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)
[Bioc-devel] BiocCheck space indentation in Rmakrdown vignette documents
5 messages · Carlos A. Catania (AKA Harpo), Mike Smith, Martin Morgan
2 days later
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
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
>
_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 s?b., 25 jul. 2020 a las 17:56, Mike Smith (<grimbough at gmail.com>) escribi?:
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
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 (
>
>
> )
> 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]]
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Bioc-devel at r-project.org mailing list
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