Error in doubScores function

[SergioManzano10]

Hi,
I am trying to add doublet scores to my ArchRproj. But I am getting the following error. I have tried to reduce the number of samples but the vector size it is trying to allocate is always the same size. Any suggestions?
Thanks!

I share:

The code:

ArrowFiles <- createArrowFiles(
  inputFiles = inputFiles,
  sampleNames = names(inputFiles),
  filterTSS = 4, # we can increase these thresholds later
  filterFrags = 1000,
  addTileMat = TRUE,
  addGeneScoreMat = TRUE
)

# check
ArrowFiles

#--- add doublet scores
doubScores <- addDoubletScores(
  input = ArrowFiles[1],
  k = 10, #Refers to how many cells near a "pseudo-doublet" to count.
  knnMethod = "UMAP", #Refers to the embedding to use for nearest neighbor search with doublet projection.
  LSIMethod = 1
)

The error:

************************************************************
2025-06-11 15:41:21.782799 : ERROR Found in Simulate LSI Project Doublets for clone18 (1 of 1) :  
LogFile = ArchRLogs/ArchR-addDoubletScores-1a1a2c1e8381bf-Date-2025-06-11_Time-15-36-30.551094.log

<simpleError in .doLoadActions(where, attach): error in load action .__A__.1 for package nabor: loadModule(module, NULL, env = where, loadNow = TRUE): Unable to load module "class_WKNNF": cannot allocate vector of size 706662.5 Gb>

************************************************************


************************************************************
2025-06-11 15:41:22.113951 : ERROR Found in .simulateProjectDoublets for clone18 (1 of 1) :  
LogFile = ArchRLogs/ArchR-addDoubletScores-1a1a2c1e8381bf-Date-2025-06-11_Time-15-36-30.551094.log

<simpleError in .logError(e, fn = "Simulate LSI Project Doublets", info = prefix,     errorList = errorList, logFile = logFile): Exiting See Error Above>

************************************************************

Error in .logError(e, fn = ".simulateProjectDoublets", info = prefix,  : 
  Exiting See Error Above

The session info:

─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.2 (2024-10-31)
 os       Debian GNU/Linux 12 (bookworm)
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Berlin
 date     2025-06-11
 rstudio  2024.12.1+563.pro5 Kousa Dogwood (server)
 pandoc   3.2 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/x86_64/ (via rmarkdown)

─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package                           * version   date (UTC) lib source
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 [1] /omics/groups/OE0219/internal/SergioM/Rlibraries
 [2] /software/R/4.4.2-GCCcore-14.1.0/lib/R/library

[immanuelazn]

Hi @SergioManzano10! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.

If you are getting an error, it is likely due to something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If your post does not contain a reproducible example, it is unlikely to receive a response.

In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information:
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Did you post your log file? If not, add it now.
3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

[SergioManzano10]

This is the log file

ArchR-addDoubletScores-c79a46a53b670-Date-2025-06-12_Time-12-05-46.604038.log