[Bioc-devel] GWASTools error on tokay related to VariantAnnotation::readVcf

[Pages, Herve]

Hi Stephanie,

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

Cheers,

H.


On 4/11/19 11:28, Shepherd, Lori wrote:
> Please ignore this ERROR for now.  It is a known issue in VariantAnnotation and we are working on the patch.  You can ignore this for now.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Stephanie Gogarten <sdmorris using uw.edu>
> Sent: Thursday, April 11, 2019 2:14:52 PM
> To: bioc-devel using r-project.org
> Subject: [Bioc-devel] GWASTools error on tokay related to VariantAnnotation::readVcf
>
> Hi,
>
> I am puzzled by the current check failure of GWASTools on tokay (but not
> any other platform). I have a unit test that writes a VCF file, which is
> then read in using VariantAnnotation::readVcf. This is the header of the
> VCF file:
>
> ##fileformat=VCFv4.1
>
> ##fileDate=2019-04-11
>
> ##source=GWASTools::vcfWrite()
>
> ##INFO=<ID=IntensityOnly,Number=1,Type=Integer,Description="Indicates
> whether Illumina defined the assay as one for which genotypes should not be
> reported. If IntensityOnly=1 then no genotypes were attempted for this
> assay.">
>
> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
>
>
> Only on tokay, readVcf generates this error:
>
>
> Error in validObject(.Object) :
>
>    invalid class "VCFHeader" object: 'geno(VCFHeader)' must be a 3 column
> DataFrame with names Number, Type, Description
>
> Calls: readVcf ... VCFHeader -> new -> initialize -> initialize ->
> validObject
>
>
> I cannot reproduce this using R-devel and current versions of all
> Bioc-devel packages (notably VariantAnnotation_1.29.25), though I don't
> have a Windows machine to test on. I also don't understand why this error
> would be platform dependent.
>
>
> thanks,
>
> Stephanie
>
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-- 
Hervé Pagès

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