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The finalizer of the externalPtr does not work when closing R?

5 messages · Jiefei Wang, Gábor Csárdi, Tomas Kalibera +1 more

Original
Jiefei Wang
# 
Hi all,

I found that the finalizer of the externalPtr is not called when R is
quitting. However, manually calling GC() works fine. This behavior is
observed on devel R 2020-04-02 r78142 on Win and R 3.6.3 on Ubuntu.  I make
a reproducible package here: https://github.com/Jiefei-Wang/example

Here is the detail of how to reproduce the problem, I create a temporary
file in the package root path and make an external pointer. The finalizer
of the external pointer will delete the  temporary file when it is called.
In the first round, I manually remove the external pointer from the global
environment and call GC() to verify if the finalizer is programmed
properly. The temporary file is deleted successfully. Then I create the
file and the pointer again and close the R session without saving the
global environment. Since the external pointer is removed when closing R,
so the finalizer should be called in this procedure. However, the temp file
still exists after closing the R session.

Here is the test code(which can be found in inst/example/example.R)

## Create a temporary file
tmpFile <- paste0(system.file(package = "testPackage"), "/tmp")
tmpFile
file.create(tmpFile)
file.exists(tmpFile)
## Create an external pointer whose finalizer will delete
## the file when the variable is not in used
x <- testPackage:::makeExtPtr(file.remove,tmpFile)
## GC is working fine
rm(list="x")
gc()
file.exists(tmpFile)

## Create the temporary file again
file.create(tmpFile)
file.exists(tmpFile)
x <- testPackage:::makeExtPtr(file.remove,tmpFile)
## Quit R session without explicitly cleaning the working space
quit(save = "no")


##=====Open a new R session=======
## The temporary file still exist
tmpFile <- paste0(system.file(package = "testPackage"), "/tmp")
file.exists(tmpFile)

Not sure if this behavior is designed on purpose, but it sounds wired to me
and can cause memory leaking if not properly handled.

Best,
Jiefei
Gábor Csárdi
# 
See R_RegisterCFinalizerEx() and set onexit to nonzero. Here:
https://github.com/wch/r-source/blob/9353ddfa8d30069ad8975e0364307d710f2488d5/src/include/Rinternals.h#L1279-L1280

Gabor
On Fri, Apr 3, 2020 at 1:56 PM Wang Jiefei <szwjf08 at gmail.com> wrote:
Tomas Kalibera
# 
+ 5.13 of Writing R Extensions

Tomas
On 4/3/20 3:04 PM, G?bor Cs?rdi wrote:
iuke-tier@ey m@iii@g oii uiow@@edu
# 
Use R_RegisterFinalizerEx in your C code. See

https://cran.r-project.org/doc/manuals/r-release/R-exts.html#External-pointers-and-weak-references

This still gives you only "best effort"; for anything stronger you
would need a different approach.

In general, finalizers should only be used as a backstop, not as a
primary resource management tool (in R or any other garbage-collected
language).

Memory leaks are not an issue -- unless you are doing very unusual
things your OS will reclaim memory resources used by your process when
it exits, cleanly or otherwise.

Best,

luke
On Fri, 3 Apr 2020, Wang Jiefei wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Jiefei Wang
    

    

      
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Thanks for all your guys responses! It is amazing to get so many answers in
a few minutes! My package needs to handle the shared memory so the
finalizer does cause memory leaking. The Ex version should be my solution
for that. Thanks for all your help.

Best
Jiefei

        
On Fri, Apr 3, 2020, 9:14 PM <luke-tierney at uiowa.edu> wrote: