Yes, moving the heavy vignette to a workflow package is probably a good
idea. See this post from last month for more info about workflow packages:
https://stat.ethz.ch/pipermail/bioc-devel/2022-February/018821.html
Cheers,
H.
On 22/03/2022 13:09, Marcel Ramos wrote:
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
discouraged.
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,
Marcel
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-boun...@r-project.org> On Behalf Of Christian
Arnold
Sent: Tuesday, March 22, 2022 3:33 PM
To:bioc-devel@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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Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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