Re: [Bioc-devel] ClassifyR Fails to Build on Windows
Thank you for the detailed explanation. I understand the cause now. Actually, the exact problem is that, in runTest, I have a condition that depends on the previous function calls : if(any(grepl(runTests, deparse(sys.calls() If runTest was called by runTests, then I intend to return a particular value that does not refer to the variable datasetName. If runTest was called directly by the user, such as when they have one training and on test dataset and don't need to do the cross-validation offered by runTests, I intend to return a ClassifyResult object, which does refer to the variable datasetName. The condition evaluates to FALSE, even when runTest was called by runTests on Windows, and executes the unintended code block which makes reference to datasetName, which is missing. How can I make my check of previously called functions platform-independent when I am also using parallelisation ? -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] ClassifyR Fails to Build on Windows
On 01/16/2015 03:00 PM, Dario Strbenac wrote:
Thank you for the detailed explanation. I understand the cause now. Actually,
the exact problem is that, in runTest, I have a condition that depends on the
previous function calls :
if(any(grepl(runTests, deparse(sys.calls()
If runTest was called by runTests, then I intend to return a particular value
that does not refer to the variable datasetName. If runTest was called directly
by the user, such as when they have one training and on test dataset and don't
need to do the cross-validation offered by runTests, I intend to return a
ClassifyResult object, which does refer to the variable datasetName. The
condition evaluates to FALSE, even when runTest was called by runTests on
Windows, and executes the unintended code block which makes reference to
datasetName, which is missing. How can I make my check of previously called
functions platform-independent when I am also using parallelisation ?
I'd just be more direct about signalling what you want runTest to do, by adding
an extra argument
fun - function(..., .init=FALSE)
## document .init as 'internal' argument not for end users
{
if (.init)
return(done)
message(doing)
fun(..., .init=TRUE)
}
If you'd like to keep .init from user view, then implement the above as .fun,
and provide an end-user wrapper
fun - function(...) .fun(..., .init=FALSE)
Martin
--
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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Re: [Bioc-devel] ClassifyR Fails to Build on Windows
There is no shared memory on windows so you need to make sure you require() any necessary packages on each node. Dan On January 15, 2015 5:00:22 PM PST, Dario Strbenac dstr7...@uni.sydney.edu.au wrote: Hello, The development version of ClassifyR won't build on Windows. It happens for a code section in the vignette that executes a function that has a bpmapply loop. However, I'm using the default parameters by calling bpparam(), so it should work on Windows. The code in the vignette executes without problems for Linux and Mac OS. Is there a flaw in the development version of BiocParallel ? -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
