do_groupChromPeaks_nearest does not accept data frame

[DWgit]

The doc for do_groupChromPeaks_nearest says

peaks: A ‘matrix’ or ‘data.frame’ with the mz values and retention ...

but the type-checking code in do_groupChromPeaks-functions.R is:

   if (!is.matrix(peaks) | is.data.frame(peaks))
        stop("Peaks has to be a 'matrix' or a 'data.frame'!")

The ! operator has higher precedence than |, so a data frame hits the stop. An obvious fix is to add parens if (! (... | ...))

[jorainer]

Good point! I'll fix.

[jorainer]

It is fixed in the current developmental version (master branch) and also in the branch matching the version from Bioconductor version 3.8. To install the latter:

devtools::install_github("sneumann/xcms", ref = "RELEASE_3_8")

[DWgit]

Thanks for the speedy fix!

[jorainer]

I'm closing the issue now. Feel free to re-open if needed.