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2019-08-10Add py-google-cloud-core package (#12369)Adam J. Stewart1-0/+19
2019-08-10Add py-google-cloud-storage package (#12370)Adam J. Stewart1-0/+21
2019-08-10Add py-google-resumable-media package (#12371)Adam J. Stewart1-0/+19
2019-08-10Add py-googleapis-common-protos package (#12372)Adam J. Stewart1-0/+18
2019-08-10Add py-oauth2client package (#12373)Adam J. Stewart1-0/+27
2019-08-10Add py-pathlib package (#12374)Adam J. Stewart1-0/+19
2019-08-10Add py-pyperclip package (#12375)Adam J. Stewart1-0/+17
2019-08-10Add py-pysmartdl package (#12376)Adam J. Stewart1-0/+18
2019-08-10Add py-retrying package (#12377)Adam J. Stewart1-0/+20
2019-08-10Add py-selenium package (#12378)Adam J. Stewart1-0/+21
2019-08-10 modified: var/spack/repos/builtin/packages/libflame/package.py (#12379)Sajid Ali1-0/+1
2019-08-10libconfig: add version 1.7.1 (#12324)Cameron Smith1-1/+4
* libconfig: add version 1.7.1 * move 1.7.1 above 1.6, latest version is preferred
2019-08-10Fix build for moab 4.9.2 on gcc8 (#12328)Seth R. Johnson2-0/+13
``` 5 errors found in build log: 609 CXX mbpart.o 610 CXX quality.o 611 CXX umr.o 612 CXX merge.o 613 CXX parread.o 614 mbpart.cpp: In function 'int main(int, char**)': >> 615 mbpart.cpp:494:19: error: no match for 'operator<<' (operand types are 'std::ostream' {aka 'std::basic_ostream<char>'} and 'std::ostri ngstream' {aka 'std::__cxx11::basic_ostringstream<char>'}) 616 std::cerr << tmp_output_file << " : failed to write file." << std::endl; 617 ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 618 mbpart.cpp:494:19: note: candidate: 'operator<<(int, int)' <built-i n> 619 mbpart.cpp:494:19: note: no known conversion for argument 2 from 'std::ostringstream' {aka 'std::__cxx11::basic_ostringstream<char>' } to 'int' 620 In file included from /software/user_tools/centos-7.2.1511/cades-ns ed-spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-8.2.0-uc6sbum ioobdbkw4rwfyn2givi4nyvwq/include/c++/8.2.0/iterator:64, 621 from /software/user_tools/centos-7.2.1511/cades-ns ed-spack/var/spack/stage/moab-4.9.2-77uuzmj4ofb7z7vz6m25sftyks7p5do 7/spack-src/src/moab/Range.hpp:167, ... 886 /software/user_tools/centos-7.2.1511/cades-nsed-spack/opt/spack/lin ux-centos7-x86_64/gcc-4.8.5/gcc-8.2.0-uc6sbumioobdbkw4rwfyn2givi4ny vwq/include/c++/8.2.0/ostream:682:5: note: candidate: 'template<cla ss _Ostream, class _Tp> typename std::enable_if<std::__and_<std::__ not_<std::is_lvalue_reference<_Tp> >, std::__is_convertible_to_basi c_ostream<_Ostream>, std::__is_insertable<typename std::__is_conver tible_to_basic_ostream<_Tp>::__ostream_type, const _Tp&, void> >::v alue, typename std::__is_convertible_to_basic_ostream<_Tp>::__ostre am_type>::type std::operator<<(_Ostream&&, const _Tp&)' 887 operator<<(_Ostream&& __os, const _Tp& __x) 888 ^~~~~~~~ 889 /software/user_tools/centos-7.2.1511/cades-nsed-spack/opt/spack/lin ux-centos7-x86_64/gcc-4.8.5/gcc-8.2.0-uc6sbumioobdbkw4rwfyn2givi4ny vwq/include/c++/8.2.0/ostream:682:5: note: template argument dedu ction/substitution failed: 890 /software/user_tools/centos-7.2.1511/cades-nsed-spack/opt/spack/lin ux-centos7-x86_64/gcc-4.8.5/gcc-8.2.0-uc6sbumioobdbkw4rwfyn2givi4ny vwq/include/c++/8.2.0/ostream: In substitution of 'template<class _ Ostream, class _Tp> typename std::enable_if<std::__and_<std::__not_ <std::is_lvalue_reference<_Tp> >, std::__is_convertible_to_basic_os tream<_Ostream>, std::__is_insertable<typename std::__is_convertibl e_to_basic_ostream<_Tp>::__ostream_type, const _Tp&, void> >::value , typename std::__is_convertible_to_basic_ostream<_Tp>::__ostream_t ype>::type std::operator<<(_Ostream&&, const _Tp&) [with _Ostream = std::basic_ostream<char>&; _Tp = std::__cxx11::basic_ostringstream <char>]': 891 mbpart.cpp:494:22: required from here >> 892 /software/user_tools/centos-7.2.1511/cades-nsed-spack/opt/spack/lin ux-centos7-x86_64/gcc-4.8.5/gcc-8.2.0-uc6sbumioobdbkw4rwfyn2givi4ny vwq/include/c++/8.2.0/ostream:682:5: error: no type named 'type' in 'struct std::enable_if<false, std::basic_ostream<char>&>' 893 CXXLD mbdepth 894 CXXLD hexmodops >> 895 make[2]: *** [mbpart.o] Error 1 896 make[2]: *** Waiting for unfinished jobs.... 897 make[2]: Leaving directory `/localscratch/tmp/s3j-spack/spack-stage /spack-stage-NT13kT/spack-src/tools' >> 898 make[1]: *** [all-recursive] Error 1 899 make[1]: Leaving directory `/localscratch/tmp/s3j-spack/spack-stage /spack-stage-NT13kT/spack-src/tools' >> 900 make: *** [all-recursive] Error 1 ```
