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

[Carlos A. Catania (AKA Harpo)]

Hello, Mike,
Thanks for your answer and info about the review process.
As recommended by Lori we filled a bug report about the issue.

Thanks again and best regards

Carlos A. Catania (AKA Harpo)


El sáb., 25 jul. 2020 a las 17:56, Mike Smith (<grimbough using gmail.com>)
escribió:

> 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)
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

	[[alternative HTML version deleted]]