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

[sylestiel]

@rcorces
Unfortunately I have encountered the same error:
Error in system2(path, "callpeak -h", stdout = TRUE, stderr = TRUE) :
error in running command

I have run the addReproduciblePeakSet command numerous times without any issue. Hence, I'm confounded. The log file is attached. Hope you can help me troubleshoot.
ArchR-addGroupCoverages-8e7d106fa905-Date-2022-06-21_Time-12-38-45.log

Originally posted by @sylestiel in #200 (comment)

[rcorces]

Hi @sylestiel! 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.

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[rcorces]

you've attached a log file for addGroupCoverages() but are reporting an error for addReproduciblePeakSet(). In all likelihood, something has changed on your end if this was working before. It is likely a problem with your macs2 installation.

[sylestiel]

Trying to reinstall ArchR.

Getting the following error

devtools::install_github("GreenleafLab/ArchR", ref="1.0.2", repos = BiocManager::repositories())
Downloading GitHub repo GreenleafLab/ArchR@1.0.2
Error in utils::download.file(url, path, method = method, quiet = quiet, :
cannot open URL 'https://api.github.com/repos/GreenleafLab/ArchR/tarball/1.0.2'

[rcorces]

1.0.2 is incorrect. its release_1.0.2

[sylestiel]

You were correct. The problem was with my path to MACS2.

[Larrycpan]

you've attached a log file for addGroupCoverages() but are reporting an error for addReproduciblePeakSet(). In all likelihood, something has changed on your end if this was working before. It is likely a problem with your macs2 installation.

@rcorces I have the same error. I have installed macs2 in my end, and there's no error when I perform macs2 callpeak -h. However, the function addReproduciblePeakSet cannot identify the macs2 application, even though I provide the full path.

proj.CRC <- addReproduciblePeakSet(ArchRProj = proj.CRC,
                                   groupBy = "Clusters",
                                   pathToMacs2 = "/media/xxx/xxx/bin/anaconda3/envs/r4-base/bin/macs2")

Look forward to your reply.
ArchR-addGroupCoverages-70c4846c19d2f-Date-2022-08-04_Time-16-55-44.log

[jum1996]

/I have been having the same issue:

`> pathToMacs2 <- findMacs2()
Searching For MACS2..
Found with $path!

projHeme4 <- addReproduciblePeakSet(

• ArchRProj = projHeme4,
• groupBy = "Clusters",
• pathToMacs2 = pathToMacs2
• )
  Error in system2(path, "callpeak -h", stdout = TRUE, stderr = TRUE) :
  error in running command`

I am following the tutorial line by line, I also tried specifying the path and same error. Also, it didn't generate a log file