Re: [R] Please don't blame your tools (was Error in autoloader)

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Fri 12 Aug 2005 - 02:26:47 EST

The problem is **NOT** in MASS. confint is in stats, not MASS, and has been (in base then stats) since R 1.7.0. You could (and should) have checked that from the (O)NEWS files of R and MASS.

Nor is there an error in autoloader, as your title stated.

Some other piece of software on your system is seriously out of date. Running traceback() might tell you what it is. My suspicion is that you have somewhere a long-outdated version of lme4.

Starting each R session with that long list of packages is surely not a good idea. Part of the homework before posting should be to run R --vanilla and see what happens there.

If this were me I would scrap all of the outdated R installation you have and start again with R 2.1.1 (or R-patched).

On Thu, 11 Aug 2005, Peter Ho wrote:

> Hi,
>
> After installing the latest versions of lme4, Matrix, VR on a Debian
> Box, I have run into a problem. When I use library(lme4) on R Version
> 2.1.0 (2005-04-18) I get the following error message:
>
> > library(lme4)
> Loading required package: Matrix
> Error in autoloader(name = "confint", package = "MASS") :
> autoloader did not find 'confint' in 'MASS'
>
> An example of the complete session is given at the end of this email. A
> search in the docs.
> At present I have 3 directories where packages are kept, as I use
> apt-get install "r-cran-package_ name" when one is available in Debian
> and when it is not R, R CMD INSTALL package_name. This gives me the
> following directories when use help.start():
>
> (1) Packages in /usr/local/lib/R/site-library (packages installed by R
> CMD INSTALL)
>
> (2) Packages in /usr/lib/R/site-library (packages installed with apt-get
> install)
>
> (3) Packages in /usr/lib/R/library (base install with apt-get install)
>
>
> Matrix, lme4 and other suggested packages were first installed with R
> CMD INSTALL. and can be found in /usr/local/lib/R/site-library. After
> the error occured, I updated VR with apt-get install (found in
> /usr/lib/R/library) and got the same error message.
>
> Installing a second version of lme4 and matrix with apt-get install puts
> these packages in /usr/lib/R/site-library and gives the same error as
> before.
>
> Looking at the MASS no function 'confint' exists, only confint.glm,
> confint.nls,confint.profile.glm and confint.profile.nls
>
> Can anyone suggest a solution to the problem or why I am unable to
> access lme4 or as the error statement suggests, a problem with the
> Matrix package and Mass?

-- 
Brian D. Ripley,                  ripley@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

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Received on Fri Aug 12 02:33:34 2005

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