Automated GHA update

patRoonDeps-4.3.tsv

@@ -5,24 +5,24 @@ affyio	1.72.0
 AnnotationFilter	1.26.0	
 askpass	1.2.0	
 assertthat	0.2.1	
-backports	1.4.1	
+backports	1.5.0	
 base64enc	0.1-3	
 BH	1.84.0-0	
 Biobase	2.62.0	
 BiocBaseUtils	1.4.0	
 BiocGenerics	0.48.1	
-BiocManager	1.30.22	
+BiocManager	1.30.23	
 BiocParallel	1.36.0	
 BiocStyle	2.30.0	
 bit	4.0.5	
 bit64	4.0.5	
 bitops	1.0-7	
 blob	1.2.4	
-bookdown	0.38	
-broom	1.0.5	
+bookdown	0.39	
+broom	1.0.6	
 bslib	0.7.0	
 ca	0.71.1	
-cachem	1.0.8	
+cachem	1.1.0	
 calibrate	1.7.7	
 callr	3.7.6	
 CAMERA	1.58.0	
@@ -62,21 +62,21 @@ digest	0.6.35
 docopt	0.7.1	
 doParallel	1.0.17	
 dplyr	1.1.4	
-DT	0.32	
+DT	0.33	
 dtplyr	1.3.1	
 dynamicTreeCut	1.63-1	
 e1071	1.7-14	
 egg	0.4.5	
 ellipsis	0.3.2	
 enviPat	2.6	
 enviPick	1.7	d346b23b1f7dc7a226c4e3a45b74fcc617e19c1b
-estimability	1.5	
+estimability	1.5.1	
 evaluate	0.23	
 fansi	1.0.6	
-farver	2.1.1	
+farver	2.1.2	
 fastAdaboost	1.0.0	f331ff8ccfe2e7f318448a29bc72af646dfaf2c1
 fastcluster	1.2.6	
-fastmap	1.1.1	
+fastmap	1.2.0	
 ff	4.0.12	
 fingerprint	3.5.7	
 flexdashboard	0.6.2	
@@ -86,7 +86,7 @@ foreach	1.5.2
 foreign	0.8-86	
 formatR	1.14	
 Formula	1.2-5	
-fs	1.6.3	
+fs	1.6.4	
 fst	0.9.8	
 fstcore	0.9.18	
 futile.logger	1.4.3	
@@ -101,7 +101,7 @@ GenomeInfoDb	1.38.8
 GenomeInfoDbData	1.2.12	19f191e01a4ca92f1b8ca4307788b08f34287b7a
 GenomicRanges	1.54.1	
 getPass	0.2-4	
-ggplot2	3.5.0	
+ggplot2	3.5.1	
 ggrepel	0.9.5	
 GlobalOptions	0.1.2	
 globals	0.16.3	
@@ -112,16 +112,16 @@ gower	1.0.1
 gplots	3.1.3.1	
 graph	1.80.0	
 gridExtra	2.3	
-gtable	0.3.4	
+gtable	0.3.5	
 gtools	3.9.5	
 hardhat	1.3.1	
 haven	2.5.4	
 heatmaply	1.5.0	
-highr	0.10	
-Hmisc	5.1-2	
+highr	0.11	
+Hmisc	5.1-3	
 hms	1.1.3	
 htmlTable	2.4.2	
-htmltools	0.5.8	
+htmltools	0.5.8.1	
 htmlwidgets	1.6.4	
 httpuv	1.6.15	
 httr	1.4.7	
@@ -138,13 +138,13 @@ jquerylib	0.1.4
 jsonlite	1.8.8	
 kableExtra	1.4.0	
 kernlab	0.9-32	
-KernSmooth	2.23-22	
+KernSmooth	2.23-24	
 keys	0.1.1	
 klaR	1.7-3	
-knitr	1.45	
+knitr	1.46	
 KPIC	2.4.0	dd0dddb0cac9bc7882eb1a420c82c9713a8aa0ce
 labeling	0.4.3	
-labelled	2.12.0	
+labelled	2.13.0	
 lambda.r	1.2.4	
 later	1.3.2	
 lattice	0.22-6	
@@ -161,14 +161,14 @@ MASS	7.3-60.0.1
 MassSpecWavelet	1.68.0	
 Matrix	1.6-5	
 MatrixGenerics	1.14.0	
-matrixStats	1.2.0	
+matrixStats	1.3.0	
 memoise	2.0.1	
 MetaboCoreUtils	1.10.0	
 MetaClean	1.0.1	d0ce1bc0b2fe4d17e7e047c8c07c75b81c4e5833
 mgcv	1.9-1	
 mime	0.12	
 miniUI	0.1.1.1	
-MLmetrics	1.1.1	
+MLmetrics	1.1.3	
 ModelMetrics	1.2.2.2	
 modelr	0.1.11	
