[Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?

The dynamic nature of R limits the extent of these checks. But as Ryan has
noted, a simple sanity check goes a long way. If what he has done could be
extended to the rest of the search path (people always forget to attach
packages), I think we've hit the 80% with 20%. Got a 404 on that URL btw.

Michael


On Mon, Nov 4, 2013 at 11:05 AM, Gabriel Becker <gmbecker at ucdavis.edu>wrote:

Hey guys,

Here is code that I have written which resolves library names into a full
list of symbols:

https://github.com/duncantl/CodeDepends/blob/forCRAN_0.3.5/R/librarySymbols.RNote
this does not require that the packages actually be loaded at the time
of the check, and does not load them (or rather, it loads them but does not
attach them, so no searchpath muddying occurs). You do need a list of
packages to check though (it adds the base ones automatically). It handles
dependency and could be easily extended to handle suggests as well I think.

When CodeDepends gets pushed to cran (not my call and not high on my
priority list to push for currently) it will actually do exactly what you
want. (the forCRAN_0.3.5 branch already does and I believe it is
documented, so you could use devtools to install it now).

As a side note, I'm not sure that existence of a symbol is sufficient (it
certainly is necessary). What about situations where the symbol exists but
is stale compared to the value in the parent? Are we sure that can never
happen?

~G


On Mon, Nov 4, 2013 at 7:29 AM, Michel Lang <michellang at gmail.com> wrote:

You might want to consider using Recall() for recursion which should

solve

this. Determining the required variables using heuristics as codetools

will

probably lead to some confusion when using functions which include calls
to, e.g., with():

f = function() {
   with(iris, Sepal.Length + Sepal.Width)
}
codetools:::findGlobals(f)

I would suggest to write up some documentation on what the function's
environment contains and how to to define variables accordingly - or why

it

can generally be considered a good idea to pass everything essential as

an

argument. Nevertheless a "bpExport" function would be a good addition for
some rare corner cases in my opinion.

Michel


2013/11/3 Henrik Bengtsson <hb at biostat.ucsf.edu>

Hi,

in BiocParallel, is there a suggested (or planned) best standards for
making *locally* assigned variables (e.g. functions) available to the
applied function when it runs in a separate R process (which will be
the most common use case)?  I understand that avoid local variables
should be avoided and it's preferred to put as mush as possible in
packages, but that's not always possible or very convenient.

EXAMPLE:

library('BiocParallel')
library('BatchJobs')

# Here I pick a recursive functions to make the problem a bit harder,

i.e.

# the function needs to call itself ("itself" = see below)
fib <- function(n=0) {
   if (n < 0) stop("Invalid 'n': ", n)
   if (n == 0 || n == 1) return(1)
   fib(n-2) + fib(n-1)
}

# Executing in the current R session
cluster.functions <- makeClusterFunctionsInteractive()
bpParams <- BatchJobsParam(cluster.functions=cluster.functions)
register(bpParams)
values <- bplapply(0:9, FUN=fib)
## SubmitJobs |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
## Waiting [S:0 R:0 D:10 E:0] |+++++++++++++++++++| 100% (00:00:00)


# Executing in a separate R process, where fib() is not defined
# (not specific to BiocParallel)
cluster.functions <- makeClusterFunctionsLocal()
bpParams <- BatchJobsParam(cluster.functions=cluster.functions)
register(bpParams)
values <- bplapply(0:9, FUN=fib)
## SubmitJobs |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
## Waiting [S:0 R:0 D:10 E:0] |+++++++++++++++++++| 100% (00:00:00)
Error in LastError$store(results = results, is.error = !ok,

throw.error =

TRUE)
:
   Errors occurred during execution. First error message:
Error in FUN(...): could not find function "fib"
[...]


# The following illustrates that the solution is not always
straightforward.
# (not specific to BiocParallel; must have been discussed previously)
values <- bplapply(0:9, FUN=function(n, fib) {
   fib(n)
}, fib=fib)
Error in LastError$store(results = results, is.error = !ok,
throw.error = TRUE) :
   Errors occurred during execution. First error message:
Error in fib(n): could not find function "fib"
[...]

# Workaround; make fib() aware of itself
# (this is something the user need to do, and would be very
#  hard for BiocParallel et al. to automate.  BTW, should all
#  recursive functions be implemented this way?).
fib <- function(n=0) {
   if (n < 0) stop("Invalid 'n': ", n)
   if (n == 0 || n == 1) return(1)
   fib <- sys.function() # Make function aware of itself
   fib(n-2) + fib(n-1)
}
values <- bplapply(0:9, FUN=function(n, fib) {
   fib(n)
}, fib=fib)


WISHLIST:
Considering the above recursive issue solved, a slightly more explicit
and standardized solution is then:

values <- bplapply(0:9, FUN=function(n, BPGLOBALS=NULL) {
   for (name in names(BPGLOBALS)) assign(name, BPGLOBALS[[name]])
   fib(n)
}, BPGLOBALS=list(fib=fib))

Could the above be generalized into something as neat as:

bpExport("fib")
values <- bplapply(0:9, FUN=function(n) {
   BiocParallel::bpImport("fib")
   fib(n)
})

or ideally just (analogously to parallel::clusterExport()):

bpExport("fib")
values <- bplapply(0:9, FUN=fib)

/Henrik

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--
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis

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