fa opa-psm2 package: correct installation prefixes and add 11.2.77 (#11658)
This PR corrects a problem with the opa-psm2 package. It was
installing headers into <prefix>/usr/include and libraries into
<prefix>/usr/lib instead of <prefix>/include and <prefix>/lib.
The extra level of usr/ subdirectories causes dependent packages
like libfabric to fail to build.
2019-07-02 10:34:58 -07:00
Mark Olesen
5fd3b5acda openfoam: rename openfoam-com to openfoam (#11876)
The original packaging, with openfoam as a virtual and with
openfoam-com, openfoam-org and openfoam-extend as
providers, adds an obfuscation layer without any benefit.

- Rename `openfoam-com` to `openfoam`, and remove the 
  `openfoam` virtual package.
2019-07-01 22:54:36 -07:00
Todd Gamblin
515b4045e9 specs: remove parse_anonymous_spec(); use Spec() instead
- `parse_anonymous_spec()` is a vestige of the days when Spack didn't
  support nameless specs.  We don't need it anymore because now we can
  write Spec() for a spec that will match anything, and satisfies()
  semantics work properly for anonymous specs.

- Delete `parse_anonymous_spec()` and replace its uses with simple calls
  to the Spec() constructor.

- make then handling of when='...' specs in directives more consistent.

- clean up Spec.__contains__()

- refactor directives and tests slightly to accommodate the change.
2019-07-01 18:45:44 -07:00
Milton Woods
1ad9f6268b New packages: libmo-unpack and py-mo-pack (#11895)
* libmo-unpack: package to encode and decode UM fields
* py-mo-pack: python interface for libmo-unpack
2019-07-01 18:24:45 -07:00
Justin S
781a115656 New package: r-gwmodel (starting at 2.0-9) (#11887) 2019-07-01 18:14:29 -07:00
Justin S
196886e708 New package: r-spatialreg (starting at 1.1-3) (#11886) 2019-07-01 18:13:06 -07:00
Justin S
a7cd7fdcd4 New package: r-spdata (starting at version 0.3.0) (#11883) 2019-07-01 18:11:16 -07:00
Milton Woods
711a80832a New package: py-nc-time-axis (#11898) 2019-07-01 18:07:57 -07:00
Glenn Johnson
b66c296562 py-markdown package: update dependency version range (#11908)
The python dependency specifies that 2.7 or 2.8 are allowed when in
fact it should specify a version range (anything between 2.7 and 2.8,
inclusive).
2019-07-01 17:52:41 -07:00
Sameer Shende
4d0926464c mpich: wrapperrpath variant allows disablement of RPATH usage in mpicc
Added a wrapperrpath variant to mpich that defaults to `True`.

Users can set this to `False` (e.g., spack install mpich~wrapperrpath) to
disable the wrapper RPATHs.  This makes it easier to replacing an MPICH
installation in a container with an MPICH for the host system,
e.g., Cray MPICH with Shifter on Cori, Intel MPI, MVAPICH2, etc.

Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2019-07-01 15:09:40 -07:00
Toyohisa Kameyama
54de03548b planck-likelihood: remove -m64 on ARM (#11902) 2019-07-01 10:48:45 -07:00
Axel Huebl
1b3c11e793 ADIOS2: v2.4.0 (#11904)
Add the latest release of ADIOS2.
2019-07-01 13:47:31 -04:00
Milton Woods
6856972745 tk: avoid search for X headers and libraries (#11892) 2019-07-01 13:47:04 -04:00
t-karatsu
8ca5c3685a camellia: fix hdf5 dependency (#11810)
* camellia: fix hdf5 dependency

* camellia: Add comment
2019-07-01 13:40:53 -04:00
Justin S
b517be2c68 r-spacetime: new package at 1.2-2 (#11885) 2019-07-01 13:39:15 -04:00
Milton Woods
0f703b7e81 py-netcdf4: depend on hdf5+hl (#11893) 2019-07-01 15:38:35 +02:00
Dr Owain Kenway
441401bb8b llvm: don't build CppBackend for flang versions of llvm (#11841)
The version of LLVM used by flang is new enough that CppBackend doesn't exist.  Unfortunately, `flang-xxxxxxxx` is seen as < `3.9.0` by the version check.  

