[Rd] Creating a vignette which depends on a non-distributable file

Henrik Bengtsson henrik.bengtsson at ucsf.edu
Fri May 15 01:33:52 CEST 2015

On May 14, 2015 15:04, "January Weiner" <january.weiner at 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).
> (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


> Kind regards,
> j.
> --
> -------- January Weiner --------------------------------------
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