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2022-11-21openvdb: update to v10.0.0 (#33835)Drew Whitehouse1-20/+21
2022-11-21texinfo: require also `makeinfo` executable (#33370)Mosè Giordano1-2/+11
* texinfo: require also `makeinfo` executable * texinfo: add versions 6.6, 6.7, 6.8 * texinfo: add `info` and `makeinfo` sanity checks
2022-11-21hugo: add v0.106.0 (#34023)Alec Scott1-2/+5
2022-11-20Python: specify tcl/tk version requirements (#34027)Adam J. Stewart1-0/+3
2022-11-20qt6: new packages (#29555)Wouter Deconinck5-0/+413
* qt6: initial commit of several basic qt6 packages * Qt6: fix style issues * [qt6] fix style issues, trailing spaces * [qt6] rename to qt-* ecosystem; remove imports * [qt6] rename dependencies; change version strings * [qt6] list_urls * [qt6] homepage links * [qt6] missing closing quotes failed style check * qt-declarative: use private _versions Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov> * qt-quick3d, qt-quicktimeline, qt-shadertools: use private _versions * qt-base: rework feature defines and use run_tests * qt: new version 6.2.4 * flake8 whitespace before comma * qt-base: variant opengl when +gui Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov> * qt6: rebase and apply new black style * qt6: apply style isort fixes * qt6: new version 6.3.0 and 6.3.1 * qt6: add 6.3.0 and 6.3.1 to versions list * qt6: multi-argument join_path Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * qt-base: fix isort * qt-shadertools: no cmake_args needed * qt-declarative: imports up front * qt-quick3d: fix import * qt-declarative: remove useless cmake_args * qt-shadertools: imports and join_path fixes * qt-quick3d: join_path fixes * qt-declarative: join_path fixes * Update features based on gui usage * Update dependencies, cmake args, mac support * Update features based on linux * More updates * qt-base: fix style * qt-base: archive_files join_path * qt-base: new version 6.3.2 * qt-{declarative,quick3d,quicktimeline,shadertools}@6.3.2 * qt-base: require libxcb@1.13: and use system xcb_xinput when on linux Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-21mold: new package for the mold linker (#34017)Pedro Ciambra1-0/+20
2022-11-21py-numpy: add v1.23.5 (#34026)Adam J. Stewart1-0/+1
2022-11-21krb5: Add new versions 1.19.4 and 1.20.1 (#34021)Bernhard Kaindl1-0/+2
Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
2022-11-20Update dask and related packages (#33925)Sam Grayson5-19/+84
* Update dask and related packages * Update package dependency specs * Run spack style * Add new version of locket * Respond to comments * Added constraints * Add version constraints for py-dask+distributed * Run spack style * Update var/spack/repos/builtin/packages/py-dask/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Deprecated dask versions * Deprecated more dask and distirbuted * spack style --fix Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-20bash: Update 5.1 to 5.1.16 (#34022)Bernhard Kaindl1-0/+8
2022-11-19py-torch: add note about MPS variant (#34018)Adam J. Stewart1-1/+1
2022-11-19New package: py-ahpy (#34008)Jen Herting1-0/+22
* first build of ahpy * updated to limit python to >4 * added from spack.package import * to >4 Co-authored-by: Sid Pendelberry <sid@rit.edu>
2022-11-19OpenMC: add v0.13.2 (#33903)Paul Romano2-5/+18
* openmc: add v0.13.2 * Fix style formatting * Update Python version dependency * Update numpy version dependency
2022-11-19spack find: remove deprecated "--bootstrap" option (#34015)Massimiliano Culpo3-30/+1
2022-11-19libxcrypt: Disable -Werror (#34013)Erik Schnetter1-1/+3
2022-11-19package_base.py: Fix #34006: test msg needs to be a string (#34007)Chris Green2-2/+10
2022-11-19Boost: enable lzma and zstd iostreams (#33998)iarspider1-2/+8
2022-11-19graphviz: remove 1. cyclic dep when +pangocairo and 2. error with ↵Olivier Cessenat1-2/+2
poppler+glib (#32120) * graphviz: remove cyclic dep to svg when pangocairo and poppler+glib failure * graphviz: remove cyclic dep to svg when pangocairo and poppler+glib failure
2022-11-19parallelio: update package to use mpi-serial, add extra module info (#33153)Jim Edwards1-6/+28
