From ripley at stats.ox.ac.uk  Wed Aug 29 23:33:54 2007
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Wed, 29 Aug 2007 22:33:54 +0100 (BST)
Subject: [Rd] R CMD check: Error in function (env) : could not find
 function "finalize"
In-Reply-To: <59d7961d0708291156tb7cdd20mc919f72325d3cc4d@mail.gmail.com>
References: <59d7961d0708281324q11f966d2y724c0bdb0a98e036@mail.gmail.com>
	<m2lkbv0wvp.fsf@ziti.fhcrc.org>
	<59d7961d0708291156tb7cdd20mc919f72325d3cc4d@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0708292200380.13321@gannet.stats.ox.ac.uk>

> 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

Not so.  R CMD check just runs the examples in a normal session after 
loading the package being tested.  Examples may themselves attach/load 
suggested packages (and if they are suggested it is likely that either 
examples or vignettes will do so).  After each group of examples 
(\examples from a single help file) any packages which have been attached 
in the course of that group are detached.

Looking at pcaMethods, function robustSvd require()s aroma.light, so this 
will happen in example(robustSvd).

I think a package that sets finalizers probably ought to ensure that they 
are run in its .Last.lib or similar hook.  There is no guarantee that they 
will be detached in a particular order, though.  (R CMD check does detach 
them in an ordering determined from the search path, but users may do 
something different.)  If namespaces are involved, similar considerations 
apply to unloading namespaces (although there are some guarantees on order 
since you cannot unload a namespace which is imported from).  Beyond that, 
you may be able to ensure by setting the environment for the 
finalizer function that what it needs will still be present at 
finalization.


On Wed, 29 Aug 2007, Henrik Bengtsson wrote:

> 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/
>>
>
> ______________________________________________
> 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] R CMD check: Error in function (env) : could not find function "finalize"
Prof Brian Ripley