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>
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