* add a special case for `flang` versions.
2019-06-30 17:04:29 -07:00
Oliver Breitwieser
cf76a143a2 libtomlc99: Update version
The PR for shared libraries has been merged upstream -> add new version.
2019-06-30 16:02:08 -07:00
Christoph Junghans
7f2e364fa1
legion: added recent releases (#11889) 2019-06-29 07:12:24 -06:00
Justin S
7f6266eef6 r-intervals: new package at 0.15.1 (#11884) 2019-06-28 19:42:55 -04:00
Carson Woods
5873beb83f qthreads package: make hwloc dependency optional and add version 1.14 (#11780) 2019-06-28 11:43:06 -07:00
Andreas Baumbach
5e9437866b New package: libtomlc99 (#11811) 2019-06-28 11:16:34 -07:00
Hironori-Yamaji
d5402147f0 bib2xhtml: replace version and change the download url (#11837)
The old version was no longer available for download
2019-06-28 11:03:54 -07:00
Matthieu Dorier
46c1513296 PMDK package: requires ncurses dependency (#11868) 2019-06-28 10:15:06 -07:00
Toyohisa Kameyama
d8f4e0a565 OTF package: use autotools. (#11873) 2019-06-28 10:13:21 -07:00
Toyohisa Kameyama
ae8710fa36 blast-plus package: remove --with-64 on ARM. (#11877)
This configure option is not supported on ARM
2019-06-28 10:11:04 -07:00
Michael Kuhn
ac76e4692f likwid package: Fix build with version 4.3.4 (#11878) 2019-06-28 10:05:38 -07:00
ktsai7
d48226b260 Update package.py (#11872) 2019-06-28 09:39:59 -06:00
Michael Kuhn
d2de78ab00 fenics, llvm: Fix package names being overriden (#11879)
Setting name within the package class allows overriding the package
name, which both packages do using several for loops.

Fixes #11789
2019-06-28 15:59:19 +02:00
Christoph Junghans
d6ecc29e4b
portage: add v1.2.2 (#11842)
* portage: add v1.2.2

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* flake8
2019-06-28 06:39:26 -06:00
Toyohisa Kameyama
ff877a567e Gotcha package: fixed to build on ARM. (#11840)
Apply patch to current version which has not yet been merged in the
upstream package repo.
2019-06-27 15:34:11 -07:00
Derick Huth
81db89b5e7 New packages: Chill and IEGenLib (#11406)
* Add Chill package
* Add IEGenLib package, a dependency of Chill
2019-06-27 13:41:06 -07:00
Michael Kuhn
f5f2b05c5b pkgconf: Add 1.6.1 (#11863) 2019-06-27 22:15:04 +02:00
Christoph Junghans
8a51215c36
bml: add v1.3.1 (#11856) 2019-06-27 10:57:09 -06:00
Hironori-Yamaji
c48b67ccd7 f90cache: change the download url (#11838)
* f90cache: change the download url

* f90cache: added the download url for ver 0.99
2019-06-27 12:55:48 -04:00
Hironori-Yamaji
9ed4db6eea tcsh: change the download url, add version 6.21.00 (#11836)
* tcsh: change the download url, add version 6.21.00

* tcsh: change the download url

* tcsh: Fix checksum for 6.20.00
2019-06-27 12:53:43 -04:00
Mark Olesen
0119812781 Update openfoam (#11866)
* OpenFOAM: rationalize architecture options

- older versions of OpenFOAM had WM_ARCH_OPTION to choose a 32-bit
  build on 64-bit architectures. This is not exactly relevant anymore
  and has now been largely removed from OpenFOAM.

