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8695 Commits

Author SHA1 Message Date
Adam J. Stewart
3c54e55546 Add py-google-cloud-storage package (#12370) 2019-08-10 11:51:27 -05:00
Adam J. Stewart
a3cc7eb4f7 Add py-google-resumable-media package (#12371) 2019-08-10 11:51:12 -05:00
Adam J. Stewart
b329d5f27f Add py-googleapis-common-protos package (#12372) 2019-08-10 11:50:58 -05:00
Adam J. Stewart
fbf386328c Add py-oauth2client package (#12373) 2019-08-10 11:50:43 -05:00
Adam J. Stewart
1d0f61816a Add py-pathlib package (#12374) 2019-08-10 11:50:24 -05:00
Adam J. Stewart
37e59cbd7e Add py-pyperclip package (#12375) 2019-08-10 11:50:10 -05:00
Adam J. Stewart
572bc5cc77 Add py-pysmartdl package (#12376) 2019-08-10 11:49:55 -05:00
Adam J. Stewart
3601f1c825 Add py-retrying package (#12377) 2019-08-10 11:49:41 -05:00
Adam J. Stewart
25b3946e0b Add py-selenium package (#12378) 2019-08-10 11:49:25 -05:00
Sajid Ali
48016366c8 modified: var/spack/repos/builtin/packages/libflame/package.py (#12379) 2019-08-10 11:48:58 -05:00
Cameron Smith
a4a30de8a1 libconfig: add version 1.7.1 (#12324) 
* libconfig: add version 1.7.1

* move 1.7.1 above 1.6, latest version is preferred
 2019-08-10 11:08:53 -05:00
Seth R. Johnson
54018b488a Fix build for moab 4.9.2 on gcc8 (#12328) 
```
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
```
 2019-08-10 11:08:13 -05:00
Adam J. Stewart
f9e6f0fb62 py-numexpr: switch from PyPI to GitHub download (#12360) 2019-08-09 22:27:34 -05:00
Ricardo Silva
c5849ce04f gromacs: fix CPU optimizations detection (simd=auto) (#12354) 
* SL-637
* https://redmine.gromacs.org/issues/2927
* tested with cmake 3.14.4 and 3.15.1
 2019-08-09 21:38:16 -05:00
Russell J. Hewett
7cc57d74e4 Updated Blaze version 3.5 and added access to master branch (#12341) 
* blaze: added version 3.5

* blaze: added access to bleeding edge
 2019-08-09 21:32:54 -05:00
Cameron Stanavige
13112d6b1c flatcc: add version 0.5.3 (#12358) 
This updates the flatcc package to have the latest version.
 2019-08-09 21:32:10 -05:00
Geoffrey Oxberry
28ffc1a4b9 gnome-common: new package (#12359) 2019-08-09 21:31:47 -05:00
Geoffrey Oxberry
92c65f3150 Add new package: libfive@master (#12334) 2019-08-09 18:10:00 -05:00
Toyohisa Kameyama
b54576abaf sdl2: fix dependency for libxext and build on ARM (#12351) 
1. add dependency for libxext2.
2. SSEMATH is off is aarch64.
3. reformat comment for flake8.
 2019-08-09 10:24:16 -05:00
Sean McGrath
74fe729be2 New Plink beta version (#12352) 
* Plink 1.9 Beta 6.10 added

* Typo Fix
 2019-08-09 10:22:18 -05:00
Sinan
a999092a93 newpackage/tippecanoe (#12319) 
* newpackage/tippecanoe

* make flake8 happy

* add "r" for raw text
 2019-08-09 10:18:26 -05:00
Geoffrey Oxberry
7b47178a53 bugfix: hunspell: add missing gettext dependency (#12347) 
* 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
 2019-08-09 10:17:57 -05:00
Derick Huth
850b2ad42e Fixed broken iegenlib package (#12229) 
* Fixed broken iegenlib package

* [IEGenLib] fixed for style

* [IEGenLib] style fixes

* [IEGenLib] removed CMAKE_BUILD_TYPE option from config_args
 2019-08-09 10:14:17 -05:00
angel-devicente
e203068125 Added checksum for binutils@2.32 (#12350) 2019-08-08 23:56:41 -05:00
Geoffrey Oxberry
9336a8be38 enchant@2.2.5: new package (#12349) 2019-08-08 22:50:06 -05:00
Toyohisa Kameyama
14bdd56004 hisea: build on ARM. (#12302) 2019-08-08 22:45:23 -05:00
Marc-Andre Hermanns
606246572a Add new releases of Cube Tools, Opari2, OTF2, and Score-P (#12303) 2019-08-08 22:44:33 -05:00
Owen Solberg
178476d8c8 new package: Cromwell (#12309) 
* 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
 2019-08-08 22:39:00 -05:00
Sinan
d1e8ea302f new package: aria2 (#12318) 
* new package: aria2

