Hi Lindsay, Is this issue specific to the Windows CRAN checks?
This Windows-specific error was also affecting several Bioconductor packages until recently but has been addressed in the latest version of Rhtslib (v 1.15.6). What version of Rhtslib are they using for the CRAN checks? They need to make sure to use the version that belongs to BioC 3.9: http://bioconductor.org/packages/3.9/Rhtslib which is the version that is known to work with R 3.6.0. BTW have you considered submitting your package to Bioconductor? We typically don't provide support for CRAN packages even if they depend on other Bioconductor packages. In other (cruder) words, by submitting to CRAN, you're on your own. Cheers, H. On 5/1/19 15:07, Clark, Lindsay V wrote: > 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lvclark_polyRAD&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=k3YdEzkx33T7tU3oJOCTF75TwVTnKpuZZGVEXnho13A&s=5zn32_iC0gM0KtfttAxA53zxyqFL3XG1NTFdrdQGCRw&e=. > 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 > > > [[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=k3YdEzkx33T7tU3oJOCTF75TwVTnKpuZZGVEXnho13A&s=7_wAV-QI5Ukxt5rkf7brSdbRiI60Rj7g80x40jsEY_M&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
