[Rd] The finalizer of the externalPtr does not work when closing R?
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 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] The finalizer of the externalPtr does not work when closing R?
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 wrote: > > 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 > > [[alternative HTML version deleted]] > > __ > 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
Re: [Rd] The finalizer of the externalPtr does not work when closing R?
+ 5.13 of Writing R Extensions Tomas On 4/3/20 3:04 PM, Gábor Csárdi wrote: 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 wrote: 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 [[alternative HTML version deleted]] __ 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [External] The finalizer of the externalPtr does not work when closing R?
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: 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 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Luke Tierney Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke-tier...@uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [External] The finalizer of the externalPtr does not work when closing R?
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 wrote: > 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: > > > 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 > > > > [[alternative HTML version deleted]] > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > -- > Luke Tierney > Ralph E. Wareham Professor of Mathematical Sciences > University of Iowa Phone: 319-335-3386 > Department of Statistics andFax: 319-335-3017 > Actuarial Science > 241 Schaeffer Hall email: luke-tier...@uiowa.edu > Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
