From ripley at stats.ox.ac.uk  Wed Feb 15 10:33:35 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Wed, 15 Feb 2006 09:33:35 +0000 (GMT)
Subject: [Rd] S3 generics without NS and cleanEx()
In-Reply-To: <Pine.LNX.4.64.0602150954340.20143@artemis.imbe.med.uni-erlangen.de>
References: <Pine.LNX.4.64.0602150954340.20143@artemis.imbe.med.uni-erlangen.de>
Message-ID: <Pine.LNX.4.64.0602150929130.19834@gannet.stats.ox.ac.uk>

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>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] S3 generics without NS and cleanEx()
Prof Brian Ripley