Automated GHA update

bin/windows/contrib/4.3/PACKAGES

@@ -328,7 +328,7 @@ License: MIT + file LICENSE
 Archs: x64
 
 Package: clue
-Version: 0.3-65
+Version: 0.3-66
 Depends: R (>= 3.2.0)
 Imports: stats, cluster, graphics, methods
 Suggests: e1071, lpSolve (>= 5.5.7), quadprog (>= 1.4-8), relations
@@ -403,7 +403,7 @@ Suggests: shiny, ggplot2, testthat (>= 2.1.0), sass, bslib
 License: MIT + file LICENSE
 
 Package: curl
-Version: 6.0.0
+Version: 6.0.1
 Depends: R (>= 3.0.0)
 Suggests: spelling, testthat (>= 1.0.0), knitr, jsonlite, later,
         rmarkdown, httpuv (>= 1.4.4), webutils
@@ -477,7 +477,7 @@ License: Artistic-2.0
 Archs: x64
 
 Package: dendextend
-Version: 1.18.1
+Version: 1.19.0
 Depends: R (>= 3.0.0)
 Imports: utils, stats, datasets, magrittr (>= 1.0.1), ggplot2, viridis
 Suggests: knitr, rmarkdown, testthat, seriation, colorspace, ape,
@@ -658,11 +658,11 @@ Suggests: testthat
 License: MIT + file LICENSE
 
 Package: fontawesome
-Version: 0.5.2
+Version: 0.5.3
 Depends: R (>= 3.3.0)
 Imports: rlang (>= 1.0.6), htmltools (>= 0.5.1.1)
-Suggests: covr, dplyr (>= 1.0.8), knitr (>= 1.31), testthat (>= 3.0.0),
-        rsvg
+Suggests: covr, dplyr (>= 1.0.8), gt (>= 0.9.0), knitr (>= 1.31),
+        testthat (>= 3.0.0), rsvg
 License: MIT + file LICENSE
 
 Package: forcats
@@ -1175,16 +1175,17 @@ Enhances: clustMixType, randomForest, ClustVarLV
 License: GPL-2 | GPL-3
 
 Package: knitr
-Version: 1.48
-Depends: R (>= 3.3.0)
+Version: 1.49
+Depends: R (>= 3.6.0)
 Imports: evaluate (>= 0.15), highr (>= 0.11), methods, tools, xfun (>=
-        0.44), yaml (>= 2.1.19)
+        0.48), yaml (>= 2.1.19)
 Suggests: bslib, codetools, DBI (>= 0.4-1), digest, formatR, gifski,
         gridSVG, htmlwidgets (>= 0.7), jpeg, JuliaCall (>= 0.11.1),
-        magick, markdown (>= 1.3), png, ragg, reticulate (>= 1.4), rgl
-        (>= 0.95.1201), rlang, rmarkdown, sass, showtext, styler (>=
-        1.2.0), targets (>= 0.6.0), testit, tibble, tikzDevice (>=
-        0.10), tinytex (>= 0.46), webshot, rstudioapi, svglite
+        magick, litedown, markdown (>= 1.3), png, ragg, reticulate (>=
+        1.4), rgl (>= 0.95.1201), rlang, rmarkdown, sass, showtext,
+        styler (>= 1.2.0), targets (>= 0.6.0), testit, tibble,
+        tikzDevice (>= 0.10), tinytex (>= 0.46), webshot, rstudioapi,
+        svglite
 License: GPL
 
 Package: KPIC
@@ -1580,7 +1581,7 @@ License: MIT + file LICENSE
 Archs: x64
 
 Package: parallelly
-Version: 1.38.0
+Version: 1.39.0
 Imports: parallel, tools, utils
 License: LGPL (>= 2.1)
 Archs: x64
@@ -1975,7 +1976,7 @@ License: GPL-2
 Archs: x64
 
 Package: Rdpack
-Version: 2.6.1
+Version: 2.6.2
 Depends: R (>= 2.15.0), methods
 Imports: tools, utils, rbibutils (>= 1.3)
 Suggests: grDevices, testthat, rstudioapi, rprojroot, gbRd
@@ -2181,13 +2182,13 @@ Suggests: emmeans (> 1.3.5.1), Vdgraph, conf.design, DoE.base, FrF2,
 License: GPL (>= 2)
 
