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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.
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
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