[Bioc-devel] Controlling vignette compilation order

[Aaron Lun]

In a number of my workflow packages (e.g., simpleSingleCell), I rely on a specific compilation order for my vignettes. This is because some vignettes set up resources or objects that are to be used by later vignettes. 

From what I understand, vignettes are compiled in alphanumeric ordering of their file names. As such, I give my vignettes fairly structured names, e.g., “work-1-reads.Rmd”, “work-2-umi.Rmd” and so on.

However, it becomes rather annoying when I want to add a new vignette in the middle somewhere. This results in some unnatural numberings, e.g., “work-0”, “3b”, which are ugly and unintuitive. This is relevant as BiocStyle::Biocpkg() links between vignettes require you to use the destination vignette’s file name; so difficult names complicate linking, especially if the names continually change to reflect new orderings.

Is there an easier way to control vignette compilation order? WRE provides no (obvious) guidance, so I would like to know what non-standard hacks are known to work on the build machines. I can imagine something dirty whereby one ”reference” vignette contains code to “rmarkdown::render" all other vignettes in the specified order… ugh. 

-A