I received this error when running cn.mops():

Error in if (all(segMedianT == 0)) { : 
  missing value where TRUE/FALSE needed

The issue occurs when the for loop reaches chrM and encounters the segment function:

> sINI[chrIdx, ,drop=FALSE]
                    WT       MUT
chrM_0_16571 0.2196978 0.2196978
> resSegmList[[chrom]] <- apply(sINI[chrIdx, ,drop=FALSE],2,
+                                       segment,
+                                       minSeg=minWidth)
Error in if (all(segMedianT == 0)) { : 
  missing value where TRUE/FALSE needed

Thought I would let you know!

Best, Henry Miller