[Bioc-devel] htSeqTools and giniCoverage error

[Shepherd, Lori]

What is your sessionInfo()? This was corrected in version 1.27.1 of the package so you could try updating to that version.



However,  htSeqTools is currently deprecated in Release Bioc 3.7 and currently scheduled to be removed in Bioc 3.8 as the maintainer has be inactive in maintaining the package and unresponsive to our requests to fix their package.



Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Nicolas Descostes <nicolas.descostes at gmail.com>
Sent: Sunday, May 13, 2018 1:35:05 PM
To: bioc-devel at r-project.org
Cc: oscar.reina at irbbarcelona.org
Subject: [Bioc-devel] htSeqTools and giniCoverage error

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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