From henrik.singmann at psychologie.uni-freiburg.de  Fri Aug 22 19:05:45 2014
From: henrik.singmann at psychologie.uni-freiburg.de (Henrik Singmann)
Date: Fri, 22 Aug 2014 19:05:45 +0200
Subject: [Rd] How to (appropropriately) use require in a package?
In-Reply-To: <CANz9Z_K5RjAKM0J7g71PJM6e6n58ez9hmPfkQ=GTgkgwqMTjsQ@mail.gmail.com>
References: <CANz9Z_+MukG_A8fc-3+b9_m6=R2tDGrq+w1WKECbFK2BNeK4sA@mail.gmail.com>	<CANz9Z_KqOMyRJ0XGr+eCYs5yzYc=v6gXptL+wZN3TpGNLyDMrw@mail.gmail.com>	<53E47285.4030604@stats.ox.ac.uk>
	<CANz9Z_K5RjAKM0J7g71PJM6e6n58ez9hmPfkQ=GTgkgwqMTjsQ@mail.gmail.com>
Message-ID: <53F77869.3030501@psychologie.uni-freiburg.de>

Dear Joshua,

Sorry for resurrecting this thread, but I was on holidays earlier. I also had that problem and unfortunately using loadNamespace() as suggested by Prof. Ripley didn't work in my case (the reason is that the cluster is created by the user and the call executed on the cluster can contain additional function calls from the loaded package which are passed by the user).

I settled on the following construct that doesn't seem to raise issues with R CMD check:

junk <- clusterCall(cl = cl, "require", package = "lme4", character.only = TRUE)

Let's hope it continues to not raise any flags.

Best,
Henrik


Am 08.08.2014 09:22, schrieb Joshua Wiley:
> Dear Professor Ripley,
>
> PkgB does not need to be on the search path---importing into the namespace
> is fine.  I did not realize that namespace scoping ensured that if a
> cluster is created from within a package, that packages entire environment
> tree is available on all the workers.
> I tried to apply how makeCluster works from an interactive R session, where
> functions from packages that are loaded when the cluster is created are not
> available on the workers, to how it works from within a package.
>
> Thanks for your reply,
>
> Josh
>
>
>
> On Fri, Aug 8, 2014 at 4:47 PM, Prof Brian Ripley <ripley at stats.ox.ac.uk>
> wrote:
>
>> The safe, elegant way to do this is to use namespace scoping: it is still
>> not at all clear why 'other code' needs PkgB *on the search path*.
>>
>> In other cases seen in CRAN submissions, 'other code' has been in PkgA's
>> namespace, and hence things in PkgB's exports have been visible as it was
>> imported by PkgA and hence in the environment tree for functions in PkgA.
>>   Then namespace scoping will ensure that PkgB's namespace is loaded on the
>> cluster workers.
>>
>>
>>
>> On 08/08/2014 00:58, Joshua Wiley wrote:
>>
>>> Someone kindly pointed out that it is not clear from my email why Depends
>>> will not work.  A more complete example is:
>>>
>>> PkgA:
>>> f <- function(ncores) {
>>>     cl <- makeCluster(ncores)
>>>
>>>     clusterEvalQ(cl, {
>>>       require(PkgB)
>>>     })
>>>     [other code]
>>>
>>>     ### this is the code I want to work and need to be able to call
>>>     ### PkgB functions on each of the cluster slaves
>>>     output <- parLapply(cl, 1:n, function(i) {
>>>       [code from my package and using some functions from PkgB]
>>>     })
>>>
>>> }
>>>
>>> As far as I know, just because I add PkgB to the Depends (or imports,
>>> whatever) of PkgA, does not mean that the cluster started by PkgA will
>>> automatically have PkgB loaded and functions available.
>>>
>>> Thanks!
>>>
>>>
>>>
>>> On Fri, Aug 8, 2014 at 9:35 AM, Joshua Wiley <jwiley.psych at gmail.com>
>>> wrote:
>>>
>>>   Dear All,
>>>>
>>>> What is the preferred way for Package A, to initialize a cluster, and
>>>> load
>>>> Package B on all nodes?
>>>>
>>>> I am writing a package that parallelizes some functions through the use
>>>> of
>>>> a cluster if useRs are on a Windows machine (using parLapply and family).
>>>>    I also make use of another package in some of my code, so it is
>>>> necessary
>>>> to load the required packages on each slave once the cluster is started.
>>>>
>>>> Right now, I have done this, by evaluating require(packages) on each
>>>> slave; however, Rcmd check has a note that I should remove the "require"
>>>> in
>>>> my code.
>>>>
>>>> Thanks!
>>>>
>>>> Josh
>>>>
>>>> --
>>>> Joshua F. Wiley
>>>> Ph.D. Student, UCLA Department of Psychology
>>>> http://joshuawiley.com/
>>>> Senior Analyst, Elkhart Group Ltd.
>>>> http://elkhartgroup.com
>>>> Office: 260.673.5518
>>>>
>>>>
>>>
>>>
>>>
>>
>> --
>> 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
>>
>
>
>

-- 
Dr. Henrik Singmann
Albert-Ludwigs-Universit?t Freiburg, Germany
http://www.psychologie.uni-freiburg.de/Members/singmann



[Rd] How to (appropropriately) use require in a package?
Henrik Singmann