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2019-08-13add charliecloud master branch; add dependencies (#12327)Jordan Ogas1-0/+13
* add master and dependencies * remove gcc and make * add variants, make doc and ch-grow dependencies optional * capitalize description sentence * move dependencies and variants below version block * fix typos
2019-08-13packages/umoci (#12346)Daryl W. Grunau1-0/+39
* bump eospac version * Revert "bump eospac version" This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da. * new package: umoci * Package -> MakefilePackage * add missing build phase * relax expand=False requirement
2019-08-13add new versions (#12393)Sinan1-0/+2
2019-08-13add new version (#12394)Sinan1-0/+1
2019-08-13add new version (#12395)Sinan1-0/+1
2019-08-13subread: build on ARM. (#12400)Toyohisa Kameyama1-0/+14
2019-08-13package/gromacs: simd optimizations autodetection for more versions (#12402)Ricardo Silva3-2/+14
* gromacs: fix simd detection for pre 2018 versions * pre 2018 the cmake file was named differently * fixed up post 2018 patch file which was non pretty * Trim patch
2019-08-13Add version 2.4.0 for cantera. (#12405)健美猞猁1-0/+1
2019-08-13patch opa-psm2 to build with spack wrappers (#12407)Gregory Lee2-1/+54
2019-08-13Fix package gpgme dependency (#12410)Daryl W. Grunau1-0/+1
* bump eospac version * Revert "bump eospac version" This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da. * build depends on gnupg which provides gpgsm binary
2019-08-13gcc: Add 9.2.0 (#12411)Michael Kuhn1-0/+1
2019-08-13Fix "spack loads" when retrieving upstream modules (#12203)Peter Scheibel1-9/+3
Fixes #12062 406c791 addressed "spack module load" for upstream modules but not the "spack module loads" command. This applies the same fixes from 406c791 to "spack module loads".
2019-08-13CP2K/SIRIUS: add support for building with CUDA, fix CP2K build with MKL ↵Tiziano Müller3-16/+169
(#11418) * cp2k/sirius: add CUDA support * cp2k: fix building with MKL * sirius: make sure to link against Spacks blas/lapack/scalapack
2019-08-13new package: asagi: create package.py (#11931)brietzke1-0/+73
* Create package.py * applied reviewer suggestions * Update package.py * remove CamelCase from variant names * add comment on why fetching package via git * found typo in variant to cmake-argumentlist translation * rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition * Revert "rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition" This reverts commit 58e8cf7d93c5665f0b4b50228946857734716cef. * remove version-preference
2019-08-12Package/grass: fix iconv linking issue (#12165)Sinan1-0/+9
* fix iconv linking issue, package_grass fix linking iconv, add more comments
2019-08-12singularity: update version to 3.3.0 (#12295)Owen Solberg1-2/+8
* add checksum for singularity release 3.3.0 * update singularity doc URL URL at the lbl.gov domain has message saying: "This website is going away soon! Update your bookmarks!" * add note about build log file for post-install step * provide links to both 2.x and 3.x security docs * remove whitespace. Passing flake8 confirmed locally this time :) * add TODO comment for fakeroot support
2019-08-12New package: TexStudio (#12301)Jean-Paul Pelteret3-3/+86
* Poppler library: Add new versions * Poppler library: Allow building with QT4 * Poppler library: Install header files * Add patch to Poppler package * Add new package: TexStudio
2019-08-12blaze: converted to CMakePackage (#12357)Russell J. Hewett1-4/+4
The previous version does not properly install the required cmake configuration files for blaze-lib, so find_package does not work correctly. This patch converts the blaze-lib package to use CMakePackage, adds the required cmake dependency, and removes the install() member function, which is not working correctly and is no longer needed.
2019-08-12gtksourceview: new package (#12387)Geoffrey Oxberry1-0/+49
2019-08-12openblas: fix target detection for cross-compiling (#12390)Janne Blomqvist1-1/+1
In a review of a previous pull request ( https://github.com/spack/spack/pull/10713 ) it was mentioned that the proper way to figure out the target architecture is via spec.architecture.target. This patch fixes this for the openblas package. Signed-off-by: Janne Blomqvist <janne.blomqvist@aalto.fi>
2019-08-12openblas@0.3.7: New version (#12391)Janne Blomqvist1-0/+1
This adds OpenBLAS 0.3.7 (released 2019-08-11).
2019-08-12Apply xl patch for cce@9: to fix cmake. (#12392)Kelly (KT) Thompson1-0/+1
2019-08-12packages/skopeo (#12348)Daryl W. Grunau1-0/+43
* bump eospac version * Revert "bump eospac version" This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da. * new package: skopeo * address flake8 issues * address adamjstewart's comments * use the Executable class and undocumented 'str' feature for output * Package -> MakefilePackage * add missing build phase * patch -> edit phase
2019-08-11bugfix: Python 2.6 parsing error (#11867)Massimiliano Culpo5-12/+4
Apparently shlex.split can't deal with unicode encoded characters in Python2.6. The solution is to convert to str before calling the function.
2019-08-11Update SWIG versions and add Fortran fork (#12185)Seth R. Johnson1-1/+17
* Add git repositories for SWIG and SWIG-Fortran * Fix typo in documentation * Move 'master' to top of SWIG version list
2019-08-11Fix py-matplotlib build with Intel compiler (#12144)Glenn Johnson1-5/+0
Not sure what happened between #5321 and now but the CC=CXX fix now prevents py-matplotlib from building with the Intel compiler. I verified with versions of py-matplotlib from 2.0.2 to 3.0.2 and intel-17.0.4 and 19.0.4 that py-matplotlib successfully builds with the Intel compiler without that code.
2019-08-11Use correct GCC installation when installing clang with GCC (#12381)Seth R. Johnson1-0/+4
2019-08-11new package: qwtpolar (#12382)Sinan1-0/+27
* create qwtpolar package * patch config files so that qwtpolar successfully builds * make flake8 happy
2019-08-11Add preCICE xSDK support (#12356)Frédéric Simonis1-13/+56
* Add preCICE xSDK support * Cleanup generation of cmake arguments * Generalize numpy include * Fix python spec Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Fix numpy spec Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-08-10Add NCCL 2.4.8-1 (#12362)Adam J. Stewart1-1/+2
2019-08-10Port py-poster to Python 3 (#12363)Adam J. Stewart2-0/+446
* Port py-poster to Python 3 * Forgot the patch
2019-08-10Add py-clipboard package (#12364)Adam J. Stewart1-0/+18
2019-08-10Add py-gee-asset-manager package (#12365)Adam J. Stewart1-0/+27
2019-08-10Add py-geeadd package (#12366)Adam J. Stewart1-0/+28
2019-08-10Add py-geeup package (#12367)Adam J. Stewart1-0/+34
2019-08-10Add py-google-api-core package (#12368)Adam J. Stewart1-0/+25
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
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