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> 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 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 mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel