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

[Shepherd, Lori]

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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