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[BUG] plotTSSEnrichment() crashes entire R‑session on native Windows #2332
Description
Environment
‑ OS: Windows 11
‑ R‑version: 4.6.0
‑ ArchR: installed from GitHub master branch
‑ Genome: mm10
Minimal reproducible code
library(ArchR)
addArchRGenome("mm10")
addArchRThreads(threads = 1)
# load valid pre‑existing ArchRProject
projncov <- ArchRProject(
ArrowFiles = c(
"D:/ATAC/snATAC-Seq/Nhlh2_P13_scATAC/fragments/ATAC_out/ArrowFiles/CKO_M_1018003.arrow",
"D:/ATAC/snATAC-Seq/Nhlh2_P13_scATAC/fragments/ATAC_out/ArrowFiles/CKO_M_1018004.arrow",
"D:/ATAC/snATAC-Seq/Nhlh2_P13_scATAC/fragments/ATAC_out/ArrowFiles/WT_M_1101005.arrow",
"D:/ATAC/snATAC-Seq/Nhlh2_P13_scATAC/fragments/ATAC_out/ArrowFiles/WT_M_1101006.arrow"
),
outputDirectory = "D:/ATAC/snATAC-Seq/Nhlh2_P13_scATAC/Proj_AllSample",
copyArrows = FALSE
)
# This works perfectly
p_test <- plotGroups(ArchRProj = projncov,
groupBy = "Sample",
colorBy = "cellColData",
name = "TSSEnrichment",
plotAs = "violin")
# Immediately crashes R, no standard R error message
p_tss <- plotTSSEnrichment(ArchRProj = projncov)
# Bug description
Calling plotTSSEnrichment() directly terminates the entire R‑session with the “R Session Aborted” popup in RStudio.
# Steps I have already tried
Set addArchRThreads(threads = 1) to disable multi‑threading
Run plotTSSEnrichment() without any extra ggplot layers
Verified enough available RAM and disk space
# Expected
Generate the TSS‑enrichment profile plot normally.
Activity
immanuelazn commentedon Aug 21, 2026
Hi @Yong-rong! 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.