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

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Thu Apr 11 20:28:21 CEST 2019

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


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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