Dear All, Since the Fedora checks on R-devel are not currently using packages from Bioconductor, one of my packages is giving new warnings. In my case (and it appears for a number of others) this is due to using BiocStyle::html_document format in the package vignette. Since BiocStyle is only required to build the vignette, I had put it in Suggests, but clearly this is not acceptable. So the question is what to do instead. Possibilities include: 1. Use bookdown::html_document2 instead. This would probably be okay to pass CRAN checks as bookdown is on CRAN, but if bookdown were not available the check would fail. The features lost are relatively minor: document styling, date line, package version line, inline table of contents, wide figures. 2. Use html_document instead. If the rmarkdown package is available, the only additional loss from 1. is figure and table referencing (the raw references are shown instead). Otherwise the knitr vignette engine reverts to R Markdown v1, losing information in the YAML header (title, authors and affiliations, abstract) and breaking citations (no references shown). As the result deteriorates moving from BiocStyle to bookdown to rmarkdown to knitr, it would be great to have a way to use the best output format given the packages available. I don't think it is possible to have conditional code in the YAML header, so I guess the only way to do this is via a custom vignette engine. Ideally this would be incorporated in knitr so that it can cope with a preference list of output formats, rather than everyone having to add custom engines to their packages. Does this sound like a good solution? If so, I'm happy to work on it and with anyone else that would like such a thing. Suggestions of how best to do this, or of better alternatives welcome. Best wishes,
Heather [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel