R help - Oct 2004 - How to install a package that needs to see oher pkg dependencies:

Hi,
I am trying to install the genetics package on a server with Linux, 
Fedora. I installed it in a PC and worked fine.

In a server since I am not used with R, I am not sure what do I need to 
change so genetics pkg can see some package dependencies:
Any suggestion is appreciated, Aldi

Note:
genetics expects gregmisc and mvtnorm to be installed already. gregmisc 
creates gdata etc dependencies.
So here is what I have done:
Retrieved the base R and installed and compiled it with make under :
/users/genetics/aldi/r/R/R-2.0.0

Under it directories:
/mvtnorm
/gregmisc
/genetics
are created.
Installed mvtnorm and gregmisc with no problem, but genetics is not 
recognizing the location of /gregmisc/gdata

The command I am using to install genetics package is the following:
../bin/R CMD ../bin/INSTALL genetics_1.1.0.tar.gz

Here is the problem:

genetics at genxeon1:/users/genetics/aldi/r/R-2.0.0/genetics% ../bin/R CMD 
../bin/INSTALL -l . genetics_1.1.0.tar.gz

* Installing *source* package 'genetics' ...

** R

** data

** inst

** preparing package for lazy loading

Error in loadNamespace(i[[1]], c(lib.loc, .libPaths()), keep.source) :

        There is no package called 'gdata'

Execution halted

ERROR: lazy loading failed for package 'genetics'

genetics at genxeon1:/users/genetics/aldi/r/R-2.0.0/genetics%

On Sat, 9 Oct 2004, Aldi Kraja wrote:
> Hi,
> I am trying to install the genetics package on a server with Linux, 
> Fedora. I installed it in a PC and worked fine.
> 
> In a server since I am not used with R, I am not sure what do I need to 
> change so genetics pkg can see some package dependencies:
> Any suggestion is appreciated, Aldi
> 
> Note:
> genetics expects gregmisc and mvtnorm to be installed already. gregmisc 
> creates gdata etc dependencies.
> So here is what I have done:
> Retrieved the base R and installed and compiled it with make under :
> /users/genetics/aldi/r/R/R-2.0.0
> 
> Under it directories:
> /mvtnorm
> /gregmisc
> /genetics
> are created.
> Installed mvtnorm and gregmisc with no problem, but genetics is not 
> recognizing the location of /gregmisc/gdata
> 
> The command I am using to install genetics package is the following:
> ../bin/R CMD ../bin/INSTALL genetics_1.1.0.tar.gz
> 
> Here is the problem:
> 
> genetics at genxeon1:/users/genetics/aldi/r/R-2.0.0/genetics% ../bin/R CMD 
> ../bin/INSTALL -l . genetics_1.1.0.tar.gz
The correct commands are

R CMD INSTALL gregmisc_2.0.0.tar.gz
R CMD INSTALL genetics_1.1.0.tar.gz

Wherever did you get `../bin/INSTALL -l .' from?

You need to install into a library that is in the library path for the 
package to be usable, and the system library (the default) is the best 
choice.  (This is no different from S-PLUS, on which you have been asking
questions on s-news for many years.)

-- 
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