R studio freezes when monocle3 is installed

[Tristan-Philippe]

Hi,

I really like the new features of monocle3, but I noticed that in my system (details below) R studio 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). I noticed the secure shell (ssh.google.cloud.com) is also slow to respond when monocle3 is installed.

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

[brgew]

Hi,

I installed RStudio version 2023.06.1+524 with R version 4.3.1on Debian bookworm and then installed Monocle3 from github without a problem. Perhaps there is a problem with RStudio Server? Have you tried running RStudio Desktop? And the most recent versions of the software?

Thank you,
Brent

[Tristan-Philippe]

Hi, Thanks for the response. Perhaps it is an issue with RStudio Server. I am not sure if I can install RStudio Desktop in the GCP environment. I can also mention it to the RStudio team.