[Bioc-devel] GenomeInfoDb is breaking bumphunter

[Samuela Pollack]

OK, thanks Bioconductor, we'll sit tight and wait for it to propagate.

- Sam


On 2/13/19 10:06 AM, Shepherd, Lori wrote:
>
> ��������External Email - Use Caution
>
>
> Herve implemented a fix in release and devel as indicated by the 
> support site question
>
> https://support.bioconductor.org/p/117808/
>
> It has yet to propagate to the system but��should be up later today.
>
>
>
> 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 using r-project.org> on behalf of 
> Samuela Pollack <spollack using jimmy.harvard.edu>
> *Sent:* Wednesday, February 13, 2019 10:00:18 AM
> *To:* Rafael Irizarry; Leonardo Collado Torres; Bioc-devel
> *Subject:* [Bioc-devel] GenomeInfoDb is breaking bumphunter
> Dear Bioconductor,
>
> The GenomeInfoDb package is generating an error in 3.8 and causing our
> package bumphunter to crash too.
>
> Our test calls GenomeInfoDb::fetchExtendedChromInfoDb and crashes with
> an error that says some UCSC seqlevels in hg38 couldn't be mapped to
> NCBI seqlevels. The release version of GenomeInfoDb is crashing in the
> same function with the same error message.
>
> The github repo for GenomeInfoDb indicates some work was done on this
> routine two days ago. It looks like maybe we need a way to set the
> drop_unmapped flag? Is that possible? What would you recommend?
>
> thanks,
>
> - Sam
>
>
>
>
>
> On 2/12/19 12:55 PM, Rafael Irizarry wrote:
> > see below
> >
> > ---------- Forwarded message ---------
> > From: <BBS-noreply using bioconductor.org>
> > Date: Tue, Feb 12, 2019 at 12:48 PM
> > Subject: bumphunter problems reported in the Multiple platform
> > build/check report for BioC 3.8
> > To: <rafa using jimmy.harvard.edu>
> >
> >
> >��������� External Email - Use Caution
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> > [This is an automatically generated email. Please don't reply.]
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> > Hi bumphunter maintainer,
> >
> > According to the Multiple platform build/check report for BioC 3.8,
> > the bumphunter package has the following problem(s):
> >
> >��� o ERROR for 'R CMD check' on malbec1. See the details here:
> > 
> https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/bumphunter/malbec1-checksrc.html
> >
> > Please take the time to address this by committing and pushing
> > changes to your package at git.bioconductor.org
> >
> > Notes:
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