p4cNewProfile runs infinitely

[CitricCoR]

CMK_fc <- p4cNewProfile(str_glue('umi4C_CMK_DS_ANK1_TSS'), scope_5=200000, scope_3=200000)

see above, when trying to run the pipeline, executing this line will result. The dot number just keep increasing (last time I checked it the number of dots reached above 300) after some debug we think the issue may be related to misha https://github.com/tanaylab/misha/blob/e97bde51f020898172d2586e676f7a9796553272/R/compute.R#L285

R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS/LAPACK: /home/jiazr18/.conda/envs/JZR_RS/lib/libopenblasp-r0.3.18.so

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

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

other attached packages:
 [1] umi4cPackage_0.0.1          misha_4.1.0                 zoo_1.8-10                  RColorBrewer_1.1-3         
 [5] VennDiagram_1.7.3           futile.logger_1.4.3         org.Mm.eg.db_3.14.0         GenomicFeatures_1.46.5     
 [9] AnnotationDbi_1.56.2        clusterProfiler_4.2.0       ChIPpeakAnno_3.28.0         rtracklayer_1.54.0         
[13] data.table_1.14.2           Biostrings_2.62.0           XVector_0.34.0              sp_1.5-0                   
[17] SeuratObject_4.1.0          Seurat_4.1.1                ChIPseeker_1.32.0           DESeq2_1.34.0              
[21] DiffBind_3.4.11             SummarizedExperiment_1.24.0 Biobase_2.54.0              MatrixGenerics_1.6.0       
[25] matrixStats_0.62.0          GenomicRanges_1.46.1        GenomeInfoDb_1.30.1         IRanges_2.28.0             
[29] S4Vectors_0.32.4            BiocGenerics_0.40.0         readxl_1.4.2                forcats_0.5.1              
[33] stringr_1.4.0               purrr_0.3.4                 readr_2.1.2                 tidyr_1.2.0                
[37] tibble_3.1.7                ggplot2_3.3.6               tidyverse_1.3.2             dplyr_1.0.9                