 Package: RSQLite
-Version: 2.3.7
+Version: 2.3.8
 Depends: R (>= 3.1.0)
 Imports: bit64, blob (>= 1.2.0), DBI (>= 1.2.0), memoise, methods,
         pkgconfig, rlang
 LinkingTo: plogr (>= 0.2.0), cpp11 (>= 0.4.0)
-Suggests: callr, DBItest (>= 1.8.0), gert, gh, hms, knitr, magrittr,
-        rmarkdown, rvest, testthat (>= 3.0.0), withr, xml2
+Suggests: callr, cli, DBItest (>= 1.8.0), decor, gert, gh, hms, knitr,
+        magrittr, rmarkdown, rvest, testthat (>= 3.0.0), withr, xml2
 License: LGPL (>= 2.1)
 Archs: x64
 
@@ -2289,7 +2290,7 @@ Suggests: htmltools (>= 0.2.9), knitr (>= 1.7), rmarkdown, shinyAce,
 License: MIT + file LICENSE
 
 Package: slam
-Version: 0.1-54
+Version: 0.1-55
 Depends: R (>= 3.4.0)
 Imports: stats
 Enhances: Matrix, SparseM, spam

bin/windows/contrib/4.4/PACKAGES

@@ -208,7 +208,7 @@ Suggests: asciicast (>= 2.3.1), cli (>= 1.1.0), mockery, ps, rprojroot,
 License: MIT + file LICENSE
 
 Package: CAMERA
-Version: 1.60.0
+Version: 1.62.0
 Depends: R (>= 3.5.0), methods, Biobase, xcms (>= 1.13.5)
 Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils,
         Hmisc, igraph
@@ -330,7 +330,7 @@ License: MIT + file LICENSE
 Archs: x64
 
 Package: clue
-Version: 0.3-65
+Version: 0.3-66
 Depends: R (>= 3.2.0)
 Imports: stats, cluster, graphics, methods
 Suggests: e1071, lpSolve (>= 5.5.7), quadprog (>= 1.4-8), relations
@@ -405,7 +405,7 @@ Suggests: shiny, ggplot2, testthat (>= 2.1.0), sass, bslib
 License: MIT + file LICENSE
 
 Package: curl
-Version: 5.2.3
+Version: 6.0.1
 Depends: R (>= 3.0.0)
 Suggests: spelling, testthat (>= 1.0.0), knitr, jsonlite, later,
         rmarkdown, httpuv (>= 1.4.4), webutils
@@ -479,7 +479,7 @@ License: Artistic-2.0
 Archs: x64
 
 Package: dendextend
-Version: 1.18.1
+Version: 1.19.0
 Depends: R (>= 3.0.0)
 Imports: utils, stats, datasets, magrittr (>= 1.0.1), ggplot2, viridis
 Suggests: knitr, rmarkdown, testthat, seriation, colorspace, ape,
@@ -654,11 +654,11 @@ Suggests: testthat
 License: MIT + file LICENSE
 
 Package: fontawesome
-Version: 0.5.2
+Version: 0.5.3
 Depends: R (>= 3.3.0)
 Imports: rlang (>= 1.0.6), htmltools (>= 0.5.1.1)
-Suggests: covr, dplyr (>= 1.0.8), knitr (>= 1.31), testthat (>= 3.0.0),
-        rsvg
+Suggests: covr, dplyr (>= 1.0.8), gt (>= 0.9.0), knitr (>= 1.31),
+        testthat (>= 3.0.0), rsvg
 License: MIT + file LICENSE
 
 Package: forcats
@@ -1171,16 +1171,17 @@ Enhances: clustMixType, randomForest, ClustVarLV
 License: GPL-2 | GPL-3
 
 Package: knitr
-Version: 1.48
-Depends: R (>= 3.3.0)
+Version: 1.49
+Depends: R (>= 3.6.0)
 Imports: evaluate (>= 0.15), highr (>= 0.11), methods, tools, xfun (>=
-        0.44), yaml (>= 2.1.19)
+        0.48), yaml (>= 2.1.19)
 Suggests: bslib, codetools, DBI (>= 0.4-1), digest, formatR, gifski,
         gridSVG, htmlwidgets (>= 0.7), jpeg, JuliaCall (>= 0.11.1),
-        magick, markdown (>= 1.3), png, ragg, reticulate (>= 1.4), rgl
-        (>= 0.95.1201), rlang, rmarkdown, sass, showtext, styler (>=
-        1.2.0), targets (>= 0.6.0), testit, tibble, tikzDevice (>=
-        0.10), tinytex (>= 0.46), webshot, rstudioapi, svglite
+        magick, litedown, markdown (>= 1.3), png, ragg, reticulate (>=
+        1.4), rgl (>= 0.95.1201), rlang, rmarkdown, sass, showtext,
+        styler (>= 1.2.0), targets (>= 0.6.0), testit, tibble,
+        tikzDevice (>= 0.10), tinytex (>= 0.46), webshot, rstudioapi,
+        svglite
 License: GPL
 
