[Bioc-devel] readVcf problems in package check

[Clark, Lindsay V]

I'm the maintainer of polyRAD, which is hosted on CRAN but dependent on several Bioconductor packages including VariantAnnotation.  I'm not sure if my problem is on CRAN's end or Bioconductor's end, but in any event I have not gotten a response from CRAN yet so I thought I would ask here.

I am running into a package check issue which is causing my CRAN submission to be rejected, but which I cannot reproduce.  I have tried fresh installs of R 3.6 and all package dependencies on three different computers and don't see this same error that CRAN reports.  My vignette uses a function that internally calls VariantAnnotation::readVcf, and when the vignette is run, CRAN reports the errors:


  Error: processing vignette 'polyRADtutorial.Rmd' failed with diagnostics:

  invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description

  invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description

I can run readVcf on the same file myself and see that the header contains info and geno DataFrames that are formatted exactly as described, so I have no idea how that error is occurring.

More confusing (and this makes me suspect that something is wrong with CRAN's check) are the messages:

  [E::bcf_hdr_parse_line] Could not parse the header line: "##contig=<ID=01,assembly=""Msi7"">"

  [W::bcf_hdr_parse] Could not parse header line: ##contig=<ID=01,assembly=""Msi7"">

  [W::bcf_hdr_check_sanity] PL should be declared as Number=G

I found these problems with the file (which is contained in inst/extdata), fixed them, resubmitted the package, yet somehow still get the same message from CRAN's checks.

If any of you want to try performing the checks yourselves, my package is hosted here: https://github.com/lvclark/polyRAD.  The call to VCF2RADdata within the vignette is where these mysterious problems are occurring.

Any help is greatly appreciated.  Perhaps this is just some weird issue with the transition from R 3.5 to 3.6.

Best wishes,

-Lindsay

Lindsay Clark, Ph.D.
Research Specialist
Department of Crop Sciences
University of Illinois, Urbana-Champaign


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