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2019-07-29PISM package: add version 1.1.4 (#12083)Adam J. Stewart1-1/+3
2019-07-29Fix some Mac constraint checks (#12138)Adam J. Stewart3-10/+6
* 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.
2019-07-29Add conflicts statement for Python-3.6.7+ and Intel compilerGlenn P Johnson1-0/+5
Python-3.6.7 and up do not build with the Intel compiler - https://bugs.python.org/issue35473 - https://bugs.python.org/issue37415
2019-07-29zeromq package: choose URL based on version; add versions (#12149)Federico Ficarelli1-4/+14
* 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
2019-07-29Gromacs package: add openmp, mdrun_only, double_precision options (#12150)Hironori-Yamaji1-0/+20
2019-07-29New package: py-pytest-isort (#12160)Adam J. Stewart1-0/+19
2019-07-29LLVM package: add optional libomp_tsan support (#11793)Jon Rood1-0/+8
This is only available for LLVM version 6 or greater. So this also adds a conflict statement for earlier versions of LLVM.
2019-07-29update cmake 3.15.1 checksum (#12182)Owen Solberg1-1/+1
2019-07-29OpenGL package: always provides gl (#12158)Adam J. Stewart1-0/+1
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).
2019-07-29py-scipy package: add version 1.3.0 (#12171)Adam J. Stewart1-9/+16
* 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
2019-07-29New package: py-torchvision (#12175)Adam J. Stewart1-0/+33
2019-07-29PyTorch package: add version 1.1.0 (#12174)Adam J. Stewart1-2/+41
* 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
2019-07-29Change dependencies to use virtual jpeg package (#12179)Seth R. Johnson6-6/+6
This prevents conflicts between descendents that depend on an unintentional arbitrary jpeg implementation.
2019-07-28Add a new version (7.2) of draco. (#11852)Kelly (KT) Thompson1-11/+40
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.
2019-07-28Update checksum of fmt 5.3.0 (#12037)Jeongseok Lee1-1/+1
2019-07-28Prevent conflicts between libuuid and Apple Cocoa Framework on Mac (#12166)Seth R. Johnson1-1/+7
* 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
2019-07-27Bump version for BLIS (#12162)Sajid Ali1-0/+2
modified: var/spack/repos/builtin/packages/blis/package.py
2019-07-27cmake: Bump to 3.15.1 (#12151)Chuck Atkins1-0/+1
2019-07-27environment-modules package: add version 4.3.0 (#12155)Xavier Delaruelle1-1/+7
2019-07-26adios2: Patch findmpi for downstream issues. (#12152)Chuck Atkins2-0/+843
2019-07-26kealib: fix incorrect md5sum for v1.4.11 (#12126)Sinan1-6/+8
* fix incorrect md5sum for v1.4.11 * fix url and replace md5 with sha256 * add mainter
2019-07-26update to kim-api-2.1.1 and openkim-models-2019-07-25 (#12137)Ryan S. Elliott2-8/+25
* 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
2019-07-26Add flake8 3.7.8 (#12141)Adam J. Stewart1-43/+34
2019-07-26libxc: Make configure recognize Fujitsu compiler (#12147)t-karatsu2-0/+23
2019-07-26py-pyomo: new package at 5.6.6 (#12134)Justin S1-0/+27
* py-pyomo: new package at 5.6.6 * py-pyomo: add missing deps, python constraint
2019-07-26Small fixes for font-util package (#12148)Rémi Lacroix1-4/+1
* 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.
2019-07-26Add GDAL 3.0.1 (#12140)Adam J. Stewart1-3/+5
2019-07-26Add Python 3.7.4 (#12142)Adam J. Stewart1-1/+4
2019-07-25googletest: Fix reversed +pthreads option (#12128)Oliver Breitwieser1-1/+1
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
2019-07-25interproscan: new package at 5.36-75.0 (#12130)Justin S1-0/+33
2019-07-25git-lfs: add version 2.8.0 (#12131)Matthias Diener1-0/+1
2019-07-25Patches for graphviz (#12133)Glenn Johnson1-0/+11
- patch to build with qt5, enabling gvedit to build - two patches to compile graphviz with icc
2019-07-25xsdk: phist has a conflict with gcc version <= gcc-4.9.1 (#11946)Satish Balay1-3/+4
* 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
2019-07-25cmake: Add a patch to revert a findmpi regression (#12129)Chuck Atkins2-0/+33
2019-07-25catch: more versions, new and older. (#12123)Chris Green1-0/+9
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.
2019-07-25lame & libmad: Added two new packages for sox mp3 support. (#11964)simo-tuomisto4-0/+163
* 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
2019-07-25gdal: added versions 2.4.2 and 3.0.1 (#12125)Sinan1-0/+2
2019-07-25geant4: improvements with respect to building against CLHEP. (#12124)Chris Green2-6/+42
2019-07-24new command: `spack maintainers` queries package maintainersTodd Gamblin2-0/+40
- 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
2019-07-24Add py-setuptools as a build dependency for py-absl-py (#12109)Glenn Johnson1-0/+1
I needed to add py-setuptools to get py-absl-py to build.
2019-07-24Add conflicts statement to freetype for icc (#12111)Glenn Johnson1-0/+4
Freetype-2.8 and above use __builtin_shuffle which is not supported by icc.
2019-07-24Perl take in flags (#12112)t-karatsu1-0/+5
* perl: perl package takes in spack cflags. * fix for flake8 test.
2019-07-24nnvm: cmake bug is fixed. (#12113)Toyohisa Kameyama2-0/+21
2019-07-24rapidjson: Don't add -march=native on ARM and gcc 5.x or before. (#12117)Toyohisa Kameyama2-0/+17
2019-07-24QMCPACK Update July 2019 (#12097)Nichols A. Romero1-16/+9
* 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
2019-07-24Do not build c-blosc test if intel in spec (#12110)Glenn Johnson1-0/+4
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.
2019-07-24cmake: fix cxx98flag's name (#12114)t-karatsu1-1/+1
2019-07-23rocksdb: Don't add -march=native on ARM and gcc 5.x or before. (#12108)Toyohisa Kameyama1-0/+7
2019-07-23added relion 3.0.7 - removed deprecated versions (#12101)Douglas Duckworth1-7/+2
* relion - added v 3.0.7 and removed deprecated versions that have inferior performance * relion 3.0.7 does require cuda 9 or above
2019-07-23isaac-server: Don't add -march=native on ARM and gcc 5.x or before. (#12042)Toyohisa Kameyama2-0/+19
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