Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

2019-01-09 Thread Erik Fasterius
Thanks for the update, Valerie! And thanks for asking the question that I also had in mind, Kevin. I’ll follow the GitHub issue and retry once the change has been reverted. Erik On 10 Jan 2019, at 03:13, Obenchain, Valerie mailto:valerie.obench...@roswellpark.org>> wrote: On 1/9/19 8:36 AM,

Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

2019-01-09 Thread Obenchain, Valerie
On 1/9/19 8:36 AM, Kevin RUE wrote: > 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 (seqCA

Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

2019-01-09 Thread Kevin RUE
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

Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

2019-01-09 Thread Obenchain, Valerie
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-thin

Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

2019-01-08 Thread Kevin RUE
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,

Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

2019-01-08 Thread Obenchain, Valerie
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 exam

[Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

2019-01-08 Thread Erik Fasterius
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