Error in addFragments when calling multiple Spectra objects

[guideflandre]

In addFragments, an error is thrown when the length of x, the Spectra object, is higher than 1:

addFragments <- function (x, tolerance = 0, ppm = 20, ...) {
    stopifnot(requireNamespace("Spectra"))
    stopifnot(inherits(x, "Spectra"), length(x) == 1)

This in itself is not a problem, but when combining with plotSpectra these different cases occur:

## Code works and plot is given with default parameters for `calculateFragments`
plotSpectra(sc[1:4], labels = addFragments)

## throws an error in addFragments, argument x is missing with no default
plotSpectra(sc[1:4], labels = addFragments(type = c("a"))) 

## thus needs to call the spectra object explicitly with the custom parameters but..
## this throws an error in `addFragments` as length(x) != 1 (see above)
plotSpectra(sc[1:4], labels = addFragments(sc[1:4], type = c("a"))) 

In short, plotSpectra coupled to addFragments only works with its default parameters. If these parameters are changed, this can only be done on 1 spectrum at a time and not multiple.

[guideflandre]

This issue might be more relevant for plotSpectra in the Spectra package