Very minor issue; I noticed that some return calls in normalizeChIPtoInput.R are missing list() at

https://github.com/Bioconductor-mirror/edgeR/blob/master/R/normalizeChIPtoInput.R#L24

which will give an error

Error in return(p = rep(0, 1), scaling.factor = 0, prop.enriched = 1) : multi-argument returns are not permitted.

It's not clear how/where to submit patches, but the github repo says bug reports should be submitted here. Sorry for the noise if this is not the right venue.

Thanks for spotting this. Yes, this is a bug, and yes, this is the right place to report it.

Posting a bug here is ok, but most Bioconductor package authors prefer for bug reports to be mailed directly to them, to the email address given in the Maintainer field of the DESCRIPTION file. Section 1.3 of the edgeR User's Guide says:

"The edgeR authors always appreciate receiving reports of bugs in the package functions or
in the documentation. The same goes for well-considered suggestions for improvements. All
other questions or problems concerning edgeR should be posted to the Bioconductor support site."

Anyway, thanks for pointing it out.