[Bioc-devel] htSeqTools and giniCoverage error

[Shepherd, Lori]

You could always reach out to the maintainer to try and get them interested again.


Or reach out on the mailing list or support site to see if anyone else is interested in taking over maintaining the package.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Nicolas Descostes <nicolas.descostes at gmail.com>
Sent: Tuesday, May 15, 2018 8:20:47 AM
To: Shepherd, Lori
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] htSeqTools and giniCoverage error

I guess I should make my package independent of it then, but that's going to ask some work. That's very unfortunate...

2018-05-15 7:24 GMT-04:00 Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>>:

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<mailto:bioc-devel-bounces at r-project.org>> on behalf of Nicolas Descostes <nicolas.descostes at gmail.com<mailto:nicolas.descostes at gmail.com>>
Sent: Sunday, May 13, 2018 1:35:05 PM
To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
Cc: oscar.reina at irbbarcelona.org<mailto: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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