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

[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 any kind of new standard?

Best,
Kevin

On Wed, Jan 9, 2019 at 3:49 PM Obenchain, Valerie <
Valerie.Obenchain using 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.Obenchain using roswellpark.org
> > <mailto: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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