R help - Sep 2008 - Trouble with R CMD check: I can't seem to get dependencies right (maybe I'm using R_LIBS incorrectly?)

Hi there,


I'm in the following directory:

~/Documents/Rstuff/diceFiles/dice_1.1

The directory "dice" is in this directory, with all the usual build
files (DESCRIPTION, NAMESPACE, etc).  I'm trying to run the following
command:

R CMD check dice

(where "dice" is the name of the package I'm checking), and I get
the following:

* checking package dependencies ... ERROR
Packages required but not available:
  gtools

My DESCRIPTION file does (correctly) list gtools as a dependency, so
I'm happy this check is ensuring its availability.  What I can't
figure out is how to get the check command to see that gtools is in
fact installed.  I've created a file called .Renviron in my home
directory that has the following line in it:

R_LIBS=~/Documents/Rstuff/library

And in the directory specified by R_LIBS above is the gtools package.
(I've also got a file called .Rprofile in my home directory, with the
line .libPaths("~/Documents/Rstuff/library")
in it.)  My reading of the R-intro manual is that setting R_LIBS in
this way should allow the R CMD check command to search in the
directory specified by R_LIBS when looking for gtools.  I'm pretty
sure at this point, though, that my understanding is incorrect.

At this point I'm in over my depth.  I'm writing because I'm hopeful
that to someone on this list my problem is trivially solvable.  My
basic question is: what must I do to get R CMD check to find the
gtools package?


Please let me know any ideas you might have for me,
Dylan

'Writing R Extensions' does say

@quotation Note
@code{R CMD check} and @code{R CMD build} run @R{} with
@option{--vanilla}, so none of the user's startup files are read.  If
you need @env{R_LIBS} set (to find packages in a non-standard library)
you will need to set it in the environment.
@end quotation

~/.Renviron is one of those startup files (and so is ~/.Rprofile).

On Thu, 4 Sep 2008, Dylan Arena wrote:
> Hi there,
>
>
> I'm in the following directory:
>
> ~/Documents/Rstuff/diceFiles/dice_1.1
>
> The directory "dice" is in this directory, with all the usual
build
> files (DESCRIPTION, NAMESPACE, etc).  I'm trying to run the following
> command:
>
> R CMD check dice
>
> (where "dice" is the name of the package I'm checking), and I
get the following:
>
> * checking package dependencies ... ERROR
> Packages required but not available:
>  gtools
>
> My DESCRIPTION file does (correctly) list gtools as a dependency, so
> I'm happy this check is ensuring its availability.  What I can't
> figure out is how to get the check command to see that gtools is in
> fact installed.  I've created a file called .Renviron in my home
> directory that has the following line in it:
>
> R_LIBS=~/Documents/Rstuff/library
>
> And in the directory specified by R_LIBS above is the gtools package.
> (I've also got a file called .Rprofile in my home directory, with the
> line .libPaths("~/Documents/Rstuff/library")
> in it.)  My reading of the R-intro manual is that setting R_LIBS in
> this way should allow the R CMD check command to search in the
> directory specified by R_LIBS when looking for gtools.  I'm pretty
> sure at this point, though, that my understanding is incorrect.
>
> At this point I'm in over my depth.  I'm writing because I'm
hopeful
> that to someone on this list my problem is trivially solvable.  My
> basic question is: what must I do to get R CMD check to find the
> gtools package?
>
>
> Please let me know any ideas you might have for me,
> Dylan
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible 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