On 11/04/2013 11:34 AM, Michael Lawrence wrote:
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
The 'foreach' framework does this sort of analysis using codetools at
least in part. You may be able to build on what they have.
luke
On Mon, 4 Nov 2013, Ryan wrote:
On 11/4/13, 11:05 AM, Gabriel Becker wrote:
As a side note, I'm not sure that existence of a symbol is sufficient (it
Actually, the check that I proposed is only supposed to check for usage
of user-defined variables, not variables from packages. Truthfully,
though, I guess I'm not the right person to work on this, since in
practice I use forked processes for the vast majority of my inside-R
parallelization,
Weird, I guess it needs to be logged in or something. I don't know if the
issue is that its in a non-master branch or waht. The repo is fully public
and the forCRAN_0.3.5 in branch definitely exists on github.
I started chrome (where I'm not logged into github) and got the same 404
error but
The code that I wrote intentionally avoids checking for package variables,
since I consider that a separate problem. Package variables can be provided
to the child by leading the package, whereas user-defined variables must be
serialized in the parent and sent to the child.
I think I could fairly
Ryan,
I agree that in some sense it is a different problem, but my point is with
a different approach we can easily answer both. The code I posted returns a
named character vector of symbol names with package name being the name.
This makes it a trivial lookup to determine both a) what symbols
On 11/4/13, 11:05 AM, Gabriel Becker wrote:
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?
I think this is a
An analog to clusterExport is a good idea. To make it even easier, we could
have a dynamic environment based on object tables that would catch missing
symbols and download them from the parent thread. But maybe there's some
benefit to being explicit?
Michael
On Sun, Nov 3, 2013 at 12:39 PM,
On Sun, Nov 3, 2013 at 1:29 PM, Michael Lawrence
lawrence.mich...@gene.com wrote:
An analog to clusterExport is a good idea. To make it even easier, we could
have a dynamic environment based on object tables that would catch missing
symbols and download them from the parent thread. But maybe
Here's an easy thing we can add to BiocParallel in the short term. The
following code defines a wrapper function withBPExtraErrorText that
simply appends an additional message to the end of any error that looks
like it is about a missing variable. We could wrap every evaluation in
a similar
Another potential easy step we can do is that if FUN function in the
user's workspace, we automatically export that function under the same
name in the children. This would make recursive functions just work, but
it might be a bit too magical.
On 11/3/13, 2:38 PM, Ryan wrote:
Here's an easy
Henrik,
See https://github.com/duncantl/CodeDepends (as used by used by
https://github.com/gmbecker/RCacheSuite). It will identify necessarily
defined symbols (input variables) for code that is not doing certain tricks
(eg get(), mixing data.frame columns and gobal variables in formulas, etc ).
I guess all we need to do is to detect whether a function would try to
access a free variable in the user's workspace, and warn/error if so.
It looks like CodeDepends could do that. I could try to come up with an
implementation. I guess we would add CodeDepends as an optional
dependency for
Ryan (et al),
FYI:
f
function() {
x = rnorm(x)
x
}
findGlobals(f)
[1] = { rnorm
x should be in the list of globals but it isn't.
~G
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3]
Ok, here is my attempt at a function to get the list of user-defined
free variables that a function refers to:
https://gist.github.com/DarwinAwardWinner/7298557
Is uses codetools, so it is subject to the limitations of that package,
but for simple examples, it successfully detects when a
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