2022-11-19py-scipy: add v1.9 (#31810)Adam J. Stewart1-36/+119
2022-11-19mercury: add version 2.2.0 (#31966)Jerome Soumagne1-1/+17
add psm, psm2 and hwloc variants Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-11-18sqlite: add 3.40.0 (#33975)Michael Kuhn1-0/+1
2022-11-18PackageBase should not define builder legacy attributes (#33942)Chris Green5-11/+23
* Add a regression test for 33928 * PackageBase should not set `(build|install)_time_test_callbacks` * Fix audits by preserving the current semantic Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-11-18Updating faiss with new versions (#33983)Robert Blake2-12/+117
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-11-18Updating hiredis with new software versions (#33982)Robert Blake1-6/+25
2022-11-18charliecloud: new version 0.30 (#34004)Richard Berger1-1/+6
2022-11-18trnascan-se: adding missing build dep (#33978)snehring1-0/+1
2022-11-18gcc: Ensure matching assembler/binutils on RHEL8 (#33994)Bernhard Kaindl1-0/+8
gcc@10: Newer binutils than RHEL7/8's are required to for guaranteed operaton. Therefore, on RHEL7/8, reject ~binutils. You need to add +binutils to be sure to have binutils which are recent enough. See this discussion with the OpenBLAS devs for reference: https://github.com/xianyi/OpenBLAS/issues/3805#issuecomment-1319878852 Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
2022-11-18pflotran: add "rxn" variant (#33995)Satish Balay1-0/+9
2022-11-18LibPressio support for MGARD (#33999)Robert Underwood2-9/+37
Co-authored-by: Robert Underwood <runderwood@anl.gov>
2022-11-18py-mypy: add new versions; add new py-types packages (#34002)Adam J. Stewart4-8/+76
* py-mypy: add new versions * Add new packages
2022-11-18py-cutadapt: adding version 4.1 (#33959)snehring2-10/+20
* py-dnaio: adding version 0.9.1 py-cutadapt: adding version 4.1 * py-cutadapt: remove old python versions * py-dnaio: remove old python versions * py-cutadapt: add cython dep
2022-11-18Improve error message for requirements (#33988)Massimiliano Culpo1-1/+1
refers #33985
2022-11-18openblas: Fix build on ARM Neoverse with gcc@:9 (no sve2+bf16) (#33968)Bernhard Kaindl1-1/+17
Also improve the InstallError message when +fortran but no FC was added. Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
2022-11-18Update libjpeg-turbo using new multibuildsystem approach (#33971)iarspider1-35/+27
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-11-17py-pytorch-lightning: add v1.8.2 (#33984)Adam J. Stewart1-0/+1
2022-11-18libxml2: make older versions depend on python@:3.9 (#33952)Ross Miller1-1/+8
Add a dependency on python versions less than 3.10 in order to work around a bug in libxml2's configure script that fails to parse python version strings with more than one character for the minor version. The bug is present in v2.10.1, but has been fixed in 2.10.2. Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-11-18libuv-julia: usa static libs for julia (#33980)Harmen Stoppels1-1/+6
2022-11-17[lerc] added version 4.0.0 (#33974)Jen Herting1-0/+2
* [lerc] added version 4.0.0 * [@spackbot] updating style on behalf of qwertos Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-11-17ParaView: add ParaView-5.11.0 new release (#33972)Cory Quammen1-5/+3
2022-11-17julia: 1.8.3 (#33976)Harmen Stoppels1-0/+1
2022-11-17ompss-2: new package (#33844)David1-0/+124
2022-11-17fixes for ndzip and sperr (#33882)Robert Underwood2-2/+4
* fixes for ndzip * fix commits in spack * new and fixed sperr release Co-authored-by: Robert Underwood <runderwood@anl.gov>
2022-11-17Spack Bioconductor package updates (#33852)Glenn Johnson196-26/+352
