From henrik.bengtsson at ucsf.edu  Fri May 15 01:33:52 2015
From: henrik.bengtsson at ucsf.edu (Henrik Bengtsson)
Date: Thu, 14 May 2015 16:33:52 -0700
Subject: [Rd] Creating a vignette which depends on a non-distributable
	file
In-Reply-To: <CA+A1kV5uemT7obxhpYu6JA5t2Dpoq7UVVowCOYKV6+dfou0qeA@mail.gmail.com>
References: <CA+A1kV5uemT7obxhpYu6JA5t2Dpoq7UVVowCOYKV6+dfou0qeA@mail.gmail.com>
Message-ID: <CAFDcVCS7_2LQNtje3H9iNQ=_mLmk1cWqGNLiDzG1KuvxduhDcw@mail.gmail.com>

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

Henrik

>
> Kind regards,
>
> j.
>
>
>
> --
> -------- January Weiner --------------------------------------
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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