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-boun...@r-project.org> on behalf of Stephanie
Gogarten <sdmor...@uw.edu>
Sent: Thursday, April 11, 2019 2:14:52 PM
To: bioc-devel@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
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited. If you have received
this message in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
