[R] What is a sane way to deal with changes in library loadings after 1.9.0?

a.prioglio@city.ac.uk a.prioglio at city.ac.uk
Mon Jul 5 14:10:08 CEST 2004

On Mon, Jul 05, 2004 at 11:51:25AM +0100, Prof Brian Ripley wrote:
> > Well, I'm certainly new to R. Still without the explicit loading of the
> > above libraries my scripts while loading on 1.8.1 were definetely not
> > loading on 1.9.1. I'm using the same account on all machines so I expect
> > to have the same environment. Or should I?
> > 
> > One thing I noticed now, a search() on a 1.8.1 machine after the loading
> > of the scripts now returns nothing (after encountering an error though).
> And what was the error?
After a call to factanal()
Error in sc %% S: non conformable arguments

If the offending line is removed search() returns its normal output

So it appears that the interpreter environment is affected by
encountering errors in the script. I did not know or noticed before.
> It seems that you have been fiddling with the default set of packages.
> Have you set R_DEFAULT_PACKAGES?  Have you set option "defaultPackages"?
> If so, set them to "", or try starting R with --vanilla.

No the R environment is "vanilla", i.e. no variables set and a call to
"set" from bash does not show any R variable. R is from official RPM binaries
for RH9 (on RH9) and the 1.9.1 from the RPM for SuSE 9.0 (on SuSE 9.0).

The only option changed in the scripts is the width of output for text
files, which is restored at the end of the script.

No other option is changed.

> Packages utils, graphics and stats are loaded by default on 1.9.1.  And
> package mva is loaded by default on 1.8.1.  People who answer here tend to
> assume that people who know enough to change the default packages loaded
> know enough to revert the changes ....

This is not my experience. The Changelog document for 1.9.0 indicates 
clearly that scripts that used to work before 1.9.0 now need to
explicitly load stats, utils and graphics libraries.
Indeed these pachages are loaded by default if
one starts R as an interpreter. This is not my the case, as I explicitly
stated as I run R with a script loaded with the .First mechanism in

My confusion derives from the fact that after I had to explicitly
load/attach the libraries to cope with the changes as described in the
Changelog document for 1.9.0, I started to experience problems that I did
not notice before and more intersting even when using the 1.8.1
version with the same script.

> > How can one know what environments are loaded? Calling R --verbose did
> > not seem to clarify this point.
> search()  (attached, not loaded, BTW, as there are loaded namespace 
> environments which are not attached).
Well, what I was hoping for was a way to see something from the unix
shell like R --show-environment (I know it's not on the man page ...) or
something like --verbose that did report the working environment. By the
time I get to the R prompt I see nothing.

Antonio Prioglio

We are what we repeatedly do. Excellence, then, is not an act, but a habit.

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