From cberry at tajo.ucsd.edu  Wed Nov 17 02:34:49 2010
From: cberry at tajo.ucsd.edu (Charles C. Berry)
Date: Tue, 16 Nov 2010 17:34:49 -0800
Subject: [Rd] unloading compiled code.
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	<alpine.LFD.2.00.1011122223410.32247@gannet.stats.ox.ac.uk>
	<AANLkTinDzRiHugMKOu+rje4PAXWReEJpQY8=6ZfUAJyL@mail.gmail.com>
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	<AANLkTi=XNYb62SOScF-=rGBPFwWOCg670zDRLSEF4tw1@mail.gmail.com>
	<Pine.LNX.4.64.1011161024180.1348@tajo.ucsd.edu>
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Message-ID: <Pine.LNX.4.64.1011161734160.2833@tajo.ucsd.edu>

On Tue, 16 Nov 2010, Andrew Redd wrote:

> so should I use reg.finalizer or overwrite .Last()?

> .Last
Error: object '.Last' not found
>

You create your own .Last - there is nothing to overwrite.

Chuck


  If I use
> reg.finalizer, what should be the environment that I specify?  The
> straight forward solution would be to have a hook .onExit that a
> package could specify to make sure  that the code was unloaded before
> the program terminates, that way I don't overwrite .Last if if has
> another purpose.
>
> -Andrew
>
> On Tue, Nov 16, 2010 at 11:27 AM, Charles C. Berry <cberry at tajo.ucsd.edu> wrote:
>> On Tue, 16 Nov 2010, Andrew Redd wrote:
>>
>>> Just found in the documentation for getHook that packages are not
>>> unloaded on quit. ?How should I force a package to unload on quit?
>>
>> See
>>
>> ? ? ? ??q
>>
>>
>> HTH,
>>
>> Chuck
>>
>>>
>>> -Andrew
>>>
>>> On Tue, Nov 16, 2010 at 10:25 AM, Andrew Redd <amredd at gmail.com> wrote:
>>>>
>>>> Are packages unloaded on quit so that the .Last.lib or .onUnload are
>>>> called for packages?
>>>>
>>>> -Andrew
>>>>
>>>> On Fri, Nov 12, 2010 at 3:52 PM, Andrew Redd <amredd at gmail.com> wrote:
>>>>>
>>>>> Perhaps you could help me make some sense of this. ?Here is a printout
>>>>> of my sessions.
>>>>> ---
>>>>> toys$R -q
>>>>>>
>>>>>> library(test2)
>>>>>> gpualloctest()
>>>>>
>>>>> testing allocation on gpu
>>>>> C Finished
>>>>> Collecting Garbage
>>>>> done.
>>>>>>
>>>>>> q()
>>>>>
>>>>> Save workspace image? [y/n/c]: n
>>>>>
>>>>> ?*** caught segfault ***
>>>>> address 0x7f12ec1add50, cause 'memory not mapped'
>>>>>
>>>>> Possible actions:
>>>>> 1: abort (with core dump, if enabled)
>>>>> 2: normal R exit
>>>>> 3: exit R without saving workspace
>>>>> 4: exit R saving workspace
>>>>> Selection: 1
>>>>> aborting ...
>>>>> Segmentation fault
>>>>> toys$R -q
>>>>>>
>>>>>> library(test2)
>>>>>> gpualloctest()
>>>>>
>>>>> testing allocation on gpu
>>>>> C Finished
>>>>> Collecting Garbage
>>>>> done.
>>>>>>
>>>>>> library.dynam.unload('test2',system.file(package='test2'))
>>>>>> q()
>>>>>
>>>>> Save workspace image? [y/n/c]: n
>>>>> toys$
>>>>> ---
>>>>>
>>>>> I have a in the test2/R/zzz.R file
>>>>> ---
>>>>> .onUnload <- function(libpath)
>>>>> ? ?library.dynam.unload("test2", libpath)
>>>>> ---
>>>>>
>>>>> so the code should be unloaded. ?But it appears that it is not from
>>>>> errors when I explicitly unload the test2.so it does not through a
>>>>> segfault. ?Why would this be happening? ?and how do I circumvent it.
>>>>>
>>>>> thanks,
>>>>> Andrew
>>>>>
>>>>>
>>>>> On Fri, Nov 12, 2010 at 3:32 PM, Prof Brian Ripley
>>>>> <ripley at stats.ox.ac.uk> wrote:
>>>>>>
>>>>>> On Fri, 12 Nov 2010, Andrew Redd wrote:
>>>>>>
>>>>>>> I have a package that I'm developing that I need to unload the
>>>>>>> library. ?Long story short I figured out that the leaving the compiled
>>>>>>> code loaded lead to a segmentation fault, but unloading the code will
>>>>>>> fix it. ?I've read the documentation and it appears that there are
>>>>>>> several ways to do this? ?What is the popper accepted current standard
>>>>>>> for unloading compiled code?
>>>>>>
>>>>>> Depends how you loaded it: you basically reverse the process.
>>>>>>
>>>>>>> The options as I understand them are:
>>>>>>> 1. dyn.unload
>>>>>>> 2. library.dynam.unload
>>>>>>> used with either
>>>>>>> A. .Last.lib
>>>>>>> B. .onUnload
>>>>>>>
>>>>>>> If it makes a difference my package does use a NAMESPACE so the
>>>>>>> package is loaded through useDynLib.
>>>>>>
>>>>>> So you need an .onUnload action calling library.dynam.unload.
>>>>>>
>>>>>> Slightly longer version: you need the DLL loaded whilst the namepace is
>>>>>> in
>>>>>> use, so it has to be in .onUnload, and useDynLib calls library.dynam so
>>>>>> you
>>>>>> need library.dynam.unload to do the housekeeping around dyn.unload
>>>>>> which
>>>>>> matches what library.dynam does around dyn.load.
>>>>>>
>>>>>> There are quite a lot of examples to look at, including in R itself.
>>>>>> MASS is
>>>>>> one example I've just checked.
>>>>>>
>>>>>> Having said all that, my experience is that unloading the DLL often
>>>>>> does not
>>>>>> help if you need to load it again (and that is why e.g. tcltk does not
>>>>>> unload its DLL).
>>>>>>
>>>>>>> Thanks,
>>>>>>> Andrew Redd
>>>>>>>
>>>>>>> ______________________________________________
>>>>>>> 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
>>>>>>
>>>>>
>>>>
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>> Charles C. Berry ? ? ? ? ? ? ? ? ? ? ? ? ? ?Dept of Family/Preventive
>> Medicine
>> cberry at tajo.ucsd.edu ? ? ? ? ? ? ? ? ? ? ? ?UC San Diego
>> http://famprevmed.ucsd.edu/faculty/cberry/ ?La Jolla, San Diego 92093-0901
>>
>>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

Charles C. Berry                            Dept of Family/Preventive Medicine
cberry at tajo.ucsd.edu			    UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901



[Rd] unloading compiled code.
Charles C. Berry