* test_suite.py: speed up slow test by using mock packages
* Don't resolve the sha during unit-tests
* Skip long-running test that fails, instead of executing it
* uninstall: fix accidental cubic complexity
Currently spack uninstall runs in worst case cubic time complexity
thanks to traversal during traversal during traversal while collecting
the specs to be uninstalled.
Also brings down the number of error messages printed to something
linear in the amount of matching specs instead of quadratic.
* 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>
* 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>
* graphviz: remove cyclic dep to svg when pangocairo and poppler+glib failure
* graphviz: remove cyclic dep to svg when pangocairo and poppler+glib failure
* 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>
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>
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>
* 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
