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

[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 (seqCAT and TVTB) VCF 
> files need to be updated to match any kind of new standard?

I don't think it's related to the vcf standard but more with handling 
buffer overflow gracefully under different circumstances.

Valerie



> 
> Best,
> Kevin
> 
> On Wed, Jan 9, 2019 at 3:49 PM Obenchain, Valerie 
> <Valerie.Obenchain using roswellpark.org 
> <mailto: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>
>      > <mailto: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]]
>      >      >
>      >      > _______________________________________________
>      >      > Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org>
>     <mailto:Bioc-devel using r-project.org <mailto:Bioc-devel using 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 using r-project.org <mailto:Bioc-devel using r-project.org>
>     <mailto:Bioc-devel using r-project.org <mailto:Bioc-devel using 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.
> 



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.