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

[Martin Morgan]

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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