* tidy up
 2019-08-08 22:36:13 -05:00
Cameron Smith
51adb6a4ef netcdf-cxx4: add m4 dep for call to autoreconf (#12325) 2019-08-08 22:29:42 -05:00
Geoffrey Oxberry
1a432fb213 guile: add versions 2.2.1 through 2.2.6 (#12333) 2019-08-08 22:22:17 -05:00
Adam J. Stewart
89af88aa02 Re-add py-cython dependency to py-tables (#12338) 2019-08-08 21:57:16 -05:00
Adam J. Stewart
b409283ad5 Add py-certifi 2019.6.16 (#12339) 2019-08-08 21:57:01 -05:00
Adam J. Stewart
0b4e13c034 openssl package: add versions including 1.1.1c (#12342) 
* 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
 2019-08-08 17:04:53 -07:00
Jon Rood
941eb5d756 Generalize STK package settings in Trilinos (#11917) 
* Making STK package in Trilinos more general.

* Remove comment about seacas exodus settings.
 2019-08-07 16:11:15 -05:00
Pariksheet Nanda
0c9bc8da86 ncbi-toolkit: add version 22_0_0 (#12278) 
* 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)
 2019-08-07 14:18:36 -05:00
Piotr Luszczek
f7026a058b Version 19.8.1 of PLASMA (#12299) 
* Remove unnecessary setting with buggy prefix

Spack adds installation prefix by default and the "self." is missing

* Add version 19.8.1 of PLASMA
 2019-08-07 00:08:59 -05:00
Daryl W. Grunau
4f6916261c new package: py-exodus (#12291) 2019-08-06 23:11:56 -05:00
Mark W. Krentel
2f84db881b ncurses: fix pic and opt flags (#12272) 
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.
 2019-08-06 22:21:25 -05:00
Cameron Smith
e077532baf pumi: new version 2.2.1 (#12282) 2019-08-06 22:09:46 -05:00
Tamara Dahlgren
951d42596b tests: explain and test dependency flattening routines (#11993) 
- Add comments to explain that `install_dependency_symlinks` and `flatten_dependencies` are actually used.
- Add a test that exercises the routines.
 2019-08-06 17:11:23 -07:00
Seth R. Johnson
09d4fcc6ad graphviz package: add MacOS fixes and quartz support (#11128) 
* 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
 2019-08-06 16:26:45 -07:00
Adam J. Stewart
66e9b1279a Overhaul numpy package (#12170) 
* Add numpy 1.17.0

* Overhaul numpy package

* Flake8 fixes

* Undefined reference fix

* HeaderList and LibraryList need an arg

* veclibfort has no headers

* Add patch for older versions of py-numpy

* Remove py-meep hack from py-numpy package

* libflame: always add max arg hack flag

* Fix build with GCC 4.8

* Compiler flags come from self.compiler

* Only apply -std=c99 to cflags

* Try to fix libflame package

* Fix ATLAS build on macOS

* --force-clang flag added in 3.10.3
 2019-08-06 18:20:23 -05:00
t-karatsu
d488d04ed3 fltk: fix about variable types (#12292) 
* fltk: fix about variable types
 2019-08-06 11:07:27 -07:00
Daryl W. Grunau
cb7e9c155e Packages/musl (#12288) 
* bump eospac version

* Revert "bump eospac version"

This reverts commit 835b1f822d.

* fix-up musl-gcc wrapper script

* address adamjstewart's comments
 2019-08-05 20:16:14 -05:00
Toyohisa Kameyama
567cef7ae3 c-blosc package: Add -std=gnu99 flag for gcc (#11959) 
When building with GCC, c-blosc requires the -std=gnu99 flag.
Before this patch, the build would only add -std=gnu99 for GCC when
building on specific architectures; this adds -std=gnu99 in all cases
when using GCC.
 2019-08-05 18:04:16 -07:00
Adam J. Stewart
2e14cdb8fd Move new packages from tutorial to builtin (#12289) 
* Move new packages from tutorial to builtin

* Remove unicode character from docstring
 2019-08-05 19:55:39 -05:00
Satish Balay
0db3d6ca37 Balay/amrex 19.08 (#12287) 
* amrex: add version 19.08

* amrex: update sundials dependency for @19.08
 2019-08-05 17:34:01 -05:00
Axel Huebl
3457dffdca openPMD-api: pre-load depend libs (#12279) 
When loading `openpmd-api` as a lib to build outside of
spack or to build depending spack packages, the "CMake-PUBLIC"
header-only library MPark.Variant must be available. Also,
the `*Config.cmake` package must be able to find dependent
libs if used.
 2019-08-05 14:02:23 -05:00
Satish Balay
5560d5b601 Add version 19.8.0 of PLASMA (#12275) 2019-08-04 20:37:46 -05:00