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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel --- Marcel Ramos Bioconductor Core Team Roswell Park Comprehensive Cancer Center Dept. of Biostatistics & Bioinformatics Elm St. & Carlton St. Buffalo, New York 14263 This email message may contain legally privileged and/or...{{dropped:4}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel