I never detach packages. I rarely load more than 6 or 7 packages directly
before restarting R. I frequently re-run my scripts in new R sessions to
confirm reproducibility.
--
Sent from my phone. Please excuse my brevity.
On September 14, 2016 1:49:55 AM PDT, Alexander Shenkin <ashen...@ufl.edu>
wrote:
>Hi Henrik,
>
>Thanks for your reply. I didn't realize that floating DLLs were an
>issue (good to know). My query is actually a bit more basic. I'm
>actually wondering how folks manage their loading and unloading of
>packages when calling scripts within scripts.
>
>Quick example:
>Script1:
> library(package1)
> source("script2.r")
> # do stuff reliant on package1
> detach("package:package1", unload=TRUE)
>
>Script2:
> library(package1)
> library(package2)
> # do stuff reliant on package1 and package2
> detach("package:package1", unload=TRUE)
> detach("package:package2", unload=TRUE)
>
>Script2 breaks Script1 by unloading package1 (though unloading package2
>
>is ok). I will have to test whether each package is loaded in Script2
>before loading it, and use that list when unloading at the end of the
>Script2. *Unless there's a better way to do it* (which is my question
>-
>is there?). I'm possibly just pushing the whole procedural scripting
>thing too far, but I also think that this likely isn't uncommon in R.
>
>Any thoughts greatly appreciated!
>
>Thanks,
>Allie
>
>On 9/13/2016 7:23 PM, Henrik Bengtsson wrote:
>> In R.utils (>= 2.4.0), which I hope to submitted to CRAN today or
>> tomorrow, you can simply call:
>>
>> R.utils::gcDLLs()
>>
>> It will look at base::getLoadedDLLs() and its content and compare to
>> loadedNamespaces() and unregister any "stray" DLLs that remain after
>> corresponding packages have been unloaded.
>>
>> Until the new version is on CRAN, you can install it via
>>
>>
>source("http://callr.org/install#HenrikBengtsson/R.utils@develop";)
>>
>> or alternatively just source() the source file:
>>
>>
>source("https://raw.githubusercontent.com/HenrikBengtsson/R.utils/develop/R/gcDLLs.R";)
>>
>>
>> DISCUSSION:
>> (this might be better suited for R-devel; feel free to move it there)
>>
>> As far as I understand the problem, running into this error / limit
>is
>> _not_ the fault of the user. Instead, I'd argue that it is the
>> responsibility of package developers to make sure to unregister any
>> registered DLLs of theirs when the package is unloaded. A developer
>> can do this by adding the following to their package:
>>
>> .onUnload <- function(libpath) {
>> library.dynam.unload(utils::packageName(), libpath)
>> }
>>
>> That should be all - then the DLL will be unloaded as soon as the
>> package is unloaded.
>>
>> I would like to suggest that 'R CMD check' would include a check that
>> asserts when a package is unloaded it does not leave any registered
>> DLLs behind, e.g.
>>
>> * checking whether the namespace can be unloaded cleanly ... WARNING
>> Unloading the namespace does not unload DLL
>> * checking loading without being on the library search path ... OK
>>
>> For further details on my thoughts on this, see
>> https://github.com/HenrikBengtsson/Wishlist-for-R/issues/29.
>>
>> Hope this helps
>>
>> Henrik
>>
>> On Tue, Sep 13, 2016 at 6:05 AM, Alexander Shenkin <ashen...@ufl.edu>
>wrote:
>>> Hello all,
>>>
>>> I have a number of analyses that call bunches of sub-scripts, and in
>the
>>> end, I get the "maximal number of DLLs reached" error. This has
>been asked
>>> before (e.g.
>>>
>http://stackoverflow.com/questions/36974206/r-maximal-number-of-dlls-reached),
>>> and the general answer is, "just clean up after yourself".
>>>
>>> Assuming there are no plans to raise this 100-DLL limit in the near
>future,
>>> my question becomes, what is best practice for cleaning up
>(detaching)
>>> loaded packages in scripts, when those scripts are sometimes called
>from
>>> other scripts? One can detach all packages at the end of a script
>that were
>>> loaded at the beginning of the script. However, if a package is
>required in
>>> a calling script, one should really make sure it hadn't been loaded
>prior to
>>> sub-script invocation before detaching it.
>>>
>>> I could write a custom function that pushes and pops package names
>from a
>>> global list, in order to keep track, but maybe there's a better way
>out
>>> there...
>>>
>>> Thanks for any thoughts.
>>>
>>> Allie
>>>
>>> ______________________________________________
>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>
>______________________________________________
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
