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.
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...@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: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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