loaded via a namespace (and not attached):
  [1] ica_1.0-3                               apeglm_1.16.0                           Rsamtools_2.10.0                       
  [4] foreach_1.5.2                           lmtest_0.9-40                           crayon_1.5.1                           
  [7] spatstat.core_2.4-2                     MASS_7.3-57                             nlme_3.1-157                           
 [10] backports_1.4.1                         reprex_2.0.1                            GOSemSim_2.20.0                        
 [13] rlang_1.0.4                             ROCR_1.0-11                             irlba_2.3.5                            
 [16] limma_3.50.3                            filelock_1.0.2                          BiocParallel_1.28.3                    
 [19] rjson_0.2.21                            bit64_4.0.5                             glue_1.6.0                             
 [22] mixsqp_0.3-43                           sctransform_0.3.3                       parallel_4.1.1                         
 [25] spatstat.sparse_2.1-1                   regioneR_1.26.0                         DOSE_3.20.0                            
 [28] spatstat.geom_2.4-0                     haven_2.5.2                             tidyselect_1.1.2                       
 [31] fitdistrplus_1.1-8                      XML_3.99-0.9                            GenomicAlignments_1.30.0               
 [34] xtable_1.8-4                            magrittr_2.0.3                          cli_3.3.0                              
 [37] zlibbioc_1.40.0                         hwriter_1.3.2.1                         rstudioapi_0.13                        
 [40] miniUI_0.1.1.1                          rpart_4.1.16                            GreyListChIP_1.26.0                    
 [43] fastmatch_1.1-3                         ensembldb_2.18.4                        lambda.r_1.2.4                         
 [46] treeio_1.18.1                           shiny_1.7.2                             clue_0.3-61                            
 [49] multtest_2.50.0                         cluster_2.1.3                           caTools_1.18.2                         
 [52] tidygraph_1.2.1                         KEGGREST_1.34.0                         ggrepel_0.9.1                          
 [55] ape_5.6-2                               listenv_0.8.0                           png_0.1-7                              
 [58] future_1.27.0                           withr_2.5.0                             bitops_1.0-7                           
 [61] ggforce_0.3.3                           RBGL_1.70.0                             plyr_1.8.7                             
 [64] cellranger_1.1.0                        AnnotationFilter_1.18.0                 coda_0.19-4                            
 [67] pillar_1.8.0                            GlobalOptions_0.1.2                     gplots_3.1.3                           
 [70] cachem_1.0.6                            fs_1.5.2                                GetoptLong_1.0.5                       
 [73] vctrs_0.4.1                             ellipsis_0.3.2                          generics_0.1.3                         
 [76] tools_4.1.1                             munsell_0.5.0                           tweenr_1.0.2                           
 [79] fgsea_1.20.0                            DelayedArray_0.20.0                     fastmap_1.1.0                          
 [82] compiler_4.1.1                          abind_1.4-5                             httpuv_1.6.5                           
 [85] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 plotly_4.10.0                           rgeos_0.5-9                            
 [88] GenomeInfoDbData_1.2.7                  gridExtra_2.3                           InteractionSet_1.22.0                  
 [91] lattice_0.20-45                         deldir_1.0-6                            utf8_1.2.2                             
 [94] later_1.3.0                             BiocFileCache_2.2.1                     jsonlite_1.8.0                         
 [97] scales_1.2.0                            graph_1.72.0                            tidytree_0.3.9                         
[100] pbapply_1.5-0                           genefilter_1.76.0                       lazyeval_0.2.2                         
[103] promises_1.2.0.1                        doParallel_1.0.17                       latticeExtra_0.6-30                    
[106] goftest_1.2-3                           spatstat.utils_2.3-1                    reticulate_1.25                        
[109] cowplot_1.1.1                           Rtsne_0.16                              downloader_0.4                         
[112] BSgenome_1.62.0                         uwot_0.1.11                             igraph_1.3.1                           
[115] survival_3.3-1                          numDeriv_2016.8-1.1                     yaml_2.3.5                             
[118] plotrix_3.8-2                           ashr_2.2-54                             SQUAREM_2021.1                         
[121] htmltools_0.5.3                         memoise_2.0.1                           BiocIO_1.4.0                           
[124] locfit_1.5-9.5                          graphlayouts_0.8.0                      viridisLite_0.4.0                      
[127] digest_0.6.29                           assertthat_0.2.1                        mime_0.12                              
[130] rappdirs_0.3.3                          futile.options_1.0.1                    emdbook_1.3.12                         
[133] RSQLite_2.2.14                          amap_0.8-18                             yulab.utils_0.0.5                      
[136] future.apply_1.9.0                      blob_1.2.3                              splines_4.1.1                          
[139] googledrive_2.0.0                       ProtGenerics_1.26.0                     RCurl_1.98-1.6                         
[142] broom_1.0.0                             hms_1.1.1                               eulerr_6.1.1                           
[145] modelr_0.1.8                            colorspace_2.0-3                        shape_1.4.6                            
[148] aplot_0.1.6                             Rcpp_1.0.8.3                            RANN_2.6.1                             
[151] circlize_0.4.15                         mvtnorm_1.1-3                           enrichplot_1.14.1                      
[154] fansi_1.0.3                             tzdb_0.3.0                              truncnorm_1.0-8                        
[157] parallelly_1.32.1                       R6_2.5.1                                ggridges_0.5.3                         
[160] lifecycle_1.0.1                         formatR_1.12                            ShortRead_1.52.0                       
[163] curl_4.3.2                              googlesheets4_1.0.0                     leiden_0.4.2                           
[166] DO.db_2.9                               Matrix_1.4-1                            qvalue_2.26.0                          
[169] RcppAnnoy_0.0.19                        iterators_1.0.14                        htmlwidgets_1.5.4                      
[172] polyclip_1.10-0                         biomaRt_2.50.3                          shadowtext_0.1.2                       
[175] gridGraphics_0.5-1                      ComplexHeatmap_2.10.0                   rvest_1.0.2                            
[178] mgcv_1.8-40                             globals_0.15.1                          patchwork_1.1.1                        
[181] spatstat.random_2.2-0                   bdsmatrix_1.3-6                         progressr_0.10.1                       
[184] codetools_0.2-18                        invgamma_1.1                            lubridate_1.8.0                        
[187] GO.db_3.14.0                            gtools_3.9.3                            prettyunits_1.1.1                      
[190] dbplyr_2.2.1                            gtable_0.3.0                            DBI_1.1.3                              
[193] ggfun_0.0.6                             tensor_1.5                              httr_1.4.3                             
[196] KernSmooth_2.23-20                      stringi_1.7.6                           progress_1.2.2                         
[199] reshape2_1.4.4                          farver_2.1.1                            annotate_1.72.0                        
[202] viridis_0.6.2                           ggtree_3.2.1                            xml2_1.3.3                             
[205] bbmle_1.0.25                            systemPipeR_2.0.8                       boot_1.3-28                            
[208] restfulr_0.0.15                         interp_1.1-3                            geneplotter_1.72.0                     
[211] ggplotify_0.1.0                         scattermore_0.8                         bit_4.0.4                              
[214] scatterpie_0.1.7                        jpeg_0.1-9                              spatstat.data_2.2-0                    
[217] ggraph_2.0.5                            pkgconfig_2.0.3                         gargle_1.2.0 

[aviezerl]

Can you please try to run:

gdb.reload()

and then rerun the above commands?