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| author | Glenn Johnson <glenn-johnson@uiowa.edu> | 2023-05-23 13:40:00 -0500 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-05-23 11:40:00 -0700 |
| commit | e4a9d9ae5bf8b7417d988ce1271d81bd99622987 (patch) | |
| tree | 4657a9c321aa47244e0196eba1fb83efab0ae575 | |
| parent | a6886983dc75e858875221b33a77565a5cebf4c8 (diff) | |
| download | spack-e4a9d9ae5bf8b7417d988ce1271d81bd99622987.tar.gz spack-e4a9d9ae5bf8b7417d988ce1271d81bd99622987.tar.bz2 spack-e4a9d9ae5bf8b7417d988ce1271d81bd99622987.tar.xz spack-e4a9d9ae5bf8b7417d988ce1271d81bd99622987.zip | |
Bioc updates (#37297)
* add version 1.48.0 to bioconductor package r-a4
* add version 1.48.0 to bioconductor package r-a4base
* add version 1.48.0 to bioconductor package r-a4classif
* add version 1.48.0 to bioconductor package r-a4core
* add version 1.48.0 to bioconductor package r-a4preproc
* add version 1.48.0 to bioconductor package r-a4reporting
* add version 1.54.0 to bioconductor package r-absseq
* add version 1.30.0 to bioconductor package r-acde
* add version 1.78.0 to bioconductor package r-acgh
* add version 2.56.0 to bioconductor package r-acme
* add version 1.70.0 to bioconductor package r-adsplit
* add version 1.72.0 to bioconductor package r-affxparser
* add version 1.78.0 to bioconductor package r-affy
* add version 1.76.0 to bioconductor package r-affycomp
* add version 1.58.0 to bioconductor package r-affycontam
* add version 1.72.0 to bioconductor package r-affycoretools
* add version 1.48.0 to bioconductor package r-affydata
* add version 1.52.0 to bioconductor package r-affyilm
* add version 1.70.0 to bioconductor package r-affyio
* add version 1.76.0 to bioconductor package r-affyplm
* add version 1.46.0 to bioconductor package r-affyrnadegradation
* add version 1.48.0 to bioconductor package r-agdex
* add version 3.32.0 to bioconductor package r-agilp
* add version 2.50.0 to bioconductor package r-agimicrorna
* add version 1.32.0 to bioconductor package r-aims
* add version 1.32.0 to bioconductor package r-aldex2
* add version 1.38.0 to bioconductor package r-allelicimbalance
* add version 1.26.0 to bioconductor package r-alpine
* add version 2.62.0 to bioconductor package r-altcdfenvs
* add version 2.24.0 to bioconductor package r-anaquin
* add version 1.28.0 to bioconductor package r-aneufinder
* add version 1.28.0 to bioconductor package r-aneufinderdata
* add version 1.72.0 to bioconductor package r-annaffy
* add version 1.78.0 to bioconductor package r-annotate
* add version 1.62.0 to bioconductor package r-annotationdbi
* add version 1.24.0 to bioconductor package r-annotationfilter
* add version 1.42.0 to bioconductor package r-annotationforge
* add version 3.8.0 to bioconductor package r-annotationhub
* add version 3.30.0 to bioconductor package r-aroma-light
* add version 1.32.0 to bioconductor package r-bamsignals
* add version 2.16.0 to bioconductor package r-beachmat
* add version 2.60.0 to bioconductor package r-biobase
* add version 2.8.0 to bioconductor package r-biocfilecache
* add version 0.46.0 to bioconductor package r-biocgeneric
* add version 1.10.0 to bioconductor package r-biocio
* add version 1.18.0 to bioconductor package r-biocneighbors
* add version 1.34.0 to bioconductor package r-biocparallel
* add version 1.16.0 to bioconductor package r-biocsingular
* add version 2.28.0 to bioconductor package r-biocstyle
* add version 3.17.1 to bioconductor package r-biocversion
* add version 2.56.0 to bioconductor package r-biomart
* add version 1.28.0 to bioconductor package r-biomformat
* add version 2.68.0 to bioconductor package r-biostrings
* add version 1.48.0 to bioconductor package r-biovizbase
* add version 1.10.0 to bioconductor package r-bluster
* add version 1.68.0 to bioconductor package r-bsgenome
* add version 1.36.0 to bioconductor package r-bsseq
* add version 1.42.0 to bioconductor package r-bumphunter
* add version 2.66.0 to bioconductor package r-category
* add version 2.30.0 to bioconductor package r-champ
* add version 2.32.0 to bioconductor package r-champdata
* add version 1.50.0 to bioconductor package r-chipseq
* add version 4.8.0 to bioconductor package r-clusterprofiler
* add version 1.36.0 to bioconductor package r-cner
* add version 1.32.0 to bioconductor package r-codex
* add version 2.16.0 to bioconductor package r-complexheatmap
* add version 1.74.0 to bioconductor package r-ctc
* add version 2.28.0 to bioconductor package r-decipher
* add version 0.26.0 to bioconductor package r-delayedarray
* add version 1.22.0 to bioconductor package r-delayedmatrixstats
* add version 1.40.0 to bioconductor package r-deseq2
* add version 1.46.0 to bioconductor package r-dexseq
* add version 1.42.0 to bioconductor package r-dirichletmultinomial
* add version 2.14.0 to bioconductor package r-dmrcate
* add version 1.74.0 to bioconductor package r-dnacopy
* add version 3.26.0 to bioconductor package r-dose
* add version 2.48.0 to bioconductor package r-dss
* add version 3.42.0 to bioconductor package r-edger
* add version 1.20.0 to bioconductor package r-enrichplot
* add version 2.24.0 to bioconductor package r-ensembldb
* add version 1.46.0 to bioconductor package r-exomecopy
* add version 2.8.0 to bioconductor package r-experimenthub
* add version 1.26.0 to bioconductor package r-fgsea
* add version 2.72.0 to bioconductor package r-gcrma
* add version 1.36.0 to bioconductor package r-gdsfmt
* add version 1.82.0 to bioconductor package r-genefilter
* add version 1.36.0 to bioconductor package r-genelendatabase
* add version 1.72.0 to bioconductor package r-genemeta
* add version 1.78.0 to bioconductor package r-geneplotter
* add version 1.22.0 to bioconductor package r-genie3
* add version 1.36.0 to bioconductor package r-genomeinfodb
* update r-genomeinfodbdata
* add version 1.36.0 to bioconductor package r-genomicalignments
* add version 1.52.0 to bioconductor package r-genomicfeatures
* add version 1.52.0 to bioconductor package r-genomicranges
* add version 2.68.0 to bioconductor package r-geoquery
* add version 1.48.0 to bioconductor package r-ggbio
* add version 3.8.0 to bioconductor package r-ggtree
* add version 2.10.0 to bioconductor package r-glimma
* add version 1.12.0 to bioconductor package r-glmgampoi
* add version 5.54.0 to bioconductor package r-globaltest
* update r-go-db
* add version 1.20.0 to bioconductor package r-gofuncr
* add version 2.26.0 to bioconductor package r-gosemsim
* add version 1.52.0 to bioconductor package r-goseq
* add version 2.66.0 to bioconductor package r-gostats
* add version 1.78.0 to bioconductor package r-graph
* add version 1.62.0 to bioconductor package r-gseabase
* add version 1.32.0 to bioconductor package r-gtrellis
* add version 1.44.0 to bioconductor package r-gviz
* add version 1.28.0 to bioconductor package r-hdf5array
* add version 1.72.0 to bioconductor package r-hypergraph
* add version 1.36.0 to bioconductor package r-illumina450probevariants-db
* add version 0.42.0 to bioconductor package r-illuminaio
* add version 1.74.0 to bioconductor package r-impute
* add version 1.38.0 to bioconductor package r-interactivedisplaybase
* add version 2.34.0 to bioconductor package r-iranges
* add version 1.60.0 to bioconductor package r-kegggraph
* add version 1.40.0 to bioconductor package r-keggrest
* add version 3.56.0 to bioconductor package r-limma
* add version 2.52.0 to bioconductor package r-lumi
* add version 1.76.0 to bioconductor package r-makecdfenv
* add version 1.78.0 to bioconductor package r-marray
* add version 1.12.0 to bioconductor package r-matrixgenerics
* add version 1.8.0 to bioconductor package r-metapod
* add version 2.46.0 to bioconductor package r-methylumi
* add version 1.46.0 to bioconductor package r-minfi
* add version 1.34.0 to bioconductor package r-missmethyl
* add version 1.80.0 to bioconductor package r-mlinterfaces
* add version 1.12.0 to bioconductor package r-mscoreutils
* add version 2.26.0 to bioconductor package r-msnbase
* add version 2.56.0 to bioconductor package r-multtest
* add version 1.38.0 to bioconductor package r-mzid
* add version 2.34.0 to bioconductor package r-mzr
* add version 1.62.0 to bioconductor package r-oligoclasses
* update r-org-hs-eg-db
* add version 1.42.0 to bioconductor package r-organismdbi
* add version 1.40.0 to bioconductor package r-pathview
* add version 1.92.0 to bioconductor package r-pcamethods
* update r-pfam-db
* add version 1.44.0 to bioconductor package r-phyloseq
* add version 1.62.0 to bioconductor package r-preprocesscore
* add version 1.32.0 to bioconductor package r-protgenerics
* add version 1.34.0 to bioconductor package r-quantro
* add version 2.32.0 to bioconductor package r-qvalue
* add version 1.76.0 to bioconductor package r-rbgl
* add version 2.40.0 to bioconductor package r-reportingtools
* add version 2.44.0 to bioconductor package r-rgraphviz
* add version 2.44.0 to bioconductor package r-rhdf5
* add version 1.12.0 to bioconductor package r-rhdf5filters
* add version 1.22.0 to bioconductor package r-rhdf5lib
* add version 1.76.0 to bioconductor package r-roc
* add version 1.28.0 to bioconductor package r-rots
* add version 2.16.0 to bioconductor package r-rsamtools
* add version 1.60.0 to bioconductor package r-rtracklayer
* add version 0.38.0 to bioconductor package r-s4vectors
* add version 1.8.0 to bioconductor package r-scaledmatrix
* add version 1.28.0 to bioconductor package r-scater
* add version 1.14.0 to bioconductor package r-scdblfinder
* add version 1.28.0 to bioconductor package r-scran
* add version 1.10.0 to bioconductor package r-scuttle
* add version 1.66.0 to bioconductor package r-seqlogo
* add version 1.58.0 to bioconductor package r-shortread
* add version 1.74.0 to bioconductor package r-siggenes
* add version 1.22.0 to bioconductor package r-singlecellexperiment
* add version 1.34.0 to bioconductor package r-snprelate
* add version 1.50.0 to bioconductor package r-snpstats
* add version 2.36.0 to bioconductor package r-somaticsignatures
* add version 1.12.0 to bioconductor package r-sparsematrixstats
* add version 1.40.0 to bioconductor package r-spem
* add version 1.38.0 to bioconductor package r-sseq
* add version 1.30.0 to bioconductor package r-summarizedexperiment
* add version 3.48.0 to bioconductor package r-sva
* add version 1.38.0 to bioconductor package r-tfbstools
* add version 1.22.0 to bioconductor package r-tmixclust
* add version 2.52.0 to bioconductor package r-topgo
* add version 1.24.0 to bioconductor package r-treeio
* add version 1.28.0 to bioconductor package r-tximport
* add version 1.28.0 to bioconductor package r-tximportdata
* add version 1.46.0 to bioconductor package r-variantannotation
* add version 3.68.0 to bioconductor package r-vsn
* add version 2.6.0 to bioconductor package r-watermelon
* add version 2.46.0 to bioconductor package r-xde
* add version 1.58.0 to bioconductor package r-xmapbridge
* add version 0.40.0 to bioconductor package r-xvector
* add version 1.26.0 to bioconductor package r-yapsa
* add version 1.26.0 to bioconductor package r-yarn
* add version 1.46.0 to bioconductor package r-zlibbioc
* Revert "add version 1.82.0 to bioconductor package r-genefilter"
This reverts commit 1702071c6d3ab83b75e0fcf493622113957223bb.
* Revert "add version 0.38.0 to bioconductor package r-s4vectors"
This reverts commit 58a7df23872ac8035fdac75c93cedf6dd7819dd0.
* add version 0.38.0 to bioconductor package r-s4vectors
* Revert "add version 1.28.0 to bioconductor package r-aneufinder"
This reverts commit 0a1f59de6c17fe6aa62bcf807826f9d2023280e6.
* add version 1.28.0 to bioconductor package r-aneufinder
* Revert "add version 2.16.0 to bioconductor package r-beachmat"
This reverts commit cd49fb8e4c84763a063f1b2d0b3bdc0179161568.
* add version 2.16.0 to bioconductor package r-beachmat
* Revert "add version 4.8.0 to bioconductor package r-clusterprofiler"
This reverts commit 6e9a951cbe08042ca5100f47b8b1680cae26cc14.
* add version 4.8.0 to bioconductor package r-clusterprofiler
* Fix syntax error
* r-genefilter: add version 1.82.0
* new package: r-basilisk-utils
* new package: r-basilisk
* new package: r-densvis
* new package: r-dir-expiry
* r-affyplm: add zlib dependency
* r-cner: add zlib dependency
* r-mzr: add zlib dependency
* r-rhdf5filters: add zstd dependency
* r-shortread: add zlib dependency
* r-snpstats: add zlib dependency
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
193 files changed, 358 insertions, 24 deletions
diff --git a/var/spack/repos/builtin/packages/r-a4/package.py b/var/spack/repos/builtin/packages/r-a4/package.py index a50c4d2c4c..d602001ddd 100644 --- a/var/spack/repos/builtin/packages/r-a4/package.py +++ b/var/spack/repos/builtin/packages/r-a4/package.py @@ -14,6 +14,7 @@ class RA4(RPackage): bioc = "a4" + version("1.48.0", commit="89ef9f4afdde5270acecc7c65be3752b71237eba") version("1.46.0", commit="1b8f1300025fb0940e7f24cff7ffec9fca02d0e4") version("1.44.0", commit="5b0fc5a9971d8f3688ad1f88a4f5ee1498e91633") version("1.42.0", commit="fc26809e2bce7cd50d99d6f6dd5f85c38342fdea") diff --git a/var/spack/repos/builtin/packages/r-a4base/package.py b/var/spack/repos/builtin/packages/r-a4base/package.py index 12177661a8..2af4e29e6c 100644 --- a/var/spack/repos/builtin/packages/r-a4base/package.py +++ b/var/spack/repos/builtin/packages/r-a4base/package.py @@ -14,6 +14,7 @@ class RA4base(RPackage): bioc = "a4Base" + version("1.48.0", commit="26d5793de3163091125feeed1de82e5406777b60") version("1.46.0", commit="be70ae723bb6031cdf9540d62dc6113761074e88") version("1.44.0", commit="9ae69e03118c7b14df0e6c9e3b25362b09f25bbe") version("1.42.0", commit="d7296e2792020e9c5b1c19101104326ee8bebfe6") diff --git a/var/spack/repos/builtin/packages/r-a4classif/package.py b/var/spack/repos/builtin/packages/r-a4classif/package.py index 9f4db0be22..7970297043 100644 --- a/var/spack/repos/builtin/packages/r-a4classif/package.py +++ b/var/spack/repos/builtin/packages/r-a4classif/package.py @@ -15,6 +15,7 @@ class RA4classif(RPackage): bioc = "a4Classif" + version("1.48.0", commit="1e2ff90d5af6332beac630395a7494c8fd30aff4") version("1.46.0", commit="96794183a76ab7da7a1863ccd421640254447af5") version("1.44.0", commit="df0fce781f9bc480a1159d958c9a63c314a9ed01") version("1.42.0", commit="820854a7ca9ed0c295479a25b7e3375c6d01d0b5") diff --git a/var/spack/repos/builtin/packages/r-a4core/package.py b/var/spack/repos/builtin/packages/r-a4core/package.py index c62598d368..a8dbd02642 100644 --- a/var/spack/repos/builtin/packages/r-a4core/package.py +++ b/var/spack/repos/builtin/packages/r-a4core/package.py @@ -14,6 +14,7 @@ class RA4core(RPackage): bioc = "a4Core" + version("1.48.0", commit="3dd09f0a662745fcfd3fee7048301f3524e8ac5c") version("1.46.0", commit="8999fe146be6d04ae36c725d2b6324a6ce8ceb83") version("1.44.0", commit="61a7f3a51a41af615bfd4c22984e4c4a82874e8c") version("1.42.0", commit="6985950b72c2a0f20ec44fe2067d8864e004bfaa") diff --git a/var/spack/repos/builtin/packages/r-a4preproc/package.py b/var/spack/repos/builtin/packages/r-a4preproc/package.py index aed9ac7200..d77b3ff598 100644 --- a/var/spack/repos/builtin/packages/r-a4preproc/package.py +++ b/var/spack/repos/builtin/packages/r-a4preproc/package.py @@ -14,6 +14,7 @@ class RA4preproc(RPackage): bioc = "a4Preproc" + version("1.48.0", commit="d3bf8b82d7cabd2ef77253bb9a741dcde3ca3a41") version("1.46.0", commit="8463958692c73fd655a6dfec39ea99c915513719") version("1.44.0", commit="252381265b96b83803a93e0c2014dd6b0574e57f") version("1.42.0", commit="773a91e884d2ada16fe9cf57d5ed53c0155e3fa2") diff --git a/var/spack/repos/builtin/packages/r-a4reporting/package.py b/var/spack/repos/builtin/packages/r-a4reporting/package.py index f03819f009..ee210045cb 100644 --- a/var/spack/repos/builtin/packages/r-a4reporting/package.py +++ b/var/spack/repos/builtin/packages/r-a4reporting/package.py @@ -14,6 +14,7 @@ class RA4reporting(RPackage): bioc = "a4Reporting" + version("1.48.0", commit="de8c4b76f6b7ef502d77d55289df0d64fe70447c") version("1.46.0", commit="00b82d25bef4d518ae92f615d3a6f7931c0618dc") version("1.44.0", commit="bfe83507daf53e2e327474ea3012f0dc920efac1") version("1.42.0", commit="b0d715b9cdac80bc412f0a9a6b33941c4a7582bb") diff --git a/var/spack/repos/builtin/packages/r-absseq/package.py b/var/spack/repos/builtin/packages/r-absseq/package.py index 6d06a658d3..83a5786bd2 100644 --- a/var/spack/repos/builtin/packages/r-absseq/package.py +++ b/var/spack/repos/builtin/packages/r-absseq/package.py @@ -17,6 +17,7 @@ class RAbsseq(RPackage): bioc = "ABSSeq" + version("1.54.0", commit="5e7de8c2a6532073012660f22243c9f7a5568ef6") version("1.52.0", commit="07038c047775e17d5d29909927d2143efb63e9cb") version("1.50.0", commit="4f384d04ebaae6ea0b56e5cff9a9dcdcb6c8afb0") version("1.48.0", commit="b237c967d44d075ca306c35e92df8b66a60ce72d") diff --git a/var/spack/repos/builtin/packages/r-acde/package.py b/var/spack/repos/builtin/packages/r-acde/package.py index 2c7ccfb0fe..af70a66c45 100644 --- a/var/spack/repos/builtin/packages/r-acde/package.py +++ b/var/spack/repos/builtin/packages/r-acde/package.py @@ -22,6 +22,7 @@ class RAcde(RPackage): bioc = "acde" + version("1.30.0", commit="4c16b9fd6c91a433bf1345252e022571c4983cb5") version("1.28.0", commit="0edccca7be2475fa2ae3b3c36d0d64924c37b3c0") version("1.26.0", commit="dfef9a435062e948efd5eda22942a0d500baa992") version("1.24.0", commit="0c3c4d47af7eaff37420032ea5245743a65124cf") diff --git a/var/spack/repos/builtin/packages/r-acgh/package.py b/var/spack/repos/builtin/packages/r-acgh/package.py index cda655f229..3295669b3a 100644 --- a/var/spack/repos/builtin/packages/r-acgh/package.py +++ b/var/spack/repos/builtin/packages/r-acgh/package.py @@ -16,6 +16,7 @@ class RAcgh(RPackage): bioc = "aCGH" + version("1.78.0", commit="75df3a4839af66ce177d1bbc3cec4ac03c21dc8e") version("1.76.0", commit="c6068522854ed0b1c3feb006619ef25590f70ad6") version("1.74.0", commit="e7ba380af0da138788eb6c86f5dbe453269c0810") version("1.72.0", commit="b5d4022ac487125194d3913f1b8c2948db6e2792") diff --git a/var/spack/repos/builtin/packages/r-acme/package.py b/var/spack/repos/builtin/packages/r-acme/package.py index 3b00ceec37..989ec5abd8 100644 --- a/var/spack/repos/builtin/packages/r-acme/package.py +++ b/var/spack/repos/builtin/packages/r-acme/package.py @@ -21,6 +21,7 @@ class RAcme(RPackage): bioc = "ACME" + version("2.56.0", commit="083af1249e67db11fd471babe67b146eb9c1700c") version("2.54.0", commit="8d39d9d6623adf427f5eba308790e1de01213870") version("2.52.0", commit="14a97c722d0201654af9e583e7e462b458c28a77") version("2.50.0", commit="d55a19a8c091e8ea5fd35041520107a7f7603e14") diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py index 8fe87f646c..182ffd14a8 100644 --- a/var/spack/repos/builtin/packages/r-adsplit/package.py +++ b/var/spack/repos/builtin/packages/r-adsplit/package.py @@ -16,6 +16,7 @@ class RAdsplit(RPackage): bioc = "adSplit" + version("1.70.0", commit="a08a994215a459b856eae051c778e2b9144f52d9") version("1.68.0", commit="705977b5e1cb7dd69793cc673fa215baaba42af5") version("1.66.0", commit="64580a6f7a9bc6b16334267c90df48fbb839cc16") version("1.64.0", commit="32f150eb51c66b867301dceeb527de5b97f9f490") diff --git a/var/spack/repos/builtin/packages/r-affxparser/package.py b/var/spack/repos/builtin/packages/r-affxparser/package.py index ddabd8d6ea..5e492394e7 100644 --- a/var/spack/repos/builtin/packages/r-affxparser/package.py +++ b/var/spack/repos/builtin/packages/r-affxparser/package.py @@ -20,6 +20,7 @@ class RAffxparser(RPackage): bioc = "affxparser" + version("1.72.0", commit="6e976af32f77835143f6b4e0c01c6016dc1b331c") version("1.70.0", commit="28f94cd3477e9500942be89cbcb5cad1bbb369fe") version("1.68.1", commit="821a01a2df18115a3b7864b3f45418255b7123eb") version("1.66.0", commit="2ea72d4c924ac14bdd807b23563c8501c226ce3a") diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py index 1be77637c3..57905c89b3 100644 --- a/var/spack/repos/builtin/packages/r-affy/package.py +++ b/var/spack/repos/builtin/packages/r-affy/package.py @@ -15,6 +15,7 @@ class RAffy(RPackage): bioc = "affy" + version("1.78.0", commit="cc7eac358b6e10ee86a7a93d2e436758f6fbd9b5") version("1.76.0", commit="3bb309388d5d6402c356d4a5270ee83c5b88942f") version("1.74.0", commit="2266c4a46eda7e5b64f7f3e17e8b61e7b85579ff") version("1.72.0", commit="3750b4eb8e5224b19100f6c881b67e568d8968a2") diff --git a/var/spack/repos/builtin/packages/r-affycomp/package.py b/var/spack/repos/builtin/packages/r-affycomp/package.py index 10359cdbcc..e7fed58a4f 100644 --- a/var/spack/repos/builtin/packages/r-affycomp/package.py +++ b/var/spack/repos/builtin/packages/r-affycomp/package.py @@ -14,6 +14,7 @@ class RAffycomp(RPackage): bioc = "affycomp" + version("1.76.0", commit="8bfc628de26a739c5e0cb47aa22bfda7c8d0a922") version("1.74.0", commit="1160d6395f23085456938ba2bd38fb45597fc92f") version("1.72.0", commit="c52baea98b80abd4a99380ac9d4b68ef91869d40") version("1.70.0", commit="487f6775975092475581a6c02ddb27590559cf07") diff --git a/var/spack/repos/builtin/packages/r-affycontam/package.py b/var/spack/repos/builtin/packages/r-affycontam/package.py index 3e4bf23919..2853c92b57 100644 --- a/var/spack/repos/builtin/packages/r-affycontam/package.py +++ b/var/spack/repos/builtin/packages/r-affycontam/package.py @@ -14,6 +14,7 @@ class RAffycontam(RPackage): bioc = "affyContam" + version("1.58.0", commit="5e91d79d7653a4f484b62eae7fd7e908de8cb9b6") version("1.56.0", commit="e2b8a4fba1648255eadce954a848f2dd8e22bcb3") version("1.54.0", commit="c5208b48b8881983ff53a4713244327e8ad13b78") version("1.52.0", commit="47c1d86da330f157d3ece0e26b0657d66a5ca0c9") diff --git a/var/spack/repos/builtin/packages/r-affycoretools/package.py b/var/spack/repos/builtin/packages/r-affycoretools/package.py index 602c22574b..64118924cb 100644 --- a/var/spack/repos/builtin/packages/r-affycoretools/package.py +++ b/var/spack/repos/builtin/packages/r-affycoretools/package.py @@ -15,6 +15,7 @@ class RAffycoretools(RPackage): bioc = "affycoretools" + version("1.72.0", commit="229ae09efc1a66e64ea395019c32d16387bf81ac") version("1.70.0", commit="f09a788aa83e1e052a7c5f148a451a99fe9c9c96") version("1.68.1", commit="69546b1fe5edd71eca130d53d33f0fb0fcf62c97") version("1.66.0", commit="6bf769d70e196634097f465ed2fa85cce5312a6d") diff --git a/var/spack/repos/builtin/packages/r-affydata/package.py b/var/spack/repos/builtin/packages/r-affydata/package.py index a57eed869a..13ce12703d 100644 --- a/var/spack/repos/builtin/packages/r-affydata/package.py +++ b/var/spack/repos/builtin/packages/r-affydata/package.py @@ -15,6 +15,7 @@ class RAffydata(RPackage): bioc = "affydata" + version("1.48.0", commit="037b86c86c114761ff1bcca64ab4e0bcd68063d3") version("1.46.0", commit="870745b886df9f1fbbd6130d266c0ef96f3afa66") version("1.44.0", commit="f18304a356cee8cd7297bab362b13c40e50439df") version("1.42.0", commit="4b54c1206bedd27ff9be32affc999a279f4e96f0") diff --git a/var/spack/repos/builtin/packages/r-affyilm/package.py b/var/spack/repos/builtin/packages/r-affyilm/package.py index 39628ea821..629a6d0e7c 100644 --- a/var/spack/repos/builtin/packages/r-affyilm/package.py +++ b/var/spack/repos/builtin/packages/r-affyilm/package.py @@ -16,6 +16,7 @@ class RAffyilm(RPackage): bioc = "affyILM" + version("1.52.0", commit="08ed8c60921ba1b9e04fa90e156eef1a3c899d15") version("1.50.0", commit="185cd8e4712a3378ce7a156d4940224bbb2c4122") version("1.48.0", commit="4603a4c4d6c2330a8a56a7bb657dc56c51a9393a") version("1.46.0", commit="67ffbfa6c881ed83d15604bf4463fe5dba81036b") diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py index 1c77995784..d196223dd1 100644 --- a/var/spack/repos/builtin/packages/r-affyio/package.py +++ b/var/spack/repos/builtin/packages/r-affyio/package.py @@ -15,6 +15,7 @@ class RAffyio(RPackage): bioc = "affyio" + version("1.70.0", commit="95560567e27088863c64e868a8e5069fc725b8d7") version("1.68.0", commit="33080c5eeb14c0ca40f0d231706af4e0c2c1ef8b") version("1.66.0", commit="3a0b90704fc46cddd99a72b985a6bdb348f69b50") version("1.64.0", commit="aa7ce48f3f4110431f6f488d45961fde4019ffb0") diff --git a/var/spack/repos/builtin/packages/r-affyplm/package.py b/var/spack/repos/builtin/packages/r-affyplm/package.py index a00bebf285..4badcd5a8a 100644 --- a/var/spack/repos/builtin/packages/r-affyplm/package.py +++ b/var/spack/repos/builtin/packages/r-affyplm/package.py @@ -17,6 +17,7 @@ class RAffyplm(RPackage): bioc = "affyPLM" + version("1.76.0", commit="45557df5a32f56aa5240439737c5718738fb4c27") version("1.74.0", commit="5f76ef92e69deabc19c5395eaec4adb85c66b63d") version("1.72.0", commit="394c0a8e213f188d0b1d01e20516df8bf1bc5c09") version("1.70.0", commit="64abfec92b347aa340b54a8c7b2fbd524fe9c312") @@ -34,3 +35,4 @@ class RAffyplm(RPackage): depends_on("r-gcrma", type=("build", "run")) depends_on("r-preprocesscore@1.5.1:", type=("build", "run")) depends_on("r-zlibbioc", type=("build", "run")) + depends_on("zlib") diff --git a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py index 7191a3d06e..9615deccf6 100644 --- a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py +++ b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py @@ -18,6 +18,7 @@ class RAffyrnadegradation(RPackage): bioc = "AffyRNADegradation" + version("1.46.0", commit="431ae61c9b3809829697ef71672c57171d93311e") version("1.44.0", commit="63881f41fc67cc7322b189446dcffb4e1060e303") version("1.42.0", commit="5775f41f538b3c8ee4d07d38cec1b49c548cebe6") version("1.40.0", commit="8539a91ee464d692a267bb17c91dc1ef9a231f41") diff --git a/var/spack/repos/builtin/packages/r-agdex/package.py b/var/spack/repos/builtin/packages/r-agdex/package.py index 5917a2d700..ba29d0e508 100644 --- a/var/spack/repos/builtin/packages/r-agdex/package.py +++ b/var/spack/repos/builtin/packages/r-agdex/package.py @@ -14,6 +14,7 @@ class RAgdex(RPackage): bioc = "AGDEX" + version("1.48.0", commit="917920b397493b0ea40093044ebe36fff7c389ad") version("1.46.0", commit="d7c38e8bdcaa7b0261117c605e7f61e2b07e8316") version("1.44.0", commit="9d3eb90eaf7bf093c7fa73facb3df89506a85185") version("1.42.0", commit="175cf1b384b0942103d841b1feb9e4f7d141ba06") diff --git a/var/spack/repos/builtin/packages/r-agilp/package.py b/var/spack/repos/builtin/packages/r-agilp/package.py index 02ea917314..c870fd6fd4 100644 --- a/var/spack/repos/builtin/packages/r-agilp/package.py +++ b/var/spack/repos/builtin/packages/r-agilp/package.py @@ -13,6 +13,7 @@ class RAgilp(RPackage): bioc = "agilp" + version("3.32.0", commit="8291f7b7c1b6167952568f51593116afc6d0fc27") version("3.30.0", commit="a2c898dc901ccdda4b8582caff079ab20b1bfc28") version("3.28.0", commit="2c6dfccc76473b5bef13b75fa59adf46b3381f55") version("3.26.0", commit="3170fe2b1cc459d5e2ca7f61a127aac17cd66a96") diff --git a/var/spack/repos/builtin/packages/r-agimicrorna/package.py b/var/spack/repos/builtin/packages/r-agimicrorna/package.py index c82fe044d9..4e27a80e81 100644 --- a/var/spack/repos/builtin/packages/r-agimicrorna/package.py +++ b/var/spack/repos/builtin/packages/r-agimicrorna/package.py @@ -14,6 +14,7 @@ class RAgimicrorna(RPackage): bioc = "AgiMicroRna" + version("2.50.0", commit="a812b0f4f215b093ca685889b65de60c6701b695") version("2.48.0", commit="4c163b1b730150a3a60a3815bd8c08fa04d71fc1") version("2.46.0", commit="8c6d73e1c3f1f9cc019bdb219b19e6179bb1efe4") version("2.44.0", commit="8b308baa3b1b0afc0855ea263630a288689e3864") diff --git a/var/spack/repos/builtin/packages/r-aims/package.py b/var/spack/repos/builtin/packages/r-aims/package.py index 69ac55d01e..47650bf153 100644 --- a/var/spack/repos/builtin/packages/r-aims/package.py +++ b/var/spack/repos/builtin/packages/r-aims/package.py @@ -17,6 +17,7 @@ class RAims(RPackage): bioc = "AIMS" + version("1.32.0", commit="019415a6362e805465d43c157606e1774aed9e51") version("1.30.0", commit="2ab61159c5aa0902cc33fc1502f7853b66912cce") version("1.28.0", commit="84608df638b5694c08158ed77ad2c8a64c4e594b") version("1.26.0", commit="5dcf60eb4cdcf563ea848482c9c488f465c27bbd") diff --git a/var/spack/repos/builtin/packages/r-aldex2/package.py b/var/spack/repos/builtin/packages/r-aldex2/package.py index 4347392f25..342644e0d7 100644 --- a/var/spack/repos/builtin/packages/r-aldex2/package.py +++ b/var/spack/repos/builtin/packages/r-aldex2/package.py @@ -23,6 +23,7 @@ class RAldex2(RPackage): bioc = "ALDEx2" + version("1.32.0", commit="ba32b9a9b6a8f42906ea094318f00116f15e42eb") version("1.30.0", commit="cb6670515a8722f9cfedac12a8c2747a5298ee46") version("1.28.1", commit="f8d8ba6d2439bff75ab80f5466c9a047c31ed0a6") version("1.26.0", commit="0876a2eac08d3f1c01df7414d97d391c80182ada") diff --git a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py index d6d05f61c7..ca2ec19e75 100644 --- a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py +++ b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py @@ -14,6 +14,7 @@ class RAllelicimbalance(RPackage): bioc = "AllelicImbalance" + version("1.38.0", commit="75a3b0fefe635a0892eae338d0fdd4a9e091f957") version("1.36.0", commit="cb4910c1fd58cc4272c21251a8f120990e1aa431") version("1.34.0", commit="290708ccc4ceae1fbb9e9257cb254916449d389b") version("1.32.0", commit="428ab8c96bb15fab45e4084da25f98b01b9d60b6") diff --git a/var/spack/repos/builtin/packages/r-alpine/package.py b/var/spack/repos/builtin/packages/r-alpine/package.py index f3134984a5..3ed48849b5 100644 --- a/var/spack/repos/builtin/packages/r-alpine/package.py +++ b/var/spack/repos/builtin/packages/r-alpine/package.py @@ -14,6 +14,7 @@ class RAlpine(RPackage): bioc = "alpine" + version("1.26.0", commit="1e317dbf2973eb4b6a3ffbf52bc0faacec76a616") version("1.24.0", commit="7e734d49881761cafaacea096ce757531b6bd522") version("1.22.0", commit="6107a82962f07e0434e93f261cd375eaaa171d91") version("1.20.0", commit="9348ef14128aa6be10cca1987736ddbc385df7e9") diff --git a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py index 4909e807df..5c3dd5428a 100644 --- a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py +++ b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py @@ -13,6 +13,7 @@ class RAltcdfenvs(RPackage): bioc = "altcdfenvs" + version("2.62.0", commit="aedf0e9f98639d60b327e50957e504cf24b64bbb") version("2.60.0", commit="0bc0b4493b8e9fe2eb47fb8e9377123ce8f472bb") version("2.58.0", commit="08255a777ffa1e1414d3dd3062d95bfdd3dfd47c") version("2.56.0", commit="941e00b97a33662a8230991e387070324b2e76bf") diff --git a/var/spack/repos/builtin/packages/r-anaquin/package.py b/var/spack/repos/builtin/packages/r-anaquin/package.py index ebea4e7464..7e0419b05c 100644 --- a/var/spack/repos/builtin/packages/r-anaquin/package.py +++ b/var/spack/repos/builtin/packages/r-anaquin/package.py @@ -17,6 +17,7 @@ class RAnaquin(RPackage): bioc = "Anaquin" + version("2.24.0", commit="0eefabdc4036b98505032c460d08375839b1fc3e") version("2.22.0", commit="d848a9bd7bf9d1d62202cc477300bf1a65b3e36c") version("2.20.0", commit="61598dd3430b09b57f31d7d550ea95126a2d73c8") version("2.18.0", commit="c8e3df3e299c32daac0dda23cea59a18673d886b") diff --git a/var/spack/repos/builtin/packages/r-aneufinder/package.py b/var/spack/repos/builtin/packages/r-aneufinder/package.py index 9c324a5215..c4fe7b5505 100644 --- a/var/spack/repos/builtin/packages/r-aneufinder/package.py +++ b/var/spack/repos/builtin/packages/r-aneufinder/package.py @@ -15,6 +15,7 @@ class RAneufinder(RPackage): bioc = "AneuFinder" + version("1.28.0", commit="e17d810171bdab1c6a26a3ab7b7931db4e073e7e") version("1.26.0", commit="7cd59a1e24c6512f2e4fcbe2c53a0d3cd2d06217") version("1.24.0", commit="4c6906eee514eba3e8ac159654a6953e37a99bba") version("1.22.0", commit="ea0beb3d827c2dd4bc56708a839a93c55304918b") @@ -33,7 +34,7 @@ class RAneufinder(RPackage): depends_on("r-aneufinderdata", type=("build", "run")) depends_on("r-foreach", type=("build", "run")) depends_on("r-doparallel", type=("build", "run")) - depends_on("r-biocgenerics", type=("build", "run"), when="@1.4.0:1.6.0") + depends_on("r-biocgenerics", type=("build", "run"), when="@1.4.0:") depends_on("r-biocgenerics@0.31.6:", type=("build", "run"), when="@1.18.0:") depends_on("r-s4vectors", type=("build", "run")) depends_on("r-genomeinfodb", type=("build", "run")) @@ -47,5 +48,5 @@ class RAneufinder(RPackage): depends_on("r-reshape2", type=("build", "run")) depends_on("r-ggdendro", type=("build", "run")) depends_on("r-ggrepel", type=("build", "run")) - depends_on("r-reordercluster", type=("build", "run")) depends_on("r-mclust", type=("build", "run")) + depends_on("r-reordercluster", type=("build", "run"), when="@:1.26.0") diff --git a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py index 697de6d96a..ba41d17972 100644 --- a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py +++ b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py @@ -14,6 +14,7 @@ class RAneufinderdata(RPackage): bioc = "AneuFinderData" + version("1.28.0", commit="d04255e60173ce478d31b1e1e5c73e6ed9e3b20c") version("1.26.0", commit="4b810599b62a3fb39239bfd98ed960c93989e86b") version("1.24.0", commit="cf6f3852702aab28e3170fc56b695d00b7389666") version("1.22.0", commit="ae8eec3b0afdc351dc447aad2024df5b2c75e56b") diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py index c04c9f1bbf..8eab7dc0c2 100644 --- a/var/spack/repos/builtin/packages/r-annaffy/package.py +++ b/var/spack/repos/builtin/packages/r-annaffy/package.py @@ -16,6 +16,7 @@ class RAnnaffy(RPackage): bioc = "annaffy" + version("1.72.0", commit="7cb439706a7e93fb5b44ead374010077a44ea78b") version("1.70.0", commit="c99e81259adb39b5d8e954fd7afe7f93675229bc") version("1.68.0", commit="fa930c0bbdca9828a130ab06d86c65d451380830") version("1.66.0", commit="aa1afa1509754128d27508228c1f39f51a8da043") diff --git a/var/spack/repos/builtin/packages/r-annotate/package.py b/var/spack/repos/builtin/packages/r-annotate/package.py index 909cb3a404..2a3cd745ec 100644 --- a/var/spack/repos/builtin/packages/r-annotate/package.py +++ b/var/spack/repos/builtin/packages/r-annotate/package.py @@ -13,6 +13,7 @@ class RAnnotate(RPackage): bioc = "annotate" + version("1.78.0", commit="ca6415a463ec682f340ba5d1dc6246a92e836143") version("1.76.0", commit="0181d5c41d594e36be06adb6a02302db0ad2c507") version("1.74.0", commit="200c71743417792880f8171d59b2ac0ddd3902a8") version("1.72.0", commit="67ac76a9ff6d60dc1620763d3aa98aef39443110") diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py index 2467f9f426..49ee0ff139 100644 --- a/var/spack/repos/builtin/packages/r-annotationdbi/package.py +++ b/var/spack/repos/builtin/packages/r-annotationdbi/package.py @@ -14,6 +14,7 @@ class RAnnotationdbi(RPackage): bioc = "AnnotationDbi" + version("1.62.0", commit="7ca03a0332d0a284ea27d16edb7b386c86cf99ea") version("1.60.0", commit="cd61bd1b1538e2f1f411fd7087820749ecf39da8") version("1.58.0", commit="05fcf7a28a6b15b195da23474d7ba89bd0cfd891") version("1.56.2", commit="13fdc4a93852199ca6ec120a2fe1078f9f445f67") diff --git a/var/spack/repos/builtin/packages/r-annotationfilter/package.py b/var/spack/repos/builtin/packages/r-annotationfilter/package.py index f05d56f2ac..3510fd3e90 100644 --- a/var/spack/repos/builtin/packages/r-annotationfilter/package.py +++ b/var/spack/repos/builtin/packages/r-annotationfilter/package.py @@ -15,6 +15,7 @@ class RAnnotationfilter(RPackage): bioc = "AnnotationFilter" + version("1.24.0", commit="172d9c149d9025154f7b26982d07f571499b03e8") version("1.22.0", commit="c9fea4a829ce9419b6e0af987915b2d469358597") version("1.20.0", commit="2818aff6502fd6fe819521cd8d97695ef6f9198e") version("1.18.0", commit="60a9b666d7362d7ed5c357fd4a5d2744d8598c20") diff --git a/var/spack/repos/builtin/packages/r-annotationforge/package.py b/var/spack/repos/builtin/packages/r-annotationforge/package.py index 69a05c4d17..e10335f6bd 100644 --- a/var/spack/repos/builtin/packages/r-annotationforge/package.py +++ b/var/spack/repos/builtin/packages/r-annotationforge/package.py @@ -14,6 +14,7 @@ class RAnnotationforge(RPackage): bioc = "AnnotationForge" + version("1.42.0", commit="2eac005012b11317c33c8b0062b968b2ac378308") version("1.40.0", commit="f77d3a942eb6b18c18888b7af3f0e652596cf19f") version("1.38.1", commit="2dcedf353bc57bf80818e6adb1f7129c21886f6b") version("1.38.0", commit="1f77750562ea3a01f0f1a46c299184fc31196ffd") diff --git a/var/spack/repos/builtin/packages/r-annotationhub/package.py b/var/spack/repos/builtin/packages/r-annotationhub/package.py index d03cd69a49..218622ccf6 100644 --- a/var/spack/repos/builtin/packages/r-annotationhub/package.py +++ b/var/spack/repos/builtin/packages/r-annotationhub/package.py @@ -20,6 +20,7 @@ class RAnnotationhub(RPackage): bioc = "AnnotationHub" + version("3.8.0", commit="975022dd33706824bd02f67cc9c3a42f3567f4a5") version("3.6.0", commit="3315a73b7803a92412ed18209dd37b378195b86f") version("3.4.0", commit="e74e54ca44f50c2c15c60f8620e3d1721f8f5b6d") version("3.2.1", commit="ad1dfe86f0b0ea4711cc9cdb89e073e8794ec9aa") diff --git a/var/spack/repos/builtin/packages/r-aroma-light/package.py b/var/spack/repos/builtin/packages/r-aroma-light/package.py