[Bioc-devel] Windows-specific build error of 'seqCAT' package

[Pages, Herve]

Hi Erik,

The 'invalid class "VCFHeader" object' error on Windows has been fixed 
in Rhtslib 1.15.6.

Cheers,

H.


On 3/18/19 00:36, Erik Fasterius wrote:
> Hi, Valerie!
>
> Thanks for looking into the problem! I hope it’ll work out.
>
> Erik
>
> On 16 Mar 2019, at 22:51, Valerie Obenchain <obenchain.valerie using gene.com<mailto:obenchain.valerie using gene.com>> wrote:
>
> It doesn't look like it was the patch - the error is still there. I'll look in to this some more.
> Valerie
>
> On Fri, Mar 15, 2019 at 11:10 AM Valerie Obenchain <obenchav using gene.com<mailto:obenchav using gene.com>> wrote:
> Hi Erik,
> I think the problem was introduced in a contributed patch applied to VariantAnnotation in devel. I've reverted the patch and expect VariantAnnotation (and downstream packages) to clear up on Windows with tomorrow's builds.
> Valerie
>
> On Thu, Mar 7, 2019 at 4:10 AM Erik Fasterius <erik.fasterius using outlook.com<mailto:erik.fasterius using outlook.com>> wrote:
> Hi,
>
> My seqCAT package recently broke building on the Windows platform, which I assume has to do with changes to the VariantAnnotation package (upon which seqCAT depends). The error (which comes during the creation of the vignette) looks like this:
>
> Quitting from lines 102-112 (seqCAT.Rmd)
> Error: processing vignette 'seqCAT.Rmd' failed with diagnostics:
> invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
> invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
> --- failed re-building 'seqCAT.Rmd'
>
> It builds and completes all checks successfully on all other platforms, though. I have no experience with Windows, so I don’t really know how to even start debugging this issue (I’m working on OS X). Given that other platforms are working fine I’m thinking (hoping) that this is some incompatibility with recent changes to VariantAnnotation (or its dependencies) and the Windows platform, but I have no clue if this is the case.
>
> Does anybody have any idea as to what is the issue here, or have any tips regarding to be debug something on a different platform than the one you are using yourself?
>
> Erik
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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