[Bioc-devel] GenomeInfoDb is breaking bumphunter

[Shepherd, Lori]

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
>
> [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
> positives,
>      either because another package (from CRAN or Bioconductor) breaks your
>      package (if yours depends on it) or because of a Build System problem.
>      If this is the case, then you can ignore this email.
>
>    * Please check the report again 24h after you've committed your changes to the
>      package and make sure that all the problems have gone.
>
>    * If you have questions about this report or need help with the
>      maintenance of your package, please use the Bioc-devel mailing list:
>
>        https://bioconductor.org/help/mailing-list/
>
>      (all package maintainers are requested to subscribe to this list)
>
> For immediate notification of package build status, please
> subscribe to your package's RSS feed. Information is at:
>
> https://bioconductor.org/developers/rss-feeds/
>
> Thanks for contributing to the Bioconductor project!

_______________________________________________
Bioc-devel using r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]