index f03d8c678b..9d1561be86 100644 --- a/var/spack/repos/builtin/packages/r-aroma-light/package.py +++ b/var/spack/repos/builtin/packages/r-aroma-light/package.py @@ -16,6 +16,7 @@ class RAromaLight(RPackage): bioc = "aroma.light" + version("3.30.0", commit="a1882c2126622cb389a7ef1ef5b5c565e603a282") version("3.28.0", commit="7749dd7033e9885ec2546a5cac0562bac2fea04d") version("3.26.0", commit="7ead7517a77bc8b4b4b42aace69957a17e8fe016") version("3.24.0", commit="3ff48b8f546acc9803b3c652363cac78d3b81ae5") diff --git a/var/spack/repos/builtin/packages/r-bamsignals/package.py b/var/spack/repos/builtin/packages/r-bamsignals/package.py index 74bc2c4541..d42d1d9a41 100644 --- a/var/spack/repos/builtin/packages/r-bamsignals/package.py +++ b/var/spack/repos/builtin/packages/r-bamsignals/package.py @@ -16,6 +16,7 @@ class RBamsignals(RPackage): bioc = "bamsignals" + version("1.32.0", commit="34bfc4e8b58e47c3b94347fd2976aeae07fc28c2") version("1.30.0", commit="aac37dffd6f6876b4626866e3d40bb7af75620fe") version("1.28.0", commit="27b70be6f73747d9d32054da043f4a37ea55b917") version("1.26.0", commit="d57643441d04f77db0907637dc9e7cd5bed5842f") diff --git a/var/spack/repos/builtin/packages/r-basilisk-utils/package.py b/var/spack/repos/builtin/packages/r-basilisk-utils/package.py new file mode 100644 index 0000000000..c6db94ccba --- /dev/null +++ b/var/spack/repos/builtin/packages/r-basilisk-utils/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class RBasiliskUtils(RPackage): + """Basilisk Installation Utilities. + + Implements utilities for installation of the basilisk package, primarily + for creation of the underlying Conda instance. This allows us to avoid + re-writing the same R code in both the configure script (for centrally + administered R installations) and in the lazy installation mechanism (for + distributed package binaries). It is highly unlikely that developers - or, + heaven forbid, end-users! - will need to interact with this package + directly; they should be using the basilisk package instead.""" + + bioc = "basilisk.utils" + + version("1.12.0", commit="8314f9a72ecc0f20b180431aec93647320de8c2c") + + depends_on("r-dir-expiry", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-basilisk/package.py b/var/spack/repos/builtin/packages/r-basilisk/package.py new file mode 100644 index 0000000000..0a94e3761a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-basilisk/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class RBasilisk(RPackage): + """Freezing Python Dependencies Inside Bioconductor Packages. + + Installs a self-contained conda instance that is managed by the + R/Bioconductor installation machinery. This aims to provide a consistent + Python environment that can be used reliably by Bioconductor packages. + Functions are also provided to enable smooth interoperability of multiple + Python environments in a single R session.""" + + bioc = "basilisk" + + version("1.12.0", commit="26c1c354526eb8d806268427a7c40b31bb89f489") + + depends_on("r-reticulate", type=("build", "run")) + depends_on("r-dir-expiry", type=("build", "run")) + depends_on("r-basilisk-utils", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-beachmat/package.py b/var/spack/repos/builtin/packages/r-beachmat/package.py index 94c3be1089..911efb01d9 100644 --- a/var/spack/repos/builtin/packages/r-beachmat/package.py +++ b/var/spack/repos/builtin/packages/r-beachmat/package.py @@ -17,6 +17,7 @@ class RBeachmat(RPackage): bioc = "beachmat" + version("2.16.0", commit="4cc8e50dcae767a2ef84ffc7a581ea182f05f300") version("2.14.0", commit="5a4b85f4a22f3447f12d03157ab95de73f6137c6") version("2.12.0", commit="3e6af145bdcdf0a0b722d8256ba1a38b8a36b2f5") version("2.10.0", commit="b7cc532d4a5b26d9073135cc9945258ea08e5079") @@ -34,7 +35,7 @@ class RBeachmat(RPackage): depends_on("r-delayedarray@0.15.14:", type=("build", "run"), when="@2.6.4") depends_on("r-biocgenerics", type=("build", "run"), when="@1.4.0:") depends_on("r-matrix", type=("build", "run"), when="@2.6.4:") - depends_on("r-rcpp@0.12.14:", type=("build", "run"), when="@1.0.2:1.4.0") + depends_on("r-rcpp@0.12.14:", type=("build", "run"), when="@1.0.2:") depends_on("r-rcpp", type=("build", "run"), when="@2.10.0:") depends_on("r-rhdf5lib", type=("build", "run"), when="@1.0.2:1.4.0") diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py index e0ae43cfb3..061dbf30f0 100644 --- a/var/spack/repos/builtin/packages/r-biobase/package.py +++ b/var/spack/repos/builtin/packages/r-biobase/package.py @@ -14,6 +14,7 @@ class RBiobase(RPackage): bioc = "Biobase" + version("2.60.0", commit="8dc10d2d26dc0847740ff2b4f16cc1ae2e936464") version("2.58.0", commit="767f2f33f158f233616178e12ce08cdb03d2a5a2") version("2.56.0", commit="3b2dd91b333677c2f27257c7624014a55e73c52b") version("2.54.0", commit="8215d76ce44899e6d10fe8a2f503821a94ef6b40") diff --git a/var/spack/repos/builtin/packages/r-biocfilecache/package.py b/var/spack/repos/builtin/packages/r-biocfilecache/package.py index bb6f6a4fb1..43679532e1 100644 --- a/var/spack/repos/builtin/packages/r-biocfilecache/package.py +++ b/var/spack/repos/builtin/packages/r-biocfilecache/package.py @@ -16,6 +16,7 @@ class RBiocfilecache(RPackage): bioc = "BiocFileCache" + version("2.8.0", commit="d088b3224bcee4661d954c77fe38ba8c45ecc51a") version("2.6.0", commit="f5b8368c1402b15e8db8eab59217f1176e902e6f") version("2.4.0", commit="2c00eee40d95fddad223f115f959b09e1a14f75d") version("2.2.1", commit="cc912123408803193bf37395f4d18baa8dcd6f47") @@ -31,7 +32,7 @@ class RBiocfilecache(RPackage): depends_on("r-dbplyr@1.0.0:", type=("build", "run"), when="@1.2.3:") depends_on("r-rsqlite", type=("build", "run")) depends_on("r-dbi", type=("build", "run")) - depends_on("r-rappdirs", type=("build", "run")) depends_on("r-filelock", type=("build", "run"), when="@2.2.1:") depends_on("r-curl", type=("build", "run"), when="@1.6.0:") depends_on("r-httr", type=("build", "run")) + depends_on("r-rappdirs", type=("build", "run"), when="@:2.6.0") diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py index 99dce4cc48..2ce882d722 100644 --- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py @@ -13,6 +13,7 @@ class RBiocgenerics(RPackage): bioc = "BiocGenerics" + version("0.46.0", commit="a90f0c5976a24417e47e009ba602fc98515ac9ab") version("0.44.0", commit="d7cd9c19958bd8d4573d980494188fa15ab16e45") version("0.42.0", commit="3582d47b836387afc08157f3d6a5013fd64334ed") version("0.40.0", commit="0bc1e0ed4d20c7101cd782a14f6373e27478acfc") diff --git a/var/spack/repos/builtin/packages/r-biocio/package.py b/var/spack/repos/builtin/packages/r-biocio/package.py index 78a4600fce..8efedf2ca9 100644 --- a/var/spack/repos/builtin/packages/r-biocio/package.py +++ b/var/spack/repos/builtin/packages/r-biocio/package.py @@ -22,11 +22,13 @@ class RBiocio(RPackage): bioc = "BiocIO" + version("1.10.0", commit="1368ff1a7ddbb62515a87a88d7ec39981de557d5") version("1.8.0", commit="4a719fa41e014b7b948f7b245e581ede6a04eda1") version("1.6.0", commit="60c8aa1a961e43bf0ee5d563a6d9fcec84f7f8f8") version("1.4.0", commit="c335932526a38c75dbfa4970c1d90b8a21466d37") depends_on("r@4.0.0:", type=("build", "run")) depends_on("r@4.0:", type=("build", "run"), when="@1.8.0:") + depends_on("r@4.3.0:", type=("build", "run"), when="@1.10.0:") depends_on("r-biocgenerics", type=("build", "run")) depends_on("r-s4vectors", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-biocneighbors/package.py b/var/spack/repos/builtin/packages/r-biocneighbors/package.py index 54cc44f158..d70fd46894 100644 --- a/var/spack/repos/builtin/packages/r-biocneighbors/package.py +++ b/var/spack/repos/builtin/packages/r-biocneighbors/package.py @@ -21,6 +21,7 @@ class RBiocneighbors(RPackage): bioc = "BiocNeighbors" + version("1.18.0", commit="4b19ef2a76baa0b001c426bad540ab9295bec78e") version("1.16.0", commit="3b227beead424314aab5ef847222f8f4243c684f") version("1.14.0", commit="670a1bd4d82636d28fbff50cea2157e16bb1a858") version("1.12.0", commit="3c8a290f75adc944b408e6e77a36f3a0c1509c4c") diff --git a/var/spack/repos/builtin/packages/r-biocparallel/package.py b/var/spack/repos/builtin/packages/r-biocparallel/package.py index 39defee82a..71ffbbd7fd 100644 --- a/var/spack/repos/builtin/packages/r-biocparallel/package.py +++ b/var/spack/repos/builtin/packages/r-biocparallel/package.py @@ -15,6 +15,7 @@ class RBiocparallel(RPackage): bioc = "BiocParallel" + version("1.34.0", commit="f3bbc0a2d38da034c50ca1e4704fc4ee99a2dc9e") version("1.32.1", commit="6c85dbad596a74a6d3022173a4a11c6b81a4a2c2") version("1.30.4", commit="1229ebe9f6d8305f9f61e562464f83f9ba86e699") version("1.30.2", commit="e7e109f7a94dbfbc50f926be030c7ad8c1a053db") diff --git a/var/spack/repos/builtin/packages/r-biocsingular/package.py b/var/spack/repos/builtin/packages/r-biocsingular/package.py index e3e9ccf6f9..7d2e240f73 100644 --- a/var/spack/repos/builtin/packages/r-biocsingular/package.py +++ b/var/spack/repos/builtin/packages/r-biocsingular/package.py @@ -17,6 +17,7 @@ class RBiocsingular(RPackage): bioc = "BiocSingular" + version("1.16.0", commit="0db9a691d4eb21551c532d8bde8f64dcc19b6c66") version("1.14.0", commit="6dc42b30110e498f6694f18037f991c1006c71b7") version("1.12.0", commit="7d1b8f4954e9e6f2c30a5111cdab9aabc8bcc3a6") version("1.10.0", commit="6615ae8cb124aba6507447c1081bd2eba655e57d") diff --git a/var/spack/repos/builtin/packages/r-biocstyle/package.py b/var/spack/repos/builtin/packages/r-biocstyle/package.py index 019801c362..4f818aeb34 100644 --- a/var/spack/repos/builtin/packages/r-biocstyle/package.py +++ b/var/spack/repos/builtin/packages/r-biocstyle/package.py @@ -14,6 +14,7 @@ class RBiocstyle(RPackage): bioc = "BiocStyle" + version("2.28.0", commit="b358aa5d3f9c68629e9abf50ffceccbf77226ea8") version("2.26.0", commit="add035498bdce76d71a0afa22a063c2d8e5588bc") version("2.24.0", commit="53095b534b7e6c80a33a67b5f2db0db8f00db902") version("2.22.0", commit="86250b637afa3a3463fac939b99c0402b47876ea") diff --git a/var/spack/repos/builtin/packages/r-biocversion/package.py b/var/spack/repos/builtin/packages/r-biocversion/package.py index f815c857da..bee3350211 100644 --- a/var/spack/repos/builtin/packages/r-biocversion/package.py +++ b/var/spack/repos/builtin/packages/r-biocversion/package.py @@ -14,6 +14,7 @@ class RBiocversion(RPackage): bioc = "BiocVersion" + version("3.17.1", commit="a2d0c4c489be1cafdb51bf8d205161429b09ac7f") version("3.16.0", commit="c681e06fe30ea6815f958c1a3c74c090863680ba") version("3.15.2", commit="818ab03b6a3551993b712e3702126040f9fb7600") version("3.14.0", commit="aa56d93d0ea5dcdbf301f120502981740fd91e1e") @@ -22,3 +23,4 @@ class RBiocversion(RPackage): depends_on("r@4.0.0:", type=("build", "run")) depends_on("r@4.1.0:", type=("build", "run"), when="@3.14.0:") depends_on("r@4.2.0:", type=("build", "run"), when="@3.15.2:") + depends_on("r@4.3.0:", type=("build", "run"), when="@3.17.1:") diff --git a/var/spack/repos/builtin/packages/r-biomart/package.py b/var/spack/repos/builtin/packages/r-biomart/package.py index 96cd35eab4..57a2ac6e8b 100644 --- a/var/spack/repos/builtin/packages/r-biomart/package.py +++ b/var/spack/repos/builtin/packages/r-biomart/package.py @@ -24,6 +24,7 @@ class RBiomart(RPackage): bioc = "biomaRt" + version("2.56.0", commit="91ca89eff52e63c225f7e4eb24b765d08faf3ed9") version("2.54.0", commit="4fb88fb56c684d5678f8288ba05db193e4881758") version("2.52.0", commit="cf4932ac02686da45ea36ff5137fa63cead8860b") version("2.50.3", commit="83a519ac13d73dc545cb6aafde5f4b5001e9e08f") diff --git a/var/spack/repos/builtin/packages/r-biomformat/package.py b/var/spack/repos/builtin/packages/r-biomformat/package.py index f9e6bdd943..d9a2cc28ec 100644 --- a/var/spack/repos/builtin/packages/r-biomformat/package.py +++ b/var/spack/repos/builtin/packages/r-biomformat/package.py @@ -21,6 +21,7 @@ class RBiomformat(RPackage): bioc = "biomformat" + version("1.28.0", commit="9240e78dc378abcf6c62ef8dbf2e60f7241232a3") version("1.26.0", commit="f851ba2428b57769f6fbb287874bad0dc84dd69c") version("1.24.0", commit="4e14692dbcc34c3bd51defd74c728df5de9d0829") version("1.22.0", commit="ab7c6411a038fec010baa72e663f362fd972cb34") diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py index 9ee31f399f..2297a0a054 100644 --- a/var/spack/repos/builtin/packages/r-biostrings/package.py +++ b/var/spack/repos/builtin/packages/r-biostrings/package.py @@ -15,6 +15,7 @@ class RBiostrings(RPackage): bioc = "Biostrings" + version("2.68.0", commit="f28b7838fb8321a9956506b3d2f4af2740bca124") version("2.66.0", commit="3470ca7da798971e2c3a595d8dc8d0d86f14dc53") version("2.64.1", commit="ffe263e958463bd1edb5d5d9316cfd89905be53c") version("2.64.0", commit="c7ad3c7af607bc8fe4a5e1c37f09e6c9bf70b4f6") diff --git a/var/spack/repos/builtin/packages/r-biovizbase/package.py b/var/spack/repos/builtin/packages/r-biovizbase/package.py index 3fc4b92418..45c015ef66 100644 --- a/var/spack/repos/builtin/packages/r-biovizbase/package.py +++ b/var/spack/repos/builtin/packages/r-biovizbase/package.py @@ -16,6 +16,7 @@ class RBiovizbase(RPackage): bioc = "biovizBase" + version("1.48.0", commit="534db77074710dae57ade81844c769fd35a2fa9c") version("1.46.0", commit="a47060cfb68e3f3b4876114af932823aed5d2d57") version("1.44.0", commit="a8f05c56c27b278524033cb896a6c97f3ee0081c") version("1.42.0", commit="f1627b2b567471837daca6e763acfc3e13937461") diff --git a/var/spack/repos/builtin/packages/r-bluster/package.py b/var/spack/repos/builtin/packages/r-bluster/package.py index 2d60bd5fec..c9f653ab41 100644 --- a/var/spack/repos/builtin/packages/r-bluster/package.py +++ b/var/spack/repos/builtin/packages/r-bluster/package.py @@ -16,6 +16,7 @@ class RBluster(RPackage): bioc = "bluster" + version("1.10.0", commit="32340420e67a184e39238e46143c00151057924c") version("1.8.0", commit="156115c8960c0b66b2c588d9fd8bbdfe56e5f0be") version("1.6.0", commit="ff86c7d8d36233e838d4f00e6a4e173e7bf16816") diff --git a/var/spack/repos/builtin/packages/r-bsgenome/package.py b/var/spack/repos/builtin/packages/r-bsgenome/package.py index a6908f58d3..5f5eb983b5 100644 --- a/var/spack/repos/builtin/packages/r-bsgenome/package.py +++ b/var/spack/repos/builtin/packages/r-bsgenome/package.py @@ -14,6 +14,7 @@ class RBsgenome(RPackage): bioc = "BSgenome" + version("1.68.0", commit="c546020750e900377fbdeae015a01a96d5962d09") version("1.66.1", commit="d1efdfa8e7242bc0f54cc1c3a9583ea555c924f6") version("1.64.0", commit="59cdebde613e9702985c003f699f4aea2b0f0e7b") version("1.62.0", commit="9b1859e11ffa082833f035a45274af6e4e83e863") diff --git a/var/spack/repos/builtin/packages/r-bsseq/package.py b/var/spack/repos/builtin/packages/r-bsseq/package.py index 136b39a123..7e83045ea3 100644 --- a/var/spack/repos/builtin/packages/r-bsseq/package.py +++ b/var/spack/repos/builtin/packages/r-bsseq/package.py @@ -14,6 +14,7 @@ class RBsseq(RPackage): bioc = "bsseq" + version("1.36.0", commit="5dd72c5a84e1fcc3389ab2a74f8ca14c399ac128") version("1.34.0", commit="98239c07d74e1362c7ba2a3bf4f6119830fc95dc") version("1.32.0", commit="a0c1eacbc479c57bd836e885e162c28bbe08e115") version("1.30.0", commit="7eb5223e9ee02fd08a52be56eaa9316a67c0d66b") diff --git a/var/spack/repos/builtin/packages/r-bumphunter/package.py b/var/spack/repos/builtin/packages/r-bumphunter/package.py index 6e0843fee0..9b560ea4d8 100644 --- a/var/spack/repos/builtin/packages/r-bumphunter/package.py +++ b/var/spack/repos/builtin/packages/r-bumphunter/package.py @@ -13,6 +13,7 @@ class RBumphunter(RPackage): bioc = "bumphunter" + version("1.42.0", commit="0eb2808a04920aaba00e1ce3e9dff503596e931f") version("1.40.0", commit="3de207a3659859737d4c748fc8023694943da43b") version("1.38.0", commit="06e2fa87b342d48793d0d2f1f7d94a95a6613995") version("1.36.0", commit="db50fcf7798c2eddfe48fd510d081dda82f2ee4e") diff --git a/var/spack/repos/builtin/packages/r-category/package.py b/var/spack/repos/builtin/packages/r-category/package.py index a3fbada129..3d8ef911dd 100644 --- a/var/spack/repos/builtin/packages/r-category/package.py +++ b/var/spack/repos/builtin/packages/r-category/package.py @@ -14,6 +14,7 @@ class RCategory(RPackage): bioc = "Category" + version("2.66.0", commit="404c5e4bebeb91b04ac62a821f9eea5610d98b96") version("2.64.0", commit="b512cbeb22fc50a2f6d767a2eef356fb143a974e") version("2.62.0", commit="0fe801c0c443aebd5d4cefa8c30e4e7d0931b673") version("2.60.0", commit="55210d8c539474954d18cf913a219dce883eac2e") diff --git a/var/spack/repos/builtin/packages/r-champ/package.py b/var/spack/repos/builtin/packages/r-champ/package.py index 473d16878e..97251babef 100644 --- a/var/spack/repos/builtin/packages/r-champ/package.py +++ b/var/spack/repos/builtin/packages/r-champ/package.py @@ -16,6 +16,7 @@ class RChamp(RPackage): bioc = "ChAMP" + version("2.30.0", commit="b6ff6670d239c2517aa57144a793ea93da3c7b42") version("2.28.0", commit="3d27ac67a738afea8cc9ece6ea1301120e4b48f7") version("2.26.0", commit="1548910bf53e1e5f7a8d80c83b742a94297d8a34") version("2.24.0", commit="7ba19da74b61e1c40ced162ba753f0f9b9c7647a") diff --git a/var/spack/repos/builtin/packages/r-champdata/package.py b/var/spack/repos/builtin/packages/r-champdata/package.py index 7ecd29132d..5714f5cf7f 100644 --- a/var/spack/repos/builtin/packages/r-champdata/package.py +++ b/var/spack/repos/builtin/packages/r-champdata/package.py @@ -14,6 +14,7 @@ class RChampdata(RPackage): bioc = "ChAMPdata" + version("2.32.0", commit="98a94978001b6a28543257e72a036c43d61e67ef") version("2.30.0", commit="6e05b8f7b004b1a5185ec4b387c32725e8bd95cb") version("2.28.0", commit="601555bf599828b6cfa125beffa51aebccdc8503") version("2.26.0", commit="ea7882707921af33eefab5133a1ccd4a409f045d") diff --git a/var/spack/repos/builtin/packages/r-chipseq/package.py b/var/spack/repos/builtin/packages/r-chipseq/package.py index f8033851d4..44983cd9da 100644 --- a/var/spack/repos/builtin/packages/r-chipseq/package.py +++ b/var/spack/repos/builtin/packages/r-chipseq/package.py @@ -15,6 +15,7 @@ class RChipseq(RPackage): maintainers("dorton21") + version("1.50.0", commit="0bdfa25828b1d65f629e96c8e832061fd7ff7935") version("1.48.0", commit="9c78296001b6dd4102318879c8504dac70015822") version("1.46.0", commit="76b00397cd117d5432158f50fc1032d50485bd24") version("1.44.0", commit="b64d0d28e9fcf0fdab9a7f9c521baf729426a594") diff --git a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py index 97b154db4b..67a0575551 100644 --- a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py +++ b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py @@ -15,6 +15,7 @@ class RClusterprofiler(RPackage): bioc = "clusterProfiler" + version("4.8.0", commit="35a69cf05855b01775658def2f3f26596902f5db") version("4.6.0", commit="2644118c36a3aa14408bc0c97ac20a545e40344d") version("4.4.4", commit="9fca9a45ca1793884d8dcfd0f077353dbf75df29") version("4.4.1", commit="daad11fb80be2dd9b825e0b484815a0a2b1592a4") @@ -41,7 +42,7 @@ class RClusterprofiler(RPackage): depends_on("r-enrichplot@1.9.3:", type=("build", "run"), when="@3.18.0:") depends_on("r-go-db", type=("build", "run")) depends_on("r-gosemsim", type=("build", "run")) - depends_on("r-gosemsim@2.0.0:", type=("build", "run"), when="@3.4.4:3.6.0") + depends_on("r-gosemsim@2.0.0:", type=("build", "run"), when="@3.4.4:") depends_on("r-gson@0.0.7:", type=("build", "run"), when="@4.6.0:") depends_on("r-magrittr", type=("build", "run")) depends_on("r-plyr", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py index 7d95907f40..bad0fad593 100644 --- a/var/spack/repos/builtin/packages/r-cner/package.py +++ b/var/spack/repos/builtin/packages/r-cner/package.py @@ -14,6 +14,7 @@ class RCner(RPackage): bioc = "CNEr" + version("1.36.0", commit="4f2feeb395cfc071ed97ba8b6327425dfd42d6b5") version("1.34.0", commit="878de98d18f6f959ad5e014ecd8165d3105d8b48") version("1.32.0", commit="1c92f3d7f3dccf76ab7d54f286117b09bc470b8f") version("1.30.0", commit="e682f2a7c8ebb561c872cf51a58ba36eed341187") @@ -46,3 +47,4 @@ class RCner(RPackage): depends_on("r-go-db@3.3.0:", type=("build", "run")) depends_on("r-r-utils@2.3.0:", type=("build", "run")) depends_on("r-keggrest@1.14.0:", type=("build", "run")) + depends_on("zlib") diff --git a/var/spack/repos/builtin/packages/r-codex/package.py b/var/spack/repos/builtin/packages/r-codex/package.py index f4b2d53bd3..6c7ec2987c 100644 --- a/var/spack/repos/builtin/packages/r-codex/package.py +++ b/var/spack/repos/builtin/packages/r-codex/package.py @@ -22,6 +22,7 @@ class RCodex(RPackage): bioc = "CODEX" + version("1.32.0", commit="83926238fb49b0e95d989612a98356d20e7caf57") version("1.30.0", commit="0694f11be9e0b02ab15047d01db2afce943f92d8") version("1.28.0", commit="c707497bd93aa4a0516fcf3671a64997c28c9f67") version("1.26.0", commit="729fd10bd42d12edcedd65b5a8fb1579e5949718") diff --git a/var/spack/repos/builtin/packages/r-complexheatmap/package.py b/var/spack/repos/builtin/packages/r-complexheatmap/package.py index 1a270e88ce..c108dbbc5f 100644 --- a/var/spack/repos/builtin/packages/r-complexheatmap/package.py +++ b/var/spack/repos/builtin/packages/r-complexheatmap/package.py @@ -16,6 +16,7 @@ class RComplexheatmap(RPackage): bioc = "ComplexHeatmap" + version("2.16.0", commit="01eb55ca9b783c6d99bdfe88aa131cc102bae5b3") version("2.14.0", commit="57fcaa040b08917c97fb66b963eb240d5fd5a8c7") version("2.12.1", commit="2c5fe70724219008174d4e6f83189cddbd895ec6") version("2.12.0", commit="8a5f060b06646f9d6a5032832ea72e3f183ca5d7") diff --git a/var/spack/repos/builtin/packages/r-ctc/package.py b/var/spack/repos/builtin/packages/r-ctc/package.py index fc6f15cecc..4aba24a7ec 100644 --- a/var/spack/repos/builtin/packages/r-ctc/package.py +++ b/var/spack/repos/builtin/packages/r-ctc/package.py @@ -14,6 +14,7 @@ class RCtc(RPackage): bioc = "ctc" + version("1.74.0", commit="00be85633de7d71ca3dc6fe6c634cf0bde6188fd") version("1.72.0", commit="0a4b464e1768e6407c1c2ce64ec4ae5a4577be65") version("1.70.0", commit="05dc046ecfddbc1eeadf77e8f3ec0ce054794437") version("1.68.0", commit="c2733534ef9d948e07ea654d1998a67ed8f7a98a") diff --git a/var/spack/repos/builtin/packages/r-decipher/package.py b/var/spack/repos/builtin/packages/r-decipher/package.py index 6728e562a0..88345c3027 100644 --- a/var/spack/repos/builtin/packages/r-decipher/package.py +++ b/var/spack/repos/builtin/packages/r-decipher/package.py @@ -13,6 +13,7 @@ class RDecipher(RPackage): bioc = "DECIPHER" + version("2.28.0", commit="9be570c9fd812139d6bf9cd0851821fe54d4d3fa") version("2.26.0", commit="7de99ec5e79f1f645f29dfbe24d2a106c2b0e69a") version("2.24.0", commit="437e60005ab281bd836f47756a367795bc16755d") version("2.22.0", commit="45da5cab5869d83af797aa82b08ebcd24f5bdab3") diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py index b885ec8b0f..bc663ccab5 100644 --- a/var/spack/repos/builtin/packages/r-delayedarray/package.py +++ b/var/spack/repos/builtin/packages/r-delayedarray/package.py @@ -20,6 +20,7 @@ class RDelayedarray(RPackage): bioc = "DelayedArray" + version("0.26.0", commit="e3bdae96838a8ed45f18697f072f3c4ec011aa03") version("0.24.0", commit="68ee3d0626c234ee1e9248a6cb95b901e4b3ad90") version("0.22.0", commit="4a5afd117b189b40bd409c7aff60e09d41797472") version("0.20.0", commit="829b52916ec54bb4f1a3c6f06c9955f3e28b3592") diff --git a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py index 7cb15ccaa7..c1db2e1345 100644 --- a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py @@ -18,6 +18,7 @@ class RDelayedmatrixstats(RPackage): bioc = "DelayedMatrixStats" + version("1.22.0", commit="e820ab9a72963badc539e38fa79dbaeab95b2d2c") version("1.20.0", commit="1ed14250e8731e60bccb44946cafad4c2b3ac5b0") version("1.18.1", commit="9c4658d11fc20b7d88e05b9c52140c2ca8a65768") version("1.18.0", commit="50c9aab259b6e8f68abf44b78122662a41c8bf47") diff --git a/var/spack/repos/builtin/packages/r-densvis/package.py b/var/spack/repos/builtin/packages/r-densvis/package.py new file mode 100644 index 0000000000..57b643271e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-densvis/package.py @@ -0,0 +1,42 @@ +# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class RDensvis(RPackage): + """Density-Preserving Data Visualization via Non-Linear Dimensionality + Reduction. + + Implements the density-preserving modification to t-SNE and UMAP described + by Narayan et al. (2020) . The non-linear dimensionality reduction + techniques t-SNE and UMAP enable users to summarise complex + high-dimensional sequencing data such as single cell RNAseq using lower + dimensional representations. These lower dimensional representations enable + the visualisation of discrete transcriptional states, as well as continuous + trajectory (for example, in early development). However, these methods + focus on the local neighbourhood structure of the data. In some cases, this + results in misleading visualisations, where the density of cells in the + low-dimensional embedding does not represent the transcriptional + heterogeneity of data in the original high-dimensional space. den-SNE and + densMAP aim to enable more accurate visual interpretation of + high-dimensional datasets by producing lower-dimensional embeddings that + accurately represent the heterogeneity of the original high-dimensional + space, enabling the identification of homogeneous and heterogeneous cell + states. This accuracy is accomplished by including in the optimisation + process a term which considers the local density of points in the original + high-dimensional space. This can help to create visualisations that are + more representative of heterogeneity in the original high-dimensional + space.""" + + bioc = "densvis" + + version("1.10.0", commit="833db1fb7b2a5667575cc2e7c2fefc8360c8d7fb") + + depends_on("r-rcpp", type=("build", "run")) + depends_on("r-basilisk", type=("build", "run")) + depends_on("r-assertthat", type=("build", "run")) + depends_on("r-reticulate", type=("build", "run")) + depends_on("r-irlba", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-deseq2/package.py b/var/spack/repos/builtin/packages/r-deseq2/package.py index ae52082ea1..45be1ed112 100644 --- a/var/spack/repos/builtin/packages/r-deseq2/package.py +++ b/var/spack/repos/builtin/packages/r-deseq2/package.py @@ -17,6 +17,7 @@ class RDeseq2(RPackage): homepage = "https://bioconductor.org/packages/DESeq2" git = "https://git.bioconductor.org/packages/DESeq2.git" + version("1.40.0", commit="c4962c3b16546e552fbc1a712258e4e21ff44241") version("1.38.0", commit="0e059f425d4ce6a5203685a4ad434f15bbd6e211") version("1.36.0", commit="2800b78ae52c0600f7e603c54af59beed3a2ed17") version("1.34.0", commit="25d4f74be59548122ccfbe8687d30c0bae5cf49a") @@ -35,11 +36,12 @@ class RDeseq2(RPackage): depends_on("r-biocgenerics@0.7.5:", type=("build", "run")) depends_on("r-biobase", type=("build", "run")) depends_on("r-biocparallel", type=("build", "run")) - depends_on("r-genefilter", type=("build", "run")) + depends_on("r-matrixstats", type=("build", "run"), when="@1.40.0:") depends_on("r-locfit", type=("build", "run")) - depends_on("r-geneplotter", type=("build", "run")) depends_on("r-ggplot2", type=("build", "run")) depends_on("r-rcpp@0.11.0:", type=("build", "run")) depends_on("r-rcpparmadillo", type=("build", "run")) depends_on("r-hmisc", type=("build", "run"), when="@:1.30.0") + depends_on("r-genefilter", type=("build", "run"), when="@:1.38.0") + depends_on("r-geneplotter", type=("build", "run"), when="@:1.38.0") diff --git a/var/spack/repos/builtin/packages/r-dexseq/package.py b/var/spack/repos/builtin/packages/r-dexseq/package.py index b76c64f587..9c4f71b439 100644 --- a/var/spack/repos/builtin/packages/r-dexseq/package.py +++ b/var/spack/repos/builtin/packages/r-dexseq/package.py @@ -21,6 +21,7 @@ class RDexseq(RPackage): maintainers("dorton21") + version("1.46.0", commit="074c0bf6776eea69e58a788a0f6904dd632a1b74") version("1.44.0", commit="9660d7372d5ced1a7e324ed9a61b935023b7d135") version("1.42.0", commit="d91de62a27d0cab2ef12ef1a5f23dc2f7a0cfadd") version("1.40.0", commit="7d2d639b3a157e443058fc557132cd2629bb36f3") @@ -32,6 +33,7 @@ class RDexseq(RPackage): depends_on("r-iranges@2.5.17:", type=("build", "run")) depends_on("r-genomicranges@1.23.7:", type=("build", "run")) depends_on("r-deseq2@1.9.11:", type=("build", "run")) + depends_on("r-deseq2@1.39.6:", type=("build", "run"), when="@1.46.0:") depends_on("r-annotationdbi", type=("build", "run")) depends_on("r-rcolorbrewer", type=("build", "run")) depends_on("r-s4vectors@0.23.18:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-dir-expiry/package.py b/var/spack/repos/builtin/packages/r-dir-expiry/package.py new file mode 100644 index 0000000000..71506ea9c0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dir-expiry/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class RDirExpiry(RPackage): + """Managing Expiration for Cache Directories. + + Implements an expiration system for access to versioned directories. + Directories that have not been accessed by a registered function within a + certain time frame are deleted. This aims to reduce disk usage by + eliminating obsolete caches generated by old versions of packages.""" + + bioc = "dir.expiry" + + version("1.8.0", commit="271f76cb2e8565817400e85fcc2c595923af4af6") + + depends_on("r-filelock", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py index 9fd1f63c5d..4d0b6ff10d 100644 --- a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py +++ b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py @@ -18,6 +18,7 @@ class RDirichletmultinomial(RPackage): bioc = "DirichletMultinomial" + version("1.42.0", commit="c388536bed4bdc57724b704edec04b28acbf48db") version("1.40.0", commit="200176f8c72ff127788c500629b71872bc6b1f83") version("1.38.0", commit="b4de83d354e974fdb7cb3526d029487f24aab670") version("1.36.0", commit="926baff6c75cb498945c5895f25cc143c907a357") diff --git a/var/spack/repos/builtin/packages/r-dmrcate/package.py b/var/spack/repos/builtin/packages/r-dmrcate/package.py index 065f2a9cae..d5ba5db45c 100644 --- a/var/spack/repos/builtin/packages/r-dmrcate/package.py +++ b/var/spack/repos/builtin/packages/r-dmrcate/package.py @@ -17,6 +17,7 @@ class RDmrcate(RPackage): bioc = "DMRcate" + version("2.14.0", commit="6e7bae0917001e7664f01c3f8d261f9fe28c2f4d") version("2.12.0", commit="560dd5067b05715631739d0fb58ef9cebdbf7078") version("2.10.0", commit="81e83701da5c55ac83d0e0b5e640a9d431f09551") version("2.8.5", commit="c65dc79a33a047c10932a98b3383709a6bcb8903") diff --git a/var/spack/repos/builtin/packages/r-dnacopy/package.py b/var/spack/repos/builtin/packages/r-dnacopy/package.py index f60a8a2257..658ec884e2 100644 --- a/var/spack/repos/builtin/packages/r-dnacopy/package.py +++ b/var/spack/repos/builtin/packages/r-dnacopy/package.py @@ -15,6 +15,7 @@ class RDnacopy(RPackage): bioc = "DNAcopy" + version("1.74.0", commit="7d22a81570c0fe76f4b5a5c25d0b8fd3696ec70e") version("1.72.0", commit="1a1ae854c3425aee68b060e3e7ab788db5bed08c") version("1.70.0", commit="9595d0ad7c78af4ed568cbd210b894d3350eae0a") version("1.68.0", commit="08f039f58bc2f5ed2cc3117ae817dbac333002a6") diff --git a/var/spack/repos/builtin/packages/r-dose/package.py b/var/spack/repos/builtin/packages/r-dose/package.py index 19f20d0670..c91be0dfee 100644 --- a/var/spack/repos/builtin/packages/r-dose/package.py +++ b/var/spack/repos/builtin/packages/r-dose/package.py @@ -18,6 +18,7 @@ class RDose(RPackage): bioc = "DOSE" + version("3.26.0", commit="9c91fb45a2ab9a875a6a7259610b7d5bc86933f6") version("3.24.1", commit="a78995d3b12bd4baabb69c497102687814cd4c68") version("3.22.1", commit="6b711a0f076a9fefcb00ddef66e8f198039e6dfa") version("3.22.0", commit="242ac1b746c44fbbf281fbe6e5e4424a8dc74375") @@ -46,5 +47,4 @@ class RDose(RPackage): depends_on("r-scales", type=("build", "run"), when="@3.2.0:3.4.0") depends_on("r-rvcheck", type=("build", "run"), when="@3.4.0") depends_on("r-igraph", type=("build", "run"), when="@3.2.0:3.4.0") - depends_on("r-do-db", type=("build", "run")) - depends_on("r-do-db", when="@:3.22.1") + depends_on("r-do-db", type=("build", "run"), when="@:3.22.1") diff --git a/var/spack/repos/builtin/packages/r-dss/package.py b/var/spack/repos/builtin/packages/r-dss/package.py index 8058cefd6d..60c72ed030 100644 --- a/var/spack/repos/builtin/packages/r-dss/package.py +++ b/var/spack/repos/builtin/packages/r-dss/package.py @@ -18,6 +18,7 @@ class RDss(RPackage): bioc = "DSS" + version("2.48.0", commit="03ceee2656e57b717e4fd7f22ff389f118421ae1") version("2.46.0", commit="debfbac4bc741961ba57915d4f2d98534f02cc21") version("2.44.0", commit="b9f44106f139c93564dfb4afab50555d24a657ba") version("2.42.0", commit="33e87450fbb64bb3e321688ff613e83cd40efe48") @@ -33,5 +34,4 @@ class RDss(RPackage): depends_on("r-bsseq", type=("build", "run")) depends_on("r-delayedarray", type=("build", "run"), when="@2.36.0:2.42.0") - depends_on("r-matrixstats", type=("build", "run"), when="@2.44.0:") - depends_on("r-matrixstats", when="@:2.44.0") + depends_on("r-matrixstats", type=("build", "run"), when="@2.44.0") diff --git a/var/spack/repos/builtin/packages/r-ecp/package.py b/var/spack/repos/builtin/packages/r-ecp/package.py index 557d65e3d5..533b5c858c 100644 --- a/var/spack/repos/builtin/packages/r-ecp/package.py +++ b/var/spack/repos/builtin/packages/r-ecp/package.py @@ -24,5 +24,4 @@ class REcp(RPackage): version("3.1.1", sha256="d2ab194e22e6ab0168222fbccfcf2e25c6cd51a73edc959086b0c6e0a7410268") depends_on("r@3.0.0:", type=("build", "run")) - depends_on("r@3.00:", type=("build", "run"), when="@3.1.4:") depends_on("r-rcpp", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py index 371af0ebc7..478323247f 100644 --- a/var/spack/repos/builtin/packages/r-edger/package.py +++ b/var/spack/repos/builtin/packages/r-edger/package.py @@ -19,6 +19,7 @@ class REdger(RPackage): bioc = "edgeR" + version("3.42.0", commit="197b9a8ccc27016611b262c2c31ca22f991661c5") version("3.40.0", commit="0b25adcc6b3cb0a8c641964d1274536ee07ee162") version("3.38.4", commit="f5a3bb568a23b34146ac66329a95ee4785093536") version("3.38.1", commit="e58bf52f34ec451096f593126922ad7e5d517f7e") diff --git a/var/spack/repos/builtin/packages/r-enrichplot/package.py b/var/spack/repos/builtin/packages/r-enrichplot/package.py index 12b4397023..0b2ae3ed1b 100644 --- a/var/spack/repos/builtin/packages/r-enrichplot/package.py +++ b/var/spack/repos/builtin/packages/r-enrichplot/package.py @@ -16,6 +16,7 @@ class REnrichplot(RPackage): bioc = "enrichplot" + version("1.20.0", commit="ae72efe5f2ded561958f95bc8b1b41c0fc79840e") version("1.18.0", commit="61ea941784a1ed6cc604af1c1cc4532b8b5fcea7") version("1.16.2", commit="eeb21345288d96c116ac308649fa772d03760259") version("1.16.1", commit="cff77b622b2312be546714ec437aa4bc585bac87") @@ -54,6 +55,4 @@ class REnrichplot(RPackage): depends_on("r-europepmc", type=("build", "run"), when="@1.2.0:1.4.0") depends_on("r-ggplotify", type=("build", "run"), when="@1.2.0:1.4.0") depends_on("r-gridextra", type=("build", "run"), when="@1.2.0:1.4.0") - depends_on("r-cowplot", type=("build", "run")) - depends_on("r-cowplot", when="@:1.16.1") - depends_on("r-cowplot", when="@:1.16.2") + depends_on("r-cowplot", type=("build", "run"), when="@:1.16.1") diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py index 967fb6469c..aa04438ae6 100644 --- a/var/spack/repos/builtin/packages/r-ensembldb/package.py +++ b/var/spack/repos/builtin/packages/r-ensembldb/package.py @@ -24,6 +24,7 @@ class REnsembldb(RPackage): bioc = "ensembldb" + version("2.24.0", commit="45a79a438fde11b0d244b071e6ae2b652100be03") version("2.22.0", commit="4dda178a14e080c643bbd8c4dd6378bfe4e6ee9f") version("2.20.2", commit="ac1fb8389efd88099600af298d6bb3384206f9ed") version("2.20.1", commit="e547d184730cfe5e65f59e4f3512395fb1cdba1a") diff --git a/var/spack/repos/builtin/packages/r-exomecopy/package.py b/var/spack/repos/builtin/packages/r-exomecopy/package.py index cc86161c13..7403272c84 100644 --- a/var/spack/repos/builtin/packages/r-exomecopy/package.py +++ b/var/spack/repos/builtin/packages/r-exomecopy/package.py @@ -17,6 +17,7 @@ class RExomecopy(RPackage): bioc = "exomeCopy" + version("1.46.0", commit="b282adb17fb05e1a940d068d27bfd9d4549a53e7") version("1.44.0", commit="2dd6598d5fb14d49f7a42e597284c7a929c0cd62") version("1.42.0", commit="ba0979cf5fbdefed841022f2dc0604941315c1b8") version("1.40.0", commit="ebde39be67baace2c326359421fd17f4a02fd4fe") diff --git a/var/spack/repos/builtin/packages/r-experimenthub/package.py b/var/spack/repos/builtin/packages/r-experimenthub/package.py index bc8f4f4413..d0cd5eb750 100644 --- a/var/spack/repos/builtin/packages/r-experimenthub/package.py +++ b/var/spack/repos/builtin/packages/r-experimenthub/package.py @@ -18,6 +18,7 @@ class RExperimenthub(RPackage): bioc = "ExperimentHub" + version("2.8.0", commit="f25c854c51878844098290a05936cb35b235f30e") version("2.6.0", commit="557ba29720bce85902a85445dd0435b7356cdd7f") version("2.4.0", commit="bdce35d3a89e8633cc395f28991e6b5d1eccbe8e") version("2.2.1", commit="4e10686fa72baefef5d2990f41a7c44c527a7a7d") @@ -29,5 +30,5 @@ class