[Bioc-devel] htSeqTools and giniCoverage error

[Nicolas Descostes]

Dear all,

I am using htseqtools on the devel version and I get the following error
when using giniCoverage:

test <- lapply(endoExoBamlist, function(bam_files){
                return(lapply(bam_files, function(bamfile){
                            ga <- if(paired)
                                        granges(readGAligmentPairs(bamfile))
                                    else granges(readGAlignments(bamfile))
                        }))
            })
    test2 <- lapply(test, GRangesList)
    giniCoverage(sample=test2[[1]])

Simulating uniformily distributed data
Error: The RangesList() constructor is defunct. Please coerce to IRangesList
  instead e.g. do 'as(list(x1, x2), "IRangesList")' instead of
  'RangesList(x1, x2)'. Alternatively, you can use the IRangesList()
  constructor e.g. 'IRangesList(x1, x2, compress=FALSE)'. See
  '?IRangesList' for more information.
In addition: Warning messages:
1: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData
2: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData


Looking at the code it seems that the problem is coming from the line 212
of giniCoverage.R:

   RD<-RangedData(RangesList(rangesl))


Would it be possible to correct this? I am using version 1.27.0

Thanks a lot,

Nicolas

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