On 05/14/2015 04:33 PM, Henrik Bengtsson wrote:
On May 14, 2015 15:04, "January Weiner" <january.wei...@gmail.com> wrote:
Dear all,
I am writing a vignette that requires a file which I am not allowed to
distribute, but which the user can easily download manually. Moreover, it
is not possible to download this file automatically from R: downloading
requires a (free) registration that seems to work only through a browser.
(I'm talking here about the MSigDB from the Broad Institute,
http://www.broadinstitute.org/gsea/msigdb/index.jsp).
In the vignette, I tell the user to download the file and then show how it
can be parsed and used in R. Thus, I can compile the vignette only if this
file is present in the vignettes/ directory of the package. However, it
would then get included in the package -- which I am not allowed to do.
What should I do?
(1) finding an alternative to MSigDB is not a solution -- there simply is
no alternative.
(2) I could enter the code (and the results) in a verbatim environment
instead of using Sweave. This has obvious drawbacks (for one thing, it
would look incosistent).
use the chunk argument eval=FALSE instead of placing the code in a verbatim
argument. See ?RweaveLatex if you're compiling a PDF vignette from Rnw or the
knitr documentation for (much nicer for users of your vignette, in my opinion)
Rmd vignettes processed to HTML.
A common pattern is to process chunks 1, 2, 3, 4, and then there is a 'leap of
faith' in chunk 5 (with eval=FALSE) and a second chunk (maybe with echo=FALSE,
eval=TRUE) that reads the _result_ that would have been produced by chunk 5 from
a serialized instance into the R session for processing in chunks 6, 7, 8...
Also very often while it might make sense to analyse an entire data set as part
of a typical work flow, for illustrative purposes a much smaller subset or
simulated data might be relevant; again a strategy would be to illustrate the
problematic steps with simulated data, and then resume the narrative with the
analyzed full data.
A secondary consideration may be that if your package _requires_ MSigDB to
function, then it can't be automatically tested by repository build machines --
you'll want to have unit tests or other approaches to ensure that 'bit rot' does
not set in without you being aware of it.
If this is a Bioconductor package, then it's appropriate to ask on the
Bioconductor devel mailing list.
http://bioconductor.org/developers/
http://bioconductor.org/packages/BiocStyle/ might be your friend for producing
stylish vignettes.
Martin
(3) I could build vignette outside of the package and put it into the
inst/doc directory. This also has obvious drawbacks.
(4) Leaving this example out defies the purpose of my package.
I am tending towards solution (2). What do you think?
Not clear how big of a static piece you're taking about, but maybe you
could set it up such that you use (2) as a fallback, i.e. have the vignette
include a static/pre-generated piece (which is clearly marked as such) only
if the external dependency is not available.
Just a thought
Henrik
Kind regards,
j.
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