Thanks, Martin, that is actually my bug report. I'm considering doing a pull-request with a fix. However, I don't have a clear idea yet on how to deal with the YAML portion of a .rmd file. Regards Carlos A. Catania (AKA Harpo)
El dom., 26 jul. 2020 a las 10:14, Martin Morgan (<mtmorgan.b...@gmail.com>) escribió: > See also this issue https://github.com/Bioconductor/BiocCheck/issues/100 . > > On 7/25/20, 4:57 PM, "Bioc-devel on behalf of Mike Smith" < > bioc-devel-boun...@r-project.org on behalf of grimbo...@gmail.com> wrote: > > Hi Carlos, > > I don't think you need to worry about this. > > The 4 space indentation is a style recommendation (not a requirement), > and > if the only place that your code isn't meeting that recommendation is > the > YAML header then I can't imagine that any reviewer will worry too much > about this. The review process is also a dialog between the package > author > and reviewer, so you have a chance to explain reasons why your code > may be > triggering BiocCheck messages, and if the explanation is reasonable (as > this sounds) then it will probably be accepted by the reviewer. > > Best wishes, > Mike > > On Thu, 23 Jul 2020 at 22:17, Carlos A. Catania (AKA Harpo) < > harpom...@gmail.com> wrote: > > > Hello BioConductor Team, > > > > We are in the final steps prior to submitting a new package to > > Bioconductor. As recommended, we want our package to pass BiocCheck > with > > no Errors, Warnings, or Notes. However, we have a problem regarding > the > > indentation of a vignette written rmarkdown. > > > > -- BEGIN BiocCheck output -- > > [3] "Consider multiples of 4 spaces for line indents, 11 lines(0%) > are not > > -- END BiocCheck output -- > > > > The problem seems to be the indentation required for yaml syntax of > the > > author section. In the section, we have several authors, > affiliations, and > > emails using just multiple of 2 space indentation. The problem is > that we > > could found a way to correctly indent such a section without > breaking the > > vignette construction process. > > > > We have observed that In section 3.1 of the biocstyle vignette about > > authoring using Rmarkdown ( > > > > > https://www.bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html > > ) > > The author and affiliation sections uses just 2 spaces instead of the > > recommended multiple of 4. > > > > So, in your opinion, what would the recommended strategy for dealing > with > > this issue? > > Regards, > > > > Carlos A. Catania (AKA Harpo) > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel