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Automated GHA update
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GHA committed Jun 19, 2024
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21 changes: 11 additions & 10 deletions bin/windows/contrib/4.3/PACKAGES
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Expand Up @@ -598,8 +598,8 @@ Suggests: knitr, rmarkdown
License: GPL (>= 3)

Package: evaluate
Version: 0.23
Depends: R (>= 3.0.2)
Version: 0.24.0
Depends: R (>= 4.0.0)
Imports: methods
Suggests: covr, ggplot2, lattice, rlang, testthat (>= 3.0.0), withr
License: MIT + file LICENSE
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Archs: x64

Package: nlme
Version: 3.1-164
Version: 3.1-165
Priority: recommended
Depends: R (>= 3.5.0)
Depends: R (>= 3.6.0)
Imports: graphics, stats, utils, lattice
Suggests: Hmisc, MASS, SASmixed
Suggests: MASS, SASmixed
License: GPL (>= 2)
Archs: x64

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License: MIT + file LICENSE

Package: rsm
Version: 2.10.4
Version: 2.10.5
Imports: estimability
Suggests: emmeans (> 1.3.5.1), Vdgraph, conf.design, DoE.base, FrF2
Suggests: emmeans (> 1.3.5.1), Vdgraph, conf.design, DoE.base, FrF2,
knitr, rmarkdown
License: GPL (>= 2)

Package: RSQLite
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License: Artistic-2.0

Package: survival
Version: 3.6-4
Version: 3.7-0
Priority: recommended
Depends: R (>= 3.5.0)
Imports: graphics, Matrix, methods, splines, stats, utils
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Archs: x64

Package: xfun
Version: 0.44
Version: 0.45
Imports: grDevices, stats, tools
Suggests: testit, parallel, codetools, methods, rstudioapi, tinytex (>=
0.30), mime, markdown (>= 1.5), knitr (>= 1.42), htmltools,
0.30), mime, markdown (>= 1.5), knitr (>= 1.47), htmltools,
remotes, pak, rhub, renv, curl, xml2, jsonlite, magick, yaml,
qs, rmarkdown
License: MIT + file LICENSE
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23 changes: 12 additions & 11 deletions bin/windows/contrib/4.4/PACKAGES
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Expand Up @@ -105,7 +105,7 @@ License: GPL-2 | GPL-3
Archs: x64

Package: BiocStyle
Version: 2.32.0
Version: 2.32.1
Imports: bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils,
yaml, BiocManager
Suggests: BiocGenerics, RUnit, htmltools
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License: GPL (>= 3)

Package: evaluate
Version: 0.23
Depends: R (>= 3.0.2)
Version: 0.24.0
Depends: R (>= 4.0.0)
Imports: methods
Suggests: covr, ggplot2, lattice, rlang, testthat (>= 3.0.0), withr
License: MIT + file LICENSE
Expand Down Expand Up @@ -788,7 +788,7 @@ Suggests: covr, pkgload, testthat (>= 3.0.0), tibble, withr
License: MIT + file LICENSE

Package: GenomeInfoDb
Version: 1.40.0
Version: 1.40.1
Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=
0.25.12), IRanges (>= 2.13.12)
Imports: stats, stats4, utils, UCSC.utils, GenomeInfoDbData
Expand All @@ -805,7 +805,7 @@ Depends: R (>= 3.3)
License: Artistic-2.0

Package: GenomicRanges
Version: 1.56.0
Version: 1.56.1
Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.37.0),
S4Vectors (>= 0.27.12), IRanges (>= 2.37.1), GenomeInfoDb (>=
1.15.2)
Expand All @@ -818,10 +818,10 @@ Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>=
AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph,
RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST,
hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr,
rmarkdown, BiocStyle
License: Artistic-2.0
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License: MIT + file LICENSE

Package: limma
Version: 3.60.2
Version: 3.60.3
Depends: R (>= 3.6.0)
Imports: grDevices, graphics, stats, utils, methods, statmod
Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines,
Expand Down Expand Up @@ -2151,9 +2151,10 @@ Suggests: covr, knitr, lifecycle, mockr, rlang, rmarkdown, testthat (>=
License: MIT + file LICENSE

Package: rsm
Version: 2.10.4
Version: 2.10.5
Imports: estimability
Suggests: emmeans (> 1.3.5.1), Vdgraph, conf.design, DoE.base, FrF2
Suggests: emmeans (> 1.3.5.1), Vdgraph, conf.design, DoE.base, FrF2,
knitr, rmarkdown
License: GPL (>= 2)

Package: RSQLite
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License: MIT + file LICENSE