 MS2Quant	1.1.0	46e0c77ef4961a29a73a388105eeb28e33839630
@@ -189,9 +189,9 @@ nnet	7.3-19
 nontarget	2.2	e30221585182bc66e1f8e1113b2c1103a0f2cb56
 nontargetData	1.1	75b2a92cd549f72cc71dfe7b86bd42947d62f2c4
 numDeriv	2016.8-1.1	
-openssl	2.1.1	
+openssl	2.2.0	
 parallelly	1.37.1	
-patRoon	2.3.1	48004a15afe9a7a220d7d36e7ad287aa6fc9a50e
+patRoon	2.3.1	870b97ba3bd778a31df34563e4385dae86d43906
 pcaMethods	1.94.0	
 permute	0.9-7	
 pillar	1.9.0	
@@ -208,22 +208,22 @@ processx	3.8.4
 prodlim	2023.08.28	
 progress	1.2.3	
 progressr	0.14.0	
-promises	1.2.1	
+promises	1.3.0	
 ProtGenerics	1.34.0	
 proxy	0.4-27	
 ps	1.7.6	
 purrr	1.0.2	
 qap	0.1-2	
 QFeatures	1.12.0	
-qlcMatrix	0.9.7	d919872f69b07b6cf892f725ed3d6e4569319206
+qlcMatrix	0.9.8	40e453a37241a0ca4a77ecf966b44b8107e644ae
 qqman	0.1.9	
 questionr	0.7.8	
 R.cache	0.16.0	
 R.methodsS3	1.8.2	
 R.oo	1.26.0	
 R.utils	2.12.3	
 R6	2.5.1	
-ragg	1.3.0	
+ragg	1.3.2	
 RAMClustR	1.3.1	e005614d808e0ca93c459ec8cc103b87cd5d11fd
 randomForest	4.7-1.1	
 RANN	2.6.1	
@@ -235,7 +235,7 @@ rcdk	3.8.1
 rcdklibs	2.9	
 RColorBrewer	1.1-3	
 Rcpp	1.0.12	
-RcppArmadillo	0.12.8.1.0	
+RcppArmadillo	0.12.8.3.0	
 RCurl	1.98-1.14	
 RDCOMClient	0.95-1	1554833f8659461427a93732119756ae1c25bc32
 Rdisop	1.62.0	
@@ -257,24 +257,24 @@ Rhdf5lib	1.24.2
 rJava	1.0-11	
 rlang	1.1.3	
 rlist	0.4.6.2	
-rmarkdown	2.26	
+rmarkdown	2.27	
 robustbase	0.99-2	
 ROCR	1.0-11	
 ropls	1.34.0	
 rpart	4.1.23	
 rprojroot	2.0.4	
 rsm	2.10.4	
-RSQLite	2.3.6	
+RSQLite	2.3.7	
 rstudioapi	0.16.0	
 rvest	1.0.4	
 S4Arrays	1.2.1	
 S4Vectors	0.40.2	
 sass	0.4.9	
 scales	1.3.0	
 selectr	0.4-2	
-seriation	1.5.4	
+seriation	1.5.5	
 shape	1.4.6.1	
-shiny	1.8.1	
+shiny	1.8.1.1	
 shinyjs	2.1.0	
 slam	0.1-50	
 snow	0.4-4	
@@ -285,29 +285,29 @@ Spectra	1.12.0
 splashR	0.0.4	174fbf289a0357535f9bacda282b9a2dbb7807cc
 SQUAREM	2021.1	
 statmod	1.5.0	
-stringi	1.8.3	
+stringi	1.8.4	
 stringr	1.5.1	
-styler	1.10.2	
+styler	1.10.3	
 SummarizedExperiment	1.32.0	
-survival	3.5-8	
+survival	3.6-4	
 svglite	2.1.3	
 sys	3.4.2	
-systemfonts	1.0.6	
-textshaping	0.3.7	
+systemfonts	1.1.0	
+textshaping	0.4.0	
 tibble	3.2.1	
 tidyr	1.3.1	
 tidyselect	1.2.1	
 tidyverse	2.0.0	
 timechange	0.3.0	
 timeDate	4032.109	
-tinytex	0.50	
+tinytex	0.51	
 TSP	1.2-4	
 tzdb	0.4.0	
 UpSetR	1.4.0	
 utf8	1.2.4	
 uuid	1.2-0	
 vctrs	0.6.5	
-vegan	2.6-4	
+vegan	2.6-6.1	
 VennDiagram	1.7.3	
 viridis	0.6.5	
 viridisLite	0.4.2	
@@ -318,7 +318,7 @@ webchem	1.3.0
 webshot	0.5.5	
 withr	3.0.0	
 xcms	4.0.2	
-xfun	0.43	
+xfun	0.44	
 xgboost	1.7.7.1	
 XML	3.99-0.16.1	
 xml2	1.3.6