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-boun...@r-project.org> on behalf of > Samuela Pollack <spoll...@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-nore...@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: <r...@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@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]]
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