From murdoch.duncan at gmail.com  Mon Jul 10 21:51:12 2017
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Mon, 10 Jul 2017 15:51:12 -0400
Subject: [Rd] 'do.call' appears to show inconsistent behavior for
 arguments of format "pkg::fun"
In-Reply-To: <837EA172-E958-4207-9C1C-F1C1F12123DC@yale.edu>
References: <837EA172-E958-4207-9C1C-F1C1F12123DC@yale.edu>
Message-ID: <ca633e0b-a43c-3f55-032a-77387b24ffa8@gmail.com>

On 10/07/2017 3:37 PM, Schlaepfer, Daniel wrote:
> Hi all,
>
> I believe that 'do.call' shows inconsistent/undocumented behavior when its 'what' argument is of the format "pkg::fun". The documentation (?do.call) suggests that
>     what: either a function or a non-empty character string naming the function to be called.

No, it is working just as documented.

>
> Thus, I expected that all four of below formats of the value for the 'what' argument would work, here I use 'utils::person' as an example:
> Three formats work:
>> do.call(person, list(given = "Jane", family = "Doe"))
>> do.call("person", list(given = "Jane", family = "Doe"))
>> do.call(utils::person, list(given = "Jane", family = "Doe"))
>
> but the format "pkg::fun" doesn't work as I expected:
>> do.call("utils::person", list(given = "Jane", family = "Doe"))
>   Error in `utils::person`(given = "Jane", family = "Doe") :
>     could not find function "utils::person"

person and utils::person are both expressions that give a function as 
the value.  "person" and "utils::person" are both expressions that give 
a character string, but "utils::person" is not the name of a function.

It's similar to this:

as.numeric(1)
as.numeric("1")
as.numeric(0+1)
as.numeric("0+1")

The 4th expression is not something that as.numeric knows how to coerce 
to a number.  The rest are expressions that evaluate to 1 or "1", and 
as.numeric() knows how to deal with both of those.


Duncan Murdoch

>
> This seemingly inconsistent behavior of 'do.call' is also exposed when working in parallel and the message doesn't make it easy to see that this error derives actually from 'do.call'.
>
>> library(parallel)
>> cl <- makePSOCKcluster(2)
>
> These work
>> clusterCall(cl, person, list(given = "Jane", family = "Doe"))
>> clusterCall(cl, "person", list(given = "Jane", family = "Doe"))
>> clusterCall(cl, utils::person, list(given = "Jane", family = "Doe"))
>
> This doesn't work
>> clusterCall(cl, "utils::person", list(given = "Jane", family = "Doe"))
>   Error in checkForRemoteErrors(lapply(cl, recvResult)) :
>     2 nodes produced errors; first error: could not find function "utils::person"
>
> This is again not obvious from the documentation (?clusterCall): fun, FUN: function or character string naming a function.
>
> This behavior of 'clusterCall' is because the function 'makePSOCKcluster' calls newPSOCKnode() which calls .slaveRSOCK(), which calls slaveLoop(). This is then waiting and on receving an appropriate message will call 'do.call':
>>  value <- tryCatch(do.call(msg$data$fun, msg$data$args, quote = TRUE), error = handler)
>
> Thus, if 'msg$data$fun' (as received from recvData() which was sent via sendData(), via postNote() from function sendCall() wrapped in clusterCall()) is of the type "pkg::fun", then this will fail as above and work otherwise.
>
> ## Temporary work-around: re-define function in local namespace and export to workers
>> temp_fun <- function(...) utils::person(...)
>> clusterExport(cl, "temp_fun")
>> clusterCall(cl, "temp_fun", list(given = "Jane", family = "Doe"))
>
> Clean up
>> stopCluster(cl)
>
>
> ## Motivation: I learned about this behavior of 'do.call' when attempting to write code such as
>> Rmpi::mpi.bcast.cmd(mypackage2::fun, ...)
>
> in my package1. The function Rmpi::mpi.bcast.cmd() calls eventually something along the lines of
>
>> scmd <- scmd <- substitute(cmd)
>> arg <- list(...)
>> scmd.arg <-serialize(list(scmd=scmd, arg=arg), NULL)
>> if (length(scmd.arg$args) > 0)
>>    do.call(as.character(scmd.arg$$scmd), scmd.arg$args, envir = .GlobalEnv)
>
> and thus expresses this same inconsistent behavior of do.call. I cannot avoid calling with pkg::fun because a package should not attach another package and change the search path of the user.
>
>
>
> ## My installation
>> sessionInfo()
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-apple-darwin16.6.0 (64-bit)
> Running under: macOS Sierra 10.12.5
>
> Matrix products: default
> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK: /opt/local/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.1
>
>
>
> I would appreciate any help with identifying whether this is indeed inconsistent/undocumented behavior of 'do.call' or whether I am simply missing the point and how to deal with the situation.
>
> Thank you,
> Daniel Schlaepfer
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] 'do.call' appears to show inconsistent behavior for arguments of format "pkg::fun"
Duncan Murdoch