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?
[Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'
7 messages · Obenchain, Valerie, Kevin RUE, Erik Fasterius
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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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 at 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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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 at roswellpark.org <mailto:Valerie.Obenchain at 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 at r-project.org <mailto:Bioc-devel at r-project.org>
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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 at 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 (
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 at roswellpark.org
<mailto:Valerie.Obenchain at 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 at r-project.org <mailto:Bioc-devel at r-project.org>
mailing list
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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 at roswellpark.org
<mailto:Valerie.Obenchain at 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
>
>
> 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 at roswellpark.org
<mailto:Valerie.Obenchain at roswellpark.org>
> <mailto:Valerie.Obenchain at roswellpark.org
<mailto:Valerie.Obenchain at 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 at r-project.org <mailto:Bioc-devel at r-project.org>
<mailto:Bioc-devel at r-project.org <mailto:Bioc-devel at 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 at r-project.org <mailto:Bioc-devel at r-project.org>
<mailto:Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>>
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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 <Valerie.Obenchain at RoswellPark.org<mailto:Valerie.Obenchain at RoswellPark.org>> wrote:
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 at roswellpark.org<mailto:Valerie.Obenchain at roswellpark.org>
<mailto:Valerie.Obenchain at 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 at roswellpark.org<mailto:Valerie.Obenchain at roswellpark.org> <mailto:Valerie.Obenchain at roswellpark.org> <mailto:Valerie.Obenchain at roswellpark.org
<mailto:Valerie.Obenchain at 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 at r-project.org<mailto:Bioc-devel at r-project.org> <mailto:Bioc-devel at r-project.org>
<mailto:Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>>
mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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that
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