Package: xcms
Version: 4.2.1
Version: 4.2.2
Depends: R (>= 4.0.0), BiocParallel (>= 1.8.0)
Imports: MSnbase (>= 2.29.3), mzR (>= 2.25.3), methods, Biobase,
BiocGenerics, ProtGenerics (>= 1.35.4), lattice,
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14 changes: 7 additions & 7 deletions patRoonDeps-4.3.tsv
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Expand Up @@ -71,7 +71,7 @@ ellipsis 0.3.2
enviPat 2.6
enviPick 1.7 d346b23b1f7dc7a226c4e3a45b74fcc617e19c1b
estimability 1.5.1
evaluate 0.23
evaluate 0.24.0
fansi 1.0.6
farver 2.1.2
fastAdaboost 1.0.0 f331ff8ccfe2e7f318448a29bc72af646dfaf2c1
Expand Down Expand Up @@ -184,14 +184,14 @@ munsell 0.5.1
mzID 1.40.0
mzR 2.36.0
ncdf4 1.22
nlme 3.1-164
nlme 3.1-165
nnet 7.3-19
nontarget 2.2 e30221585182bc66e1f8e1113b2c1103a0f2cb56
nontargetData 1.1 75b2a92cd549f72cc71dfe7b86bd42947d62f2c4
numDeriv 2016.8-1.1
openssl 2.2.0
parallelly 1.37.1
patRoon 2.3.1 21b00b7fc364c818271a81e9e97322a56d0a01d7
patRoon 2.3.1 02e71665cb9c53ef1e89a17f26560d45ae5419d8
pcaMethods 1.94.0
permute 0.9-7
pillar 1.9.0
Expand All @@ -215,7 +215,7 @@ ps 1.7.6
purrr 1.0.2
qap 0.1-2
QFeatures 1.12.0
qlcMatrix 0.9.8 40e453a37241a0ca4a77ecf966b44b8107e644ae
qlcMatrix 0.9.8 d4f0cc2619e262b00514aa838675d4713cab5565
qqman 0.1.9
questionr 0.7.8
R.cache 0.16.0
Expand Down Expand Up @@ -263,7 +263,7 @@ ROCR 1.0-11
ropls 1.34.0
rpart 4.1.23
rprojroot 2.0.4
rsm 2.10.4
rsm 2.10.5
RSQLite 2.3.7
rstudioapi 0.16.0
rvest 1.0.4
Expand All @@ -289,7 +289,7 @@ stringi 1.8.4
stringr 1.5.1
styler 1.10.3
SummarizedExperiment 1.32.0
survival 3.6-4
survival 3.7-0
svglite 2.1.3
sys 3.4.2
systemfonts 1.1.0
Expand Down Expand Up @@ -318,7 +318,7 @@ webchem 1.3.0
webshot 0.5.5
withr 3.0.0
xcms 4.0.2
xfun 0.44
xfun 0.45
xgboost 1.7.7.1
XML 3.99-0.16.1
xml2 1.3.6
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18 changes: 9 additions & 9 deletions patRoonDeps-4.4.tsv
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Expand Up @@ -13,7 +13,7 @@ BiocBaseUtils 1.6.0
BiocGenerics 0.50.0
BiocManager 1.30.23
BiocParallel 1.38.0
BiocStyle 2.32.0
BiocStyle 2.32.1
bit 4.0.5
bit64 4.0.5
bitops 1.0-7
Expand Down Expand Up @@ -70,7 +70,7 @@ ellipsis 0.3.2
enviPat 2.6
enviPick 1.7 d346b23b1f7dc7a226c4e3a45b74fcc617e19c1b
estimability 1.5.1
evaluate 0.23
evaluate 0.24.0
fansi 1.0.6
farver 2.1.2
fastAdaboost 1.0.0 f331ff8ccfe2e7f318448a29bc72af646dfaf2c1
Expand All @@ -96,9 +96,9 @@ GA 3.2.4
gargle 1.5.2
gclus 1.3.2
generics 0.1.3
GenomeInfoDb 1.40.0
GenomeInfoDb 1.40.1
GenomeInfoDbData 1.2.12 19f191e01a4ca92f1b8ca4307788b08f34287b7a
GenomicRanges 1.56.0
GenomicRanges 1.56.1
getPass 0.2-4
ggplot2 3.5.1
ggrepel 0.9.5
Expand Down Expand Up @@ -150,7 +150,7 @@ lattice 0.22-6
lava 1.8.0
lazyeval 0.2.2
lifecycle 1.0.4
limma 3.60.2
limma 3.60.3
listenv 0.9.1
lubridate 1.9.3
magick 2.8.3
Expand Down Expand Up @@ -189,7 +189,7 @@ nontargetData 1.1 75b2a92cd549f72cc71dfe7b86bd42947d62f2c4
numDeriv 2016.8-1.1
openssl 2.2.0
parallelly 1.37.1
patRoon 2.3.1 21b00b7fc364c818271a81e9e97322a56d0a01d7
patRoon 2.3.1 02e71665cb9c53ef1e89a17f26560d45ae5419d8
pcaMethods 1.96.0
permute 0.9-7
pillar 1.9.0
Expand All @@ -214,7 +214,7 @@ PSMatch 1.8.0
purrr 1.0.2
qap 0.1-2
QFeatures 1.14.1
qlcMatrix 0.9.8 40e453a37241a0ca4a77ecf966b44b8107e644ae
qlcMatrix 0.9.8 d4f0cc2619e262b00514aa838675d4713cab5565
qqman 0.1.9
questionr 0.7.8
R.cache 0.16.0
Expand Down Expand Up @@ -259,7 +259,7 @@ ROCR 1.0-11
ropls 1.36.0
rpart 4.1.23
rprojroot 2.0.4
rsm 2.10.4
rsm 2.10.5
RSQLite 2.3.7
rstudioapi 0.16.0
rvest 1.0.4
Expand Down Expand Up @@ -314,7 +314,7 @@ vsn 3.72.0
webchem 1.3.0
webshot 0.5.5
withr 3.0.0
xcms 4.2.1
xcms 4.2.2
xfun 0.44
xgboost 1.7.7.1
XML 3.99-0.16.1
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