problem with peak to genes

[A-legac45]

Hello @immanuelazn @jeffmgranja @Goultard59 @rcorces @joshchiou ,

I was able before to run peak to genes and now it is not working anymore due to Error in distance(rowRanges(seRNA)[o[, 1]], rowRanges(seATAC)[o[, 2]]) :
unused argument (rowRanges(seATAC)[o[, 2]]):

The command I am using is the following

archr <- addPeak2GeneLinks(
ArchRProj = archr,useMatrix = "GeneExpressionMatrix",
reducedDims = "LSI_ATAC")

Error message

ArchR logging to : ArchRLogs/ArchR-addPeak2GeneLinks-acf91c90f8e9-Date-2025-05-21_Time-00-51-20.120264.log
If there is an issue, please report to github with logFile!
2025-05-21 00:51:20.227687 : Getting Available Matrices, 0.002 mins elapsed.
No predictionScore found. Continuing without predictionScore!
2025-05-21 00:51:20.264585 : Filtered Low Prediction Score Cells (0 of 3733, 0), 0 mins elapsed.
Filtering 1 dims correlated > 0.75 to log10(depth + 1)
2025-05-21 00:51:20.302828 : Computing KNN, 0.001 mins elapsed.
2025-05-21 00:51:20.338491 : Identifying Non-Overlapping KNN pairs, 0.001 mins elapsed.
2025-05-21 00:51:26.508833 : Identified 496 Groupings!, 0.104 mins elapsed.
2025-05-21 00:51:26.525131 : Getting Group RNA Matrix, 0.104 mins elapsed.
2025-05-21 00:51:47.246276 : Getting Group ATAC Matrix, 0.45 mins elapsed.
2025-05-21 00:52:18.64677 : Normalizing Group Matrices, 0.973 mins elapsed.
2025-05-21 00:52:20.586676 : Finding Peak Gene Pairings, 1.006 mins elapsed.
Error in distance(rowRanges(seRNA)[o[, 1]], rowRanges(seATAC)[o[, 2]]) :
unused argument (rowRanges(seATAC)[o[, 2]])

I do not understand why?

can you help?

best

ArchR-addPeak2GeneLinks-acf91c90f8e9-Date-2025-05-21_Time-00-51-20.120264.log