Error: package or namespace load failed for ‘marge’

[xeccm]

Hi!

I have some installation problems with marge. This is the error:

''' marge 0.0.4.9999 (dev version) Checking for HOMER installation... HOMER installation found. Error: package or namespace load failed for ‘marge’: .onAttach failed in attachNamespace() for 'marge', details: call: system("type -a findMotifsGenome.pl", intern = TRUE) error: error in running command '''

[El-Castor]

Hi weccm,

I've the same issue, do you have fix it ? Thanks in advance

[monovich]

Also same issue. Seems like its an issue with marge being able to run the findMotifsGenome.pl script. I really only want to use marge for the downstream processing of the html files so I find it ~~really~~ mildly annoying that homer configuration is a requirement to utilize this package.

[robertamezquita]

Sorry @monovich you find this to be "really annoying", I would welcome a PR to help fix the issue, as I have limited time these days to maintain this package (esp since I am no longer working actively with motif analysis).

I agree though with your assertion that it would be desirable to modularize the package into two parts: one containing the scripts to run HOMER (such as that using the findMotifsGenome.pl script) and the other to read HOMER results. Not a bad idea!

[monovich]

@robertamezquita I apologize if that came off as rude! I should have said "mildly annoying" as opposed to "really annoying". I neglected to add that I really appreciate the work you've done on this. Your package is definitely the most complete HOMER helper/output parser I've come across. Anything that saves me the trouble of writing my own regular expressions to parse HOMER's rather inaccessible output is fantastic.

I'm glad you're open to the idea of modularization. Given the development status of the package, I think it makes total sense to break off the output parsing from the HOMER calls, especially because everything in the parser seems to work perfectly out of the box when the scripts are simply sourced directly and supplemented with tidyverse. I think you'd have a totally stable HOMER complement package on your hands if you did so. In my book a stable, lightweight, & reproducible package > semi-stable but more feature-rich package.