S4 summary method not being called (VGAM)

A relevant report, not just for VGAM but for maintainers of other
packages that define methods for functions that have both generic and
non-generic versions in other packages.

The problem is that VGAM "Depends" on stats4 but does not import from
it. So when VGAM is loaded, only the old version of summary() is
available. Importing the relevant functions from stats4 in VGAM should
fix the problem.

With the current R 2.14.1 this happens silently. With the latest
r-devel, the installation of VGAM produces a warning:

"Functions for exporting methods must have been made generic, explicitly
or implicitly; not true when loading 'VGAM' for 'AIC', 'coef', 'logLik',
'plot', 'summary', 'vcov' "

This implies (a bit obscurely) that the package has generic versions in
its dependencies, but has not imported them.

Maintainers of CRAN packages should check installation against the
development version. Warning messages like this suggest a problem with
the imports.


John

On 1/9/12 5:05 PM, Mark.Bravington at csiro.au wrote:

The symptom triggering this email is that an S4 summary method
sometimes refuses to be invoked, even when a package is explicitly
loaded, if the first load of the package is implicit. It may or may
not be specific to 'summary' methods and/or the 'VGAM' package. I've
sent to R-devel because (i) it looks like some kind of bug to me, but
I'm not sure; (ii) it's not something I personally need any help with;
and (iii) it seems a bit specialized for R-help.

Here's the case notes. I have an object 'nf1' of S4 class 'vglm',
created by calling 'vglm(...)' from package 'VGAM' (you can create
your own from the examples in VGAM). It's save()d into a file
"nf1.rda". If I start a new R session, call 'library( VGAM)', and then
'load("nf1.rda")', then 'summary(nf1)' works fine. But if instead I
start a pretty basic R session and load() the file *without* having
explicitly called library( VGAM), the summary method for 'vglm'
doesn't get called whether or not I subsequently call library( VGAM).
Transcript below.

I'm using R 2.13.2 on Windows XP, VGAM 0.8-4. The same thing happens
with R 2.15 devel v57866.

bye
Mark

Mark Bravington
CSIRO CMIS
Marine Lab
Hobart
Australia


#############################
# Start a basic R session, and then:

search()

[1] ".GlobalEnv" "package:stats4" "package:splines" "package:stats"
"package:graphics"
[6] "package:grDevices" "package:utils" "package:datasets"
"package:methods" "Autoloads" "package:base"

print( load( "nf1.rda")) # which should implicitly load VGAM, but not
attach it

[1] "nf1"

search()

# ...snipped. No explicit VGAM

loadedNamespaces()

# ...snipped. VGAM is there at the end.

nf1

Call:
vglm(formula = form, family = posbinomial, data = data, trace = TRUE)

Coefficients:
# ...snipped. The print() or show() or whatever method seems to get
called OK

summary( nf1)

Length Class Mode
1 vglm S4

# Hmmm... default method is being called, that's wrong. Try explicitly
attaching 'VGAM':

library( VGAM)

Loading required package: splines
Loading required package: stats4

Attaching package: 'VGAM'

The following object(s) are masked from 'package:splines':

bs, ns

The following object(s) are masked from 'package:stats':

biplot, case.names, coefficients, df.residual, fitted, fitted.values,
formula, poly, residuals,
variable.names, weights

The following object(s) are masked from 'package:base':

identity, print, scale.default

summary( nf1)

Length Class Mode
1 vglm S4
# Hmmm... even though VGAM is on the search path etc, the wrong method
is being called

###############################