Thanks for the update Valerie. Needless to say, I ran R CMD check locally yesterday, and it crashed with the same issue.
Naive question, without looking into the original issue: is it purely a programming issue, or is there a chance that our (seqCAT and TVTB) VCF files need to be updated to match any kind of new standard? Best, Kevin On Wed, Jan 9, 2019 at 3:49 PM Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > The problem is related to a change I made to handle buffer overflow: > > https://github.com/Bioconductor/VariantAnnotation/issues/19 > > This clearly doesn't work for all cases, thanks for reporting the > problems with seqCAT and TVTB. I've reverted the change so your packages > will build and will re-think the fix. > > Valerie > > > On 1/8/19 10:45 AM, Kevin RUE wrote: > > Hi all, > > > > Same kind of error for my TVTB package > > ( > https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/TVTB/malbec1-checksrc.html). > > > > > I'll run R CMD check locally ASAP to see whether I need to update TVTB > > or if it's something upstream. > > > > Best, > > Kevin > > > > On Tue, Jan 8, 2019 at 5:05 PM Obenchain, Valerie > > <valerie.obench...@roswellpark.org > > <mailto:valerie.obench...@roswellpark.org>> wrote: > > > > Hi Erik, > > > > There have been a few changes to VariantAnnotation lately. I'll take > a > > look at seqCAT and get back to you. > > > > Valerie > > > > > > On 1/8/19 6:07 AM, Erik Fasterius wrote: > > > I recently started to get a weird error when building the > > vignette to my seqCAT package, related to a VCF file I use as > > example data. The error itself looks like this: > > > > > > scanVcf: _DNAencode(): invalid DNAString input character: '1' > > (byte value 49) path: (...)/seqCAT/extdata/example.vcf.gz > > > > > > I can also reproduce the error by a simple > > `VariantAnnotation::readVCF()` call. It has worked fine until the > > latest devel-updates of other Bioconductor packages, so I assumed it > > was some new change that caused the error, but I cannot find > > anything in the NEWS seemingly related to this. I also tried to > > troubleshoot by manually inspecting my file, and it seems that the > > ANN field is the culprit; I can read the VCF if I remove the > > entirety of the INFO column. I cannot, however, seem to locate the > > erroneous data itself. > > > > > > Does anybody have any idea what causes this? > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org <mailto: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. > > _______________________________________________ > > Bioc-devel@r-project.org <mailto: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]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel