[Bioc-devel] BiocCheck space indentation in Rmakrdown vignette documents

[Carlos A. Catania (AKA Harpo)]

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 using 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-bounces using r-project.org on behalf of grimbough using 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 using 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)
>     >
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>     >
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