Hi. 2009/6/1 Hervé Pagès <hpa...@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 > } > } > ) > �...@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 > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
