decoupler script crashes because it uses all CPUs

Hi, I have been facing this weird issue. Evrytime I run the run_ulm function, suddenly all my cores are used and the machine crashes.

This is the code I was trying to run from the CollecTRI package:

library(tidyverse)
library(decoupleR)
library(magrittr)

## Load files
dorothea_ABC <- read.csv("data/networks/dorothea_ABC.csv")
CollecTRI <- read.csv("output/CollecTRI/CollecTRI_GRN.csv") %>% rename(mor = weight)

# In this use case we use data from CPTAC and three cancer types:
# UCEC: Uterine Corpus Endometrial Carcinoma
# LUAD: Lung Adenocarcinoma
# CCRCC: Clear Cell Renal Cell Carcinoma
download.file("https://zenodo.org/record/7773985/files/ucec_counts_tvalues.csv?download=1", file.path("data", "CPTAC_DEGs", "ucec_counts_tvalues.csv"))
download.file("https://zenodo.org/record/7773985/files/luad_counts_tvalues.csv?download=1", file.path("data", "CPTAC_DEGs", "luad_counts_tvalues.csv"))
download.file("https://zenodo.org/record/7773985/files/ccrcc_counts_tvalues.csv?download=1", file.path("data", "CPTAC_DEGs", "ccrcc_counts_tvalues.csv"))

# Read data in a list of dataframes
file_names = list.files(path ="data/CPTAC_DEGs", pattern="*.csv", full.names = T)
file_list = lapply(file_names, read.csv)
file_list = setNames(file_list, gsub("data/CPTAC_DEGs/|.csv|_counts_tvalues","",file_names))

# Format input for decoupleR
decoupler_inputs <- lapply(file_list, function(x) as.data.frame(x) %>%
                             set_rownames(.$ID) %>% dplyr::select(NATvsTUM_t) %>% filter(!is.na(NATvsTUM_t)))

res_decoupler_CollecTRI <- lapply(decoupler_inputs, function(x) run_ulm(as.matrix(x),network = CollecTRI,.source='source',
                                                                         .target='target', minsize = 5))

After this point I get an R session error and the session crashes.

This is the output of the session info:

R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

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

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
 [1] magrittr_2.0.3  decoupleR_2.8.0 lubridate_1.9.3 forcats_1.0.0   stringr_1.5.1   dplyr_1.1.4    
 [7] purrr_1.0.2     readr_2.1.5     tidyr_1.3.1     tibble_3.2.1    ggplot2_3.5.1   tidyverse_2.0.0

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       cli_3.6.2         rlang_1.1.3       stringi_1.8.3     generics_0.1.3   
 [6] glue_1.7.0        colorspace_2.1-0  hms_1.1.3         scales_1.3.0      fansi_1.0.6      
[11] grid_4.3.3        munsell_0.5.1     tzdb_0.4.0        lifecycle_1.0.4   compiler_4.3.3   
[16] timechange_0.3.0  pkgconfig_2.0.3   rstudioapi_0.16.0 lattice_0.22-6    R6_2.5.1         
[21] tidyselect_1.2.1  utf8_1.2.4        pillar_1.9.0      Matrix_1.6-5      tools_4.3.3      
[26] withr_3.0.0       gtable_0.3.5

Your help is much appreciated.

saezlab / decoupleR

decoupler script crashes because it uses all CPUs #136