Package versions:

glmnet 4.1-8 Matrix 1.6-5 plyr 1.8.9 reshape2 1.4.4 metacell 0.3.7 devtools 2.4.5 usethis 2.2.3 httr 1.4.7 pkgload 1.4.0 tidyr 1.3.1 splines 4.2.2 foreach 1.5.2 jsonlite 1.9.0 tgconfig 0.1.2 shiny 1.10.0 askpass 1.2.1 stats4 4.2.2 yaml 2.3.7 remotes 2.5.0 sessioninfo 1.2.2 pillar 1.10.1 lattice 0.22-6 glue 1.8.0 reticulate 1.40.0 uuid 1.2-1 digest 0.6.37 promises 1.3.2 colorspace 2.1-1 htmltools 0.5.8.1 httpuv 1.6.15 pkgconfig 2.0.3 purrr 1.0.4 xtable 1.8-4 scales 1.3.0 RSpectra 0.16-2 later 1.4.1 tgutil 0.1.17 tibble 3.2.1 openssl 2.3.2 generics 0.1.3 dbscan 1.1-12 ggplot2 3.5.1 ellipsis 0.3.2 pdist 1.2.1 cachem 1.1.0 umap 0.2.10.0 repr 1.1.7 BiocGenerics 0.44.0 cli 3.6.4 survival 3.8-3 magrittr 2.0.3 crayon 1.5.3 mime 0.12 memoise 2.0.1 evaluate 1.0.3 fs 1.6.5 pkgbuild 1.4.6 graph 1.76.0 profvis 0.3.8 tools 4.2.2 lifecycle 1.0.4 stringr 1.5.1 munsell 0.5.1 cluster 2.1.3 compiler 4.2.2 rlang 1.1.5 grid 4.2.2 iterators 1.0.14 pbdZMQ 0.3-13 IRkernel 1.3.2 htmlwidgets 1.6.4 igraph 2.1.4 miniUI 0.1.1.1 base64enc 0.1-3 tgstat 2.3.28 codetools 0.2-20 gtable 0.3.6 curl 6.2.1 R6 2.6.1 zoo 1.8-12 dplyr 1.1.4 fastmap 1.2.0 shape 1.4.6.1 Rgraphviz 2.42.0 stringi 1.8.4 IRdisplay 1.1 Rcpp 1.0.14 vctrs 0.6.5 png 0.1-8 tidyselect 1.2.1 urlchecker 1.0.1