 Package: KPIC
@@ -1458,7 +1459,7 @@ Suggests: testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown
 License: Artistic-2.0
 
 Package: MSnbase
-Version: 2.30.1
+Version: 2.32.0
 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.7.1), Biobase (>=
         2.15.2), mzR (>= 2.29.3), S4Vectors, ProtGenerics (>= 1.29.1)
 Imports: MsCoreUtils, PSMatch, BiocParallel, IRanges (>= 2.13.28),
@@ -1467,10 +1468,10 @@ Imports: MsCoreUtils, PSMatch, BiocParallel, IRanges (>= 2.13.28),
         MASS, Rcpp
 LinkingTo: Rcpp
 Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>=
-        1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>=
-        0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>=
-        2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny,
-        magrittr, SummarizedExperiment
+        1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.43.3), magick,
+        msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub,
+        BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots,
+        XML, shiny, magrittr, SummarizedExperiment
 License: Artistic-2.0
 Archs: x64
 
@@ -1567,7 +1568,7 @@ License: MIT + file LICENSE
 Archs: x64
 
 Package: parallelly
-Version: 1.38.0
+Version: 1.39.0
 Imports: parallel, tools, utils
 License: LGPL (>= 2.1)
 Archs: x64
@@ -1935,9 +1936,9 @@ License: GPL (>= 2)
 Archs: x64
 
 Package: RcppArmadillo
-Version: 14.0.2-1
+Version: 14.2.0-1
 Depends: R (>= 3.3.0)
-Imports: Rcpp (>= 1.0.8), stats, utils, methods
+Imports: Rcpp (>= 1.0.12), stats, utils, methods
 LinkingTo: Rcpp
 Suggests: tinytest, Matrix (>= 1.3.0), pkgKitten, reticulate, slam
 License: GPL (>= 2)
@@ -1958,7 +1959,7 @@ License: GPL-2
 Archs: x64
 
 Package: Rdpack
-Version: 2.6.1
+Version: 2.6.2
 Depends: R (>= 2.15.0), methods
 Imports: tools, utils, rbibutils (>= 1.3)
 Suggests: grDevices, testthat, rstudioapi, rprojroot, gbRd
@@ -2103,7 +2104,7 @@ Suggests: testthat, stringdist
 License: MIT + file LICENSE
 
 Package: rmarkdown
-Version: 2.28
+Version: 2.29
 Depends: R (>= 3.0)
 Imports: bslib (>= 0.2.5.1), evaluate (>= 0.13), fontawesome (>=
         0.5.0), htmltools (>= 0.5.1), jquerylib, jsonlite, knitr (>=
@@ -2153,13 +2154,13 @@ Suggests: emmeans (> 1.3.5.1), Vdgraph, conf.design, DoE.base, FrF2,
 License: GPL (>= 2)
 
 Package: RSQLite
-Version: 2.3.7
+Version: 2.3.8
 Depends: R (>= 3.1.0)
 Imports: bit64, blob (>= 1.2.0), DBI (>= 1.2.0), memoise, methods,
         pkgconfig, rlang
 LinkingTo: plogr (>= 0.2.0), cpp11 (>= 0.4.0)
-Suggests: callr, DBItest (>= 1.8.0), gert, gh, hms, knitr, magrittr,
-        rmarkdown, rvest, testthat (>= 3.0.0), withr, xml2
+Suggests: callr, cli, DBItest (>= 1.8.0), decor, gert, gh, hms, knitr,
+        magrittr, rmarkdown, rvest, testthat (>= 3.0.0), withr, xml2
 License: LGPL (>= 2.1)
 Archs: x64
 
@@ -2261,7 +2262,7 @@ Suggests: htmltools (>= 0.2.9), knitr (>= 1.7), rmarkdown, shinyAce,
 License: MIT + file LICENSE
 