* add version 1.46.0 to bioconductor package r-a4 * add version 1.46.0 to bioconductor package r-a4base * add version 1.46.0 to bioconductor package r-a4classif * add version 1.46.0 to bioconductor package r-a4core * add version 1.46.0 to bioconductor package r-a4preproc * add version 1.46.0 to bioconductor package r-a4reporting * add version 1.52.0 to bioconductor package r-absseq * add version 1.28.0 to bioconductor package r-acde * add version 1.76.0 to bioconductor package r-acgh * add version 2.54.0 to bioconductor package r-acme * add version 1.68.0 to bioconductor package r-adsplit * add version 1.70.0 to bioconductor package r-affxparser * add version 1.76.0 to bioconductor package r-affy * add version 1.74.0 to bioconductor package r-affycomp * add version 1.58.0 to bioconductor package r-affycompatible * add version 1.56.0 to bioconductor package r-affycontam * add version 1.70.0 to bioconductor package r-affycoretools * add version 1.46.0 to bioconductor package r-affydata * add version 1.50.0 to bioconductor package r-affyilm * add version 1.68.0 to bioconductor package r-affyio * add version 1.74.0 to bioconductor package r-affyplm * add version 1.44.0 to bioconductor package r-affyrnadegradation * add version 1.46.0 to bioconductor package r-agdex * add version 3.30.0 to bioconductor package r-agilp * add version 2.48.0 to bioconductor package r-agimicrorna * add version 1.30.0 to bioconductor package r-aims * add version 1.30.0 to bioconductor package r-aldex2 * add version 1.36.0 to bioconductor package r-allelicimbalance * add version 1.24.0 to bioconductor package r-alpine * add version 2.60.0 to bioconductor package r-altcdfenvs * add version 2.22.0 to bioconductor package r-anaquin * add version 1.26.0 to bioconductor package r-aneufinder * add version 1.26.0 to bioconductor package r-aneufinderdata * add version 1.70.0 to bioconductor package r-annaffy * add version 1.76.0 to bioconductor package r-annotate * add version 1.60.0 to bioconductor package r-annotationdbi * add version 1.22.0 to bioconductor package r-annotationfilter * add version 1.40.0 to bioconductor package r-annotationforge * add version 3.6.0 to bioconductor package r-annotationhub * add version 3.28.0 to bioconductor package r-aroma-light * add version 1.30.0 to bioconductor package r-bamsignals * add version 2.14.0 to bioconductor package r-beachmat * add version 2.58.0 to bioconductor package r-biobase * add version 2.6.0 to bioconductor package r-biocfilecache * add version 0.44.0 to bioconductor package r-biocgenerics * add version 1.8.0 to bioconductor package r-biocio * add version 1.16.0 to bioconductor package r-biocneighbors * add version 1.32.1 to bioconductor package r-biocparallel * add version 1.14.0 to bioconductor package r-biocsingular * add version 2.26.0 to bioconductor package r-biocstyle * add version 3.16.0 to bioconductor package r-biocversion * add version 2.54.0 to bioconductor package r-biomart * add version 1.26.0 to bioconductor package r-biomformat * add version 2.66.0 to bioconductor package r-biostrings * add version 1.46.0 to bioconductor package r-biovizbase * add version 1.8.0 to bioconductor package r-bluster * add version 1.66.1 to bioconductor package r-bsgenome * add version 1.34.0 to bioconductor package r-bsseq * add version 1.40.0 to bioconductor package r-bumphunter * add version 2.64.0 to bioconductor package r-category * add version 2.28.0 to bioconductor package r-champ * add version 2.30.0 to bioconductor package r-champdata * add version 1.48.0 to bioconductor package r-chipseq * add version 4.6.0 to bioconductor package r-clusterprofiler * add version 1.34.0 to bioconductor package r-cner * add version 1.30.0 to bioconductor package r-codex * add version 2.14.0 to bioconductor package r-complexheatmap * add version 1.72.0 to bioconductor package r-ctc * add version 2.26.0 to bioconductor package r-decipher * add version 0.24.0 to bioconductor package r-delayedarray * add version 1.20.0 to bioconductor package r-delayedmatrixstats * add version 1.38.0 to bioconductor package r-deseq2 * add version 1.44.0 to bioconductor package r-dexseq * add version 1.40.0 to bioconductor package r-dirichletmultinomial * add version 2.12.0 to bioconductor package r-dmrcate * add version 1.72.0 to bioconductor package r-dnacopy * add version 3.24.1 to bioconductor package r-dose * add version 2.46.0 to bioconductor package r-dss * add version 3.40.0 to bioconductor package r-edger * add version 1.18.0 to bioconductor package r-enrichplot * add version 2.22.0 to