Hi,
R studio server freezes and the .Rproj.user and .Rhistory files must be deleted to connect to an already running session. This behaviour is only resolved by uninstalling monocle3 and comes back when I re-install monocle3. I tried the development and beta branch of Monocle3. I had the same issue with an older version of Rstudio server (I can't recall which). So this seems to be an issue between the two.
See my post to the monocle3 devs here: R studio freezes when monocle3 is installed · Issue #646 · cole-trapnell-lab/monocle3 · GitHub
Environment:
Google Cloud virtual machine (n2d-highmem-16)
RStudio Server 2022.12.0 Build 353
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
release
"5.10.0-20-cloud-amd64"
Running under: Debian GNU/Linux 11 (bullseye)
version
"#1 SMP Debian 5.10.158-2 (2022-12-13)"
Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ComplexHeatmap_2.12.1 ggplot2_3.4.1
[3] data.table_1.14.8 fgsea_1.25.1
[5] limma_3.54.1 DESeq2_1.36.0
[7] SummarizedExperiment_1.28.0 Biobase_2.58.0
[9] MatrixGenerics_1.10.0 matrixStats_0.63.0
[11] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[13] IRanges_2.32.0 S4Vectors_0.36.1
[15] BiocGenerics_0.44.0 nebula_1.2.2
[17] SeuratObject_4.1.3 sp_1.6-0
loaded via a namespace (and not attached):
[1] utf8_1.2.3 spatstat.explore_3.0-6
[3] reticulate_1.28 R.utils_2.12.2
[5] tidyselect_1.2.0 RSQLite_2.2.20
[7] AnnotationDbi_1.58.0 htmlwidgets_1.6.1
[9] BiocParallel_1.32.5 Rtsne_0.16
[11] munsell_0.5.0 codetools_0.2-18
[13] ica_1.0-3 future_1.31.0
[15] miniUI_0.1.1.1 withr_2.5.0
[17] spatstat.random_3.1-3 colorspace_2.1-0
[19] progressr_0.13.0 knitr_1.42
[21] rstudioapi_0.14 Seurat_4.3.0
[23] ROCR_1.0-11 tensor_1.5
[25] listenv_0.9.0 GenomeInfoDbData_1.2.9
[27] polyclip_1.10-4 bit64_4.0.5
[29] parallelly_1.34.0 vctrs_0.5.2
[31] generics_0.1.3 xfun_0.37
[33] R6_2.5.1 doParallel_1.0.17
[35] clue_0.3-64 rsvd_1.0.5
[37] locfit_1.5-9.7 RcppZiggurat_0.1.6
[39] bitops_1.0-7 spatstat.utils_3.0-1
[41] cachem_1.0.6 DelayedArray_0.24.0
[43] promises_1.2.0.1 scales_1.2.1
[45] gtable_0.3.1 globals_0.16.2
[47] goftest_1.2-3 rlang_1.0.6
[49] genefilter_1.78.0 GlobalOptions_0.1.2
[51] splines_4.2.2 lazyeval_0.2.2
[53] trust_0.1-8 spatstat.geom_3.0-6
[55] BiocManager_1.30.19 yaml_2.3.7
[57] reshape2_1.4.4 abind_1.4-5
[59] Rfast_2.0.6 httpuv_1.6.9
[61] tools_4.2.2 ellipsis_0.3.2
[63] RColorBrewer_1.1-3 ggridges_0.5.4
[65] Rcpp_1.0.10 plyr_1.8.8
[67] zlibbioc_1.44.0 purrr_1.0.1
[69] RCurl_1.98-1.10 deldir_1.0-6
[71] pbapply_1.7-0 GetoptLong_1.0.5
[73] cowplot_1.1.1 zoo_1.8-11
[75] ggrepel_0.9.3 cluster_2.1.4
[77] magrittr_2.0.3 scattermore_0.8
[79] circlize_0.4.15 lmtest_0.9-40
[81] RANN_2.6.1 fitdistrplus_1.1-8
[83] patchwork_1.1.2 mime_0.12
[85] evaluate_0.20 xtable_1.8-4
[87] XML_3.99-0.13 gridExtra_2.3
[89] shape_1.4.6 compiler_4.2.2
[91] tibble_3.1.8 KernSmooth_2.23-20
[93] crayon_1.5.2 R.oo_1.25.0
[95] htmltools_0.5.4 later_1.3.0
[97] tidyr_1.3.0 geneplotter_1.74.0
[99] DBI_1.1.3 MASS_7.3-58.1
[101] Matrix_1.5-3 cli_3.6.0
[103] R.methodsS3_1.8.2 parallel_4.2.2
[105] igraph_1.4.0 pkgconfig_2.0.3
[107] plotly_4.10.1 spatstat.sparse_3.0-0
[109] foreach_1.5.2 annotate_1.74.0
[111] XVector_0.38.0 stringr_1.5.0
[113] digest_0.6.31 sctransform_0.3.5
[115] RcppAnnoy_0.0.20 spatstat.data_3.0-0
[117] Biostrings_2.64.1 rmarkdown_2.20
[119] leiden_0.4.3 fastmatch_1.1-3
[121] uwot_0.1.14 shiny_1.7.4
[123] rjson_0.2.21 nloptr_2.0.3
[125] lifecycle_1.0.3 nlme_3.1-160
[127] jsonlite_1.8.4 SeuratWrappers_0.3.1
[129] viridisLite_0.4.1 fansi_1.0.4
[131] pillar_1.8.1 lattice_0.20-45
[133] KEGGREST_1.36.3 fastmap_1.1.0
[135] httr_1.4.4 survival_3.4-0
[137] glue_1.6.2 remotes_2.4.2
[139] png_0.1-8 iterators_1.0.14
[141] bit_4.0.5 stringi_1.7.12
[143] blob_1.2.3 memoise_2.0.1
[145] dplyr_1.1.0 irlba_2.3.5.1
[147] future.apply_1.10.0
Thanks!