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

[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-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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