[R] Unable to load foreign after upgrade on ubuntu

[Prof Brian Ripley]

On Tue, 24 Oct 2006, Dirk Eddelbuettel wrote:

>
> On 24 October 2006 at 15:47, Van Campenhout Bjorn wrote:
> | I am running R on ubuntu dapper.  The version that is in the ubuntu
> | repos is 2.2.1, so I decided to upgrade by adding
> |
> | deb http://cran.R-project.org/bin/linux/ubuntu dapper/
> |
> | to my sources.list, as advised on the web page.  After sudo apt-get
> | update and upgrade, I have version 2.3.1.  However, when I try to load
> | the library 'foreign', I get the following error:
> |
> | Error in dyn.load(x, as.logical(local), as.logical(now)):
> | Unable to load shared library
> | '/usr/lib/R/library/foreign/libs/foreign.so':
> | /usr/lib/R/library/foreign/libs/foreign.so: undefined symbol: isfinite
> | Error: package/namespace load failed for 'foreign'
> |
> | What is going wrong?
>
> There are interdependencies between the R binary and the dynamically loaded
> libraries it loads.  By upgrading R, you have agreed to the Faustian bargain
> of potentially having to upgrade these libraries too.
>
> So reinstalling foreign from CRAN should do. R can do that for you, see
> 	help("update.packages")
> and make sure you also have r-base-dev installed as this will cover most if
> not all of the tools

But since foreign is part of R, installing a new version of R will update 
the standard and recommended packages including foreign. So this suggests 
that what is being picked up is another copy of foreign from another 
library.

Make sure R_LIBS is not set, and then start R --vanilla and try again.
If that works (as I suspect), check start R again normally, and look at

> .libPaths()

Then check all those directories other than the last for 
previously-installed packages and delete duplicates.  As Dirk suggests,

update.packages(ask=FALSE, checkBuilt=TRUE)

will update them all, *provided* you have sufficient file permissions.

-- 
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