Re: [Rd] formal argument "envir" matched by multiple actual arguments

From: Henrik Bengtsson <hb_at_stat.berkeley.edu>
Date: Tue, 02 Jun 2009 01:13:12 -0700

Hi.

2009/6/1 Hervé Pagès <hpages_at_fhcrc.org>:
> Hi list,
>
> This looks similar to the problem reported here
>  https://stat.ethz.ch/pipermail/r-devel/2006-April/037199.html
> by Henrik Bengtsson a long time ago. It is very sporadic and
> non-reproducible.
> Henrik, do you remember if your code was using reg.finalizer()?
> I tend to suspect it but I'm not sure.

Yes. This was/is observed with object extending the Object class of R.oo, and the constructor of Object use reg.finalizer() [which then calls finalize() that can be "overloaded"]. The fact that the garbage collector is involved could explain why this bug(?) is hard to reproduce.

It's been a while since I saw this problem (and we do instantiate way more Object:s these days). Looking at my source code comments and the post you refers to, I suspect that I manage to circumvent the issue by the following trick (looking at my code, I have several of those statements):

envir2 <- envir
get(name, envir=envir2)

Also, on March 6, 2008 I reported to R-devel on a related problem with '%in%':

  http://tolstoy.newcastle.edu.au/R/e4/devel/08/03/0708.html

That one I circumvent by now only using is.element(a,b) instead of a %in% b.

Maybe this gives you further clues.

/Henrik

BTW. You need to be careful when you register a finalizer and that uses code in a package, which may have been detached. This may cause an error in the finalizer which can give further side effects. See here:

  http://tolstoy.newcastle.edu.au/R/e2/devel/07/08/4251.html

>
> I've been hunting this bug for months but today, and we the help of other
> Bioconductor users, I was able to isolate it and to write some code that
> seems to "almost" reproduce it (i.e. not systematically but most of the
> times).
>
> (Just to put some context to the code below: it's a simplified version
> of some more complex code that we use in Bioconductor to manage memory
> caching of some big objects stored on disk. The idea is that objects of
> class A can be named. All A objects with the same name form a group.
> The code below implements a simple mechanism to trigger some action when
> a group is completely removed from memory i.e. when the last object in
> a group is garbage collected.)
>
>
>  setClassUnion("environmentORNULL", c("environment", "NULL"))
>
>  setClass("A",
>    representation(
>      aa="integer",
>      groupname="character",
>      groupanchor="environmentORNULL"
>    )
>  )
>
>  .A.group.sizes <- new.env(hash=TRUE, parent=emptyenv())
>
>  .inc.A.group.size <- function(groupname)
>  {
>    group.size <- 1L
>    if (exists(groupname, envir=.A.group.sizes, inherits=FALSE))
>        group.size <- group.size +
>                      get(groupname, envir=.A.group.sizes, inherits=FALSE)
>    assign(groupname, group.size, envir=.A.group.sizes, inherits=FALSE)
>  }
>
>  .dec.A.group.size <- function(groupname)
>  {
>    group.size <- get(groupname, envir=.A.group.sizes, inherits=FALSE) - 1L
>    assign(groupname, group.size, envir=.A.group.sizes, inherits=FALSE)
>    return(group.size)
>  }
>
>  newA <- function(groupname="")
>  {
>    a <- new("A", groupname=groupname)
>    if (!identical(groupname, "")) {
>        .inc.A.group.size(groupname)
>        groupanchor <- new.env(parent=emptyenv())
>        reg.finalizer(groupanchor,
>                      function(e)
>                      {
>                          group.size <- .dec.A.group.size(groupname)
>                          if (group.size == 0L) {
>                              cat("no more object of group",
>                                  groupname, "in memory\n")
>                              # take some action
>                          }
>                      }
>        )
>        a_at_groupanchor <- groupanchor
>    }
>    return(a)
>  }
>
>
> The following commands seem to trigger the problem:
>
>  > for (i in 1:2000) {a1 <- newA("group1")}
>  > as.list(.A.group.sizes)
>  > gc()
>  > as.list(.A.group.sizes)
>  > for (i in 1:2000) {a2 <- newA("group2")}
>  Error in assign(".Method", method, envir = envir) :
>    formal argument "envir" matched by multiple actual arguments
>
> If it doesn't, then adding more rounds should finally do it:
>
>  gc()
>  for (i in 1:2000) {a3 <- newA("group3")}
>  gc()
>  for (i in 1:2000) {a4 <- newA("group4")}
>
>  etc...
>
> Thanks in advance for any help with this!
>
> H.
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages_at_fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



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