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2023-05-18Cran updates (#37296)Glenn Johnson321-174/+965
* add version 1.28.3 to r-hexbin * add version 5.0-1 to r-hmisc * add version 0.5.5 to r-htmltools * add version 1.6.2 to r-htmlwidgets * add version 1.4.2 to r-igraph * add version 0.42.19 to r-imager * add version 1.0-5 to r-inum * add version 0.9-14 to r-ipred * add version 1.3.2 to r-irkernel * add version 2.2.0 to r-janitor * add version 0.1-10 to r-jpeg * add version 1.2.2 to r-jsonify * add version 0.9-32 to r-kernlab * add version 1.7-2 to r-klar * add version 1.42 to r-knitr * add version 1.14.0 to r-ks * add version 2.11.0 to r-labelled * add version 1.7.2.1 to r-lava * add version 0.6-15 to r-lavaan * add version 2.1.2 to r-leaflet * add version 2.9-0 to r-lfe * add version 1.1.6 to r-lhs * add version 1.1-33 to r-lme4 * add version 1.5-9.7 to r-locfit * add version 0.4.3 to r-log4r * add version 5.6.18 to r-lpsolve * add version 0.2-11 to r-lwgeom * add version 2.7.4 to r-magick * add version 1.22.1 to r-maldiquant * add version 1.2.11 to r-mapproj * add version 1.6 to r-markdown * add version 7.3-59 to r-mass * add version 1.5-4 to r-matrix * add version 0.63.0 to r-matrixstats * add version 4.2-3 to r-memuse * add version 4.0-0 to r-metafor * add version 1.8-42 to r-mgcv * add version 3.15.0 to r-mice * add version 0.4-5 to r-mitml * add version 2.0.0 to r-mixtools * add version 0.1.11 to r-modelr * add version 1.4-23 to r-multcomp * add version 0.1-9 to r-multcompview * add version 0.1-13 to r-mutoss * add version 1.18.1 to r-network * add version 3.3.4 to r-nleqslv * add version 3.1-162 to r-nlme * add version 0.26 to r-nmf * add version 0.60-17 to r-np * add version 4.2.5.2 to r-openxlsx * add version 2022.11-16 to r-ordinal * add version 0.6.0.8 to r-osqp * add version 0.9.1 to r-packrat * add version 1.35.0 to r-parallelly * add version 1.3-13 to r-party * add version 1.2-20 to r-partykit * add version 1.7-0 to r-pbapply * add version 0.3-9 to r-pbdzmq * add version 1.2 to r-pegas * add version 1.5-1 to r-phytools * add version 1.9.0 to r-pillar * add version 1.4.0 to r-pkgbuild * add version 2.1.0 to r-pkgcache * add version 0.5.0 to r-pkgdepends * add version 2.0.7 to r-pkgdown * add version 1.3.2 to r-pkgload * add version 0.1-8 to r-png * add version 1.1.22 to r-polspline * add version 1.0.1 to r-pool * add version 1.4.1 to r-posterior * add version 3.8.1 to r-processx * add version 2023.03.31 to r-prodlim * add version 1.0-12 to r-proj4 * add version 2.5.0 to r-projpred * add version 0.1.6 to r-pryr * add version 1.7.5 to r-ps * add version 1.0.1 to r-purrr * add version 1.3.2 to r-qqconf * add version 0.25.5 to r-qs * add version 1.60 to r-qtl * add version 0.4.22 to r-quantmod * add version 5.95 to r-quantreg * add version 0.7.8 to r-questionr * add version 1.2.5 to r-ragg * add version 0.15.1 to r-ranger * add version 3.6-20 to r-raster * add version 2.2.13 to r-rbibutils * add version 1.0.10 to r-rcpp * add version 0.12.2.0.0 to r-rcpparmadillo * add version 0.1.7 to r-rcppde * add version 0.3.13 to r-rcppgsl * add version 1.98-1.12 to r-rcurl * add version 1.2-1 to r-rda * add version 2.1.4 to r-readr * add version 1.4.2 to r-readxl * add version 1.0.6 to r-recipes * add version 1.1.6 to r-repr * add version 1.2.16 to r-reproducible * add version 0.3.0 to r-require * add version 1.28 to r-reticulate * add version 2.0.7 to r-rfast * add version 1.6-6 to r-rgdal * add version 0.6-2 to r-rgeos * add version 1.1.3 to r-rgl * add version 0.2.18 to r-rinside * add version 4-14 to r-rjags * add version 1.3-1.8 to r-rjsonio * add version 2.21 to