- simultaneously the newest version of OpenFOAM has rationalized the
  handling of special settings for KNL by rolling these into the
  compiler options. We now do the same thing here in spack.

  1. Reuse the internal variable arch_option to convey processor-specific
     optimizations and add these into the C++OPT=... statement.
  2. Drop spack support for configuring a 32-bit build on 64-bit
     hardware.

These changes can also be applied to older OpenFOAM versions, and to
various OpenFOAM forks without issue.

* update openfoam versions. New release 1906, patched 1812 version.
2019-06-27 11:14:33 -05:00
Michael Kuhn
eb00436ec8 font-util: Add missing mkfontdir build dependency (#11865)
Some of the fonts now included in font-util need mkfontdir to build.
2019-06-27 15:53:05 +02:00
Michael Kuhn
5669144d22 Fix pkgconfig dependencies (#11864)
pkgconfig is the correct virtual dependency.
2019-06-27 14:56:42 +02:00
Toyohisa Kameyama
1c779608b2 cbtf-krell: fixed to build on ARM. (#11859) 2019-06-27 11:55:15 +02:00
Toyohisa Kameyama
977b2621f9 font-util: fix fontname. (#11860) 2019-06-27 11:54:23 +02:00
Satish Balay
85372ae102 petsc: add version 3.11.3 (#11857) 2019-06-27 07:02:03 +02:00
Michael Kuhn
75adb54d51 cdo: Remove obsolete patch (#11854)
Commit ea3e1521fe removed version
1.9.7rc2, making the patch for gcc@9 obsolete.
2019-06-26 19:36:41 -05:00
Michael Kuhn
0ef3b4c578 ncl: Fix build (#11855)
ncl does not build with newer versions of gdal (or rather proj). This
also needs a small change to gdal, otherwise we end up with both proj@5
and proj@6 in the spec.
2019-06-26 19:36:29 -05:00
Greg Becker
a0f2d6a8b9 Make yaml-cpp build with libc++ (#10504)
- Separate `yaml-cpp` tests into variant
- Make conflict between `yaml-cpp` tests and `libc++` explicit
2019-06-26 14:29:09 -07:00
ktsai7
ba5530bb42 added min version for gasnet and legion (#11853)
* added min version for gasnet and legion

* Update package.py

* Update package.py

* Update package.py
2019-06-26 14:46:18 -06:00
Douglas Duckworth
27b07811dd RELION package: add version 3.0.6 (#11851) 2019-06-26 09:57:14 -07:00
Toyohisa Kameyama
e49c101f05 X11fonts: use autotools for new architecture host (#11785)
* Remove individual font-* packages and add them as resources of the
  font-util package
* Update font-util package to Autotools-based package, and call
  autoreconf to regenerate the old configure script
* Add font-adobe-utopia-type1
2019-06-26 08:26:37 -07:00
Adam J. Stewart
5c5d6cad44 Rename py-pytables -> py-tables (#11847) 2019-06-25 21:32:49 -04:00
Satish Balay
ef48219f15 remove binary file that got added inadvertently via #11828 (#11848) 2019-06-25 21:31:36 -04:00
Christoph Junghans
718af821d1 pfunit: fixed a typo (#11843) 2019-06-25 14:06:52 -04:00
Chuck Atkins
f20c97168d
gnutls: workaround guile build error on macos (#11751) 2019-06-25 13:08:28 -04:00
jthies
6bbc7e8d9b phist can't be compiled with gcc older than 4.9.2 (#11677)
* phist can't be compiled with gcc older than 4.9.2
2019-06-25 12:53:21 -04:00
Ben Morgan
531114cd6c
fmt: Add version 5.3.0 with cxxstd variant support (#11799)
* fmt: Add cxxstd variant, plus cmake/c++ patches

Spack supported versions of fmt default to C++11 for versions
less than 5, C++14 greater than 5, with fmt implementing
fallbacks to whatever compiler supports.

