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2021-06-16Set r-chipseq to bioconductor format (#24315)Glenn Johnson1-3/+5
- added description - converted to git from url - set commit rather than sha256
2021-06-16QNNPACK: add py-torch submodule commits (#24329)Adam J. Stewart1-14/+21
2021-06-16ParFlow: add new package (#24331)Steven Smith1-0/+81
2021-06-16r-effects: new package (#24342)Glenn Johnson1-0/+27
2021-06-16kaldi: fix building with mkl (#24338)archxlith1-1/+1
2021-06-16openfst: add v1.7.3 (#24339)archxlith1-0/+1
It's the highest version allowed in kaldi package
2021-06-16openmolcas: add v21.02, add mpi variant (#24343)snehring1-2/+21
2021-06-16cpuinfo: prevent downloads during build (#24345)Adam J. Stewart1-1/+29
2021-06-16pthreadpool: more specific resource destination (#24346)Adam J. Stewart1-6/+12
2021-06-15p4est: add v2.3.2 (#24311)Marc Fehling1-1/+2
2021-06-15openPMD-api: Build with Legacy API (#24341)Axel Huebl2-18/+34
Allow to build with `^hdf5@1.12.0 api=v110` and `v18`.
2021-06-15e4s ci: specs: add datatransferkit (#24325)eugeneswalker1-0/+1
2021-06-15add irep and lua-lang virtual dependency (#22492)Richarda Butler4-0/+50
This adds a package for `irep`, a tool for reading `lua` input decks from Fortran, C, and C++. `irep` can be built with either `lua` or `luajit`. To address this, we also add a virtual package for lua called `lua-lang`. `luajit` isn't, by default, a drop-in replacement for `lua`, but we add a `+lualinks` variant to it that adds symlinks that make it behave like `lua@5.1`. With this variant enabled, it provides the `lua-lang` virtual. `lua` always provides `lua-lang`. - [x] add `irep` package - [x] add `+lualinks` variant to `lua-luajit` - [x] create `lua-lang` virtual, provided by `lua` and `luajit+lualinks` Co-authored-by: Kayla Richarda Butler <butler59@quartz1148.llnl.gov> Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2021-06-15cairo: fix gtkdocize patch (#24332)Seth R. Johnson1-3/+3
Patch in #23971 was not correct
2021-06-15adding spack upload command (#24321)Vanessasaurus4-9/+126
this will first support uploads for spack monitor, and eventually could be used for other kinds of spack uploads Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-06-15pthreadpool: add new package (#24324)Adam J. Stewart1-0/+47
2021-06-15dd4hep: add v1.17 and a patch for cmake issues (#24274)Thomas Madlener2-0/+20
2021-06-15libdrm: fix one error, mark another conflict (#24309)Seth R. Johnson2-3/+7
* libdrm: fix one configure error and require libpciaccess Failure with `LIBS`: the linker can't find `-lrt` so configure fails on darwin-bigsur %apple-clang@12.0.5 ``` >> 22 configure: error: in `/private/var/folders/gy/mrg1ffts2h945qj9k29s1l1dvvmbqb/T/s3j/spack-s tage/spack-stage-libdrm-2.4.100-ofhk6m25n2pi427ihnxmvjkfmgyzlrqc/spack-src': >> 23 configure: error: C compiler cannot create executables 24 See `config.log' for more details See build log for details: /var/folders/gy/mrg1ffts2h945qj9k29s1l1dvvmbqb/T/s3j/spack-stage/spack-stage-libdrm-2.4.100-ofhk6m25n2pi427ihnxmvjkfmgyzlrqc/spack-build-out.txt ``` * libpciaccess: Mark conflict with darwin ``` make[2]: *** [common_init.lo] Error 1 make[2]: *** Waiting for unfinished jobs.... common_interface.c:75:10: fatal error: 'sys/endian.h' file not found ^~~~~~~~~~~~~~ ``` and ``` common_init.c:73:3: error: "Unsupported OS" ``` and others
2021-06-15r-insight: new package (#24313)Glenn Johnson1-0/+27
2021-06-15openmc: add v0.12.2, v0.12.1 (#24320)Paul Romano2-5/+9
2021-06-15openpmd-api: conflicts w hdf5 api=v110, v16, v18 (#24323)eugeneswalker1-0/+6
* openpmd-api: conflicts w hdf5 api=v110, v16, v18 * Update var/spack/repos/builtin/packages/openpmd-api/package.py * Add reference Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-06-14extending example for buildcaches (#22504)Vanessasaurus1-6/+78
* extending example for buildcaches I was attempting to create a local build cache from a directory, and I found the docs for both buildcaches and mirrors, but did not connect the docs that the url variable could be the local filesystem variable. I am extending the docs for buildcaches with an example of creating and interacting with one on the filesystem because I suspect other users will run into this need and possibly not find what they are looking for. Signed-off-by: vsoch <vsoch@users.noreply.github.com> * adding as follows to spack mirror list Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-06-14e4s ci environment: packages: update to newer versions (#24308)eugeneswalker1-6/+6
2021-06-14paraver: rename package to wxparaver, add new versions and fix installation ↵Hervé Yviquel2-9/+58
