From january.weiner at gmail.com  Fri May 15 00:04:32 2015
From: january.weiner at gmail.com (January Weiner)
Date: Fri, 15 May 2015 00:04:32 +0200
Subject: [Rd] Creating a vignette which depends on a non-distributable file
Message-ID: <CA+A1kV5uemT7obxhpYu6JA5t2Dpoq7UVVowCOYKV6+dfou0qeA@mail.gmail.com>

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?

Kind regards,

j.



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-------- January Weiner --------------------------------------

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