bioconductor package r-ensembldb * add version 1.44.0 to bioconductor package r-exomecopy * add version 2.6.0 to bioconductor package r-experimenthub * add version 1.24.0 to bioconductor package r-fgsea * add version 2.70.0 to bioconductor package r-gcrma * add version 1.34.0 to bioconductor package r-gdsfmt * add version 1.80.0 to bioconductor package r-genefilter * add version 1.34.0 to bioconductor package r-genelendatabase * add version 1.70.0 to bioconductor package r-genemeta * add version 1.76.0 to bioconductor package r-geneplotter * add version 1.20.0 to bioconductor package r-genie3 * add version 1.34.3 to bioconductor package r-genomeinfodb * update r-genomeinfodbdata * add version 1.34.0 to bioconductor package r-genomicalignments * add version 1.50.2 to bioconductor package r-genomicfeatures * add version 1.50.1 to bioconductor package r-genomicranges * add version 2.66.0 to bioconductor package r-geoquery * add version 1.46.0 to bioconductor package r-ggbio * add version 3.6.2 to bioconductor package r-ggtree * add version 2.8.0 to bioconductor package r-glimma * add version 1.10.0 to bioconductor package r-glmgampoi * add version 5.52.0 to bioconductor package r-globaltest * update r-go-db * add version 1.18.0 to bioconductor package r-gofuncr * add version 2.24.0 to bioconductor package r-gosemsim * add version 1.50.0 to bioconductor package r-goseq * add version 2.64.0 to bioconductor package r-gostats * add version 1.76.0 to bioconductor package r-graph * add version 1.60.0 to bioconductor package r-gseabase * add version 1.30.0 to bioconductor package r-gtrellis * add version 1.42.0 to bioconductor package r-gviz * add version 1.26.0 to bioconductor package r-hdf5array * add version 1.70.0 to bioconductor package r-hypergraph * add version 1.34.0 to bioconductor package r-illumina450probevariants-db * add version 0.40.0 to bioconductor package r-illuminaio * add version 1.72.0 to bioconductor package r-impute * add version 1.36.0 to bioconductor package r-interactivedisplaybase * add version 2.32.0 to bioconductor package r-iranges * add version 1.58.0 to bioconductor package r-kegggraph * add version 1.38.0 to bioconductor package r-keggrest * add version 3.54.0 to bioconductor package r-limma * add version 2.50.0 to bioconductor package r-lumi * add version 1.74.0 to bioconductor package r-makecdfenv * add version 1.76.0 to bioconductor package r-marray * add version 1.10.0 to bioconductor package r-matrixgenerics * add version 1.6.0 to bioconductor package r-metapod * add version 2.44.0 to bioconductor package r-methylumi * add version 1.44.0 to bioconductor package r-minfi * add version 1.32.0 to bioconductor package r-missmethyl * add version 1.78.0 to bioconductor package r-mlinterfaces * add version 1.10.0 to bioconductor package r-mscoreutils * add version 2.24.0 to bioconductor package r-msnbase * add version 2.54.0 to bioconductor package r-multtest * add version 1.36.0 to bioconductor package r-mzid * add version 2.32.0 to bioconductor package r-mzr * add version 1.60.0 to bioconductor package r-oligoclasses * update r-org-hs-eg-db * add version 1.40.0 to bioconductor package r-organismdbi * add version 1.38.0 to bioconductor package r-pathview * add version 1.90.0 to bioconductor package r-pcamethods * update r-pfam-db * add version 1.42.0 to bioconductor package r-phyloseq * add version 1.60.0 to bioconductor package r-preprocesscore * add version 1.30.0 to bioconductor package r-protgenerics * add version 1.32.0 to bioconductor package r-quantro * add version 2.30.0 to bioconductor package r-qvalue * add version 1.74.0 to bioconductor package r-rbgl * add version 2.38.0 to bioconductor package r-reportingtools * add version 2.42.0 to bioconductor package r-rgraphviz * add version 2.42.0 to bioconductor package r-rhdf5 * add version 1.10.0 to bioconductor package r-rhdf5filters * add version 1.20.0 to bioconductor package r-rhdf5lib * add version 2.0.0 to bioconductor package r-rhtslib * add version 1.74.0 to bioconductor package r-roc * add version 1.26.0 to bioconductor package r-rots * add version 