2019-08-09py-numexpr: switch from PyPI to GitHub download (#12360)Adam J. Stewart1-7/+7
2019-08-09gromacs: fix CPU optimizations detection (simd=auto) (#12354)Ricardo Silva2-0/+14
* SL-637 * https://redmine.gromacs.org/issues/2927 * tested with cmake 3.14.4 and 3.15.1
2019-08-09Updated Blaze version 3.5 and added access to master branch (#12341)Russell J. Hewett1-1/+4
* blaze: added version 3.5 * blaze: added access to bleeding edge
2019-08-09flatcc: add version 0.5.3 (#12358)Cameron Stanavige1-1/+2
This updates the flatcc package to have the latest version.
2019-08-09gnome-common: new package (#12359)Geoffrey Oxberry1-0/+34
2019-08-09Add new package: libfive@master (#12334)Geoffrey Oxberry1-0/+24
2019-08-09sdl2: fix dependency for libxext and build on ARM (#12351)Toyohisa Kameyama1-3/+11
1. add dependency for libxext2. 2. SSEMATH is off is aarch64. 3. reformat comment for flake8.
2019-08-09New Plink beta version (#12352)Sean McGrath1-0/+6
* Plink 1.9 Beta 6.10 added * Typo Fix
2019-08-09newpackage/tippecanoe (#12319)Sinan1-0/+23
* newpackage/tippecanoe * make flake8 happy * add "r" for raw text
2019-08-09bugfix: hunspell: add missing gettext dependency (#12347)Geoffrey Oxberry1-0/+8
* hunspell: write autoreconf method to triage error This commit fixes the error described in GitHub issue `AutotoolsPackage` class attempts to call `libtoolize`, which doesn't exist on macOS systems that externally install `libtool` in Spack via Homebrew -- Homebrew installzes GNU libtoolize as `glibtoolize`. The fix is to call `autoreconf` only, and GitHub pull request #12344 makes this change in AutotoolsPackage (https://github.com/spack/spack/pull/12344). However, while waiting for that pull request to be merged, overriding the `autoreconf` method achieves the same result for a self-contained fix. This self-contained fix is necessary to fix a dependency bug in the `hunspell` package. * hunspell: add missing gettext dependency * hunspell: add version 1.7.0
2019-08-09Fixed broken iegenlib package (#12229)Derick Huth1-2/+18
* Fixed broken iegenlib package * [IEGenLib] fixed for style * [IEGenLib] style fixes * [IEGenLib] removed CMAKE_BUILD_TYPE option from config_args
2019-08-08Added checksum for binutils@2.32 (#12350)angel-devicente1-0/+1
2019-08-08bugfix: nested matrices in spec lists (#12320)Greg Becker6-27/+88
* stack concretization: fix handling of variant names with dashes * spec_list: bugfix for handling nested matrices
2019-08-08enchant@2.2.5: new package (#12349)Geoffrey Oxberry1-0/+45
2019-08-08hisea: build on ARM. (#12302)Toyohisa Kameyama1-0/+4
2019-08-08Add new releases of Cube Tools, Opari2, OTF2, and Score-P (#12303)Marc-Andre Hermanns6-0/+8
2019-08-08new package: Cromwell (#12309)Owen Solberg4-0/+86
* add new package cromwell * fix flake8 errors, add cromwell-womtool package * change name of cromwell to cromwell-server * renamed cromwell-server to just cromwell * update description to what is in the project docs * fixing format call for python2.6 compatibility
2019-08-08new package: aria2 (#12318)Sinan1-0/+23
* new package: aria2 * tidy up
2019-08-08netcdf-cxx4: add m4 dep for call to autoreconf (#12325)Cameron Smith1-0/+1
2019-08-08guile: add versions 2.2.1 through 2.2.6 (#12333)Geoffrey Oxberry1-0/+6
2019-08-08Re-add py-cython dependency to py-tables (#12338)Adam J. Stewart1-4/+7
2019-08-08Add py-certifi 2019.6.16 (#12339)Adam J. Stewart1-1/+3
2019-08-08Allow Spack to uninstall external extensions without permissions (#11991)Adam J. Stewart1-3/+7
* Allow Spack to uninstall external extensions without permissions Raise when self.projections is not empty
2019-08-08openssl package: add versions including 1.1.1c (#12342)Adam J. Stewart1-11/+19
* Add comment that 1.0.1 versions are no longer supported * Add comment that 1.0.2 versions are only supported up to December 2019 * Add versions 1.0.2s, 1.0.2r, and 1.0.2p * Add versions 1.1.0k, 1.1.0j, and 1.1.0i * Add version 1.1.1c * Add comment that 1.1.0 versions are only supported up to September 2019
2019-08-08docs: fix compiler config (#12330)Pariksheet Nanda1-2/+3
It's no longer possible to set compiler flags under as an entry under "paths" in compilers.yaml; instead the user must list these under the "flags" section. This updates the docs accordingly.
