[Bioc-devel] Controlling vignette compilation order

Michael Lawrence l@wrence@mich@el @ending from gene@com
Tue Dec 18 14:34:36 CET 2018

I would recommend against dependencies across vignettes. Ideally someone
can pick up a vignette and execute the code independently of any other
documentation. Perhaps you could move the code generating those shared
resources to the package. They could behave lazily, only generating the
resource if necessary, otherwise reusing it. That would also make it easy
for people to write their own documents using those resources.


On Tue, Dec 18, 2018 at 5:22 AM Aaron Lun <
infinite.monkeys.with.keyboards using gmail.com> wrote:

> 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
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