RStudio is crashing when running compareCluster

[nfancy]

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Hi, I have run compareCluster before but never had this issue. This time, Rstudio is repeatedly crashing if I am running compareCluster() in a for loop for multiple genelists. I am using the latest version of clusterProfiler. Please see the sessioninfo below. Any pointer is highly appreciated.

Nurun

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/London
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] org.Hs.eg.db_3.19.1    AnnotationDbi_1.66.0   IRanges_2.38.1         S4Vectors_0.42.1      
 [5] Biobase_2.64.0         BiocGenerics_0.50.0    clusterProfiler_4.13.2 lubridate_1.9.3       
 [9] forcats_1.0.0          stringr_1.5.1          dplyr_1.1.4            purrr_1.0.2           
[13] readr_2.1.5            tidyr_1.3.1            tibble_3.2.1           ggplot2_3.5.1         
[17] tidyverse_2.0.0       

loaded via a namespace (and not attached):
  [1] DBI_1.2.3               gson_0.1.0              shadowtext_0.1.4       
  [4] gridExtra_2.3           httr2_1.0.3             rlang_1.1.4            
  [7] magrittr_2.0.3          DOSE_3.30.2             compiler_4.4.1         
 [10] RSQLite_2.3.7           png_0.1-8               vctrs_0.6.5            
 [13] reshape2_1.4.4          pkgconfig_2.0.3         crayon_1.5.3           
 [16] fastmap_1.2.0           XVector_0.44.0          ggraph_2.2.1           
 [19] utf8_1.2.4              HDO.db_0.99.1           tzdb_0.4.0             
 [22] enrichplot_1.22.0       UCSC.utils_1.0.0        bit_4.0.5              
 [25] zlibbioc_1.50.0         cachem_1.1.0            aplot_0.2.3            
 [28] GenomeInfoDb_1.40.1     jsonlite_1.8.8          blob_1.2.4             
 [31] BiocParallel_1.38.0     tweenr_2.0.3            parallel_4.4.1         
 [34] R6_2.5.1                stringi_1.8.4           RColorBrewer_1.1-3     
 [37] qs_0.26.3               GOSemSim_2.30.0         Rcpp_1.0.13            
 [40] Matrix_1.7-0            splines_4.4.1           igraph_2.0.3           
 [43] timechange_0.3.0        tidyselect_1.2.1        qvalue_2.36.0          
 [46] rstudioapi_0.16.0       viridis_0.6.5           stringfish_0.16.0      
 [49] codetools_0.2-20        lattice_0.22-6          plyr_1.8.9             
 [52] treeio_1.28.0           withr_3.0.1             KEGGREST_1.44.1        
 [55] gridGraphics_0.5-1      scatterpie_0.2.3        RcppParallel_5.1.8     
 [58] polyclip_1.10-7         Biostrings_2.72.1       ggtree_3.12.0          
 [61] pillar_1.9.0            ggfun_0.1.5             generics_0.1.3         
 [64] hms_1.1.3               tidytree_0.4.6          munsell_0.5.1          
 [67] scales_1.3.0            RApiSerialize_0.1.3     glue_1.7.0             
 [70] lazyeval_0.2.2          tools_4.4.1             data.table_1.15.4      
 [73] fgsea_1.30.0            fs_1.6.4                graphlayouts_1.1.1     
 [76] fastmatch_1.1-4         tidygraph_1.3.1         cowplot_1.1.3          
 [79] grid_4.4.1              ape_5.8                 colorspace_2.1-1       
 [82] nlme_3.1-165            patchwork_1.2.0         GenomeInfoDbData_1.2.12
 [85] ggforce_0.4.2           cli_3.6.3               rappdirs_0.3.3         
 [88] fansi_1.0.6             viridisLite_0.4.2       gtable_0.3.5           
 [91] yulab.utils_0.1.6       digest_0.6.37           ggplotify_0.1.2        
 [94] ggrepel_0.9.5           farver_2.1.2            memoise_2.0.1          
 [97] lifecycle_1.0.4         httr_1.4.7              GO.db_3.19.1           
[100] bit64_4.0.5             MASS_7.3-61  

[guidohooiveld]

The obvious question is whether your code runs fine when NOT using R-studio, thus directly in R....

In case debugging is needed: could you provide a reproducible example that triggers this behavior?