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2021-04-23r-colourpicker: new package (#23136)Glenn Johnson1-0/+31
2021-04-23r-isva: new package (#23137)Glenn Johnson1-0/+22
2021-04-23r-dmrcate: new package (#23151)Glenn Johnson1-0/+36
2021-04-23mpa and fgfs: add v1.1.1 (#23173)Gregory Lee2-0/+2
2021-04-23gmap-gsnap: add v2021-03-08 (#23178)snehring1-0/+1
2021-04-23augustus: add v3.4.0 and update package (#22879)Glenn Johnson2-38/+112
- add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23shadow: add v4.8.1 (#23185)Robert Mijakovic1-2/+3
Co-authored-by: Robert Mijakovic <robert.mijakovic@lxp.lu>
2021-04-23fontconfig: resolve tarball issue fcobjshash.h (#23190)Tamara Dahlgren1-0/+6
2021-04-23docs: be more precise on what `spack add ...` does (#23204)George Hartzell1-3/+3
This is as much a question as it is a minor fine-tuning of the docs. I've been known to add things to an environment by editing the `spack.yaml` file directly. When I read the previous version of this sentence, I was afraid that `spack add` was actually doing *two* things, modifying the `spack.yaml` and updating something else that defined the roots of the Environment. A bit of experimentation suggests that editing the `spack.yaml` file is sufficient to change the roots. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-04-23mpich: post-configure patch for cce (#23193)Greg Becker1-0/+11
2021-04-23pythia8: add v8304, fix copy-paste errors in configure arguments (#23028)Valentin Volkl1-2/+3
2021-04-23er: add v0.0.4 (#23022)Cameron Stanavige1-8/+13
This adds that new version to the package, updates the url, and updates the hash of v0.0.3 for the new url. This also updates the KVTree dependency as MPI is required to be enabled in KVTree for er to work. rankstr is now also required by er for recently added tests.
2021-04-23py-particle: add v0.14.1 (#23216)Valentin Volkl1-0/+1
2021-04-22Docs: Updated copyrights in files still using 2020 as ending year (#23215)Tamara Dahlgren42-42/+42
2021-04-22Initial Version of Ascent Miniapp Spackage (#23170)Robert Pavel1-0/+22
Initial version of ascent miniapp spackage
2021-04-22hpctoolkit: fix patch from #22864 (#23149)Mark W. Krentel2-6/+17
PR #22864 added a patch to hpctoolkit to fix an issue with gcc 10.x, and the patch was applied to all revs unconditionally. But this was fixed in hpctoolkit master on Aug 11, 2020, so the patch should only apply to old revs. Fixes #22951.
2021-04-22NEST package: add version @master; fix ~python (#23211)Itaru Kitayama1-2/+4
2021-04-22[AMD] - rocm-openmp-extras 4.1 updates. (#22998)estewart081-20/+53
Update package with 4.1 sha keys. Use variant to disable openmp in the build of llvm-amdgpu. Set CPATH, LIBRARY_PATH so that clang knows to look in the rocm-openmp-extras for headers/libraries. Disable flang warnings as Spack thinks they are errors. In ROCm 4.1, the plugin changed names from hsa -> amdgpu. Update HSA_INCLUDE for 4.1.0.
