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

Stephanie Gogarten @dmorr|@ @end|ng |rom uw@edu
Thu Apr 11 20:14:52 CEST 2019


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:




whether Illumina defined the assay as one for which genotypes should not be
reported. If IntensityOnly=1 then no genotypes were attempted for this


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 ->

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.



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