RExperimenthub(RPackage): depends_on("r-biocfilecache@1.5.1:", type=("build", "run")) depends_on("r-s4vectors", type=("build", "run")) depends_on("r-biocmanager", type=("build", "run")) - depends_on("r-curl", type=("build", "run")) depends_on("r-rappdirs", type=("build", "run")) + depends_on("r-curl", type=("build", "run"), when="@:2.6.0") diff --git a/var/spack/repos/builtin/packages/r-fgsea/package.py b/var/spack/repos/builtin/packages/r-fgsea/package.py index 58ca517050..1719bde23a 100644 --- a/var/spack/repos/builtin/packages/r-fgsea/package.py +++ b/var/spack/repos/builtin/packages/r-fgsea/package.py @@ -16,6 +16,7 @@ class RFgsea(RPackage): bioc = "fgsea" + version("1.26.0", commit="102b439e2208ae415dc19d3d1ac8936f9c5999f1") version("1.24.0", commit="ac74ccd935c15623b8584caa791835aec514144b") version("1.22.0", commit="e4e203aa64faa984e0406fed5d87a422d9df92f2") version("1.20.0", commit="b704f81687dc16afdaafc6d30108c62a067856b2") @@ -34,6 +35,7 @@ class RFgsea(RPackage): depends_on("r-cowplot", type=("build", "run"), when="@1.24.0:") depends_on("r-fastmatch", type=("build", "run")) depends_on("r-matrix", type=("build", "run"), when="@1.6.0:") + depends_on("r-scales", type=("build", "run"), when="@1.26.0:") depends_on("r-bh", type=("build", "run"), when="@1.10.1:") - depends_on("r-gridextra", type=("build", "run")) - depends_on("r-gridextra", when="@:1.22.0") + + depends_on("r-gridextra", type=("build", "run"), when="@:1.22.0") diff --git a/var/spack/repos/builtin/packages/r-gcrma/package.py b/var/spack/repos/builtin/packages/r-gcrma/package.py index 352d98ef7c..565ca6c86d 100644 --- a/var/spack/repos/builtin/packages/r-gcrma/package.py +++ b/var/spack/repos/builtin/packages/r-gcrma/package.py @@ -13,6 +13,7 @@ class RGcrma(RPackage): bioc = "gcrma" + version("2.72.0", commit="5cfccc7c684283dc3a82830bad75aad254efcb01") version("2.70.0", commit="095f38914525d8812524a3cb38db8075382f8121") version("2.68.0", commit="c14063ff5490fac8d60530826613d728e68b3d66") version("2.66.0", commit="ba134b392def89d36b5639a187e0c25a4353457b") diff --git a/var/spack/repos/builtin/packages/r-gdsfmt/package.py b/var/spack/repos/builtin/packages/r-gdsfmt/package.py index 84786be946..c0aa0aeb49 100644 --- a/var/spack/repos/builtin/packages/r-gdsfmt/package.py +++ b/var/spack/repos/builtin/packages/r-gdsfmt/package.py @@ -24,6 +24,7 @@ class RGdsfmt(RPackage): bioc = "gdsfmt" + version("1.36.0", commit="39ba0af93d499b0f9ef53f04d4f15e5436616f1a") version("1.34.0", commit="ab912c393d8eb6dc26f844a13422a29b9ce7265b") version("1.32.0", commit="06f2097cc10b1888739f86e635383a0f2ee7e208") version("1.30.0", commit="d27dde6a70bb2295f5bbc8961152b45ccee7a652") diff --git a/var/spack/repos/builtin/packages/r-genefilter/package.py b/var/spack/repos/builtin/packages/r-genefilter/package.py index 0313e5e6b0..ce8764eadd 100644 --- a/var/spack/repos/builtin/packages/r-genefilter/package.py +++ b/var/spack/repos/builtin/packages/r-genefilter/package.py @@ -13,6 +13,7 @@ class RGenefilter(RPackage): bioc = "genefilter" + version("1.82.0", commit="1ee4bdc65b0144853211354f8fabf8b497d9a565") version("1.80.0", commit="14fbc2d776916e572583e3c268ea9ba60ed60a9a") version("1.78.0", commit="2f574388971641d3a71858f5c34606c04fcd2ba2") version("1.76.0", commit="8d630fd25f0d2a4101e05e123c3959591203a7ea") @@ -24,11 +25,11 @@ class RGenefilter(RPackage): version("1.60.0", commit="c98f695253c330a9380b2b4ffa27f3b7d66773e4") version("1.58.1", commit="ace2556049677f60882adfe91f8cc96791556fc2") - depends_on("r-biocgenerics", type=("build", "run"), when="@1.78.0:") - depends_on("r-biocgenerics@0.31.2:", type=("build", "run"), when="@1.68.0:") + depends_on("r-matrixgenerics@1.11.1:", type=("build", "run"), when="@1.82.0:") depends_on("r-annotationdbi", type=("build", "run")) depends_on("r-annotate", type=("build", "run")) depends_on("r-biobase", type=("build", "run")) depends_on("r-survival", type=("build", "run")) - depends_on("r-s4vectors@0.9.42:", type=("build", "run"), when="@:1.66.0") + depends_on("r-biocgenerics", type=("build", "run"), when="@1.78.0:1.80.0") + depends_on("r-biocgenerics@0.31.2:", type=("build", "run"), when="@1.68.0:1.80.0") diff --git a/var/spack/repos/builtin/packages/r-genelendatabase/package.py b/var/spack/repos/builtin/packages/r-genelendatabase/package.py index 8c1c141ff0..3d583803af 100644 --- a/var/spack/repos/builtin/packages/r-genelendatabase/package.py +++ b/var/spack/repos/builtin/packages/r-genelendatabase/package.py @@ -14,6 +14,7 @@ class RGenelendatabase(RPackage): bioc = "geneLenDataBase" + version("1.36.0", commit="e8f37dd2a63cf10ba946958362192909fec64a10") version("1.34.0", commit="e26cf8e3fc20b5d183cbd39b7b28a8cc866f6ead") version("1.32.0", commit="eaa193a2c6d502c6d59113fd42f66761b8730594") version("1.30.0", commit="b3cc755f1ffcbb2eacd9ea45e11f39f1639782b1") diff --git a/var/spack/repos/builtin/packages/r-genemeta/package.py b/var/spack/repos/builtin/packages/r-genemeta/package.py index 32dec3cd5b..ed6458cc9b 100644 --- a/var/spack/repos/builtin/packages/r-genemeta/package.py +++ b/var/spack/repos/builtin/packages/r-genemeta/package.py @@ -14,6 +14,7 @@ class RGenemeta(RPackage): bioc = "GeneMeta" + version("1.72.0", commit="1cb047172f54c12c5dc5a9b39358ea04cbeff8a2") version("1.70.0", commit="e5db82e04efc4572358abce7e0c09273f94c9d72") version("1.68.0", commit="4213c0205d477660195300a0aa9751972f86bf91") version("1.66.0", commit="c16eb09492f08f6cc0f253fafa3fa5dce35dcdba") diff --git a/var/spack/repos/builtin/packages/r-geneplotter/package.py b/var/spack/repos/builtin/packages/r-geneplotter/package.py index 92ef1c1819..74caffa944 100644 --- a/var/spack/repos/builtin/packages/r-geneplotter/package.py +++ b/var/spack/repos/builtin/packages/r-geneplotter/package.py @@ -13,6 +13,7 @@ class RGeneplotter(RPackage): bioc = "geneplotter" + version("1.78.0", commit="a105c51d2f7a097ea33c3aad8f2345e9a51406d3") version("1.76.0", commit="4eb6a787d0c66110ec9a7d34fc76b64030fbde5d") version("1.74.0", commit="ca819565829eac7a9a98e3cafafd6c06a466fddf") version("1.72.0", commit="57a1d830ba7844fda5236af0153d5b5587634f96") diff --git a/var/spack/repos/builtin/packages/r-genie3/package.py b/var/spack/repos/builtin/packages/r-genie3/package.py index 1cf6b8e7e0..f07a94e7ed 100644 --- a/var/spack/repos/builtin/packages/r-genie3/package.py +++ b/var/spack/repos/builtin/packages/r-genie3/package.py @@ -14,6 +14,7 @@ class RGenie3(RPackage): bioc = "GENIE3" + version("1.22.0", commit="e0b7f23a1ac5b01c937a351bb530b2dc6b76711f") version("1.20.0", commit="aea2e686a262f30b16c068241938d04f21251a0d") version("1.18.0", commit="f16b25ef50978a4a497eb2f911e21f2e839fa33c") version("1.16.0", commit="5543b1b883d3a1c92e955de6668444278edc2bdf") diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py index 7c65e0fea3..4f04c16c23 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py @@ -17,6 +17,7 @@ class RGenomeinfodb(RPackage): bioc = "GenomeInfoDb" + version("1.36.0", commit="c380bb93a5480b48e0efbf6d107cefc10d574438") version("1.34.3", commit="ea6f131f1d1ee61535d6733ce76fabf3c62185fc") version("1.32.4", commit="69df6a5a10027fecf6a6d1c8298f3f686b990d8f") version("1.32.2", commit="2e40af38f00ee86d2c83d140e234c1349baa27de") diff --git a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py index 0de0ff2f50..cfb5093c11 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py @@ -14,6 +14,11 @@ class RGenomeinfodbdata(RPackage): url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz" version( + "1.2.10", + url="https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GenomeInfoDbData_1.2.10.tar.gz", + sha256="74c5db556d163e8f512d55f5c0d8ce315fb13ac822d31b4b030c20036d58f864", + ) + version( "1.2.9", url="https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz", sha256="e63a719a8eceefeda39fc95de83e7aa41caad39705efc712a44ab4021adc45fa", diff --git a/var/spack/repos/builtin/packages/r-genomicalignments/package.py b/var/spack/repos/builtin/packages/r-genomicalignments/package.py index 3904f134e6..f3e8a24e47 100644 --- a/var/spack/repos/builtin/packages/r-genomicalignments/package.py +++ b/var/spack/repos/builtin/packages/r-genomicalignments/package.py @@ -16,6 +16,7 @@ class RGenomicalignments(RPackage): bioc = "GenomicAlignments" + version("1.36.0", commit="cdc1aa49f14d3effe2540380a04fe1fc72c00f04") version("1.34.0", commit="c6eb78079c8aa21d47c95b3d16a606e8c2c5d799") version("1.32.1", commit="2553580d0b8a8a5fd7835c1446616b39f707b8a9") version("1.32.0", commit="7a660a914a04e2eb0758082b6f64c4124a887ef3") diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py index 8d83d23613..0ca2561f35 100644 --- a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py +++ b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py @@ -20,6 +20,7 @@ class RGenomicfeatures(RPackage): bioc = "GenomicFeatures" + version("1.52.0", commit="207ff08b38421f0394a8f6450e00fb8713ab463c") version("1.50.2", commit="4fc9120ceed9ff59f390c8bbdbd79b212ee35b84") version("1.48.4", commit="06e37dc1847d49d91391264caec877ed33abf359") version("1.48.3", commit="b0ddea0e101e3861928f3ad353348df047d90382") @@ -43,6 +44,7 @@ class RGenomicfeatures(RPackage): depends_on("r-genomeinfodb@1.15.4:", type=("build", "run"), when="@1.32.3:") depends_on("r-genomeinfodb@1.25.7:", type=("build", "run"), when="@1.42.1:") depends_on("r-genomeinfodb@1.34.1:", type=("build", "run"), when="@1.50.2:") + depends_on("r-genomeinfodb@1.35.8:", type=("build", "run"), when="@1.52.0:") depends_on("r-genomicranges@1.27.6:", type=("build", "run")) depends_on("r-genomicranges@1.29.14:", type=("build", "run"), when="@1.30.3:") depends_on("r-genomicranges@1.31.17:", type=("build", "run"), when="@1.32.3:") diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py index 0b406237fe..cad44e125d 100644 --- a/var/spack/repos/builtin/packages/r-genomicranges/package.py +++ b/var/spack/repos/builtin/packages/r-genomicranges/package.py @@ -22,6 +22,7 @@ class RGenomicranges(RPackage): bioc = "GenomicRanges" + version("1.52.0", commit="883f125ea593099293dc808ec2188be3cbdbd3a7") version("1.50.1", commit="6b3fb388ec038fb43f3cd26684ce778ee0e80e81") version("1.48.0", commit="2bce60814db7c20949892587740fb484aa435978") version("1.46.1", commit="e422642f64815cdfee8fc340681ad87a7eafc3bb") diff --git a/var/spack/repos/builtin/packages/r-geoquery/package.py b/var/spack/repos/builtin/packages/r-geoquery/package.py index 3810f346f0..7b31628598 100644 --- a/var/spack/repos/builtin/packages/r-geoquery/package.py +++ b/var/spack/repos/builtin/packages/r-geoquery/package.py @@ -16,6 +16,7 @@ class RGeoquery(RPackage): bioc = "GEOquery" + version("2.68.0", commit="7995c579b068f98ebf3f1cd2cfd0575c3d73530c") version("2.66.0", commit="00a954e9f8223607b43cf112943ab575d03a0eb6") version("2.64.2", commit="e9b7f075a4a6a952660443ca93ed392d7a4fd6d7") version("2.62.2", commit="1966c108fe8a58ac39ef53c3c452fd160efa526e") diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py index 50fb2ddb83..bc4b7f0946 100644 --- a/var/spack/repos/builtin/packages/r-ggbio/package.py +++ b/var/spack/repos/builtin/packages/r-ggbio/package.py @@ -21,6 +21,7 @@ class RGgbio(RPackage): bioc = "ggbio" + version("1.48.0", commit="fd4ebca44151e8f8e20ad2a38292398a3a4bb948") version("1.46.0", commit="d9c6cb495c7268bcaaab141231a9038aec8498bc") version("1.44.1", commit="0301d9464e304a8113ea4479185cd358855ca365") version("1.44.0", commit="cb21284a9803917fa76e116adfc456525c95f660") diff --git a/var/spack/repos/builtin/packages/r-ggtree/package.py b/var/spack/repos/builtin/packages/r-ggtree/package.py index 182d2f2992..db34d3dae4 100644 --- a/var/spack/repos/builtin/packages/r-ggtree/package.py +++ b/var/spack/repos/builtin/packages/r-ggtree/package.py @@ -16,6 +16,7 @@ class RGgtree(RPackage): bioc = "ggtree" + version("3.8.0", commit="e7c989085d0848e4d5f82aa8000422c71458a9a8") version("3.6.2", commit="431ec37bc0f0159b08a7990ce1d9374e160b9f44") version("3.4.4", commit="8e48d3e2ea445b6c2213f0471462108a7a72b333") version("3.4.0", commit="23f08a3da1829d1bbb6827ed1c4cf878daa4b539") @@ -28,11 +29,13 @@ class RGgtree(RPackage): depends_on("r-dplyr", type=("build", "run")) depends_on("r-ggplot2@3.0.0:", type=("build", "run")) depends_on("r-ggplot2@3.4.0:", type=("build", "run"), when="@3.6.2:") + depends_on("r-ggplot2@UNKNOWN:", type=("build", "run"), when="@3.8.0:") depends_on("r-magrittr", type=("build", "run")) depends_on("r-purrr", type=("build", "run")) depends_on("r-rlang", type=("build", "run")) depends_on("r-ggfun", type=("build", "run")) depends_on("r-ggfun@0.0.6:", type=("build", "run"), when="@3.4.0:") + depends_on("r-ggfun@0.0.9:", type=("build", "run"), when="@3.8.0:") depends_on("r-yulab-utils", type=("build", "run")) depends_on("r-tidyr", type=("build", "run")) depends_on("r-tidytree@0.2.6:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-glimma/package.py b/var/spack/repos/builtin/packages/r-glimma/package.py index c943e511dc..abf310b469 100644 --- a/var/spack/repos/builtin/packages/r-glimma/package.py +++ b/var/spack/repos/builtin/packages/r-glimma/package.py @@ -17,6 +17,7 @@ class RGlimma(RPackage): bioc = "Glimma" + version("2.10.0", commit="ea1257614c5fca0cedf5805d5b9a21e8b7d15d18") version("2.8.0", commit="09cec82e9af9c6775192570f8c28f050c0df08ac") version("2.6.0", commit="23220d9b90476059aab035b5de11b7ce04b331c8") version("2.4.0", commit="caa270e44ec6994035d2e915c0f68a14ccbb58db") diff --git a/var/spack/repos/builtin/packages/r-glmgampoi/package.py b/var/spack/repos/builtin/packages/r-glmgampoi/package.py index 275cef8688..b36ac7d263 100644 --- a/var/spack/repos/builtin/packages/r-glmgampoi/package.py +++ b/var/spack/repos/builtin/packages/r-glmgampoi/package.py @@ -16,6 +16,7 @@ class RGlmgampoi(RPackage): bioc = "glmGamPoi" + version("1.12.0", commit="5fdfa5ca1a56b19e51bc6e307ca6015cc56109a0") version("1.10.0", commit="048e17384209fc07031e09875ec6eea35e90ef46") version("1.8.0", commit="b723d61e05c1ad50a3cf6a6393ec3d97adc7edb4") @@ -29,5 +30,6 @@ class RGlmgampoi(RPackage): depends_on("r-singlecellexperiment", type=("build", "run"), when="@1.10.0:") depends_on("r-biocgenerics", type=("build", "run")) depends_on("r-rlang", type=("build", "run"), when="@1.10.0:") + depends_on("r-vctrs", type=("build", "run"), when="@1.12.0:") depends_on("r-rcpparmadillo", type=("build", "run")) depends_on("r-beachmat", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-globaltest/package.py b/var/spack/repos/builtin/packages/r-globaltest/package.py index 831652e813..461aed1f03 100644 --- a/var/spack/repos/builtin/packages/r-globaltest/package.py +++ b/var/spack/repos/builtin/packages/r-globaltest/package.py @@ -18,6 +18,7 @@ class RGlobaltest(RPackage): bioc = "globaltest" + version("5.54.0", commit="bb8bc5f757c8b7c020da31b6a3f500075715ab8e") version("5.52.0", commit="a1fc3ad206454d1151bcc940644fd8a5c4164d63") version("5.50.0", commit="08612a06eb1cc7381f9bf70f6fe198bb401a21df") version("5.48.0", commit="86c2c8f35734dcbc8c8ca791d8a190dc525beac9") diff --git a/var/spack/repos/builtin/packages/r-go-db/package.py b/var/spack/repos/builtin/packages/r-go-db/package.py index 53be469518..c5dfb5e6ff 100644 --- a/var/spack/repos/builtin/packages/r-go-db/package.py +++ b/var/spack/repos/builtin/packages/r-go-db/package.py @@ -16,6 +16,11 @@ class RGoDb(RPackage): url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/GO.db_3.4.1.tar.gz" version( + "3.17.0", + url="https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GO.db_3.17.0.tar.gz", + sha256="5dbe48060813c8c39a725b34d9c793ca76ef8e568fdc49f96f4a4bd8ba30401c", + ) + version( "3.16.0", url="https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GO.db_3.16.0.tar.gz", sha256="4652812d8ba380aeeb9b136efbc9365156397eec99c5ca36cfb8294139493b8e", @@ -46,3 +51,5 @@ class RGoDb(RPackage): depends_on("r-annotationdbi@1.51.3:", type=("build", "run"), when="@3.12.1:") depends_on("r-annotationdbi@1.55.1:", type=("build", "run"), when="@3.14.0:") depends_on("r-annotationdbi@1.57.1:", type=("build", "run"), when="@3.15.0:") + depends_on("r-annotationdbi@1.59.1:", type=("build", "run"), when="@3.16.0:") + depends_on("r-annotationdbi@1.61.0:", type=("build", "run"), when="@3.17.0:") diff --git a/var/spack/repos/builtin/packages/r-gofuncr/package.py b/var/spack/repos/builtin/packages/r-gofuncr/package.py index 88c4dcbae8..db691bdb28 100644 --- a/var/spack/repos/builtin/packages/r-gofuncr/package.py +++ b/var/spack/repos/builtin/packages/r-gofuncr/package.py @@ -28,6 +28,7 @@ class RGofuncr(RPackage): bioc = "GOfuncR" + version("1.20.0", commit="2374d68fdd13a72bc8d43cc3b5e6735228996ff1") version("1.18.0", commit="49182411e40a5d72abf99a5cca9287f34f870b19") version("1.16.0", commit="603fc79e13b58ec4612b6092f37d2450078dbfe1") version("1.14.0", commit="b3d445acf95851241d1fdb673d108ee115bdc17b") diff --git a/var/spack/repos/builtin/packages/r-gosemsim/package.py b/var/spack/repos/builtin/packages/r-gosemsim/package.py index 91f84e33f2..65fb0705c3 100644 --- a/var/spack/repos/builtin/packages/r-gosemsim/package.py +++ b/var/spack/repos/builtin/packages/r-gosemsim/package.py @@ -19,6 +19,7 @@ class RGosemsim(RPackage): bioc = "GOSemSim" + version("2.26.0", commit="ef3d5a7fb37b43603de4f43aa4fecadaa47f93e0") version("2.24.0", commit="ed7334f3cf3ac7ce5be76003934c29b598089f4d") version("2.22.0", commit="fd74aeba2371ebf9db0595cf18674441bdac9618") version("2.20.0", commit="fa82442aaa4ad1a8dacc05ee2c54f5e5e770a794") diff --git a/var/spack/repos/builtin/packages/r-goseq/package.py b/var/spack/repos/builtin/packages/r-goseq/package.py index ad2d9c4566..5f9ae293e0 100644 --- a/var/spack/repos/builtin/packages/r-goseq/package.py +++ b/var/spack/repos/builtin/packages/r-goseq/package.py @@ -14,6 +14,7 @@ class RGoseq(RPackage): bioc = "goseq" + version("1.52.0", commit="d6b0cfddf887a074acf18c77c2ea4cb3a9202bd8") version("1.50.0", commit="f9fad238e2d08a87b14c3c8c228ad332efa60f14") version("1.48.0", commit="d077fda56986cc7218a88f7db37a42412b227025") version("1.46.0", commit="1fb5626cc80f595499af511a830322ed12bbe144") diff --git a/var/spack/repos/builtin/packages/r-gostats/package.py b/var/spack/repos/builtin/packages/r-gostats/package.py index d1c2b928d8..e021f6c9c3 100644 --- a/var/spack/repos/builtin/packages/r-gostats/package.py +++ b/var/spack/repos/builtin/packages/r-gostats/package.py @@ -15,6 +15,7 @@ class RGostats(RPackage): bioc = "GOstats" + version("2.66.0", commit="dbfc8a7646b53db53b0c329e0e1c77c0f202f08f") version("2.64.0", commit="62813253249dc02d2ddaafa7f0249e69d6f2c6b0") version("2.62.0", commit="217db032272010ebb8fe3af4647153428f42cd47") version("2.60.0", commit="a20055cc1c04a91b0291a918dadd9ea912c187ce") diff --git a/var/spack/repos/builtin/packages/r-graph/package.py b/var/spack/repos/builtin/packages/r-graph/package.py index d5c06dffa3..c9c3ddb4a1 100644 --- a/var/spack/repos/builtin/packages/r-graph/package.py +++ b/var/spack/repos/builtin/packages/r-graph/package.py @@ -13,6 +13,7 @@ class RGraph(RPackage): bioc = "graph" + version("1.78.0", commit="9df68e8f74e2b807b033f991d21142edfd1bc090") version("1.76.0", commit="e3efc108716e98bd3363621d17a6f9c3ef975d19") version("1.74.0", commit="4af608a5d9e1de33fda6ae28fb73bff9272ee296") version("1.72.0", commit="7afbd26ecd76e55e6bbd74915a561d7a9b15f907") diff --git a/var/spack/repos/builtin/packages/r-gseabase/package.py b/var/spack/repos/builtin/packages/r-gseabase/package.py index 175db0dc36..318e2417f3 100644 --- a/var/spack/repos/builtin/packages/r-gseabase/package.py +++ b/var/spack/repos/builtin/packages/r-gseabase/package.py @@ -14,6 +14,7 @@ class RGseabase(RPackage): bioc = "GSEABase" + version("1.62.0", commit="fc20cbcd85da0202eb0f2316dcf63f6fb1372b3e") version("1.60.0", commit="aae4e52b50b076550967601f98031e952fb97765") version("1.58.0", commit="7de04442fb1ab63ffde29f4e3daf13ad32e90bdb") version("1.56.0", commit="ee7c3ca4ad0f1f3e9b9162db1515413802860ecc") diff --git a/var/spack/repos/builtin/packages/r-gtrellis/package.py b/var/spack/repos/builtin/packages/r-gtrellis/package.py index e1308b36e5..90fea73d53 100644 --- a/var/spack/repos/builtin/packages/r-gtrellis/package.py +++ b/var/spack/repos/builtin/packages/r-gtrellis/package.py @@ -18,6 +18,7 @@ class RGtrellis(RPackage): bioc = "gtrellis" + version("1.32.0", commit="4c2361bde90a556aa5a585d45f056b3ddc806f9b") version("1.30.0", commit="da93b30ef812e231c47aa83da5c521f1801b3d14") version("1.28.0", commit="d770a7b3441e4003869c88cfd8e21fd6508b86c4") version("1.26.0", commit="f2c3121b31ad1b422e2cf503435d0590e903ff3f") diff --git a/var/spack/repos/builtin/packages/r-gviz/package.py b/var/spack/repos/builtin/packages/r-gviz/package.py index acc38c2584..d102bf17c5 100644 --- a/var/spack/repos/builtin/packages/r-gviz/package.py +++ b/var/spack/repos/builtin/packages/r-gviz/package.py @@ -18,6 +18,7 @@ class RGviz(RPackage): bioc = "Gviz" + version("1.44.0", commit="e70aaa7dd27df8482ee854395475a87ec2121279") version("1.42.0", commit="4eddb688bca3fdeb65fd536d653d7ba7f7976121") version("1.40.1", commit="d21843710cd05135353de5cd4ce4d35cdd333b7c") version("1.38.3", commit="c4b352a16455a5744533c511e59354977814cb9e") @@ -32,6 +33,7 @@ class RGviz(RPackage): depends_on("r@4.0:", type=("build", "run"), when="@1.34.0:") depends_on("r@4.1:", type=("build", "run"), when="@1.38.3:") depends_on("r@4.2:", type=("build", "run"), when="@1.40.1:") + depends_on("r@4.3:", type=("build", "run"), when="@1.44.0:") depends_on("r-s4vectors@0.9.25:", type=("build", "run")) depends_on("r-iranges@1.99.18:", type=("build", "run")) depends_on("r-genomicranges@1.17.20:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-hdf5array/package.py b/var/spack/repos/builtin/packages/r-hdf5array/package.py index f55d3261d6..dcb575aa95 100644 --- a/var/spack/repos/builtin/packages/r-hdf5array/package.py +++ b/var/spack/repos/builtin/packages/r-hdf5array/package.py @@ -20,6 +20,7 @@ class RHdf5array(RPackage): bioc = "HDF5Array" + version("1.28.0", commit="8c839417c4a37c35330bd6f02b79dda9f48e76ae") version("1.26.0", commit="38b7bd603f7281245605048d8d57237e00b74d79") version("1.24.2", commit="fb213ba36631b04dfe754705f701f3a015c4fc82") version("1.24.1", commit="d002fe70c84baaadb62058ce467d6c1ea032d8f5") diff --git a/var/spack/repos/builtin/packages/r-hypergraph/package.py b/var/spack/repos/builtin/packages/r-hypergraph/package.py index 046789d818..37fcca408f 100644 --- a/var/spack/repos/builtin/packages/r-hypergraph/package.py +++ b/var/spack/repos/builtin/packages/r-hypergraph/package.py @@ -14,6 +14,7 @@ class RHypergraph(RPackage): bioc = "hypergraph" + version("1.72.0", commit="1b619b8dfeaf13dca7857013495d52dcfe4276b4") version("1.70.0", commit="a5ffeafa8b999b5e7e77f93f4e6284abafc81621") version("1.68.0", commit="7d53b5050f4ebe0a7007c02b76e93498195da3a4") version("1.66.0", commit="e9c47336df6409006622818f541f258103163a39") diff --git a/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py b/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py index 84b0061331..8b638114d8 100644 --- a/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py +++ b/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py @@ -15,6 +15,7 @@ class RIllumina450probevariantsDb(RPackage): bioc = "Illumina450ProbeVariants.db" + version("1.36.0", commit="aaa4254cebb352730779677cef7a7c99c1447e7a") version("1.34.0", commit="6c0f0b4d2bcf13da852b2f132a8ce1229fa5269e") version("1.32.0", commit="a15602253e675a104303627957653a08876d8d7c") version("1.30.0", commit="ba1296b4aafc287dea61f5f37c6c99fd553e52a2") diff --git a/var/spack/repos/builtin/packages/r-illuminaio/package.py b/var/spack/repos/builtin/packages/r-illuminaio/package.py index 52ee887a1c..33d212a04b 100644 --- a/var/spack/repos/builtin/packages/r-illuminaio/package.py +++ b/var/spack/repos/builtin/packages/r-illuminaio/package.py @@ -13,6 +13,7 @@ class RIlluminaio(RPackage): bioc = "illuminaio" + version("0.42.0", commit="d72b85c57ea9bcba8d652e3a66fddf5dcc59dda6") version("0.40.0", commit="1d7045697eaf09e5c61447a6f61e2eeaaf7a5095") version("0.38.0", commit="b16231b7417b4d6e9cff1e2724ed3529871dff92") version("0.36.0", commit="c5b6e9164b73c650c0a9f055f4fd0580ac64fae7") diff --git a/var/spack/repos/builtin/packages/r-impute/package.py b/var/spack/repos/builtin/packages/r-impute/package.py index 68c05bbf3a..d1c25eea64 100644 --- a/var/spack/repos/builtin/packages/r-impute/package.py +++ b/var/spack/repos/builtin/packages/r-impute/package.py @@ -13,6 +13,7 @@ class RImpute(RPackage): bioc = "impute" + version("1.74.0", commit="6dc26573263e337d4b521f006701f022bbad21b9") version("1.72.0", commit="638ac916464f5a392b947ef5bb426b8445d27325") version("1.70.0", commit="970b2c28d908e26369b01dddf36dab2f8916d4af") version("1.68.0", commit="fa4e4d883e609633c49d865a44acd6a79954eaac") diff --git a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py index fce74e0712..2ee8dc7223 100644 --- a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py +++ b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py @@ -16,6 +16,7 @@ class RInteractivedisplaybase(RPackage): bioc = "interactiveDisplayBase" + version("1.38.0", commit="3b3a3fdc4bafca767ae66c5f8869e2d93a9a4cb3") version("1.36.0", commit="79a0552bd467367866ceda2efc2b60a04a81f5fb") version("1.34.0", commit="fafbb13a42bb7549f17aa08cdb0e51728c5e825e") version("1.32.0", commit="0f88b2ac3689d51abb6ac0045b3207ca77963a5a") diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py index 259700fa1e..55b509f2a0 100644 --- a/var/spack/repos/builtin/packages/r-iranges/package.py +++ b/var/spack/repos/builtin/packages/r-iranges/package.py @@ -18,6 +18,7 @@ class RIranges(RPackage): bioc = "IRanges" + version("2.34.0", commit="dcddf934384e05dccffb2a8a808147c963ff0c3e") version("2.32.0", commit="2b5c9fc706c8cdc96f0c46508087863df1502f81") version("2.30.1", commit="ead506a14d6cc89ac2f14b55a4b04496755e4e50") version("2.30.0", commit="9b5f3ca12812fb76c23b1550aa3a794384384d9b") diff --git a/var/spack/repos/builtin/packages/r-kegggraph/package.py b/var/spack/repos/builtin/packages/r-kegggraph/package.py index 44cb4fdfe0..02480e023b 100644 --- a/var/spack/repos/builtin/packages/r-kegggraph/package.py +++ b/var/spack/repos/builtin/packages/r-kegggraph/package.py @@ -18,6 +18,7 @@ class RKegggraph(RPackage): bioc = "KEGGgraph" + version("1.60.0", commit="9fc1e371309193e7ff47b0e9d9937cbeed830a1c") version("1.58.0", commit="7c3f148b57903b8df517f94824f07f38bbd3b591") version("1.56.0", commit="e95cbf9f8a095d59b78a053463191b89c00d5ded") version("1.54.0", commit="135ee3dad30ca208e21acd0a2d81120b74b64079") diff --git a/var/spack/repos/builtin/packages/r-keggrest/package.py b/var/spack/repos/builtin/packages/r-keggrest/package.py index 397eb6566c..7b11221c76 100644 --- a/var/spack/repos/builtin/packages/r-keggrest/package.py +++ b/var/spack/repos/builtin/packages/r-keggrest/package.py @@ -15,6 +15,7 @@ class RKeggrest(RPackage): bioc = "KEGGREST" + version("1.40.0", commit="1bdb0b57d7e9b708da14d2847c2a17ca35500b21") version("1.38.0", commit="4dfbff9f6662227bd49d64d18a342f469dd88ad3") version("1.36.3", commit="1827cde76863aa80c83264a0dd95514654358df3") version("1.36.0", commit="591818bbc9195bfd0657cf4f5c7c771ea7f86830") diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py index 358cc1a3eb..99f01b292d 100644 --- a/var/spack/repos/builtin/packages/r-limma/package.py +++ b/var/spack/repos/builtin/packages/r-limma/package.py @@ -14,6 +14,7 @@ class RLimma(RPackage): bioc = "limma" + version("3.56.0", commit="efe857829233edb11ae317ce5d1ad4ea3073cf7f") version("3.54.0", commit="1d1fa843d4fe2f8c94fd843bb1e80b8384d8306e") version("3.52.4", commit="3226c29ad8c18aa7e6722f4a2c95ff8ac900437e") version("3.52.1", commit="c81c539a217ac1cf46e850f8a20266cecfafed50") diff --git a/var/spack/repos/builtin/packages/r-lumi/package.py b/var/spack/repos/builtin/packages/r-lumi/package.py index b837a78d8a..5206ac2b4b 100644 --- a/var/spack/repos/builtin/packages/r-lumi/package.py +++ b/var/spack/repos/builtin/packages/r-lumi/package.py @@ -19,6 +19,7 @@ class RLumi(RPackage): bioc = "lumi" + version("2.52.0", commit="c6aa992a622dbaba4dae1b54c61835a37cce8e95") version("2.50.0", commit="8711b77a1b5b0a58770d25d3d079ad02208704f5") version("2.48.0", commit="1f988ffe04d2c0707b2202d2074d02b679a3204b") version("2.46.0", commit="a68932c17a61c99e58ebbd8008d078bec6adb4e7") diff --git a/var/spack/repos/builtin/packages/r-makecdfenv/package.py b/var/spack/repos/builtin/packages/r-makecdfenv/package.py index 4d75dcdb7c..307ae72906 100644 --- a/var/spack/repos/builtin/packages/r-makecdfenv/package.py +++ b/var/spack/repos/builtin/packages/r-makecdfenv/package.py @@ -16,6 +16,7 @@ class RMakecdfenv(RPackage): bioc = "makecdfenv" + version("1.76.0", commit="8196d4886db1d8e51821bfe9f727a30666d53801") version("1.74.0", commit="412affc333ba51cad0ff3c7919e2eadaaf426359") version("1.72.0", commit="85c89688e6b6e8bff46b92cbeba49e38c510492e") version("1.70.0", commit="82ecd0fa8ac401e4ac8f1e9139556d2be4a3c4f3") diff --git a/var/spack/repos/builtin/packages/r-marray/package.py b/var/spack/repos/builtin/packages/r-marray/package.py index 6a3c83a92a..6d181c0eef 100644 --- a/var/spack/repos/builtin/packages/r-marray/package.py +++ b/var/spack/repos/builtin/packages/r-marray/package.py @@ -14,6 +14,7 @@ class RMarray(RPackage): bioc = "marray" + version("1.78.0", commit="97d74b2af40568eda445378b4708a2e2d33291cd") version("1.76.0", commit="88cb0fd21cc60ac65410ca4314eca2e351933ec5") version("1.74.0", commit="9130a936fffb7d2d445ff21d04520e78b62625ac") version("1.72.0", commit="da35e8b8d2c9ef17e779013a5d252f38a1c66633") diff --git a/var/spack/repos/builtin/packages/r-matrixgenerics/package.py b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py index f5872454f8..b5df37b26c 100644 --- a/var/spack/repos/builtin/packages/r-matrixgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py @@ -19,6 +19,7 @@ class RMatrixgenerics(RPackage): bioc = "MatrixGenerics" + version("1.12.0", commit="442fde27fdf18ee3460ea0258a74a847b2c99cf3") version("1.10.0", commit="6d9d907e8c4d1fc96a32160fb9f3ab805d6eb356") version("1.8.1", commit="a4a21089e9f78275dd4a6f0df0c4b6b45c4650c7") version("1.8.0", commit="e4cc34d53bcfb9a5914afd79fda31ecd5037a47a") diff --git a/var/spack/repos/builtin/packages/r-metapod/package.py b/var/spack/repos/builtin/packages/r-metapod/package.py index 30c7329995..b2156dfae6 100644 --- a/var/spack/repos/builtin/packages/r-metapod/package.py +++ b/var/spack/repos/builtin/packages/r-metapod/package.py @@ -19,6 +19,7 @@ class RMetapod(RPackage): bioc = "metapod" + version("1.8.0", commit="6ac6999182d581ed579d2f7535e838b084f67b8d") version("1.6.0", commit="cfeaa959f5c6b2119df270f40af9c3ea718c4b00") version("1.4.0", commit="e71c2072e5b39f74599e279b28f4da7923b515fb") diff --git a/var/spack/repos/builtin/packages/r-methylumi/package.py b/var/spack/repos/builtin/packages/r-methylumi/package.py index e7483c39ef..1fb9aa9ab7 100644 --- a/var/spack/repos/builtin/packages/r-methylumi/package.py +++ b/var/spack/repos/builtin/packages/r-methylumi/package.py @@ -20,6 +20,7 @@ class RMethylumi(RPackage): bioc = "methylumi" + version("2.46.0", commit="eb09e6508f1619c789d6b3091a8065cb6571cdac") version("2.44.0", commit="8f1f1f944993800da2776cb3240b4482c09429ad") version("2.42.0", commit="73e9c7fe1252c4ca20dc7b4e58decf04bf22d5e0") version("2.40.1", commit="211039225ca6fca9af75b8266f656161912ce10f") diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py index 5d73ed66f7..2431d77055 100644 --- a/var/spack/repos/builtin/packages/r-minfi/package.py +++ b/var/spack/repos/builtin/packages/r-minfi/package.py @@ -13,6 +13,7 @@ class RMinfi(RPackage): bioc = "minfi" + version("1.46.0", commit="1d063178fb27d577c260f8b7626b982c9a6585cc") version("1.44.0", commit="7c89fefc2e174d43ed9891b3f30b51ee19e916a6") version("1.42.0", commit="30fc7059460a9ec0be734fc26e608426ca9f5614") version("1.40.0", commit="17fa2b5d6cdbef6cbfb690242bd3f660731431f1") diff --git a/var/spack/repos/builtin/packages/r-missmethyl/package.py b/var/spack/repos/builtin/packages/r-missmethyl/package.py index a31dee292c..9190733b12 100644 --- a/var/spack/repos/builtin/packages/r-missmethyl/package.py +++ b/var/spack/repos/builtin/packages/r-missmethyl/package.py @@ -23,6 +23,7 @@ class RMissmethyl(RPackage): bioc = "missMethyl" + version("1.34.0", commit="57db57c48ab79c36eb89726afc2833a981cbaf3d") version("1.32.0", commit="969b892e400b9821398099bcea46f2d0431daedf") version("1.30.0", commit="734846653f332f10e557b87aca4cb5d100b62469") version("1.28.0", commit="6a36aee28837736291ac630c1da3909f0e9c8d6a") diff --git a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py index 92d0a1c7c8..b1c04a6591 100644 --- a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py +++ b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py @@ -15,6 +15,7 @@ class RMlinterfaces(RPackage): bioc = "MLInterfaces" + version("1.80.0", commit="275f8d39f05c46ab3ab7096d1e0539a33bab3a54") version("1.78.0", commit="0988b95d282a6bffe56b7df4da2e23485e96d12c") version("1.76.0", commit="935323d8ce1e4bbf41844a1f9b6c946c5a30c673") version("1.74.0", commit="5ee73b6491b1d68d7b49ddce6483df98ad880946") diff --git a/var/spack/repos/builtin/packages/r-mscoreutils/package.py b/var/spack/repos/builtin/packages/r-mscoreutils/package.py index c4b88cfeec..e8be0bb0df 100644 --- a/var/spack/repos/builtin/packages/r-mscoreutils/package.py +++ b/var/spack/repos/builtin/packages/r-mscoreutils/package.py @@ -19,6 +19,7 @@ class RMscoreutils(RPackage): bioc = "MsCoreUtils" + version("1.12.0", commit="14a3fdb2fecca41ef0acb67bc8356227a1491c56") version("1.10.0", commit="742c0c7143b1c32f75cc96b555e9f8cd265096c9") version("1.8.0", commit="8b7e2c31009276aad0b418ba5cdfc94d03e1973e") version("1.6.0", commit="9ed95b2d20dacaa83567fadd04349c81db9127ef") diff --git a/var/spack/repos/builtin/packages/r-msnbase/package.py b/var/spack/repos/builtin/packages/r-msnbase/package.py index ce4efe03da..434ef49d02 100644 --- a/var/spack/repos/builtin/packages/r-msnbase/package.py +++ b/var/spack/repos/builtin/packages/r-msnbase/package.py @@ -15,6 +15,7 @@ class RMsnbase(RPackage): bioc = "MSnbase" + version("2.26.0", commit="3e6268a86b93c474e37b21a9b8f564812202b2b6") version("2.24.0", commit="b96e0142c663c2cb01e92479816a503c46caa1a8") version("2.22.0", commit="4f6e5767eee91b2105781b494fcabcfed16eba2d") version("2.20.4", commit="c86ac8b341832f2b577f2153258c1abf064e6448") diff --git a/var/spack/repos/builtin/packages/r-multtest/package.py b/var/spack/repos/builtin/packages/r-multtest/package.py index 1eb412a15c..43b2d96bef 100644 --- a/var/spack/repos/builtin/packages/r-multtest/package.py +++ b/var/spack/repos/builtin/packages/r-multtest/package.py @@ -29,6 +29,7 @@ class RMulttest(RPackage): bioc = "multtest" + version("2.56.0", commit="619975704a271cdb74d97a75bee7e2df0028b4d3") version("2.54.0", commit="4e2c9e939dfd9984d8ff4bab0a95e1bd0457ec72") version("2.52.0", commit="00cfc9beb6d063c2b04fc83495a76824f8a33a64") version("2.50.0", commit="1de96649a942b115d3d554394514745e86eb3fd3") diff --git a/var/spack/repos/builtin/packages/r-mzid/package.py b/var/spack/repos/builtin/packages/r-mzid/package.py index 8ddabcb5c2..85e9db1e8b 100644 --- a/var/spack/repos/builtin/packages/r-mzid/package.py +++ b/var/spack/repos/builtin/packages/r-mzid/package.py @@ -17,6 +17,7 @@ class RMzid(RPackage): bioc = "mzID" + version("1.38.0", commit="d87d8b83d27876d3c12cd437499b87a5856f397d") version("1.36.0", commit="d6525edce3389fd4a05ff5fd42e9d611f00a545d") version("1.34.0", commit="bef64db159a0a4d241ba2ba271f70266c1522b2b") version("1.32.0", commit="d4146385b54f4d8361e23fc2c2aef79e952f4730") diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py index 420fb5595c..b083a4d14b 100644 --- a/var/spack/repos/builtin/packages/r-mzr/package.py +++ b/var/spack/repos/builtin/packages/r-mzr/package.py @@ -19,6 +19,7 @@ class RMzr(RPackage): bioc = "mzR" + version("2.34.0", commit="14ccc37ab3efd4b6003442a0268668258ccb7df9") version("2.32.0", commit="ef57d59205398558898a748ba9c8de66b0bddb81") version("2.30.0", commit="563ae755cfc7de1ac8862247779182b7b3aebdcc") version("2.28.0", commit="bee7d6fb5f99e1fab5444ae1ad27b0bc6e83be9e") @@ -39,5 +40,6 @@ class RMzr(RPackage): depends_on("r-ncdf4", type=("build", "run"), when="@2.16.2:") depends_on("r-rhdf5lib@1.1.4:", type=("build", "run"), when="@2.14.0:") depends_on("gmake", type="build") + depends_on("zlib") depends_on("r-zlibbioc", type=("build", "run"), when="@:2.28.0") diff --git a/var/spack/repos/builtin/packages/r-oligoclasses/package.py b/var/spack/repos/builtin/packages/r-oligoclasses/package.py index 9c29b73095..92c8e49a3b 100644 --- a/var/spack/repos/builtin/packages/r-oligoclasses/package.py +++ b/var/spack/repos/builtin/packages/r-oligoclasses/package.py @@ -15,6 +15,7 @@ class ROligoclasses(RPackage): bioc = "oligoClasses" + version("1.62.0", commit="2de6126d2a98f78d6dc80ffeef8bc76782a6dbdf") version("1.60.0", commit="cf9d76c2551ad061d8b882ff1dc0a5cadc64a8a7") version("1.58.0", commit="5544e937913bb0df54c66d738d279c38efeb30cd") version("1.56.0", commit="6e6c7b4ba54095d1d3c44c081839f57af9261cbf") diff --git a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py index 4c2be56074..ae6e5fca68 100644 --- a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py +++ b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py @@ -16,6 +16,11 @@ class ROrgHsEgDb(RPackage): url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz" version( + "3.17.0", + url="https://www.bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Hs.eg.db_3.17.0.tar.gz", + sha256="94714ea22b50d20523becbb665d9b27f2f147d3b1f77bc24ddcd3a245e201a0e", + ) + version( "3.16.0", url="https://www.bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Hs.eg.db_3.16.0.tar.gz", sha256="2d2e6fdefa0dbb61c86d4736e5a0d430745ae733e310f240b97b2cb3703a2c0a", @@ -52,3 +57,5 @@ class ROrgHsEgDb(RPackage): depends_on("r-annotationdbi@1.51.3:", type=("build", "run"), when="@3.12.0:") depends_on("r-annotationdbi@1.55.1:", type=("build", "run"), when="@3.14.0:") depends_on("r-annotationdbi@1.57.1:", type=("build", "run"), when="@3.15.0:") + depends_on("r-annotationdbi@1.59.1:", type=("build", "run"), when="@3.16.0:") + depends_on("r-annotationdbi@1.61.0:", type=("build", "run"), when="@3.17.0:") diff --git a/var/spack/repos/builtin/packages/r-organismdbi/package.py b/var/spack/repos/builtin/packages/r-organismdbi/package.py index 3df0fe6a1c..6231b229e6 100644 --- a/var/spack/repos/builtin/packages/r-organismdbi/package.py +++ b/var/spack/repos/builtin/packages/r-organismdbi/package.py @@ -16,6 +16,7 @@ class ROrganismdbi(RPackage): bioc = "OrganismDbi" + version("1.42.0", commit="29fcd5c47f8c479edac630a8e2a05ec5facb1328") version("1.40.0", commit="fac971dabef3b6d2473d2061bc1723e3de59c9d7") version("1.38.1", commit="fa8da4dd42ab15e1d21fd9f8286440596d50b1ec") version("1.38.0", commit="2ca01830a6ffcd0c0018d2bdbd3de8b4df716771") diff --git a/var/spack/repos/builtin/packages/r-pathview/package.py b/var/spack/repos/builtin/packages/r-pathview/package.py index 560c276b33..bf201d9d76 100644 --- a/var/spack/repos/builtin/packages/r-pathview/package.py +++ b/var/spack/repos/builtin/packages/r-pathview/package.py @@ -20,6 +20,7 @@ class RPathview(RPackage): bioc = "pathview" + version("1.40.0", commit="6546c6139f797bdff2fcc0645030a5de3588f2eb") version("1.38.0", commit="8229376ffd45278b74a6e4ccfb3abea8992667f7") version("1.36.1", commit="f2e86b106c1cd91aac703337f968b7593a61c68d") version("1.36.0", commit="4f6be090a4089b5259d8e796d62f9830e2d63943") diff --git a/var/spack/repos/builtin/packages/r-pcamethods/package.py b/var/spack/repos/builtin/packages/r-pcamethods/package.py index cf4d64a1c5..26fdbd0884 100644 --- a/var/spack/repos/builtin/packages/r-pcamethods/package.py +++ b/var/spack/repos/builtin/packages/r-pcamethods/package.py @@ -21,6 +21,7 @@ class RPcamethods(RPackage): bioc = "pcaMethods" + version("1.92.0", commit="ecbbc5b96b8fa79342611af8f798dd43c36d6699") version("1.90.0", commit="52474bc6d125122e89834328a1a780988349756f") version("1.88.0", commit="02fb58d6fe35579b86fb2ebd2eaf92e6b53444d2") version("1.86.0", commit="9419cfa18c18dfbd1e1194127fd120ab456c3657") diff --git a/var/spack/repos/builtin/packages/r-pfam-db/package.py b/var/spack/repos/builtin/packages/r-pfam-db/package.py index 3878f361ec..1a9705e88a 100644 --- a/var/spack/repos/builtin/packages/r-pfam-db/package.py +++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py @@ -16,6 +16,11 @@ class RPfamDb(RPackage): url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz" version( + "3.17.0", + url="https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PFAM.db_3.17.0.tar.gz", + sha256="8c4f8bebbf002df87ef7e4c4116be1676072e5c3ba0af1070d281a2ea6101712", + ) + version( "3.16.0", url="https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PFAM.db_3.16.0.tar.gz", sha256="8082aaa94eb962b2cf42cfaead8ff9e1bdbd12fdeae82a49d0f3b37bd50eb30c", @@ -52,3 +57,5 @@ class RPfamDb(RPackage): depends_on("r-annotationdbi@1.51.3:", type=("build", "run"), when="@3.12.0:") depends_on("r-annotationdbi@1.55.1:", type=("build", "run"), when="@3.14.0:") depends_on("r-annotationdbi@1.57.1:", type=("build", "run"), when="@3.15.0:") + depends_on("r-annotationdbi@1.59.1:", type=("build", "run"), when="@3.16.0:") + depends_on("r-annotationdbi@1.61.0:", type=("build", "run"), when="@3.17.0:") diff --git a/var/spack/repos/builtin/packages/r-phyloseq/package.py b/var/spack/repos/builtin/packages/r-phyloseq/package.py index 57c6407f20..5da02d1f58 100644 --- a/var/spack/repos/builtin/packages/r-phyloseq/package.py +++ b/var/spack/repos/builtin/packages/r-phyloseq/package.py @@ -14,6 +14,7 @@ class RPhyloseq(RPackage): bioc = "phyloseq" + version("1.44.0", commit="03b74f7d7aa866f5f9a84c7368da57b7a168967e") version("1.42.0", commit="de6be71fe9902bdfe7791163acb7b67d238424dc") version("1.40.0", commit="20bb27d5e6e0d4368978a15671b829990b1f4568") version("1.38.0", commit="1e2409a6ed3c23e308275098c2dc9fdba9d5e5f6") diff --git a/var/spack/repos/builtin/packages/r-preprocesscore/package.py b/var/spack/repos/builtin/packages/r-preprocesscore/package.py index 2522531663..c6c9f5ece4 100644 --- a/var/spack/repos/builtin/packages/r-preprocesscore/package.py +++ b/var/spack/repos/builtin/packages/r-preprocesscore/package.py @@ -13,6 +13,7 @@ class RPreprocesscore(RPackage): bioc = "preprocessCore" + version("1.62.0", commit="a6e3d339bc8204d15db4e750bd98f0313490b658") version("1.60.0", commit="7f62a7d54776a21ab6c2d3df4668382d531d1ee8") version("1.58.0", commit="2995e3e1a8f428a80aee200db42ee44743d893f6") version("1.56.0", commit="8f3272219507aa85e0c876fb434dc3b926c22c5d") diff --git a/var/spack/repos/builtin/packages/r-protgenerics/package.py b/var/spack/repos/builtin/packages/r-protgenerics/package.py index bf5a28d4fa..75271dd5c8 100644 --- a/var/spack/repos/builtin/packages/r-protgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-protgenerics/package.py @@ -13,6 +13,7 @@ class RProtgenerics(RPackage): bioc = "ProtGenerics" + version("1.32.0", commit="30c6458568c43fc7d769b0aef855d6e90b314eaa") version("1.30.0", commit="fcd566bf04034cf52db3338b5d6de7447443cf77") version("1.28.0", commit="cfcd0a9ebd642515764ba70c5c4e9c2a0f2f07ac") version("1.26.0", commit="2033289ab928034b86c321e56c37e502e557c7a1") diff --git a/var/spack/repos/builtin/packages/r-quantro/package.py b/var/spack/repos/builtin/packages/r-quantro/package.py index b3cea7aa05..1811b7b9eb 100644 --- a/var/spack/repos/builtin/packages/r-quantro/package.py +++ b/var/spack/repos/builtin/packages/r-quantro/package.py @@ -18,6 +18,7 @@ class RQuantro(RPackage): bioc = "quantro" + version("1.34.0", commit="c769d21ce5ccb6f33c35e6e1dbb901ea8afad4b1") version("1.32.0", commit="0c70b787866d915abb720f2ab326a83eb1e775b7") version("1.30.0", commit="e756c439cdc5a6fb4d7879aff56a8368475513b5") version("1.28.0", commit="109e7452a349f273e10d2ffb79d5624260b67dd5") diff --git a/var/spack/repos/builtin/packages/r-qvalue/package.py b/var/spack/repos/builtin/packages/r-qvalue/package.py index a82e98c4be..defcc31eb6 100644 --- a/var/spack/repos/builtin/packages/r-qvalue/package.py +++ b/var/spack/repos/builtin/packages/r-qvalue/package.py @@ -23,6 +23,7 @@ class RQvalue(RPackage): bioc = "qvalue" + version("2.32.0", commit="a6272dc68f9d91de63e04fae28476e4ec016ee89") version("2.30.0", commit="e8a4c22d035f860ee730aa7c5a4dbc7460afcedc") version("2.28.0", commit="aaa62d5ab5a960e0a626928abaf5b3a5c5f73374") version("2.26.0", commit="6d7410d4b8673bcf9065e054670c1fbcb917a27e") diff --git a/var/spack/repos/builtin/packages/r-rbgl/package.py b/var/spack/repos/builtin/packages/r-rbgl/package.py index d79488c5e1..8db4889873 100644 --- a/var/spack/repos/builtin/packages/r-rbgl/package.py +++ b/var/spack/repos/builtin/packages/r-rbgl/package.py @@ -14,6 +14,7 @@ class RRbgl(RPackage): bioc = "RBGL" + version("1.76.0", commit="18b7cc5f002435aa83e8b693e7bf269fc0b096a5") version("1.74.0", commit="e698db897b719992a8c0747138735c0e7d9dfb21") version("1.72.0", commit="a86f3102f2795e1ffb530bb061247e3a42ca22f7") version("1.70.0", commit="9cfd5fdad4f1f438ff748317f32e822aede8921b") diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py index 558a0b1dfa..e288876151 100644 --- a/var/spack/repos/builtin/packages/r-reportingtools/package.py +++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py @@ -23,6 +23,7 @@ class RReportingtools(RPackage): bioc = "ReportingTools" + version("2.40.0", commit="808af36aa9756be8c907a8669726c90dcd02c73c") version("2.38.0", commit="5c4971eebbaf3577ef20b74bf36c2db4e91561cc") version("2.36.0", commit="34122d4bde5ce43415f63f2e39e3a088c55282cc") version("2.34.0", commit="fb5aef0b6e1c6166d0f025d9e6ca60e54c68dbaf") diff --git a/var/spack/repos/builtin/packages/r-rgraphviz/package.py b/var/spack/repos/builtin/packages/r-rgraphviz/package.py index e77cade48a..85d98ab601 100644 --- a/var/spack/repos/builtin/packages/r-rgraphviz/package.py +++ b/var/spack/repos/builtin/packages/r-rgraphviz/package.py @@ -14,6 +14,7 @@ class RRgraphviz(RPackage): bioc = "Rgraphviz" + version("2.44.0", commit="1a1540d66afa0b5a693eee2acac8ad96cfc0a2e6") version("2.42.0", commit="f6877441ab256876ef6a62c2e6faf980c2190b20") version("2.40.0", commit="d864c9741c9177bc627cca1198673be2b1bfbc3e") version("2.38.0", commit="004de09a5b171211aff6cbaa1969ab8e3a5d6c61") diff --git a/var/spack/repos/builtin/packages/r-rhdf5/package.py b/var/spack/repos/builtin/packages/r-rhdf5/package.py index dc3277e07a..1acd747396 100644 --- a/var/spack/repos/builtin/packages/r-rhdf5/package.py +++ b/var/spack/repos/builtin/packages/r-rhdf5/package.py @@ -19,6 +19,7 @@ class RRhdf5(RPackage): bioc = "rhdf5" + version("2.44.0", commit="0f6e367ca9e97c37c683cd0f97c06732a67146f0") version("2.42.0", commit="fa26027d57b5b6d1c297446d9bbed74d5710c5d2") version("2.40.0", commit="fb6c15a3199f3ffd746fb9a381d574d17fef45a2") version("2.38.0", commit="f6fdfa807f5cd5a4d11d4aa6ebfaa81c118b4c3f") diff --git a/var/spack/repos/builtin/packages/r-rhdf5filters/package.py b/var/spack/repos/builtin/packages/r-rhdf5filters/package.py index c7db011469..b13de3ad5e 100644 --- a/var/spack/repos/builtin/packages/r-rhdf5filters/package.py +++ b/var/spack/repos/builtin/packages/r-rhdf5filters/package.py @@ -13,6 +13,7 @@ class RRhdf5filters(RPackage): bioc = "rhdf5filters" + version("1.12.0", commit="4deabdef71c0349c4eaf7e5604cb7f389809f006") version("1.10.0", commit="6131538e2c5896dca0af33882bc2da961d79e49a") version("1.8.0", commit="b0b588b71a5595b30f4e698a50b84310dc19745d") version("1.6.0", commit="5f7f3a5b7dabd6e7d0c50cda70290e2472ff4f53") @@ -21,6 +22,7 @@ class RRhdf5filters(RPackage): depends_on("r-rhdf5lib", type=("build", "run")) depends_on("gmake", type="build") depends_on("zlib") + depends_on("zstd") def configure_args(self): args = [] diff --git a/var/spack/repos/builtin/packages/r-rhdf5lib/package.py b/var/spack/repos/builtin/packages/r-rhdf5lib/package.py index 014cf9ff60..8005ec16f9 100644 --- a/var/spack/repos/builtin/packages/r-rhdf5lib/package.py +++ b/var/spack/repos/builtin/packages/r-rhdf5lib/package.py @@ -13,6 +13,7 @@ class RRhdf5lib(RPackage): bioc = "Rhdf5lib" + version("1.22.0", commit="2bf06b364e8d478549b07a298eaf60177a050dc9") version("1.20.0", commit="760679995f17996a9de328cf7a8bcaa6c87286d4") version("1.18.2", commit="d104bbfdb91ac5ec7db3c453f23e4d1d6feb671f") version("1.16.0", commit="534c49705dbdb27ae0c564acff2c72df2b27b3f1") @@ -24,5 +25,6 @@ class RRhdf5lib(RPackage): depends_on("r@3.3.0:", type="build", when="@1.12.1:") depends_on("r@4.0.0:", type="build", when="@1.16.0:") + depends_on("r@4.2.0:", type=("build", "run"), when="@1.22.0:") depends_on("gmake", type="build") depends_on("zlib") diff --git a/var/spack/repos/builtin/packages/r-roc/package.py b/var/spack/repos/builtin/packages/r-roc/package.py index 38903beab1..3343237f82 100644 --- a/var/spack/repos/builtin/packages/r-roc/package.py +++ b/var/spack/repos/builtin/packages/r-roc/package.py @@ -13,6 +13,7 @@ class RRoc(RPackage): bioc = "ROC" + version("1.76.0", commit="905ee01be734ed0a5674a4ce2cdc0cdea9d01cb9") version("1.74.0", commit="982ad4d3606b19b8460e8a8af7cfe7c30b83f9b9") version("1.72.0", commit="c5d083b01314280dd43eb4cddd8a7fde8b5dce18") version("1.70.0", commit="44fd639958b9b1be4f8f731dc2be9dd91b2fa632") diff --git a/var/spack/repos/builtin/packages/r-rots/package.py b/var/spack/repos/builtin/packages/r-rots/package.py index fd686454c5..4556d3a1c1 100644 --- a/var/spack/repos/builtin/packages/r-rots/package.py +++ b/var/spack/repos/builtin/packages/r-rots/package.py @@ -14,6 +14,7 @@ class RRots(RPackage): bioc = "ROTS" + version("1.28.0", commit="032cb97ed6fe303758856c669a4f63fb9e43d124") version("1.26.0", commit="8bb45fe78779583ae4d30cf0dc3af0d8de405fdf") version("1.24.0", commit="372e4623b39f585d4196d21164436c1ba013173f") version("1.22.0", commit="a53ec77c40ed3b3c84e91d794c1602dd509cad83") diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py index 134d4362b5..4e6ae59f91 100644 --- a/var/spack/repos/builtin/packages/r-rsamtools/package.py +++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py @@ -17,6 +17,7 @@ class RRsamtools(RPackage): bioc = "Rsamtools" + version("2.16.0", commit="3eb6d03acecb8d640ec5201cacdc322e9e0c2445") version("2.14.0", commit="8302eb7fa1c40384f1af5855222d94f2efbdcad1") version("2.12.0", commit="d6a65dd57c5a17e4c441a27492e92072f69b175e") version("2.10.0", commit="b19738e85a467f9032fc7903be3ba10e655e7061") diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py index 0426ba67a2..81412dc8e2 100644 --- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py +++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py @@ -18,6 +18,7 @@ class RRtracklayer(RPackage): bioc = "rtracklayer" + version("1.60.0", commit="de35bc03116fc7ad30f0e425b41715c3cb2e783b") version("1.58.0", commit="54a74972c08775fdf1e83e6e22cd0b8fad677fc1") version("1.56.1", commit="4c6d2201fcb102d471bd88f4f51cc34317669955") version("1.56.0", commit="1d70f7dc464ad87a1fde61588cd9ae0cb86b6e86") diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py index 66476dbdcb..bb8848ff29 100644 --- a/var/spack/repos/builtin/packages/r-s4vectors/package.py +++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py @@ -20,6 +20,7 @@ class RS4vectors(RPackage): bioc = "S4Vectors" + version("0.38.0", commit="e80c24e1481033741147a0677fb42ce455e7da74") version("0.36.0", commit="af58701957ffdd9209031dd6a8dee3acdc58e999") version("0.34.0", commit="f590de3ec4d896a63351d0c1925d3856c0bd5292") version("0.32.3", commit="ad90e78fd3a4059cfcf2846498fb0748b4394e1a") @@ -34,7 +35,7 @@ class RS4vectors(RPackage): depends_on("r@3.3.0:", type=("build", "run")) depends_on("r@4.0.0:", type=("build", "run"), when="@0.28.1:") depends_on("r-biocgenerics@0.21.1:", type=("build", "run")) - depends_on("r-biocgenerics@0.23.3:", type=("build", "run"), when="@0.16.0:0.22.1") + depends_on("r-biocgenerics@0.23.3:", type=("build", "run"), when="@0.16.0:") depends_on("r-biocgenerics@0.31.1:", type=("build", "run"), when="@0.26.1:") depends_on("r-biocgenerics@0.36.0:", type=("build", "run"), when="@0.28.1:") depends_on("r-biocgenerics@0.37.0:", type=("build", "run"), when="@0.32.3:") diff --git a/var/spack/repos/builtin/packages/r-scaledmatrix/package.py b/var/spack/repos/builtin/packages/r-scaledmatrix/package.py index 2b5ca585e5..4f8349781e 100644 --- a/var/spack/repos/builtin/packages/r-scaledmatrix/package.py +++ b/var/spack/repos/builtin/packages/r-scaledmatrix/package.py @@ -16,6 +16,7 @@ class RScaledmatrix(RPackage): bioc = "ScaledMatrix" + version("1.8.0", commit="122f2c43d496bd420f0aff7cd96728a11bd7fa07") version("1.6.0", commit="45a29d3662e2766f973b281ed86ce2654be84b70") version("1.4.1", commit="15e2efcb6b11e26c31ef2d44968355f71cc1f4fc") version("1.4.0", commit="32e6e918bc7bb64bbf75613d353ca268c7d04292") diff --git a/var/spack/repos/builtin/packages/r-scater/package.py b/var/spack/repos/builtin/packages/r-scater/package.py index 133777d7e1..c8778d192f 100644 --- a/var/spack/repos/builtin/packages/r-scater/package.py +++ b/var/spack/repos/builtin/packages/r-scater/package.py @@ -15,6 +15,7 @@ class RScater(RPackage): bioc = "scater" + version("1.28.0", commit="e654498c3fa9f769b794f840f230720333bd9555") version("1.26.0", commit="a548ddc8424e185bfb06f48bfc174071e69fc687") version("1.24.0", commit="013f0935a1a225139986ca5a3f0e9d08a1558153") version("1.22.0", commit="ea2c95c53adb8c6fab558c1cb869e2eab36aa9f8") @@ -32,14 +33,13 @@ class RScater(RPackage): depends_on("r-singlecellexperiment", type=("build", "run"), when="@1.6.3:") depends_on("r-scuttle", type=("build", "run"), when="@1.18.3:") depends_on("r-ggplot2", type=("build", "run")) - depends_on("r-gridextra", type=("build", "run"), when="@1.18.3:") depends_on("r-matrix", type=("build", "run")) depends_on("r-biocgenerics", type=("build", "run")) depends_on("r-s4vectors", type=("build", "run"), when="@1.6.3:") depends_on("r-summarizedexperiment", type=("build", "run"), when="@1.6.3:") depends_on("r-delayedarray", type=("build", "run"), when="@1.8.4:") depends_on("r-delayedmatrixstats", type=("build", "run"), when="@1.8.4:") - depends_on("r-beachmat", type=("build", "run"), when="@1.6.3:1.12.2,1.22.0:") + depends_on("r-beachmat", type=("build", "run"), when="@1.6.3:") depends_on("r-biocneighbors", type=("build", "run"), when="@1.12.2:") depends_on("r-biocsingular", type=("build", "run"), when="@1.12.2:") depends_on("r-biocparallel", type=("build", "run"), when="@1.10.1:") @@ -53,6 +53,7 @@ class RScater(RPackage): depends_on("r-pheatmap", type=("build", "run"), when="@1.26.0:") depends_on("r-uwot", type=("build", "run"), when="@1.26.0:") depends_on("r-ggrepel", type=("build", "run"), when="@1.22.0:") + depends_on("r-densvis", type=("build", "run"), when="@1.28.0:") depends_on("r-biobase", type=("build", "run"), when="@1.4.0:1.8.4") depends_on("r-biomart", type=("build", "run"), when="@1.4.0:1.6.3") @@ -71,3 +72,4 @@ class RScater(RPackage): depends_on("r-rcpp", type=("build", "run"), when="@1.6.3:1.12.2") depends_on("r-rcpp@0.12.14:", type=("build", "run"), when="@1.8.4:1.12.2") depends_on("r-rhdf5lib", type=("build", "run"), when="@1.6.3:1.10.1") + depends_on("r-gridextra", type=("build", "run"), when="@1.18.3:1.26.0") diff --git a/var/spack/repos/builtin/packages/r-scdblfinder/package.py b/var/spack/repos/builtin/packages/r-scdblfinder/package.py index 57e437977b..8a6ef79ba1 100644 --- a/var/spack/repos/builtin/packages/r-scdblfinder/package.py +++ b/var/spack/repos/builtin/packages/r-scdblfinder/package.py @@ -16,6 +16,7 @@ class RScdblfinder(RPackage): bioc = "scDblFinder" + version("1.14.0", commit="6191ed09b87d7c54809a721d1d6c50c0027cf0a9") version("1.12.0", commit="65a88be3a4ca98ccad0a1829a19652df1a3c94fd") version("1.10.0", commit="03512cad0cdfe3cddbef66ec5e330b53661eccfc") diff --git a/var/spack/repos/builtin/packages/r-scran/package.py b/var/spack/repos/builtin/packages/r-scran/package.py index 4cf1873080..7ed0479b18 100644 --- a/var/spack/repos/builtin/packages/r-scran/package.py +++ b/var/spack/repos/builtin/packages/r-scran/package.py @@ -17,6 +17,7 @@ class RScran(RPackage): bioc = "scran" + version("1.28.0", commit="2e542b929b231fb5bb8c40af0f6ccea97f79234d") version("1.26.0", commit="df66576d6958a088c38bd45e1cad9c16cbb52991") version("1.24.1", commit="1a83eb7c948b1dc49253080c23b26cefb3a0f3b9") version("1.24.0", commit="c3f9e169c4538ce827d4f14a4141571c2366cd31") diff --git a/var/spack/repos/builtin/packages/r-scuttle/package.py b/var/spack/repos/builtin/packages/r-scuttle/package.py index 2f038efecf..9601d33c5e 100644 --- a/var/spack/repos/builtin/packages/r-scuttle/package.py +++ b/var/spack/repos/builtin/packages/r-scuttle/package.py @@ -16,6 +16,7 @@ class RScuttle(RPackage): bioc = "scuttle" + version("1.10.0", commit="02e864cb80414f71bb312cdf6d68e0036326e10b") version("1.8.0", commit="dabf6b95e478d599557ebbed03edd44031fd6b78") version("1.6.3", commit="df23680da9fa4d685df77e4561467f491c850b50") version("1.6.2", commit="afdfc555151d84cc332757b4ec0b97cb7f39d2d5") diff --git a/var/spack/repos/builtin/packages/r-seqlogo/package.py b/var/spack/repos/builtin/packages/r-seqlogo/package.py index b84114f7d5..c854dd9ae9 100644 --- a/var/spack/repos/builtin/packages/r-seqlogo/package.py +++ b/var/spack/repos/builtin/packages/r-seqlogo/package.py @@ -15,6 +15,7 @@ class RSeqlogo(RPackage): bioc = "seqLogo" + version("1.66.0", commit="6214c1733fe25da86071afba4210068816e4d74f") version("1.64.0", commit="75ff6c0689fce541f054d33750acb6224d14ed4e") version("1.62.0", commit="f2d0b53b1411ea98299201a8125a85f4cbf7c9cd") version("1.60.0", commit="4115c8e1d01accb8c8cc1cf96f23359466827e16") diff --git a/var/spack/repos/builtin/packages/r-shortread/package.py b/var/spack/repos/builtin/packages/r-shortread/package.py index 7cdd5a0b58..15cee95dae 100644 --- a/var/spack/repos/builtin/packages/r-shortread/package.py +++ b/var/spack/repos/builtin/packages/r-shortread/package.py @@ -18,6 +18,7 @@ class RShortread(RPackage): bioc = "ShortRead" + version("1.58.0", commit="433d18266b141ddcc9dc590f5244163a04efebe3") version("1.56.0", commit="df25d0872d52aac3610998abda0d7bfd37298726") version("1.54.0", commit="a1082a335120860d019aa0065a975d41890351f7") version("1.52.0", commit="4d7304d7b5a0ca5c904c0b919d6c95599db72a39") @@ -52,3 +53,4 @@ class RShortread(RPackage): depends_on("r-latticeextra", type=("build", "run")) depends_on("r-xvector", type=("build", "run")) depends_on("r-rhtslib", type=("build", "run"), when="@1.48.0:") + depends_on("zlib") diff --git a/var/spack/repos/builtin/packages/r-siggenes/package.py b/var/spack/repos/builtin/packages/r-siggenes/package.py index bc1d354c52..d857b2c7c4 100644 --- a/var/spack/repos/builtin/packages/r-siggenes/package.py +++ b/var/spack/repos/builtin/packages/r-siggenes/package.py @@ -16,6 +16,7 @@ class RSiggenes(RPackage): bioc = "siggenes" + version("1.74.0", commit="02e0e825eae0e1fa8ffda0c826ddc176cb67cb0a") version("1.72.0", commit="4f93d1a28087c941b275e6c6bae9e42d721cf422") version("1.70.0", commit="c263daa14cf87c61b41e3a9e88573ba339c66179") version("1.68.0", commit="a29bf02b19cc9003c8401608831232b7c2af26e7") diff --git a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py index f108194ff4..b41e444e8a 100644 --- a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py +++ b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py @@ -16,6 +16,7 @@ class RSinglecellexperiment(RPackage): bioc = "SingleCellExperiment" + version("1.22.0", commit="d477e8ef442dec60576e08bb660081b8bccc978c") version("1.20.0", commit="467f02c0346e3ca5ec8825a6faa80a90d20fcd29") version("1.18.1", commit="db7768a7cb5eca724bcf7e4cea3234992ac714a1") version("1.18.0", commit="3a72dcd97e628055b2d02294eaecca9a41aba604") diff --git a/var/spack/repos/builtin/packages/r-snprelate/package.py b/var/spack/repos/builtin/packages/r-snprelate/package.py index 6fb4682efd..b61a9bcf2e 100644 --- a/var/spack/repos/builtin/packages/r-snprelate/package.py +++ b/var/spack/repos/builtin/packages/r-snprelate/package.py @@ -29,6 +29,7 @@ class RSnprelate(RPackage): bioc = "SNPRelate" + version("1.34.0", commit="27a7c9658b974f9887f48a4a3ed1a7621b141488") version("1.32.0", commit="2e8cc807baa74fca5137148b672f3945c36689b2") version("1.30.1", commit="baef8a71d3908287a2307768348c02db0720d125") version("1.28.0", commit="8fcd837f4627a3bb77cb8d992b2baedd0589d123") diff --git a/var/spack/repos/builtin/packages/r-snpstats/package.py b/var/spack/repos/builtin/packages/r-snpstats/package.py index c62b8ec4b0..cf6460c2f9 100644 --- a/var/spack/repos/builtin/packages/r-snpstats/package.py +++ b/var/spack/repos/builtin/packages/r-snpstats/package.py @@ -15,6 +15,7 @@ class RSnpstats(RPackage): bioc = "snpStats" + version("1.50.0", commit="b6d42f93f2ce510cc10a1668809218f317c23d2a") version("1.48.0", commit="7d4cec7275b9360d98cb59d15c4140bed3e6a74c") version("1.46.0", commit="1e70784b113eaca231bc5f91fc8ae5aadb151ddb") version("1.44.0", commit="72392dab4e75de2da459b1e95f1d48947811597b") diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py index 9ae52a14af..ebc211ad61 100644 --- a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py +++ b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py @@ -16,6 +16,7 @@ class RSomaticsignatures(RPackage): bioc = "SomaticSignatures" + version("2.36.0", commit="26ce72c1fc771f711796eccee0a24c1070d33066") version("2.34.0", commit="249b1ef7cef3c94cfb96cc8aa2a16e00c2bd5d1f") version("2.32.0", commit="444d37661d147618f6830fd5de01a83ddf2a694d") version("2.30.0", commit="03f7ad707f6530fa7f62093f808884b6e83b0526") diff --git a/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py b/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py index c467dc901d..7bb2e38b0c 100644 --- a/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py @@ -17,6 +17,7 @@ class RSparsematrixstats(RPackage): bioc = "sparseMatrixStats" + version("1.12.0", commit="054bf939cd7220deaf8e768ff7029d0d38483c91") version("1.10.0", commit="75d85ba2c9c4c36887fef1a007883167aa85bd94") version("1.8.0", commit="4f1e2213e5b0d6b3d817c2c9129b7566288916f6") version("1.6.0", commit="78627a842790af42b6634893087b2bb1f4ac0392") diff --git a/var/spack/repos/builtin/packages/r-spem/package.py b/var/spack/repos/builtin/packages/r-spem/package.py index c2ccd2bfa7..5ddb1b986a 100644 --- a/var/spack/repos/builtin/packages/r-spem/package.py +++ b/var/spack/repos/builtin/packages/r-spem/package.py @@ -14,6 +14,7 @@ class RSpem(RPackage): bioc = "SPEM" + version("1.40.0", commit="2eb948950c01ced90ebf27558817e2849da81a32") version("1.38.0", commit="43ff6b0a84e7aef947d1a793583d2e9a0119c99d") version("1.36.0", commit="75832966ba3e2bae6b56aa138764f7a98c7ba9b1") version("1.34.0", commit="53fd404638a04ec8e2e826e55c3f2d91d8b28e3d") diff --git a/var/spack/repos/builtin/packages/r-sseq/package.py b/var/spack/repos/builtin/packages/r-sseq/package.py index 429b18d212..db132609cb 100644 --- a/var/spack/repos/builtin/packages/r-sseq/package.py +++ b/var/spack/repos/builtin/packages/r-sseq/package.py @@ -23,6 +23,7 @@ class RSseq(RPackage): bioc = "sSeq" + version("1.38.0", commit="09242bb94d72ff13e3f18c3588934149f27ac374") version("1.36.0", commit="0345ac579c4bdcc9c42c24831ad86fc6225c5cb9") version("1.34.0", commit="882bea1664f55d85550a7185cbd4a0108c35df36") version("1.32.0", commit="c0d3c305755d888f64d334a4ab5fa54c623054cf") diff --git a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py index 06e52ced93..bb074df20f 100644 --- a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py +++ b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py @@ -16,6 +16,7 @@ class RSummarizedexperiment(RPackage): bioc = "SummarizedExperiment" + version("1.30.0", commit="a2843fbced9fc345c9061b2e52244f3263326e2e") version("1.28.0", commit="ba55dac12224f0aafe8f52f1397611b5efb41626") version("1.26.1", commit="c8cbd3b4f0fa1d686c4d7ce5b8614a24c74b2074") version("1.24.0", commit="d37f19383d03c107a8a41c0df2326e28efe46b28") diff --git a/var/spack/repos/builtin/packages/r-sva/package.py b/var/spack/repos/builtin/packages/r-sva/package.py index 305fb2f75c..10c6d5d225 100644 --- a/var/spack/repos/builtin/packages/r-sva/package.py +++ b/var/spack/repos/builtin/packages/r-sva/package.py @@ -30,6 +30,7 @@ class RSva(RPackage): bioc = "sva" + version("3.48.0", commit="f1657af586d402598df71ade10dfeb28aa28b5c4") version("3.46.0", commit="4aac49cf806f05bb98e08a6be539adebbecbfdb2") version("3.44.0", commit="45ab2c1d6643bcda4de2d95a81b9b28d33a1a8a1") version("3.42.0", commit="54c843cc46437be233ecb43b6aa868e968d71138") diff --git a/var/spack/repos/builtin/packages/r-tfbstools/package.py b/var/spack/repos/builtin/packages/r-tfbstools/package.py index b235894651..3c808e10bf 100644 --- a/var/spack/repos/builtin/packages/r-tfbstools/package.py +++ b/var/spack/repos/builtin/packages/r-tfbstools/package.py @@ -18,6 +18,7 @@ class RTfbstools(RPackage): bioc = "TFBSTools" + version("1.38.0", commit="2ce17166b6f73b5093acec2a3dde33b6bcfa56bc") version("1.36.0", commit="3358c89227a4d2e237ee5f8c532f468460a16ee2") version("1.34.0", commit="7f8d0cb58a527a5d7ba94a773279f13aedca6ec7") version("1.32.0", commit="235505626b910de29156a07e1f990daa3b5d57d9") diff --git a/var/spack/repos/builtin/packages/r-tmixclust/package.py b/var/spack/repos/builtin/packages/r-tmixclust/package.py index 04e048166a..269f12fadd 100644 --- a/var/spack/repos/builtin/packages/r-tmixclust/package.py +++ b/var/spack/repos/builtin/packages/r-tmixclust/package.py @@ -18,6 +18,7 @@ class RTmixclust(RPackage): bioc = "TMixClust" + version("1.22.0", commit="bb750ce4682542ba8e2cb5bfbdb5eff839ffacd4") version("1.20.0", commit="df27f53d088b02cf596504b44909f2762900ab49") version("1.18.0", commit="71f80a7ace481f46471f36c91223effb85e17186") version("1.16.0", commit="e525cfd9c729a73a1964c243e5c34c37343f7bfa") diff --git a/var/spack/repos/builtin/packages/r-topgo/package.py b/var/spack/repos/builtin/packages/r-topgo/package.py index 33a6c331f7..cc79a5842c 100644 --- a/var/spack/repos/builtin/packages/r-topgo/package.py +++ b/var/spack/repos/builtin/packages/r-topgo/package.py @@ -16,6 +16,7 @@ class RTopgo(RPackage): bioc = "topGO" + version("2.52.0", commit="214db210d1757231eb9b2889288dc385553525cd") version("2.50.0", commit="befbff4e67c1b01e23f111d147274641a8b7b0f5") version("2.48.0", commit="a47f0079319c7d74db4aeda6399e06f12a34b585") version("2.46.0", commit="2bfa9dff41fff261aa6188f8368aebd6e8250b18") diff --git a/var/spack/repos/builtin/packages/r-treeio/package.py b/var/spack/repos/builtin/packages/r-treeio/package.py index 0ef9e71cb8..ef065df5de 100644 --- a/var/spack/repos/builtin/packages/r-treeio/package.py +++ b/var/spack/repos/builtin/packages/r-treeio/package.py @@ -18,6 +18,7 @@ class RTreeio(RPackage): bioc = "treeio" + version("1.24.0", commit="81425559d71ab87ee683c6a8833f0f165632e416") version("1.22.0", commit="eb24a854806a671e7b37ef36dafc60b4eb9ddaa1") version("1.20.2", commit="ed457d6fd85a50e0993c8c9acbd9b701be01a348") version("1.20.0", commit="5f7c3704fc8202c52451d092148fdcfe683f026a") @@ -32,3 +33,4 @@ class RTreeio(RPackage): depends_on("r-tibble", type=("build", "run")) depends_on("r-tidytree@0.3.0:", type=("build", "run")) depends_on("r-tidytree@0.3.9:", type=("build", "run"), when="@1.20.0:") + depends_on("r-cli", type=("build", "run"), when="@1.24.0:") diff --git a/var/spack/repos/builtin/packages/r-tximport/package.py b/var/spack/repos/builtin/packages/r-tximport/package.py index d280537040..d4e585e1ca 100644 --- a/var/spack/repos/builtin/packages/r-tximport/package.py +++ b/var/spack/repos/builtin/packages/r-tximport/package.py @@ -19,6 +19,7 @@ class RTximport(RPackage): bioc = "tximport" + version("1.28.0", commit="9acd3640c034655ffba12044ed2982fab57d4fbb") version("1.26.0", commit="5ae7139edf9d3445210ea014026813fd030212a8") version("1.24.0", commit="58524f39bdd55299cfe80a726f99b714b724be20") version("1.22.0", commit="335213baee3492fbf6baaa8b4e067ac0ef384684") diff --git a/var/spack/repos/builtin/packages/r-tximportdata/package.py b/var/spack/repos/builtin/packages/r-tximportdata/package.py index 6dd7d69678..0dd8c26137 100644 --- a/var/spack/repos/builtin/packages/r-tximportdata/package.py +++ b/var/spack/repos/builtin/packages/r-tximportdata/package.py @@ -18,6 +18,7 @@ class RTximportdata(RPackage): bioc = "tximportData" + version("1.28.0", commit="7de494ba12168e2766baffdd177d9cecc0642820") version("1.26.0", commit="8f6ef3e3ae54e6eb99fe915364f5174c4f50a986") version("1.24.0", commit="646f366fb25be359c95dc97c9369961c8d5ed942") version("1.22.0", commit="c576b18e43985baf8beab327cbc54afe8324659c") diff --git a/var/spack/repos/builtin/packages/r-variantannotation/package.py b/var/spack/repos/builtin/packages/r-variantannotation/package.py index e87d89c75d..5bb805c340 100644 --- a/var/spack/repos/builtin/packages/r-variantannotation/package.py +++ b/var/spack/repos/builtin/packages/r-variantannotation/package.py @@ -14,6 +14,7 @@ class RVariantannotation(RPackage): bioc = "VariantAnnotation" + version("1.46.0", commit="80d43e024bead5afd48cb86910ba4670d8d37424") version("1.44.0", commit="2e7e0a3b7c1918c0d64170dc7c173a636d3764f4") version("1.42.1", commit="d1121696c76c189d6b4df9914806bf585a495845") version("1.40.0", commit="50ead7cb60cedf3c053853fab92d9f104f9f85bd") diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py index ca97f09978..30bdedbbc7 100644 --- a/var/spack/repos/builtin/packages/r-vsn/package.py +++ b/var/spack/repos/builtin/packages/r-vsn/package.py @@ -24,6 +24,7 @@ class RVsn(RPackage): bioc = "vsn" + version("3.68.0", commit="b8c9cef9730a00a810e8ec08e472b26d0bff5357") version("3.66.0", commit="ddccd6c74ebea426056794c2bfad2dfd02631092") version("3.64.0", commit="1f09f20ee7f81100fb0bf66288c4caf0049b5508") version("3.62.0", commit="6ae7f4e07ec1a5a9482cab892d98175983bfcd50") diff --git a/var/spack/repos/builtin/packages/r-watermelon/package.py b/var/spack/repos/builtin/packages/r-watermelon/package.py index db2885cc04..4663ad90bb 100644 --- a/var/spack/repos/builtin/packages/r-watermelon/package.py +++ b/var/spack/repos/builtin/packages/r-watermelon/package.py @@ -14,6 +14,7 @@ class RWatermelon(RPackage): bioc = "wateRmelon" + version("2.6.0", commit="a46541ffcc08efebf08ea29cb214a45f51f5cb72") version("2.4.0", commit="31c15255511940b8b83d039c42ec89e43ceb0885") version("2.2.0", commit="6ec49efe98aef31d0789b31ab048eb46edec762c") version("2.0.0", commit="f6a331bdf50e0e5c94009fb67be873d996348ade") diff --git a/var/spack/repos/builtin/packages/r-xde/package.py b/var/spack/repos/builtin/packages/r-xde/package.py index 92b30f3891..97d8af821d 100644 --- a/var/spack/repos/builtin/packages/r-xde/package.py +++ b/var/spack/repos/builtin/packages/r-xde/package.py @@ -15,6 +15,7 @@ class RXde(RPackage): bioc = "XDE" + version("2.46.0", commit="f94324fba1ad6dca129d86e61abc219f766321e8") version("2.44.0", commit="a6ddedb91afe381f223e52ae49c6704f8f046916") version("2.42.0", commit="298e83eff7fc5f72a2bb76b559c5115c6cd3ee84") version("2.40.0", commit="bfc3c54787aec97b70bef7b99a6adc75d2cf5ed2") diff --git a/var/spack/repos/builtin/packages/r-xmapbridge/package.py b/var/spack/repos/builtin/packages/r-xmapbridge/package.py index 489aa9e549..584612f2d8 100644 --- a/var/spack/repos/builtin/packages/r-xmapbridge/package.py +++ b/var/spack/repos/builtin/packages/r-xmapbridge/package.py @@ -14,6 +14,7 @@ class RXmapbridge(RPackage): bioc = "xmapbridge" + version("1.58.0", commit="905077b7935c4678376f3f2afd9881ff0c45ad00") version("1.56.0", commit="fdf2cafca8ad348813d3381fee57623fab53f0ab") version("1.54.0", commit="a316e2399894191646c229378fa138b7461c75ab") version("1.52.0", commit="fe32fcd2a83432c721eb948cb3af73dd187065f6") diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py index a5e04fd66d..7f4d0cc7a6 100644 --- a/var/spack/repos/builtin/packages/r-xvector/package.py +++ b/var/spack/repos/builtin/packages/r-xvector/package.py @@ -15,6 +15,7 @@ class RXvector(RPackage): bioc = "XVector" + version("0.40.0", commit="875b4b4469e125737bee42362e7a3c75edd642f1") version("0.38.0", commit="8cad08446091dcc7cd759e880c0f3e47228278dd") version("0.36.0", commit="ff6f818ff4357eb9bf00654de9e0f508a5285408") version("0.34.0", commit="06adb25ac51c707b90fb8e0637fa06df237a863c") diff --git a/var/spack/repos/builtin/packages/r-yapsa/package.py b/var/spack/repos/builtin/packages/r-yapsa/package.py index 2b7e73dced..8c90980a6c 100644 --- a/var/spack/repos/builtin/packages/r-yapsa/package.py +++ b/var/spack/repos/builtin/packages/r-yapsa/package.py @@ -18,6 +18,7 @@ class RYapsa(RPackage): bioc = "YAPSA" + version("1.26.0", commit="eab6bbd7a44e1368c7827e4717439de445303868") version("1.24.0", commit="68d1c9c71af3ade4a44237ec2d3003688378f898") version("1.22.0", commit="55c2886874f154c737264ce6843089bf3565fa57") version("1.20.1", commit="6c3f437911859df6f6e4a9af5571c3a5aafbffb2") diff --git a/var/spack/repos/builtin/packages/r-yarn/package.py b/var/spack/repos/builtin/packages/r-yarn/package.py index 92af93d49d..3f2901fef7 100644 --- a/var/spack/repos/builtin/packages/r-yarn/package.py +++ b/var/spack/repos/builtin/packages/r-yarn/package.py @@ -18,6 +18,7 @@ class RYarn(RPackage): bioc = "yarn" + version("1.26.0", commit="54dac4a6afe6b036bac60482cf268aa0cf28cec4") version("1.24.0", commit="d3a9c5cc1f97bff111dc9332f32ded676e3709d3") version("1.22.0", commit="0d94152eee4224bf1ca467fad7f2b35c2e1df6b2") version("1.20.0", commit="b41e4ef14f980518af2fc59f202ad8ec148e8b47") diff --git a/var/spack/repos/builtin/packages/r-zlibbioc/package.py b/var/spack/repos/builtin/packages/r-zlibbioc/package.py index 0f542a1865..33da7c380f 100644 --- a/var/spack/repos/builtin/packages/r-zlibbioc/package.py +++ b/var/spack/repos/builtin/packages/r-zlibbioc/package.py @@ -16,6 +16,7 @@ class RZlibbioc(RPackage): bioc = "zlibbioc" + version("1.46.0", commit="f475457ece2c2b5fc9e6a91a3084dcba2345ab0a") version("1.44.0", commit="d39f0b02fa108ab907b4042c00a114569430a333") version("1.42.0", commit="aa074d72515df745ad65133ca21d3cad778ccc0e") version("1.40.0", commit="3f116b39d104c1ea8288f6b8f0ef94bb95f41f69") |