2021-04-22Update patchfile to allow xl+cuda builds. (#23201)Kelly (KT) Thompson1-1/+16
2021-04-22SIRIUS 7.2.1 (#23199)Harmen Stoppels1-0/+1
2021-04-22minisign: add v0.9 and v0.8 (#23202)Massimiliano Culpo1-1/+2
2021-04-22prepend missing self. to spec (#23172)Frank Willmore1-1/+1
2021-04-22qa: install clingo-cffi from pip (#23163)Massimiliano Culpo1-23/+54
Clingo has been released on PyPI, so there are no more concerns on our CI depending on pypy.test for installing the wheel. Apparently we have parts of Spack which are not compatible with kcov > 3.4
2021-04-21boost: only apply boostrap-toolset.patch for version 1.75 (#23174)Gregory Lee1-1/+1
2021-04-22ncbi-rmblastn: add v2.11.0 (#22788)Glenn Johnson2-0/+328
2021-04-21New package: r-assertive-files (#23183)Jen Herting1-0/+26
Co-authored-by: Alex Leute <acl2809@rit.edu> Co-authored-by: Alex C Leute <aclrc@rit.edu>
2021-04-21New package: r-assertive-matrices (#23184)Jen Herting1-0/+26
Co-authored-by: Alex Leute <acl2809@rit.edu> Co-authored-by: Alex C Leute <aclrc@rit.edu>
2021-04-21New package: r-assertive-datetimes (#23180)Jen Herting1-0/+25
Co-authored-by: Alex Leute <acl2809@rit.edu> Co-authored-by: Alex C Leute <aclrc@rit.edu>
2021-04-21Disable multithreaded version of zstd by default (#23167)Harmen Stoppels2-2/+7
* Disable multithreaded version of zstd by default * zstd pthreads by default again! but configurable, and turned off in GCC
2021-04-21New package: r-assertive-numbers (#23181)Jen Herting1-0/+25
Co-authored-by: Alex C Leute <aclrc@rit.edu>
2021-04-21MAGMA: Add e4s testsuite-inspired smoke test (#23011)Sergei Shudler1-0/+31
2021-04-21lbann: remove deprecated variants in opencv (#23176)Massimiliano Culpo1-4/+5
2021-04-21axl: add version 0.4.0 (#23044)Cameron Stanavige1-16/+24
* Swap .zip downloads with .tar.gz downloads (and update download hashes) * New variants: intel_cppr and bbapi_fallback support
2021-04-21unifyfs: add version 0.9.2 (#22390)Cameron Stanavige2-53/+17
UnifyFS has been integrated with updated versions of its mochi-margo dependency (and mochi-margo's mercury and libfabric dependencies). This removes support for version 0.9.0
2021-04-21Fix GCC with zstd on CCentOS 7 where it doesn't consider the lib64 directory ↵Harmen Stoppels1-1/+4
(#23169)
2021-04-21conduit package: avoid issue with subclass case (#23156)Cyrus Harrison1-3/+7
* avoid issue with subclass case * catch named exception
2021-04-21OpenCV: overhaul package (#22340)Adam J. Stewart1-229/+167
2021-04-21ASP-based solve: minimize compiler mismatches (#23016)Massimiliano Culpo2-32/+26
fixes #22718 Instead of trying to maximize the number of matches (preferred behavior), try to minimize the number of mismatches (unwanted behavior).
2021-04-21ASP-based solver: suppress warnings when constructing facts (#23090)Massimiliano Culpo1-1/+4
fixes #22786 Trying to get optimization flags for a specific target from a compiler may trigger warnings. In the context of constructing facts for the ASP-based solver we don't want to show these warnings to the user, so here we simply ignore them.
2021-04-20lbann: requirements of the new variants for the legacy versions (#23159)Brian Van Essen1-1/+7
Fixed the range of conduit for legacy versions of LBANN.
2021-04-20check for package in spec not variant (#23157)Chris White1-3/+3
2021-04-20Catch rstudio based URL for `cran` attribute in create.py (#23072)Glenn Johnson1-1/+1
2021-04-20Removed unnecessary code to put cuda_arch in DiHydrogen (#23158)Brian Van Essen2-14/+4
These were deprecated when the custom cuda_arch list was removed. Also fixed up the Aluminum dependencies for Hydrogen and DiHydrogen. Turns out that Aluminum v0.6.0 didn't have a correct version in CMake and thus the interaction with older versions of Hydrogen and DiHydrogen needed to be corrected.
2021-04-20libsigsegv: update to version 2.13. (#23155)Mansour Moufid1-1/+2
2021-04-20Fixing typo tty.fail -> tty.die and monitor docstrings (#23152)Vanessasaurus1-37/+90
This isn't a significant issue, but I noticed that the docstring incorrectly references "tty.fail" and I wanted to quickly fix it to reflect the correct command, tty.die. I also wanted to fix the docstrings to not be large clumps, to what @tgamblin suggested after I wrote this - having one line at the top that is a quick summary, and more verbose after that.
2021-04-20Use xz instead of lzma. XZ utils provides lzma dev files (#23144)Ethan Stam1-1/+1
2021-04-20redset: add versions 0.0.5 and 0.0.4 (#22977)Cameron Stanavige1-2/+4
Also update the url and hash of v0.0.3.
2021-04-20shuffile: add version 0.0.4 (#22976)Cameron Stanavige1-3/+4
Also update the url and hash for v0.0.3.
2021-04-20New package: pmemkvKoyamaSohei1-0/+88
2021-04-20Package libsecret: turn off gobj variant by default (#23070)Sinan1-1/+1
Co-authored-by: sbulut <sbulut@3vgeomatics.com>