Age | Commit message (Collapse) | Author | Files | Lines |
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* 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
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refers #33985
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Also improve the InstallError message when +fortran but no FC was added.
Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
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Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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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>
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* [lerc] added version 4.0.0
* [@spackbot] updating style on behalf of qwertos
Co-authored-by: qwertos <qwertos@users.noreply.github.com>
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* fixes for ndzip
* fix commits in spack
* new and fixed sperr release
Co-authored-by: Robert Underwood <runderwood@anl.gov>
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* 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
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* 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>
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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>
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Fix erroneous duplication of `build_time_test_callbacks` in
`legacy_attributes`: one of the duplicates should be
`install_time_test_callbacks`
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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.
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These commands are slated for removal in v0.20
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* replace mpi as a variant instead of dependency
* separate serial and MPI dependencies
* configure args depending on serial or mpi variant
* reformat with black
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Typo introduced in #33847
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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>
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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
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Reviewed-by: haampie, bernhardkaindl
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Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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Delete statements related to Python 2.7, and avoid installing
patchelf since now we can bootstrap it.
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#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).
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Co-authored-by: Stephen Sachs <stesachs@amazon.com>
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* add sz3 and mdz smoke test
Co-authored-by: Robert Underwood <runderwood@anl.gov>
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* py-isal: adding some missing build deps
* py-isal: use external libisal
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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.
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target (#33936)
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