[Rd] modifying a persistent (reference) class

Ross Boylan ross at biostat.ucsf.edu
Fri Aug 1 19:53:37 CEST 2014

I saved objects that were defined using several reference classes.
Later I modified the definition of reference classes a bit, creating new
functions and deleting old ones.  The total number of functions did not
change.  When I read them back I could only access some of the original

I asked on the user list and someone suggested sticking with the old
class definitions, creating new classes, reading in the old data, and
converting it to the new classes.  This would be awkward (I want the
"new" classes to have the same name as the "old" ones), and I can
probably just leave the old definitions and define the new functions I
need outside of the reference classes.

Are there any better alternatives?

On reflection, it's a little surprising that changing the code for a
reference class makes any difference to an existing instance, since all
the function definitions seem to be attached to the instance.  One
problem I've had in the past was precisely that redefining a method in a
reference class did not change the behavior of existing instances.  So
I've tried to follow the advice to keep the methods light-weight.

In this case I was trying to move from a show method (that just printed)
to a summary method that returned a summary object.  So I wanted to add
a summary method and redefine the show to call summary in the base
class, removing all the subclass definitions of show.

Regular S4 classes are obviously not as sensitive since they usually
don't include the functions that operate on them, but I suppose if you
changed the slots you'd be in similar trouble.

Some systems keep track of versions of class definitions and allow one
to write code to migrate old to new forms automatically when the data
are read in.  Does R have anything like that?

The system on which I encountered the problems was running R 2.15.

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