2019-08-08Fix typo in yaml config docs (#12312)Adam J. Stewart1-1/+1
2019-08-07bugfix: spack stacks mixed dependency and non-dep constraints (#12315)Greg Becker1-1/+1
Spack stacks drop invalid dependencies applied to packages by a spec_list matrix operation Without this fix, Spack would raise an error if orthogonal dependency constraints and non-dependency constraints were applied to the same package by a matrix and the dependency constraint was invalid for that package. This is an error, fixed by this PR. An example failing configuration: spack: definitions: - packages: [libelf, hdf5+mpi] - compilers: ['%gcc'] - mpis: [^openmpi] specs: - matrix: - $packages - $compilers - $mpis
2019-08-07Revert "add maintainer review action to main.workflow" (#12316)Peter Scheibel1-9/+0
This reverts commit 54e3bc31f991200688044431f57ad8b3a25c12e8.
2019-08-07compiler bootstrapping: enable both single-node and multi-node DAGS(#12310)Peter Scheibel1-7/+15
5f74f22 enabled installing compilers for dependencies but not for the root package (and in particular not for DAGs which consist of one package) this enables bootstrapping compilers for both types of DAGs
2019-08-07Generalize STK package settings in Trilinos (#11917)Jon Rood1-21/+10
* Making STK package in Trilinos more general. * Remove comment about seacas exodus settings.
2019-08-07ncbi-toolkit: add version 22_0_0 (#12278)Pariksheet Nanda1-7/+36
* ncbi-toolkit: fix compiler+version restriction (spack/spack#12276) * ncbi-toolkit: update urls for current and archive releases * ncbi-toolkit: add compatibility for boost@1.69: * ncbi-toolkit: add compatibility for boost@1.70: * ENH: Add debug variant to significantly reduce install size * ncbi-toolkit: add archive url for 22_0_0 (spack/spack#12278)
2019-08-07Version 19.8.1 of PLASMA (#12299)Piotr Luszczek1-2/+1
* Remove unnecessary setting with buggy prefix Spack adds installation prefix by default and the "self." is missing * Add version 19.8.1 of PLASMA
2019-08-06new package: py-exodus (#12291)Daryl W. Grunau1-0/+20
2019-08-06ncurses: fix pic and opt flags (#12272)Mark W. Krentel1-2/+6
Resolves #11932. Move the PIC flags from CFLAGS on the configure line to the spack compiler wrapper for ncurses. The problem with the configure line for autotools is that specifying CFLAGS sets the entire flags, thus deleting the flags that configure would add itself. By default, if CFLAGS is unspecified, then configure picks a sensible default of `-g -O2`. But adding `-fPIC` erases these and it ends up building unoptimized.
2019-08-06pumi: new version 2.2.1 (#12282)Cameron Smith1-0/+1
2019-08-06tests: explain and test dependency flattening routines (#11993)Tamara Dahlgren3-1/+63
- Add comments to explain that `install_dependency_symlinks` and `flatten_dependencies` are actually used. - Add a test that exercises the routines.
2019-08-06graphviz package: add MacOS fixes and quartz support (#11128)Seth R. Johnson2-129/+112
* Add patch to detect newer versions of MacOS and to fix a typo in configure.ac (AM_LIBTOOLSFLAGS should be AM_LIBTOOLFLAGS) * Remove variant declarations for unsupported languages * Add support for quartz on MacOS * Add optional X Window support * Specifically build against qt@4 when building QT support * Point to appropriate C++ standard libraries when building with Clang on MacOS * Disable parallel build (for all platforms) * Increase verbosity of configure script by adding --disable-silent-rules
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