r-rmarkdown * add version 0.9-2 to r-rmpfr * add version 0.7-1 to r-rmpi * add version 6.6-0 to r-rms * add version 0.10.25 to r-rmysql * add version 0.8.7 to r-rncl * add version 2.4.11 to r-rnexml * add version 0.95-1 to r-robustbase * add version 1.3-20 to r-rodbc * add version 7.2.3 to r-roxygen2 * add version 1.4.5 to r-rpostgres * add version 0.7-5 to r-rpostgresql * add version 0.8.29 to r-rsconnect * add version 0.4-15 to r-rsnns * add version 2.3.1 to r-rsqlite * add version 0.7.2 to r-rstatix * add version 1.1.2 to r-s2 * add version 0.4.5 to r-sass * add version 0.1.9 to r-scatterpie * add version 0.3-43 to r-scatterplot3d * add version 3.2.4 to r-scs * add version 1.6-4 to r-segmented * add version 4.2-30 to r-seqinr * add version 0.26 to r-servr * add version 4.3.0 to r-seurat * add version 1.0-12 to r-sf * add version 0.4.2 to r-sfheaders * add version 1.1-15 to r-sfsmisc * add version 1.7.4 to r-shiny * add version 1.9.0 to r-signac * add version 1.6.0.3 to r-smoof * add version 0.1.7-1 to r-sourcetools * add version 1.6-0 to r-sp * add version 1.3-0 to r-spacetime * add version 7.3-16 to r-spatial * add version 2.0-0 to r-spatialeco * add version 1.2-8 to r-spatialreg * add version 3.0-5 to r-spatstat * add version 3.0-1 to r-spatstat-data * add version 3.1-0 to r-spatstat-explore * add version 3.1-0 to r-spatstat-geom * add version 3.1-0 to r-spatstat-linnet * add version 3.1-4 to r-spatstat-random * add version 3.0-1 to r-spatstat-sparse * add version 3.0-2 to r-spatstat-utils * add version 2.2.2 to r-spdata * add version 1.2-8 to r-spdep * add version 0.6-1 to r-stars * add version 1.5.0 to r-statmod * add version 4.8.0 to r-statnet-common * add version 1.7.12 to r-stringi * add version 1.5.0 to r-stringr * add version 1.9.1 to r-styler * add version 3.5-5 to r-survival * add version 1.5-4 to r-tclust * add version 1.7-29 to r-terra * add version 3.1.7 to r-testthat * add version 1.1-2 to r-th-data * add version 1.2 to r-tictoc * add version 1.3.2 to r-tidycensus * add version 1.2.3 to r-tidygraph * add version 1.3.0 to r-tidyr * add version 2.0.0 to r-tidyverse * add version 0.2.0 to r-timechange * add version 0.45 to r-tinytex * add version 0.4.1 to r-triebeard * add version 1.0-9 to r-truncnorm * add version 0.10-53 to r-tseries * add version 0.8-1 to r-units * add version 4.3.0 to r-v8 * add version 1.4-11 to r-vcd * add version 1.14.0 to r-vcfr * add version 0.6.2 to r-vctrs * add version 1.1-8 to r-vgam * add version 0.4.0 to r-vioplot * add version 1.6.1 to r-vroom * add version 1.72-1 to r-wgcna * add version 0.4.1 to r-whisker * add version 0.7.2 to r-wk * add version 0.39 to r-xfun * add version 1.7.5.1 to r-xgboost * add version 1.0.7 to r-xlconnect * add version 3.99-0.14 to r-xml * add version 0.13.1 to r-xts * add version 2.3.7 to r-yaml * add version 2.3.0 to r-zip * add version 1.8-12 to r-zoo * r-bigmem: dependency on uuid * r-bio3d: dependency on zlib * r-devtools: dependency cleanup * r-dose: dependency cleanup * r-dss: dependency cleanup * r-enrichplot: dependency cleanup * r-fgsea: dependency cleanup * r-geor: dependency cleanup * r-ggridges: dependency cleanup * r-lobstr: dependency cleanup * r-lubridate: dependency cleanup * r-mnormt: dependency cleanup * r-sctransform: version format correction * r-seuratobject: dependency cleanup * r-tidyselect: dependency cleanup * r-tweenr: dependency cleanup * r-uwot: dependency cleanup * new package: r-clock * new package: r-conflicted * new package: r-diagram * new package: r-doby * new package: r-httr2 * new package: r-kableextra * new package: r-mclogit * new package: r-memisc * new package: r-spatstat-model * r-rmysql: use mariadb-client * r-snpstats: add zlib dependency * r-qs: add zstd dependency * r-rcppcnpy: add zlib dependency * black reformatting * Revert "r-dose: dependency cleanup" This reverts commit 4c8ae8f5615ee124fff01ce43eddd3bb5d06b9bc. * Revert "r-dss: dependency cleanup" This reverts commit a6c5c15c617a9a688fdcfe2b70c501c3520d4706. * Revert "r-enrichplot: dependency cleanup" This reverts commit 65e116c18a94d885bc1a0ae667c1ef07d1fe5231. * Revert "r-fgsea: dependency cleanup" This reverts commit ffe2cdcd1f73f69d66167b941970ede0281b56d7. * r-rda: this package is back in CRAN * r-sctransform: fix copyright * r-seurat: fix copyright * r-seuratobject: fix copyright * Revert "add version 6.0-94 to r-caret" This reverts commit 236260597de97a800bfc699aec1cd1d0e3d1ac60. * add version 6.0-94 to r-caret * Revert "add version 1.8.5 to r-emmeans" This reverts commit 64a129beb0bd88d5c88fab564cade16c03b956ec. * add version 1.8.5 to r-emmeans * Revert "add version 5.0-1 to r-hmisc" This reverts commit 517643f4fd8793747365dfcfc264b894d2f783bd. * add version 5.0-1 to r-hmisc * Revert "add version 1.42 to r-knitr" This reverts commit 2a0d9a4c1f0ba173f7423fed59ba725bac902c37. * add version 1.42 to r-knitr * Revert "add version 1.6 to r-markdown" This reverts commit 4b5565844b5704559b819d2e775fe8dec625af99. * add version 1.6 to r-markdown * Revert "add version 0.26 to r-nmf" This reverts commit 4c44a788b17848f2cda67b32312a342c0261caec. * add version 0.26 to r-nmf * Revert "add version 2.3.1 to r-rsqlite" This reverts commit 5722ee2297276e4db8beee461d39014b0b17e420. * add version 2.3.1 to r-rsqlite * Revert "add version 1.0-12 to r-sf" This reverts commit ee1734fd62cc02ca7a9359a87ed734f190575f69. * add version 1.0-12 to r-sf * fix syntax error
2023-05-18unifyfs: new v1.1 release (#37756)Cameron Stanavige1-3/+7
Add v1.1 release Update mochi-margo dependency compatible versions Update version range of libfabric conflict
2023-05-18[xrootd] New variants, new version, improve build config (#37682)Chris Green3-20/+128
* Add FNAL Spack team to maintainers * New variants and configuration improvements * Version dependent "no-systemd" patches. * New variants `client_only`, and `davix` * Better handling of `cxxstd` for different versions, including improved patching and CMake options. * Version-specific CMake requirements. * Better version-specific handling of `openssl` dependency. * `py-setuptools` required for `+python` build. * Specific enable/disable of CMake options and use of `-DFORCE_ENABLED=TRUE` to prevent unwanted/non-portable activation of features. * Better handling of `+python` configuration. * New version 5.5.5
2023-05-18Bump Spack version on develop to 0.21.0.dev0 (#37760)Massimiliano Culpo1-1/+1
2023-05-18Bugfix: allow preferred new versions from externals (#37747)Peter Scheibel2-92/+126
2023-05-17maintainers: switch from list to directive (#37752)Tamara Dahlgren30-1221/+1310
2023-05-17Add aws-plcuster[-aarch64] stacks (#37627)Stephen Sachs9-0/+394
Add aws-plcuster[-aarch64] stacks. These stacks build packages defined in https://github.com/spack/spack-configs/tree/main/AWS/parallelcluster They use a custom container from https://github.com/spack/gitlab-runners which includes necessary ParallelCluster software to link and build as well as an upstream spack installation with current GCC and dependencies. Intel and ARM software is installed and used during the build stage but removed from the buildcache before the signing stage. Files `configs/linux/{arch}/ci.yaml` select the necessary providers in order to build for specific architectures (icelake, skylake, neoverse_{n,v}1).
