Re: [Rd] R CMD check warning about boot ?

From: Prof Brian Ripley <>
Date: Fri 01 Dec 2006 - 11:27:28 GMT

On Fri, 1 Dec 2006, Martin Maechler wrote:

>>>>>> "Dirk" == Dirk Eddelbuettel <>
>>>>>> 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/ it is like R --vanilla, which is what is used for a lot of batch testing code.

Brian D. Ripley,        
Professor of Applied Statistics,
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

______________________________________________ mailing list
Received on Fri Dec 01 22:39:03 2006

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.1.8, at Fri 01 Dec 2006 - 14:00:48 GMT.

Mailing list information is available at Please read the posting guide before posting to the list.