To give better ABI compatibility and use of newer standards, provide
a `cxxstd` variant defaulting to 11 with 98-17 options. Use cmake_args
to set CMAKE_CXX_STANDARD as appropriate, plus use of `FMT_USE_CPP11`
option for C++98 builds. Use `conflicts` to disable use of certain
standards in versions that don't support, or fail the build, with
those standards.

Add patches to unify use of `CMAKE_CXX_STANDARD` in 3.0 versions,
remove hard-coding of compiler flags in `fmt-config.cmake`, and
prevent use of C++11 features in 4.1.0 when in supported C++98
mode.

Default to not building documents as no dependency on Doxygen is
yet present, and they are not part of the "all" build.

* Use CMake to enforce C++ standard support

Fail configure step if fmt tries to build with a cxxstd variant
not supported by the compiler (or known to CMake).

* fmt: New version 5.3.0
2019-06-25 12:01:31 +01:00
rvinaybharadwaj
fa563f0f55 Bumping-up miniVite to version 1.1 (#11828)
* Bumping-up miniVite to version 1.1

* Keeping both version of miniVite

* Changed to >=
2019-06-24 19:41:01 -06:00
Justin S
5b3f196bc2 New package: Rodinia (starting at 3.1) (#11650) 2019-06-24 18:32:46 -07:00
Carson Woods
ad14432e66 UCX package: add versions 1.5.1/1.5.2 (#11832) 2019-06-24 18:21:06 -07:00
Carson Woods
f10b806bde Singularity package: add version 3.2.1 (#11833) 2019-06-24 18:20:23 -07:00
Denis Davydov
8e89a82076 clamav: add new package (#11818)
* clamav: add new package

* fix flake8

* remove --dsable lines
2019-06-24 19:47:15 -04:00
Gregory Lee
16ff38b784 add glx variant to libepoxy (#11814) 2019-06-24 17:57:17 -04:00
Glenn Johnson
c575cc46db The py-pytables package depends on hdf5-blosc (#11823)
* The py-pytables package depends on hdf5-blosc

* Further modifications to py-pytables package

The 3.2.2 version of py-pytables should still build with internal blosc.
The issue with locking in a multithreaded environment has been
fixed/worked around in version 3.3.

Also, add bzip2 and lzo variants.
2019-06-24 17:56:51 -04:00
Satish Balay
1ec3d78441 hypre: superlu-dist-link-2.15.0.patch is now in hypre@develop (#11829) 2019-06-24 17:55:04 -04:00
Andreas Baumbach
b39a992528 add new package py-absl-py (#11812)
* add new package py-absl-py

Change-Id: I248d30e0a3e5e05d9ea4027d97a85545c63d1125

* Update package.py

* Update package.py

* Update package.py

* Update package.py
2019-06-23 17:33:36 -04:00
Andreas Baumbach
2687af2c53 New package py-astor (and test dependency py-astunparse) (#11813)
* add package py-astor

Change-Id: I2f6becfb5e9771170bf2df5eb629920e1c0998d7

* add new package py-astunparse

Change-Id: Id2d3e8dec28e720ed1cb121dad0d1a405c27ca29

* Update package.py

* Update package.py

* Update package.py
2019-06-23 17:33:22 -04:00
Christoph Junghans
d65e6ad7e3 hypre: add v2.16.0 (#11821)
* hypre: add v2.16.0

* update checksums

* hypre: xsdk-0.2.0 tag is missing on the new repo
2019-06-23 17:33:05 -04:00
Neil Flood
681245c7ed awscli: new package (#11796)
* awscli: new package

* More precise py-pyyaml version dep, as per setup.py
2019-06-23 14:54:48 -04:00
Adam J. Stewart
9c54d8ef6c
r-sf may not support PROJ.6 (#11767)
* r-sf may not support PROJ.6