2023-05-17Added version 1.3.1 (#37735)Brian Van Essen1-0/+1
2023-05-17lmod: fix build, bump patch version (#37744)Harmen Stoppels1-0/+3
2023-05-17Limit deepcopy to just the initial "all" section (#37718)Massimiliano Culpo1-12/+7
Modifications: - [x] Limit the scope of the deepcopy when initializing module file writers
2023-05-17gitlab ci: no copy-only pipelines w/ deprecated config (#37720)Scott Wittenburg1-6/+22
Make it clear that copy-only pipelines are not supported while still using the deprecated ci config format. Also ensure that the deprecated stack does not fail on spack pipelines for tags.
2023-05-17whizard: build newer versions in parallel (#37422)Juan Miguel Carceller1-9/+6
2023-05-17libxcb: depend on python, remove releases that need python 2 (#37698)Harmen Stoppels1-10/+3
2023-05-17spack test: fix stand-alone test suite status reporting (#37602)Tamara Dahlgren5-43/+198
* Fix reporting of packageless specs as having no tests * Add test_test_output_multiple_specs with update to simple-standalone-test (and tests) * Refactored test status summary; added more tests or checks
2023-05-17celeritas: new version 0.2.2 (#37731)Seth R. Johnson1-1/+6
* celeritas: new version 0.2.2 * [@spackbot] updating style on behalf of sethrj
2023-05-17Tk/Tcl packages: speed up file search (#35902)Peter Scheibel2-4/+32
2023-05-17Add recently added Spack Docker Images to documentation (#37732)Yoshiaki Senda1-0/+20
Signed-off-by: Yoshiaki Senda <yoshiaki@live.it>
2023-05-17emacs: convert to new stand-alone test process (#37725)Tamara Dahlgren1-15/+30
2023-05-17Fix `spack find` not able to display version ranges in compilers (#37715)Massimiliano Culpo2-1/+16
2023-05-16libxpm package: fix RHEL8 build with libintl (#37713)Chris Green1-1/+1
Set LDFLAGS rather than LDLIBS
2023-05-16Windows: fix MSVC version handling (#37711)John W. Parent1-2/+2
MSVC compiler logic was using string parsing to extract version from compiler spec, which was fragile. This broke in #37572, so has been fixed and made more robust by using attribute access.
2023-05-16CI: Expand E4S ROCm stack to include missing DaV packages (#36843)kwryankrattiger4-4/+8
* CI: Expand E4S ROCm stack to include missing DaV packages Ascent: Fixup for VTK-m with Kokkos backend * DaV SDK: Removed duplicated openmp variant for ascent * Drop visit and add conflict for Kokkos * E4S: Drop ascent from CUDA builds
2023-05-16gha rhel8-platform-python: configure git safe.directory (#37708)Harmen Stoppels1-0/+1
2023-05-16Revert "hdf5: fix showconfig (#34920)" (#37707)Harmen Stoppels1-18/+0
This reverts commit 192e564e26e919169aa926e92af7bd9a28cbb4f1.
2023-05-16Requirements and preferences should not define (non-git) versions (#37687)Peter Scheibel6-11/+177
Ensure that requirements `packages:*:require:@x` and preferences `packages:*:version:[x]` fail concretization when no version defined in the package satisfies `x`. This always holds except for git versions -- they are defined on the fly.
