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-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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=g_Cu4yEp7EWlBco2REuFpytpOSxt4wgJeUQWw3A0zF8&s=7YumO178tpblZmRhmq1bo2X9DlPLETsWOT3wUp2ciU4&e= > > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=g_Cu4yEp7EWlBco2REuFpytpOSxt4wgJeUQWw3A0zF8&s=7YumO178tpblZmRhmq1bo2X9DlPLETsWOT3wUp2ciU4&e= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