* Add comment explaining dep
2019-06-23 11:35:33 -05:00
Sinan
c83f8a425d new package/py-blessed (#11656)
* new package/py-blessed

* make flake8 happy

* fix docstring

* tab to spaces

* Update var/spack/repos/builtin/packages/py-blessed/package.py

specify dependency version.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-blessed/package.py

specify dependency version

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* add setuptools as depedency
2019-06-22 17:05:03 -05:00
Gerasimos Chourdakis
98d21193ff precice: add version 1.5.1 (#11809) 2019-06-21 07:56:35 -04:00
Toyohisa Kameyama
e19d7b9a49 exonerate use autotools. (#11805) 2019-06-21 07:55:29 -04:00
Toyohisa Kameyama
1827b4c5cb mpileaks: use autotools. (#11808) 2019-06-21 07:55:04 -04:00
Toyohisa Kameyama
9955b15f4e mpe2 use autotools and add libx11 dependency. (#11807) 2019-06-21 07:54:51 -04:00
Gregory Lee
894d01e482 converting to launchmon to autotools package (#11794) 2019-06-21 07:47:42 -04:00
Valentin Reis
e6264030d7 New packages: nrm and libnrm (#11777)
Also add new py-warlock, py-jsonpatch, and py-jsonpointer packages as
dependencies of nrm.
2019-06-20 19:21:44 -07:00
Mark W. Krentel
a76bacd594 boost: add variant for symbol visibility (#11801)
Starting with 1.69.0, boost added a bjam option for the default symbol
visibility.  Up to 1.68.0, the value was always 'global'.  1.69.0
changed the default to 'hidden' but added an option.

Most packages will work with hidden and won't notice.  But some
packages may discover that an interface that they rely on is now
hidden and inaccessible.

https://boostorg.github.io/build/manual/develop/index.html#bbv2.builtin.features.visibility
2019-06-20 17:43:25 -04:00
Justin S
686eaff30c subread: add 1.6.4 (#11800) 2019-06-20 13:54:20 -05:00
Peter Scheibel
284ae9d1cc
Resources: use expanded archive name by default (#11688)
For resources, it is desirable to use the expanded archive name of
the resource as the name of the directory when adding it to the root
staging area.

#11528 established 'spack-src' as the universal directory where
source files are placed, which also affected the behavior of
resources managed with Stages.

This adds a new property ('srcdir') to Stage to remember the name of
the expanded source directory, and uses this as the default name when
placing a resource directory in the root staging area.

This also:

* Ensures that downloaded sources are archived using the expanded
  archive name (otherwise Spack will not be able to determine the
  original directory name when using a cached archive).
* Updates working_dir context manager to guarantee restoration of
  original working directory when an exception occurs
* Adds a "temp_cwd" context manager which creates a temporary
  directory and sets it as the working directory
2019-06-20 11:09:31 -07:00
Adam J. Stewart
4858d8c275 Add GDL 0.9.9 (#11760)
* Add GDL 0.9.9

* Add comment on PROJ dependency
2019-06-20 13:36:10 -04:00
Neil Flood
0cec7c6590 py-python-dateutil: Version 2.7.0 acquired dependency on setuptools-scm (#11795) 2019-06-20 09:18:04 -05:00
Carson Woods
e7eb9ce1af Bump netcdf-fortran version to 4.4.5 (#11790) 2019-06-19 17:38:17 -05:00
Oliver Breitwieser
8b1575fa0a py-matplotlib: Fix dependencies in [2.1.0:3.0.0) (#11787)
Starting with 2.1.0, backports.functools_lru_cache replaces functools32
when using python 2.7.x until python2 support is dropped in 3.0.0.

Change-Id: I8db61eac975da0042f6f5babe0f5f0c92807200e
2019-06-19 17:38:04 -05:00