[Bioc-devel] GenomeInfoDb is breaking bumphunter

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Wed Feb 13 16:06:57 CET 2019

Herve implemented a fix in release and devel as indicated by the support site question


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?


- 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
> [This is an automatically generated email. Please don't reply.]
> 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:
>    * This was the status of your package at the time this email was sent to you.
>      Given that the online report is updated daily (in normal conditions) you
>      could see something different when you visit the URL(s) above, especially if
>      you do so several days after you received this email.
>    * It is possible that the problems reported in this report are false
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>      either because another package (from CRAN or Bioconductor) breaks your
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