cmdError in system2(path, "callpeak -h", stdout = TRUE, stderr = TRUE)

[aowenson-imm]

Attach your log file ArchR.log

Describe the bug ArchR function addReproduciblePeakSet tries to call program callpeak here: https://github.com/GreenleafLab/ArchR/blob/6feec354ad6c8052ddbc4626a2ca2d858ed465bf/R/ReproduciblePeakSet.R#L788

Problem is that is not a program. It is a command of program macs2, so you actually want macs2 callpeak.

$ callpeak
callpeak: command not found
$ macs2 callpeak
usage: macs2 callpeak [-h] -t TFILE [TFILE ...] ...

Similarly for other macs2 commands:

usage: macs2 [-h] [--version] {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak} ...

I'm confused current ArchR can work for other users. Did an old version of Macs2 create aliases but not anymore? Are they manually creating aliases?

To Reproduce

python -m venv macs2
source macs2/bin/activate
pip install macs2
callpeak
# callpeak: command not found
macs2 callpeak
# usage: macs2 callpeak [-h] ...

Additional information

I'm aware of closed issue #1483, but replies are being ignored. Those replies corroborate my experience.