Message-ID: <CAKDhoDrmY55fkhSd=KM+QtipGbN1BH+Ds_CaZQmJfPezcnSYTw@mail.gmail.com>
Date: 2020-07-27T11:25:29Z
From: Carlos A. Catania (AKA Harpo)
Subject: [Bioc-devel] BiocCheck space indentation in Rmakrdown vignette documents
In-Reply-To: <BL0PR04MB6609313BD9AAD32649E4CE2FF9750@BL0PR04MB6609.namprd04.prod.outlook.com>
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.bioc at gmail.com>)
escribi?:
> 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-bounces at r-project.org on behalf of grimbough at 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) <
> harpomaxx at 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 at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
[[alternative HTML version deleted]]