[Bioc-devel] Controlling vignette compilation order

Martin Morgan mtmorg@n@bioc @ending from gm@il@com
Tue Dec 18 15:14:39 CET 2018

Also perhaps using BiocFileCache so that the result object is only generated once, then cached for future (different session) use.

On 12/18/18, 8:35 AM, "Bioc-devel on behalf of Michael Lawrence" <bioc-devel-bounces using r-project.org on behalf of lawrence.michael using gene.com> wrote:

    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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