2.14.0 to bioconductor package r-rsamtools * add version 1.58.0 to bioconductor package r-rtracklayer * add version 0.36.0 to bioconductor package r-s4vectors * add version 1.6.0 to bioconductor package r-scaledmatrix * add version 1.26.0 to bioconductor package r-scater * add version 1.12.0 to bioconductor package r-scdblfinder * add version 1.26.0 to bioconductor package r-scran * add version 1.8.0 to bioconductor package r-scuttle * add version 1.64.0 to bioconductor package r-seqlogo * add version 1.56.0 to bioconductor package r-shortread * add version 1.72.0 to bioconductor package r-siggenes * add version 1.20.0 to bioconductor package r-singlecellexperiment * add version 1.32.0 to bioconductor package r-snprelate * add version 1.48.0 to bioconductor package r-snpstats * add version 2.34.0 to bioconductor package r-somaticsignatures * add version 1.10.0 to bioconductor package r-sparsematrixstats * add version 1.38.0 to bioconductor package r-spem * add version 1.36.0 to bioconductor package r-sseq * add version 1.28.0 to bioconductor package r-summarizedexperiment * add version 3.46.0 to bioconductor package r-sva * add version 1.36.0 to bioconductor package r-tfbstools * add version 1.20.0 to bioconductor package r-tmixclust * add version 2.50.0 to bioconductor package r-topgo * add version 1.22.0 to bioconductor package r-treeio * add version 1.26.0 to bioconductor package r-tximport * add version 1.26.0 to bioconductor package r-tximportdata * add version 1.44.0 to bioconductor package r-variantannotation * add version 3.66.0 to bioconductor package r-vsn * add version 2.4.0 to bioconductor package r-watermelon * add version 2.44.0 to bioconductor package r-xde * add version 1.56.0 to bioconductor package r-xmapbridge * add version 0.38.0 to bioconductor package r-xvector * add version 1.24.0 to bioconductor package r-yapsa * add version 1.24.0 to bioconductor package r-yarn * add version 1.44.0 to bioconductor package r-zlibbioc * make version resource consistent for r-bsgenome-hsapiens-ucsc-hg19 * make version resource consistent for r-go-db * make version resource consistent for r-kegg-db * make version resource consistent for r-org-hs-eg-db * make version resource consistent for r-pfam-db * new package: r-ggrastr * Patches not needed for new version * new package: r-hdo-db * new package: r-ggnewscale * new package: r-gson * Actually depends on ggplot2@3.4.0: * Fix formatting of r-hdo-db * Fix dependency version specifiers * Clean up duplicate dependency references
2022-11-17glib: fix URLs (#33919)Erik Heeren1-2/+2
2022-11-17py-tensorflow: add patch releases, remove v0.X (#33963)Adam J. Stewart3-100/+7
2022-11-17Hdf5 package: build on Windows (#31141)Jared Popelar6-21/+94
* Enable hdf5 build (including +mpi) on Windows * This includes updates to hdf5 dependencies openssl (minor edit) and bzip2 (more-extensive edits) * Add binary-based installation of msmpi (this is currently the only supported MPI implementation in Spack for Windows). Note that this does not install to the Spack-specified prefix. This implementation will be replaced with a source-based implementation Co-authored-by: John Parent <john.parent@kitware.com>
2022-11-17Update CMake version to 3.25.0 (#33957)John W. Parent1-0/+1
CMake had official release 3.25.0, update package version to reflect Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-11-17Waf build system: fix typo in legacy_attributes (#33958)Chris Green2-3/+1
Fix erroneous duplication of `build_time_test_callbacks` in `legacy_attributes`: one of the duplicates should be `install_time_test_callbacks`
2022-11-17Python: do not set PYTHONHOME during build (#33956)Massimiliano Culpo1-6/+1
Setting PYTHONHOME is rarely needed (since each interpreter has various ways of setting it automatically) and very often it is difficult to get right manually. For instance, the change done to set PYTHONHOME to sysconfig["base_prefix"] broke bootstrapping dev dependencies of Spack for me, when working inside a virtual environment in Linux.
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-11-09 08:12:29 +0000