(#24307) * update url, add all new versions and fix installation * add wxparaver package and set the old paraver package as deprecated * remove update of deprecated package * remove old version from new wxparaver * Update url Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-06-14Made mxnet's cuda dependency conditional on +cuda. (#24305)David M. Rogers1-2/+2
2021-06-14adding more description to binary caches (#23934)Vanessasaurus1-0/+23
It is currently kind of confusing to the reader to distinguish spack buildcache install and spack install, and it is not clear how to use a build cache once a mirror is added. Hopefully this little big of description can help (and I hope I got it right!) Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-06-14New package: rmgdft. (#23313)Emil Briggs1-0/+96
2021-06-14Caliper: add v2.6.0 (#24303)QuellynSnead1-1/+2
2021-06-14oneAPI packages: fix install for python2 (#24296)Robert Cohn11-22/+22
Fix platform detection logic to work for Python 2 and 3
2021-06-14HiPACE: new package (#24070)Axel Huebl2-1/+70
Co-authored-by: Severin Diederichs <65728274+SeverinDiederichs@users.noreply.github.com>
2021-06-14leptonica: add v1.81.0 and missing dependencies (#24302)Glenn Johnson1-1/+9
- add version 1.81.0 - add dependencies - giflib - jpeg - libpng - libtiff - libwebp - openjpeg - build shared libs
2021-06-14libwebp: add v1.2.0 and new variants (#24301)Glenn Johnson1-26/+20
- add version 1.2.0 - add variants - giflib - jpeg - libpng - libtiff
2021-06-14Fix the branch for the develop version of IOR (#24079)Sergio1-1/+1
2021-06-14fast-global-file-status: depends_on libtool (#24293)eugeneswalker1-0/+1
2021-06-12gnutls: added unconditional dependency on libidn2 (#21471)Jen Herting1-0/+1
2021-06-12IntelPackage: use 'version_yearlike' in check for libfabrics RPATH. (#16700)Dominik Gresch1-1/+1
Use the 'version_yearlike' attribute instead of 'version' to check if the SPACK_COMPILER_EXTRA_RPATHS should be set to include the built-in 'libfabrics'. When using the bare 'version', the comparison is wrong when building with 'intel-parallel-studio', which has the version format '<edition>.YYYY.Nupdate', due to the leading '<edition>'.
2021-06-12nss: new package (#24288)Michael Kuhn1-0/+69
2021-06-12Ensure all roots of an installed environment are marked explicit in db (#24277)Greg Becker2-0/+28
2021-06-12graphviz: add v2.47.2 (#24273)Olivier Cessenat1-5/+11
Updated dependencies
2021-06-12libinih: add new package (#24289)Vanessasaurus2-0/+19
xfsprogs currently does not install with error message: FATAL ERROR: could not find a valid ini.h header. Adding this package libinih, and including it as a dependency for xfsprogs seems to fix the issue. It could be that we only need to add it for newer versions (if it worked before) and maybe a maintainer can comment on that. Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-06-12py-pytorch-sphinx-theme: add new package (#24283)Adam J. Stewart1-0/+18
2021-06-12nspr: add v4.31 (#24284)Michael Kuhn1-2/+10
2021-06-11llvm: add conflicts for newer gcc (#24281)Seth R. Johnson1-1/+2
Closes #24270
2021-06-11cp2k: add v8.2 (#24265)Robert Mijakovic1-0/+1
Co-authored-by: Robert Mijakovic <robert.mijakovic@lxp.lu>
2021-06-11ipopt: add versions up to v3.13.0 (#16706)Adrien Bernede1-12/+21
Pagination on Github prevent spack from easily parse all available versions. Also, due to recent migration to GitHub, tarballs for versions up to 3.12.13 have be regenerated, changing the hash. The current URL will apparently be supported, so we keep it, and give the alternative one as a comment.
2021-06-11setup-env: allow users to skip module function setup (#24236)Adam J. Stewart3-5/+11
* setup-env: allow users to skip module function setup * Add documentation on SPACK_SKIP_MODULES
2021-06-11[py-ippython]: Start py-backcall dependency to start at py-ipython@7.3.0: ↵Tom Payerle1-1/+1
(#24279) This should fix #24278 $INSTALLDIR/lib/python3.7/site-packages/IPython/core/events.py contains an import from backcall even in @7.3.0, so dependency on py-backcall needs to start earlier.
2021-06-11qt+webkit: fix python2 dependency and add opengl conflict (#24276)Manuela Kuhn1-1/+4
2021-06-11py-distributed: restrict py-contextvars dep to newer versions (#23841)Andreas Baumbach1-1/+1
* py-distributed: restrict py-contextvars dep to newer versions Change-Id: I8a6d55b840309aa6966ab310d42252f45b0ef9c7 * fixup dependency on py-contextvars Change-Id: I56b729394af0f5a6fc283344d8af87990c97426b
2021-06-11texlive: restrict poppler version (#24222)Tom Payerle1-1/+1
Restrict poppler version for texlive to poppler@:0.84 Should fix #19946 See also https://github.com/NixOS/nixpkgs/issues/79170 Looks like poppler@0.84 upgraded their header files to use the C++ cstdio instead of the C stdio.h. Since TeX is using C, not C++. this causes problems.