From ripley at stats.ox.ac.uk  Tue Mar 11 11:02:13 2003
From: ripley at stats.ox.ac.uk (ripley@stats.ox.ac.uk)
Date: Tue Mar 11 12:02:24 2003
Subject: Problems with affy (was [Rd] R CMD check (again))
In-Reply-To: <20030311104401.GB297025@genome.cbs.dtu.dk>
Message-ID: <Pine.LNX.4.44.0303111054500.27403-100000@gannet.stats>

Please use a meaningful subject line: yours was far too vague.

On Tue, 11 Mar 2003, Laurent Gautier wrote:

> Hi,
> 
> R-devel causes me still trouble. It dies with
> Error: couldn't find function "predict.loess"
> Execution halted
> for the package affy, but
> bash-2.04$ grep predict.loess ~/R-devel/src/library/modreg/R/*.R
> /misc/homes/laurent/R-devel/src/library/modreg/R/loess.R:predict.loess <- function(object, newdata = NULL, se = FALSE, ...)
> bash-2.04$ 
> 
> 
> ..the function seems to be there...

That's a problem with the package, not R-devel: it should not be calling a
method.  Do note the USER-VISIBLE CHANGES in the NEWS file:

    o   Namespaces can now be defined for packages other than `base':
        see `Writing R Extensions'.  This hides some internal objects
        and changes the search path from objects in a namespace.  All
        the base packages (except methods and tcltk) have namespaces,
        as well as the recommended packages `KernSmooth', `MASS',
        `boot', `class', `nnet', `rpart' and `spatial'.

predict.loess is no longer user-visible. Calling predict() will work with
correctly-written code.

There are still a few (three I think) such problems in the CRAN packages, 
and you can't expect all packages to have been updated for a version that 
is not even feature-frozen as yet.

-- 
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


Problems with affy (was [Rd] R CMD check (again))
ripley@stats.ox.ac.uk