2023-05-16gha bootstrap-dev-rhel8: configure git safe.directory (#37702)Harmen Stoppels1-0/+1
git has been updated to something more recent
2023-05-16check_modules_set_name: do not check for "enable" key (#37701)Harmen Stoppels2-14/+46
2023-05-16Update llvm recipe regarding libomptarget. (#36675)Ye Luo1-7/+28
2023-05-16libxcb/xcb-proto: Enable internal Python dependency (#37575)QuellynSnead2-7/+2
In the past, Spack did not allow two different versions of the same package within a DAG. That led to difficulties with packages that still required Python 2 while other packages had already switched to Python 3. The libxcb and xcb-proto packages did not have Python 3 support for a time. To get around this issue, Spack maintainers disabled their dependency on an internal (i.e., Spack-provided) Python (see #4145),forcing these packages to look for a system-provided Python (see #7646). This has worked for us all right, but with the arrival of our most recent platform we seem to be missing the critical xcbgen Python module on the system. Since most software has largely moved on to Python 3 now, let's re-enable internal Spack dependencies for the libxcb and xcb-proto packages.
2023-05-16Add conflict for pika with fmt@10 and +cuda/rocm (#37679)Mikael Simberg1-0/+3
2023-05-16unify: when_possible and unify: true -- Bugfix for error in 37438 (#37681)Greg Becker1-6/+15
Two bugs came in from #37438 1. `unify: when_possible` was broken, because of an incorrect assertion. abstract/concrete spec pairs were compared against the results that were in the process of being computed, rather than against the previous results. 2. `unify: true` had an ordering bug that could mix the association between abstract and concrete specs - [x] 1 is resolved by creating a lookup from old concrete specs to old abstract specs, and we use that to associate the "new" concrete specs that happen to be the old ones with their abstract specs (since those are stripped out for concretization - [x] 2 is resolved by combining the new and old abstract as lists instead of combining them as sets. This is important because `set() | set()` does not make any ordering promises, even though set ordering is otherwise guaranteed in `python@3.7:`
2023-05-16Upgrading kosh to 3.0 (#37471)Robert Blake2-1/+18
* Upgrading kosh to 3.0. * Accidentally regressed the package, changing back. * Updating py-hdbscan versions for kosh. * Fixing bug in patch. * Adding 3.0.1 * Removing 3.0. * Updating package deps for hdbscan to match requirements.txt. * Version reqs for 3.0.*, need newer numpy and networkx * spack style * Reordering to match setup.py, adding "type" to python depends.
2023-05-15trilinos: @develop fixes (#37615)eugeneswalker1-1/+4
* trilinos@develop fixes * Update var/spack/repos/builtin/packages/trilinos/package.py Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov> --------- Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2023-05-16gitlab ci: reduce job name length of build_systems pipeline (#37686)Scott Wittenburg1-1/+1
2023-05-15circos: add v0.69-9 (#37479)Alec Scott1-0/+1
2023-05-15alluxio: add v2.9.3 (#37488)Alec Scott1-0/+1
2023-05-15codec2: add v1.1.0 (#37480)Alec Scott1-0/+1
2023-05-15coinutils: add v2.11.9 (#37481)Alec Scott1-0/+1
2023-05-15g2c: add v1.7.0 (#37482)Alec Scott1-0/+1
2023-05-15shadow: add v4.13 (#37485)Alec Scott1-0/+1
2023-05-15yoda: add v1.9.8 (#37487)Alec Scott1-0/+1
2023-05-15cpp-httplib: add v0.12.3 (#37490)Alec Scott1-0/+1
2023-05-15entt: add v3.11.1 (#37491)Alec Scott1-0/+1
2023-05-15harfbuzz: add v7.2.0 (#37492)Alec Scott1-0/+1
2023-05-15libconfuse: add v3.3 (#37493)Alec Scott1-0/+1
2023-05-15libnsl: add v2.0.0 (#37494)Alec Scott1-0/+1
2023-05-15p11-kit: add v0.24.1 (#37495)Alec Scott1-0/+1
2023-05-15packmol: add v20.0.0 (#37496)Alec Scott2-1/+2
* packmol: add v20.0.0 * Fix zoltan homepage url
2023-05-15perl-module-build-tiny: add v0.044 (#37497)Alec Scott1-0/+1
2023-05-15zoltan: add v3.901 (#37498)Alec Scott1-0/+1
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