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

[Erik Fasterius]

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 
mailto:valerie.obench...@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
mailto:valerie.obench...@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
mailto:valerie.obench...@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@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@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, 

Re: [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 
>  > 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
>  >  
>  >  >> 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@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@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 

Re: [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.obench...@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
> >  > > 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@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@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.
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [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 
>  > 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@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@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [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.obench...@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@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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

[Obenchain, Valerie]

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@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

[Erik Fasterius]

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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel