findIsotopes throws "Error in mint[ipeak, , drop = FALSE] : subscript out of bounds

[jmorim]

Happens when I tried processing a single data file. The other annotation functions work except this one. CAMERA version 1.44.0.
Debugging shows ipeak is a list from 1947:1963, when the mint matrix only has length 1843.

[jmorim]

Seems to be an issue with

CAMERA/R/xsAnnotate.R

Lines 609 to 627 in 0ff0ebf

	# get mz,rt and intensity values from peaktable
	if(nrow(groups(object@xcmsSet)) > 0){
	##multiple sample or grouped single sample
	if(is.na(object@sample[1])){
	index <- 1:length(object@xcmsSet@filepaths);
	}else{
	index <- object@sample;
	}
	cat("Generating peak matrix!\n");
	mint <- groupval(object@xcmsSet,value=intval)[,index,drop=FALSE];
	imz <- object@groupInfo[, "mz", drop=FALSE];
	irt <- object@groupInfo[, "rt", drop=FALSE];
	}else{
	##one sample case
	cat("Generating peak matrix!\n");
	imz <- object@groupInfo[, "mz", drop=FALSE];
	irt <- object@groupInfo[, "rt", drop=FALSE];
	mint <- object@groupInfo[, intval, drop=FALSE];
	}

A single file doesn't trigger the else condition, is
if(nrow(groups(object@xcmsSet)) > 0)
supposed to be
if(length(object@xcmsSet@filepaths) > 1)?
It seems the point is to tell whether or not the dataset is a single file.

[sneumann]

The nrow(groups(object@xcmsSet)) > 0 checks if group() had been called before.
Best thing to get this right would be unit tests for all combinations of

1. one 2) multiple files a) grouped b) not grouped (where 1a probably does not exist).
   Yours, Steffen

[jmorim]

I don't understand why 1a wouldn't exist since grouping in xcms groups within samples according to the docs.
I'm also stuck on why groupval(object@xcmsSet) returns a shorter list than the number of peaks in all pspectra, length(unlist(object@pspectra)) for a single file, but not multiple.

For now I'm changing

CAMERA/R/xsAnnotate.R

Line 610 in 0ff0ebf

if(nrow(groups(object@xcmsSet)) > 0){

to
if(nrow(groups(object@xcmsSet)) > 0 && length(object@sample) > 1){...