 Package: slam
-Version: 0.1-54
+Version: 0.1-55
 Depends: R (>= 3.4.0)
 Imports: stats
 Enhances: Matrix, SparseM, spam
@@ -2635,14 +2636,14 @@ Suggests: callr, DBI, knitr, methods, rlang, rmarkdown (>= 2.12),
 License: MIT + file LICENSE
 
 Package: xcms
-Version: 4.2.3
+Version: 4.4.0
 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,
+        BiocGenerics, ProtGenerics (>= 1.37.1), lattice,
         MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges,
         SummarizedExperiment, MsCoreUtils (>= 1.15.5), MsFeatures,
-        MsExperiment (>= 1.5.4), Spectra (>= 1.13.7), progress,
-        jsonlite, RColorBrewer, MetaboCoreUtils (>= 1.11.2)
+        MsExperiment (>= 1.5.4), Spectra (>= 1.15.7), progress,
+        RColorBrewer, MetaboCoreUtils (>= 1.11.2)
 Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>=
         0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown,
         MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal,

patRoonDeps-4.3.tsv

@@ -38,7 +38,7 @@ cli	3.6.3
 clipr	0.8.0	
 cliqueMS	1.7.1	cb569e0b78ce0fa4254f1393874762bed08fa855
 clock	0.7.1	
-clue	0.3-65	
+clue	0.3-66	
 cluster	2.1.6	
 codetools	0.2-20	
 colorspace	2.1-1	
@@ -48,14 +48,14 @@ conflicted	1.2.0
 cpp11	0.5.0	
 crayon	1.5.3	
 crosstalk	1.2.1	
-curl	6.0.0	
+curl	6.0.1	
 data.table	1.16.2	
 data.tree	1.1.0	
 DBI	1.2.3	
 dbplyr	2.5.0	
 dbscan	1.2-0	
 DelayedArray	0.28.0	
-dendextend	1.18.1	
+dendextend	1.19.0	
 DEoptimR	1.1-3	
 diagram	1.6.5	
 digest	0.6.37	
@@ -79,7 +79,7 @@ fastmap	1.2.0
 ff	4.5.0	
 fingerprint	3.5.7	
 flexdashboard	0.6.2	
-fontawesome	0.5.2	
+fontawesome	0.5.3	
 forcats	1.0.0	
 foreach	1.5.2	
 foreign	0.8-87	
@@ -140,7 +140,7 @@ kernlab	0.9-33
 KernSmooth	2.23-24	
 keys	0.1.1	
 klaR	1.7-3	
-knitr	1.48	
+knitr	1.49	
 KPIC	2.4.0	dd0dddb0cac9bc7882eb1a420c82c9713a8aa0ce
 labeling	0.4.3	
 labelled	2.13.0	
@@ -189,8 +189,8 @@ nontarget	2.2	e30221585182bc66e1f8e1113b2c1103a0f2cb56
 nontargetData	1.1	75b2a92cd549f72cc71dfe7b86bd42947d62f2c4
 numDeriv	2016.8-1.1	
 openssl	2.2.2	
-parallelly	1.38.0	
-patRoon	2.3.3	b07292f4cb40c48a97a179e30c3eb025c7576f71
+parallelly	1.39.0	
+patRoon	2.3.3	cbc12002ac7fc40d2478dd86d83a0c690f3dff2a
 pcaMethods	1.94.0	
 permute	0.9-7	
 pillar	1.9.0	
@@ -238,7 +238,7 @@ RcppArmadillo	14.0.2-1
 RCurl	1.98-1.16	
 RDCOMClient	0.95-1	1554833f8659461427a93732119756ae1c25bc32
 Rdisop	1.65.2	
-Rdpack	2.6.1	
+Rdpack	2.6.2	
 reactable	0.4.4	
 reactR	0.6.1	
 readMzXmlData	2.8.3	
@@ -263,7 +263,7 @@ ropls	1.34.0
 rpart	4.1.23	
 rprojroot	2.0.4	
 rsm	2.10.5	
-RSQLite	2.3.7	
+RSQLite	2.3.8	
 rstudioapi	0.17.1	
 rvest	1.0.4	
 S4Arrays	1.2.1	
@@ -275,7 +275,7 @@ seriation	1.5.6
 shape	1.4.6.1	
 shiny	1.9.1	
 shinyjs	2.1.0	
-slam	0.1-54	
+slam	0.1-55	
 snow	0.4-4	
 sourcetools	0.1.7-1	
 SparseArray	1.2.4