[Bioc-devel] htSeqTools and giniCoverage error
But ... yes. The package is scheduled to be removed unless it is fixed before the next release so it is not advisable in its current state to utilize its functionality. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Shepherd, Lori
Sent: Tuesday, May 15, 2018 8:30:32 AM
To: Nicolas Descostes
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] htSeqTools and giniCoverage error
Sent: Tuesday, May 15, 2018 8:30:32 AM
To: Nicolas Descostes
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] htSeqTools and giniCoverage error
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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