S3 generics without NS and cleanEx()

which is exported in party's namespace

    S3method(sctest, mob)

Torsten,

The error is that .__S3MethodsTable__. ends up in the global environment.
Are you importing sctest (I can't see it)?  I think that's the problem.

From R-exts:

The standard method for S3-style @code{UseMethod} dispatching might fail
to locate methods defined in a package that is imported but not attached
to the search path.  To ensure that these methods are available the
packages defining the methods should ensure that the generics are
imported and register the methods using @code{S3method} directives.
^^^^^^^^

Brian

On Wed, 15 Feb 2006, Torsten Hothorn wrote:

Good morning,

we recently observed a problem with importing S3 generics from a foreign
package (without namespace), defining a S3 method in a package _with_
namespace and the `cleanEx()' function which is automatically generated
and executed before examples are run by R CMD check.

To be more precise. Package `strucchange' defines a S3 generic

    sctest <- function(x, ...) UseMethod("sctest")

and the development version of `party' defines

    sctest.mob <- function(x, node = NULL, ...) {
        ...

which is exported in party's namespace

    S3method(sctest, mob)

Creating a `mob' object and running `sctest' on it works fine.

However, when we attach `party' and run `cleanEx()', the `sctest' method
for `mob' is no longer found. Before `cleanEx()' we get

R> methods(sctest)
[1] sctest.Fstats  sctest.efp     sctest.formula sctest.gefp
sctest.mob*

and afterwards

R> methods(sctest)
[1] sctest.Fstats  sctest.efp     sctest.formula sctest.gefp

is missing.

Debugging `cleanEx()' shows that those objects are removed from the
global environment:

ls(envir = env, all.names = TRUE)
[1] ".Random.seed"         ".__S3MethodsTable__." "GCtorture"
[4] "a"                    "euro"

where the second one looks very suspicious.

`party_0.4-0.tar.gz' is available from

    http://www.imbe.med.uni-erlangen.de/~hothorn/party_0.4-0.tar.gz

and

    http://www.imbe.med.uni-erlangen.de/~hothorn/modeltools_0.2-3.tar.gz

is required.

The example below can be reproduced with both R-2.2.1 and R-2.3.0.

Best wishes,

Torsten



R> invisible(options(echo = TRUE))
R> ### * <HEADER>
R> ###
R> attach(NULL, name = "CheckExEnv")
R> assign(".CheckExEnv", as.environment(2), pos = length(search())) # base
R> ## add some hooks to label plot pages for base and grid graphics
R> setHook("plot.new", ".newplot.hook")
R> setHook("persp", ".newplot.hook")
R> setHook("grid.newpage", ".gridplot.hook")
R>
R> assign("cleanEx",
+        function(env = .GlobalEnv) {
+ 	   rm(list = ls(envir = env, all.names = TRUE), envir = env)
+            RNGkind("default", "default")
+ 	   set.seed(1)
+    	   options(warn = 1)
+ 	   delayedAssign("T", stop("T used instead of TRUE"),
+ 		  assign.env = .CheckExEnv)
+ 	   delayedAssign("F", stop("F used instead of FALSE"),
+ 		  assign.env = .CheckExEnv)
+ 	   sch <- search()
+ 	   newitems <- sch[! sch %in% .oldSearch]
+ 	   for(item in rev(newitems))
+                eval(substitute(detach(item), list(item=item)))
+ 	   missitems <- .oldSearch[! .oldSearch %in% sch]
+ 	   if(length(missitems))
+ 	       warning("items ", paste(missitems, collapse=", "),
+ 		       " have been removed from the search path")
+        },
+        env = .CheckExEnv)
R> assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now
R> assign("ptime", proc.time(), env = .CheckExEnv)
R> grDevices::postscript("party-Ex.ps")
R> assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv)
R> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
R> options(warn = 1)
R> library('party')
Loading required package: survival
Loading required package: splines
Loading required package: grid
Loading required package: modeltools
Loading required package: coin
Loading required package: mvtnorm
Loading required package: zoo
Loading required package: sandwich
Loading required package: strucchange
R>
R> methods(sctest)
[1] sctest.Fstats  sctest.efp     sctest.formula sctest.gefp    sctest.mob*

   Non-visible functions are asterisked
R>
R> assign(".oldSearch", search(), env = .CheckExEnv)
R> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
R> cleanEx(); ..nameEx <- "BinaryTree-class"
R>
R> methods(sctest)
[1] sctest.Fstats  sctest.efp     sctest.formula sctest.gefp
R>
R>
R> proc.time()
[1] 1.77 0.01 1.97 0.00 0.00
R>