From ripley at stats.ox.ac.uk  Fri Dec  1 12:27:28 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Fri, 1 Dec 2006 11:27:28 +0000 (GMT)
Subject: [Rd] R CMD check warning about boot ?
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	<17776.2383.700920.192129@stat.math.ethz.ch>
Message-ID: <Pine.LNX.4.64.0612011105540.12054@gannet.stats.ox.ac.uk>

On Fri, 1 Dec 2006, Martin Maechler wrote:

>>>>>> "Dirk" == Dirk Eddelbuettel <edd at debian.org>
>>>>>>     on Thu, 30 Nov 2006 08:06:46 -0600 writes:
>
> 	  [.............]
>
>    Dirk> The boot package loads fine, and is current.  Why does
>    Dirk> R CMD check think it is an error that boot happens to
>    Dirk> live in a particular directory, for as long as that
>    Dirk> directory is known to .libPaths() ?
>
> There's quite a difference between
> .libPaths()  in interactive and in "R CMD check" use :
>
> 'R CMD check' does not use your R_ENVIRON where you probably set
> your R_LIBS .

That's not the issue here.  Even if R_LIBS is set, R CMD check looks for 
the copies of the standard and recommended packages in .Library 
(specifically .check_Rd_xrefs does): that is a safety measure as those are 
the ones against which the checks should be done even if you have 
development versions elsewhere in R_LIBS.  (Not my design, but one that 
seems highly defensible.)

There is no provision in the R scripts to install the recommended 
packages elsewhere than .Library, but I believe Dirk has a post-install 
script that breaks the assumptions so this is a Debian-packaging-specific 
issue.

> I vaguely remember that there a good reasons for this behavior,
> but I don't recall them at the moment.

R CMD does not make use of ~/.Renviron nor R_HOME/etc/Renviron.site:
it is like R --vanilla, which is what is used for a lot of batch testing 
code.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] R CMD check warning about boot ?
Prof Brian Ripley