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List:       bioc-devel
Subject:    Re: [Bioc-devel] htSeqTools and giniCoverage error
From:       "Shepherd, Lori" <Lori.Shepherd () RoswellPark ! org>
Date:       2018-05-15 12:31:53
Message-ID: MW2PR12MB236459B07E50B3C0E9589678F9930 () MW2PR12MB2364 ! namprd12 ! prod ! outlook ! com
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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@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@gmail.com>
Sent: Tuesday, May 15, 2018 8:20:47 AM
To: Shepherd, Lori
Cc: bioc-devel@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@roswellpark.org<mailto:Lori.Shepherd@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@r-project.org<mailto:bioc-devel-bounces@r-project.org>> \
on behalf of Nicolas Descostes \
                <nicolas.descostes@gmail.com<mailto:nicolas.descostes@gmail.com>>
Sent: Sunday, May 13, 2018 1:35:05 PM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Cc: oscar.reina@irbbarcelona.org<mailto:oscar.reina@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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