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

[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, Valerie <
Valerie.Obenchain using 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]]
> >
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>
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