R Error in labelsMatrix[A, 1] == labelsMatrix[i, 1] && labelsMatrix[A, 2] == :

Question

I am using X13CMS package and after updating R from 4.1 to 4.3.1 it stoped working with the same input.

Using the R 4.1 the code worked fine:

labelsM<-getIsoLabelReport(xcmsSet = xs3, sampleNames = sNE, unlabeledSamples = "C12", labeledSamples = "C13", isotopeMassDiff = 1.00335, RTwindow = 10, ppm=15, massOfLabeledAtom = 12, noiseCutoff = 10000, intChoice = "intb", varEq = FALSE, alpha = 0.05, singleSample = FALSE, compareOnlyDistros = FALSE, monotonicityTol = FALSE, enrichTol = 0.1)

But after I updated to R 4.3.1, I am keep getting following error:

Error in labelsMatrix[A, 1] == labelsMatrix[i, 1] && labelsMatrix[A, 2] ==  : 
  'length = 16929' in coercion to 'logical(1)'

Could anyone please tell me, how can I fix this problem?