[Bioc-devel] htSeqTools and giniCoverage error

[Nicolas Descostes]

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>:

> 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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>
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