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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.
2022-11-17py-rasterio: add v1.3.4 (#33961)Adam J. Stewart1-2/+4
2022-11-17docs: fix typo in multiple build systems (#33965)Harmen Stoppels1-1/+1
2022-11-17relocate.py: small refactor for file_is_relocatable (#33967)Harmen Stoppels4-39/+31
2022-11-17Remove deprecated subcommands from "spack bootstrap" (#33964)Massimiliano Culpo3-61/+24
These commands are slated for removal in v0.20
2022-11-17Octopus : Separate serial and MPI dependencies (#33836)Ashwin Kumar1-7/+30
* replace mpi as a variant instead of dependency * separate serial and MPI dependencies * configure args depending on serial or mpi variant * reformat with black
2022-11-17py-torchmetrics: add v0.10.3 (#33962)Adam J. Stewart1-0/+1
2022-11-17Add sgid notice when running on AFS (#30247)Michael Kuhn1-0/+7
2022-11-17Python: fix bug detection, trying to access self (#33955)Massimiliano Culpo1-1/+1
Typo introduced in #33847
2022-11-16zlib, openssl: return to `http` URLs (#33324)Ben Boeckel2-2/+2
In #3113, `https` was removed to ensure that `curl` can be bootstrapped without SSL being present. This was lost in #25672 which aimed to use `https` where possible. Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-11-16[xz] icc does not support attribute __symver__ (#33839)Stephen Sachs1-0/+4
xz have added attribute __symver__ for compilers that identify as GCC>=10.0 via __GNUC__. Intels `icc` sets __GNUC__ but currently does not support this attribute: https://community.intel.com/t5/Intel-C-Compiler/symver-not-supported/m-p/1429028/emcs_t/S2h8ZW1haWx8dG9waWNfc3Vic2NyaXB0aW9ufExBQVRWMjIyUFFZTlZTfDE0MjkwMjh8U1VCU0NSSVBUSU9OU3xoSw#M40459
2022-11-16serialbox: update patch to handle UTF-8 conversion errors (#33317)Sergey Kosukhin2-7/+32
2022-11-16py-jupyter-server: add 1.21.0 (#33310)Manuela Kuhn1-2/+7
2022-11-17lib/spack/spack/store.py: Fix #28170 for padding relocation (#33122)Brian Vanderwende1-0/+1
2022-11-16py-jupyterlab: add 3.4.8 (#33308)Manuela Kuhn1-5/+9
2022-11-17blast-plus: update to 2.13.0 and add cpio as build dependency (#33187)Christian Kniep1-1/+4
2022-11-17* ninja: Set min. required version of re2c dependency, fixes #33127 (#33128)Sebastian Grabowski1-0/+1
Reviewed-by: haampie, bernhardkaindl
2022-11-17gettext: On ppc64le, for older versions, use system cdefs.h (#33411)Jonathon Anderson1-0/+7
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-11-16Clean unit-test workflow file (#33945)Massimiliano Culpo1-16/+5
Delete statements related to Python 2.7, and avoid installing patchelf since now we can bootstrap it.
2022-11-16updated v2.11.8 (#33944)chenwany1-2/+4
2022-11-16initial implementation of slingshot detection (#33793)Greg Becker2-2/+7
2022-11-16Upstreams: add canonicalize path (#33946)psakievich1-1/+3
2022-11-16Windows bootstrapping: remove unneeded call to add dll to PATH (#33622)John W. Parent1-7/+0
#32942 fixed bootstrapping on Windows by having the core Spack code explicitly add the Clingo package bin/ directory as a DLL path. Since then, #33400 has been merged, which ensures that the Python module installed by the Spack `clingo` package can find the DLLs in bin/. Note that this only works for Spack instances which have been bootstrapped after #33400: for installations bootstrapped before then, you will need to run `spack clean -b` (this would only be needed for Spack instances running on Windows).
2022-11-16SIP build system: fix "python not defined in builder" (#33906)Stephen Sachs1-1/+1
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-11-16qt: new version 5.15.6 and 5.15.7 (#33933)Wouter Deconinck1-0/+2
2022-11-16add sz3 and mdz smoke test for inclusion in e4s (#33864)Robert Underwood1-0/+14
* add sz3 and mdz smoke test Co-authored-by: Robert Underwood <runderwood@anl.gov>
2022-11-16py-isal: use external libisal (#33932)snehring1-0/+4
* py-isal: adding some missing build deps * py-isal: use external libisal
2022-11-16New Package: rarpd (#28686)Pat Riehecky1-0/+26
2022-11-16docs updates for spack env depfile (#33937)Harmen Stoppels1-6/+10
2022-11-16neovim: fix build dependencies (#33935)Matthias Wolf1-2/+2
Buildin neovim@0.8.0 complains (for me) about Lua's lpeg and mpack packages not being available at build time. Removing the link-only setting in the dependencies for these two packages fixes the build for me.
2022-11-16spack env depfile in Gitlab CI should use `install-deps/pkg-version-hash` ↵Harmen Stoppels1-3/+1
target (#33936)
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