Re: [Rd] R CMD check: Error in function (env) : could not find function "finalize"

From: Henrik Bengtsson <hb_at_stat.berkeley.edu>
Date: Wed, 29 Aug 2007 11:56:27 -0700

Hi, thanks Seth and others (I've got some offline replies); all feedback has been useful indeed.

The short story is that as the author of R.oo I am actually the bad guy here (but not for long since I'm soon committing a fix for R.oo).

REPRODUCIBLE EXAMPLE #1:
% R --vanilla
> library(R.oo)
R.oo v1.2.8 (2006-06-09) successfully loaded. See ?R.oo for help.
> detach("package:R.oo")
> gc()

Error in function (env)  : could not find function "finalize"
Error in function (env)  : could not find function "finalize"
Error in function (env)  : could not find function "finalize"
Error in function (env)  : could not find function "finalize"
Error in function (env)  : could not find function "finalize"
         used (Mb) gc trigger (Mb) max used (Mb)
Ncells 142543  3.9     350000  9.4   350000  9.4
Vcells  82660  0.7     786432  6.0   478255  3.7

REPRODUCIBLE EXAMPLE #2:
Here is another example without R.oo illustrating what is going on. % R --vanilla
> e <- new.env()
> e$foo <- "foo"
> e$foo <- 1
> e <- new.env()
> e$foo <- 1
> reg.finalizer(e, function(env) { print(ls.str(envir=env)) })
> detach("package:utils")
> rm(e)
> gc()

Error in print(ls.str(envir = env)) : could not find function "ls.str"

         used (Mb) gc trigger (Mb) max used (Mb)
Ncells 158213  4.3     350000  9.4   350000  9.4
Vcells  86800  0.7     786432  6.0   478255  3.7


WHY ONLY WHEN RUNNING R CMD CHECK?
So, the problem I had was with 'affxparser' examples failing in R CMD check, but not when I tested them manually. Same thing was happening with the 'pcaMethods' package. The common denominator was that both 'affxparser' and 'pcaMethods' had R.oo dependent package in DESCRIPTION/Suggests; 'affxparser' used Suggests: R.utils (which depends on R.oo), and 'pcaMethods' used Suggests: aroma.light (which in turn *suggests* R.utils). To the best of my understanding, when R CMD check runs examples, it will load *all* suggested packages, and when done, detach them. When the garbage collector later runs and cleans out objects, the generic function finalize() in R.oo called by the registered finalize hook is not around anymore. FYI, if you move the R.oo-dependent package from Suggests: to Depends:, there is no longer a problem because then the package is never detached. It all makes sense.

CONCLUSION:
When registering finalizers for object using reg.finalizer() there is always the risk of the finalizer code to be broken because a dependent package has been detached.

SOLUTION:
At least make the finalizer hook function robust against these things.  For instance, check if required packages are loaded etc, or just add a tryCatch() statement. However, since finalizers are typically used to deallocate resources, much more effort has to be taken to make sure that is still work, which is not easy. For instance, one could make sure to require() the necessary packages in the finalizer, but that has side effects and it is not necessarily sufficient, e.g. you might only load a generic function, but the method for a specific subclass might be in a package out of your control. Same problem goes with explicit namespace calls to generic functions, e.g. R.oo::finalize(). If you have more clever suggestions, please let me know.

SOME MORE DETAILS ON R.OO:
This is what R.oo looks like now:

Object <- function (core = NA) {
  this <- core
  attr(this, ".env") <- new.env()
  class(this) <- "Object"
  attr(this, "...instanciationTime") <- Sys.time()   reg.finalizer(attr(this, ".env"), function(env) finalize(this))   this
}

finalize.Object <- function(this, ...) {}

finalize <- function(...) UseMethod("finalize")

As you see, when detaching R.oo, finalize() is no longer around.

Lesson learned!

Cheers

Henrik

On 8/28/07, Seth Falcon <sfalcon_at_fhcrc.org> wrote:
> Hi Henrik,
>
> "Henrik Bengtsson" <hb_at_stat.berkeley.edu> writes:
>
> > Hi,
> >
> > does someone else get this error message:
> >
> > Error in function (env) : could not find function "finalize"?
> >
> > I get an error when running examples in R CMD check (v2.6.0; session
> > info below):
> [snip]
> > The error occurs in R CMD check but also when start a fresh R session
> > and run, in this case, affxparser.Rcheck/affxparser-Ex.R. It always
> > occur on the same line.
>
> So does options(error=recover) help in determining where the error is
> coming from?
>
> If you can narrow it down, gctorture may help or running the examples
> under valgrind.
>
> + seth
>
> --
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
> BioC: http://bioconductor.org/
> Blog: http://userprimary.net/user/
>



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