PeakCallTiles-groupMat: Error in vapply(all_objects, nrow, integer(1L), USE.NAMES = FALSE) :

[drowsygoat]

ArchR-addReproduciblePeakSet-47655b744492-Date-2024-06-11_Time-11-14-47.log

Error in vapply(all_objects, nrow, integer(1L), USE.NAMES = FALSE) :
  values must be length 1,
 but FUN(X[[2]]) result is length 0
Calls: addReproduciblePeakSet ... Reduce -> f -> rbind -> bindROWS -> bindROWS -> vapply
Execution halted

Reproduced with different parameters using custom genome reference.

[rcorces]

Hi @drowsygoat! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

[erflynn]

FYI I resolved this and similar issues by switching to running ArchR with only one thread for these functions.