Re: [R] R_LIBS difficulty ?

From: François Pinard <pinard_at_iro.umontreal.ca>
Date: Fri 15 Apr 2005 - 08:47:44 EST

[Prof Brian Ripley]
> [François Pinard]

> >Now using this line within `~/.Renviron':
> > R_LIBS=/home/pinard/etc/R
> >my tiny package is correctly found by R. However, R does not seem to
> >see any library within that directory if I rather use either of:
> > R_LIBS=$HOME/etc/R
> > R_LIBS="$HOME/etc/R"

> Correct, and as documented. See the description in ?Startup,
> which says things like ${foo-bar} are allowed but not $HOME, and
> not ${HOME}/bah or even ${HOME}. But R_LIBS=~/etc/R will work in
> .Renviron since ~ is intepreted by R in paths.

Hello, Brian (or should I rather write Prof Ripley?).

Thanks for having replied. I was not sure how to read "but not", which could be associated either with "which says" or "are allowed". My English knowledge is not fully solid, and I initially read you meant the later, but it seems the former association is probably the correct one.

The fact is the documentation never says that `$HOME' or `${HOME} are forbidden. It is rather silent on the subject, except maybe for this sentence: "value is processed in a similar way to a Unix shell" in the Details section, which vaguely but undoubtedly suggests that `$HOME' and `${HOME}' might be allowed. Using `~/' is not especially documented either, except from the Examples section, where it is used. I probably thought it was an example of how shell-alike R processes `~/.Renviron'.

> >The last writing (I mean, something similar) is suggested somewhere in
> >the R manuals (but I do not have the manual with me right now to give
> >the exact reference, I'm in another town).

> It is not mentioned in an R manual, but it is mentioned in the FAQ.

I tried checking in the FAQ. By the way, http://www.r-project.org presents a menu on the left, and there is a group of items under the title `Documentation'. `FAQs' is shown under that title, but is not clickable. I would presume it was meant to be? However, the `Other' item is itself clickable, and offers a link to what appears to be an FAQs page.

The only thing I saw, in item 5.2 of the FAQ (How can add-on packages be installed?) says that one may use `$HOME/' while defining `R_LIBS' in a Bourne shell profile, or _preferably_ use `~/` while defining `R_LIBS' within file `~/.Renviron`. The FAQ does not really say that `$HOME' is forbidden. The FAQ then refers to `?Startup' for more information, and `?Startup' is not clear on this thing, in my opinion at least.

> R_LIBS=$HOME/etc/R will work in a shell (and R_LIBS=~/etc/R may not).

> >Another hint that it could be expected to work is that the same
> >`~/.Renviron' once contained the line:

> > R_BROWSER=$HOME/bin/links

> >which apparently worked as expected. (This `links' script launches
> >the real program with `-g' appended whenever `DISPLAY' is defined.)

> Yes, but that was not interpreted by R, rather a shell script called by R.

Granted, thanks for pointing this out.

The documentation does not really say either (or else I missed it) if the value of R_BROWSER is given to exec, or given to an exec'ed shell. If a shell is called, it means in particular that we can use options, and this is a useful feature, worth being known I guess.

Once again, thanks for having replied, and for caring.

-- 
François Pinard   http://pinard.progiciels-bpi.ca

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Received on Fri Apr 15 08:53:02 2005

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