[R-pkg-devel] Avoid reprocessing Rmd vignette

You can make things even a bit easier by setting "eval=myeval" and set
"myeval <- FALSE" at the top of the vignette. In case you want to update
the figures, you only have to set "myeval <- TRUE" and run the vignette.

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx at inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

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To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
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<https://www.inbo.be>

2018-03-19 8:18 GMT+01:00 I?aki ?car <i.ucar86 at gmail.com>:

2018-03-19 3:57 GMT+01:00 Tim Keitt <tkeitt at utexas.edu>:

http://www.keittlab.org/

On Sun, Mar 18, 2018 at 8:14 PM, Dirk Eddelbuettel <edd at debian.org>

wrote:

Tim,

On 18 March 2018 at 18:58, Tim Keitt wrote:
| I have an Rmd vignette that runs some benchmarks. It takes long

enough

(20+
| minutes) that eg TravisCI will choke. I've not tried submitting to

CRAN.

| What is the best practice for handling this situation? Do I generate
| HTML/PDF output locally and try to make them static? The vignette

builder

| is knitr. I know about the R.rsp package but I do not know if it

handles

| Rmd files.

Tests are tickled from a runner script such as either one of

      tests/doRUnit.R
      tests/testthat.R

so you have an entry point to control for environment variables.

Travis clearly documents what theirs are -- so you could just turn it

off

--
and I have opted (years ago) for a more endogeneous scheme of

suppressing

tests on CRAN based on version numbers (as I suppress tests when

version

numbers are "release-style" form 'a.b.c', but then run the tests when

the

version number is "dev-style" ie a.b.c.d).

That's a great idea, however my problem is with building a vignette,

not

running tests, unless they are linked in some way I'm not

understanding.

One of my packages on CRAN contains a vignette with a benchmark. You
can check what I do here (search for "microbenchmark"):

https://raw.githubusercontent.com/r-simmer/simmer/master/
vignettes/simmer-07-ctmc.Rmd

Basically, those chunks that use microbenchmark are marked as
"eval=FALSE", and the resulting figures are static images. I run those
manually and update the images from time to time if something relevant
changed. Apart from saving compilation time, this way I don't need to
include microbenchmark as a dependency.

I?aki

THK

You can alternatively check for CRAN via an env.var; I forget what it

is

called and cannot grep for it as my scheme does not need it. WRE may

tell

you
what it is.

Hth,  Dirk

--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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