Problem to kill jobs with Rstudio

[ArthurPERE]

Hello,

I have a very strange bug that appear on Rstudio alone. When I run code on Biocparallele with R command (in a terminal). The function work perfectly, no probleme. But when I run it in Rstudio, the function run forever.

When I consult htop, I see that multiple process named rsession is running, but failed to stop, even if there is no running function inside of it.

I am on ubuntu 25.10. With rstudio 2025.09.2

I really don't know what happend. With Debian (12) it worked on rstudio.

Thanks,
Regards.

PS: This is my sessionInfo() :

R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 25.10

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.1 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.1;  LAPACK version 3.12.0

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

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

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

other attached packages:
 [1] BiocParallel_1.44.0         stringr_1.6.0               devtools_2.4.6              usethis_3.2.1               ggplotify_0.1.3             pdftools_3.6.0              UpSetR_1.4.0               
 [8] data.table_1.17.8           coseq_1.34.0                SummarizedExperiment_1.40.0 Biobase_2.70.0              GenomicRanges_1.62.0        Seqinfo_1.0.0               IRanges_2.44.0             
[15] S4Vectors_0.48.0            BiocGenerics_0.56.0         generics_0.1.4              MatrixGenerics_1.22.0       matrixStats_1.5.0           RColorBrewer_1.1-3          dplyr_1.1.4                
[22] plyr_1.8.9                  ggpubr_0.6.2                reshape2_1.4.5              gplots_3.2.0                FactoMineR_2.12             ggplot2_4.0.1               edgeR_4.8.0                
[29] limma_3.66.0               

loaded via a namespace (and not attached):
 [1] bitops_1.0-9         gridExtra_2.3        HTSFilter_1.50.0     remotes_2.5.0        rlang_1.1.6          magrittr_2.0.4       e1071_1.7-16         compiler_4.5.1       vctrs_0.6.5         
[10] Rmixmod_2.1.10       pkgconfig_2.0.3      fastmap_1.2.0        ellipsis_0.3.2       backports_1.5.0      XVector_0.50.0       caTools_1.18.3       sessioninfo_1.2.3    purrr_1.2.0         
[19] cachem_1.1.0         flashClust_1.01-2    DelayedArray_0.36.0  broom_1.0.10         parallel_4.5.1       cluster_2.1.8.1      R6_2.6.1             stringi_1.8.7        compositions_2.0-9  
[28] pkgload_1.4.1        car_3.1-3            estimability_1.5.1   Rcpp_1.1.0           Matrix_1.7-3         tidyselect_1.2.1     rstudioapi_0.17.1    abind_1.4-8          codetools_0.2-20    
[37] pkgbuild_1.4.8       qpdf_1.4.1           lattice_0.22-7       tibble_3.3.0         withr_3.0.2          S7_0.2.1             askpass_1.2.1        gridGraphics_0.5-1   bayesm_3.1-7        
[46] proxy_0.4-27         capushe_1.1.3        pillar_1.11.1        BiocManager_1.30.27  carData_3.0-5        tensorA_0.36.2.1     KernSmooth_2.23-26   corrplot_0.95        DT_0.34.0           
[55] scales_1.4.0         gtools_3.9.5         xtable_1.8-4         leaps_3.2            class_7.3-23         glue_1.8.0           emmeans_2.0.0        scatterplot3d_0.3-44 tools_4.5.1         
[64] robustbase_0.99-6    locfit_1.5-9.12      ggsignif_0.6.4       fs_1.6.6             mvtnorm_1.3-3        grid_4.5.1           plotrix_3.8-13       tidyr_1.3.1          Formula_1.2-5       
[73] cli_3.6.5            rappdirs_0.3.3       S4Arrays_1.10.0      gtable_0.3.6         DEoptimR_1.1-4       yulab.utils_0.2.1    rstatix_0.7.3        DESeq2_1.50.2        digest_0.6.38       
[82] HTSCluster_2.0.11    SparseArray_1.10.1   ggrepel_0.9.6        htmlwidgets_1.6.4    farver_2.1.2         memoise_2.0.1        htmltools_0.5.8.1    lifecycle_1.0.4      multcompView_0.1-10 
[91] statmod_1.5.1        MASS_7.3-65         

[Jiefei-Wang]

Hello,

It is very hard to tell what happens without a REPEX, but I see you mentioned failed to stop, even if there is no running function inside of it. Do you mean you cannot stop a BPPARAM even when no task is running? What backend did you use in BPPARAM? It will be helpful to have a minimal example here.

Jiefei

[ArthurPERE]

Hello,

I can't really give you a minimal example, because on all others computer my code is working in Rstudio normaly. So I don't really know if it will not work on your computer. And I don't really know what happend so I really can't reproduce that minimaly.

I mean by 'failed to stop', that when I run the code I see the CPU running with htop, and goes back to normal but there is some process spawn 'rsession' (2 or more of those, it depend) that continue to run (with a sleeping status). The function that I called to run the bplapply is stop at this call. And when I stopped the function manually, I get the hand in Rstudio, but the spawn 'rsession' processes are still up. And now I can't run another bplapply, I think because it think that another bplapply is running. I must kill the 'rsession' that spawn all the other 'rsession' (so kill the session of Rstudio), if I try to kill the spawn it make it to zombie status.

My BPPARAM :

> bpparam()
class: MulticoreParam
  bpisup: FALSE; bpnworkers: 30; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
  bpexportglobals: TRUE; bpexportvariables: FALSE; bpforceGC: FALSE
  bpfallback: TRUE
  bplogdir: NA
  bpresultdir: NA
  cluster type: FORK

Arthur