[Bioc-devel] Vignettes with many output graphics - How to fulfill the Bioc build requirements, best practises?

Marcel Ramos m@rce|@r@mo@perez @end|ng |rom ro@we||p@rk@org
Tue Mar 22 21:09:58 CET 2022

Hi Christian,

Thanks for reaching out.

 From what I gather, perhaps a workflow package submission is more 
appropriate for the
details that you would like to submit within the vignette. We recommend 
vignettes that have
small and run-able examples (possibly from simulated data) that 
demonstrate package functionality.

I haven't taken a look at the 'mysterious' package but perhaps consider 
breaking up the functionality
into separate packages, if possible. For example, you could have one 
package for each of the facilities
(e.g., stats, viz, utils, etc).

As for producing PDFs from plotting functions, this is generally 
Plotting functions should work like plot(1:10) and should output a 
single plot (or grouped plots)
to the graphics device. The user should then be free to choose the file 
format for any plot produced.
This approach may in turn resolve the issues you describe with plots in 
the vignette.

It may require some time re-designing the package(s) but I think your 
users would benefit
in the long run.

Best regards,


On 3/22/22 4:05 PM, James W. MacDonald wrote:
> If the pages from the PDF are essentially static (for your vignette, that is), why not run it once, get the pngs, save them somewhere, and use eval = FALSE in the knitr headers for the plot* fuctions. Then you will speed things up, there won't be all this extra PDF documentation that's +/- not part of the vignette, and it should run much faster.
> -----Original Message-----
> From: Bioc-devel<bioc-devel-bounces using r-project.org>  On Behalf Of Christian Arnold
> Sent: Tuesday, March 22, 2022 3:33 PM
> To:bioc-devel using r-project.org
> Subject: [Bioc-devel] Vignettes with many output graphics - How to fulfill the Bioc build requirements, best practises?
> Hi, I wanted to reach out for some thoughts on the following problem I am facing with a package I recently submitted to Bioc. In essence, I am struggling with the 15 minutes time limit for R CMD check as well as the package size limit of 5 MB. The latter is more important, so let's focus on that:
> It is a quite large package with many functions, a full workflow for building gene-regulatory networks, and we want to include a detailed workflow vignette where the most important output plots are shown and explained, to make it user-friendly and easy to apply.
> For various plot* functions produce PDFs that have many pages (sometimes dozens or even hundreds), only some of which should be shown in the vignette (say page 2 and 5 from PDF A, and page 1 and 2 from PDF B, etc). Including selected pages from a PDF doesnt seem to be possible with BiocStyle (please correct me if I am wrong), so currently, I am automatically converting each page of each of the various PDFs as a png image, to include selected pages then in the Vignette via knitr::include_graphics. This works well, but leads to the repo being too big (currently 11 MB) when being build - because the original images as well as the resulting htmls in the inst folder contain the images, making it bigger than 5 MB. I could reduce the resolution of the images much further, but this feels wrong also. In total, we talk about 40 or so images that I wanted to share across the different vignettes.
> Are there any thoughts on how I can proceed here without spending a lot of time on re-designing the package logic (which I unfortunately dont have at this point) and without sacrificing the usability of the package (I could just remove the Workflow vignette or host it externally I guess)?
> Thanks, your input is very appreciated.
> Best
> Christian
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Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263

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