[Bioc-devel] BiocParallel-devel error

[Valerie Obenchain]

Hi Thomas,

Just wanted to let you know I saw this and am looking into it.

Valerie

On 09/20/2014 02:54 PM, Thomas Girke wrote:
> Hi Martin, Micheal and Vincent,
>
> If I run the following code, with the release version of BiocParallel then it
> works (took me some time to actually realize that), but with the development
> version I am getting an error shown after the test code below. If I run the
> same test with BatchJobs from the devel branch alone then there is no problem.
> Thus, it seems there is some change in the devel version of BiocParallel
> causing this error? The torque.tmpl file I am using on our cluster is the
> standard one from BatchJobs here:
> https://github.com/tudo-r/BatchJobs/blob/master/examples/cfTorque/simple.tmpl
>
> For my application, I could stick with BatchJobs, but it would be nicer if I
> could get things to work with BiocParallel.
>
> Thanks,
>
> Thomas
>
> ###############
> ## Test Code ##
> ###############
> FUN <- function(i) system("hostname", intern=TRUE)
> library(BiocParallel); library(BatchJobs)
> funs <- makeClusterFunctionsTorque("torque.tmpl")
> param <- BatchJobsParam(4, resources=list(walltime="48:00:00", nodes="1:ppn=4", memory="4gb"), cluster.functions=funs)
> register(param)
> xx <- bplapply(1:4, FUN)
>
> Error: 4 errors; first error:
>
> For more information, use bplasterror(). To resume calculation, re-call the function and
> set the argument 'BPRESUME' to TRUE or wrap the previous call in bpresume()
>
>> bplasterror()
> Error in vapply(head(which(is.error), n.print), f, character(1L)) :
>    values must be length 1,
>   but FUN(X[[1]]) result is length 0
>
>> sessionInfo()
> R Under development (unstable) (2014-05-05 r65530)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  utils     datasets  grDevices methods   base
>
> other attached packages:
> [1] BatchJobs_1.3        BBmisc_1.7           BiocParallel_0.99.19
>
> loaded via a namespace (and not attached):
>   [1] BiocGenerics_0.11.4 DBI_0.3.0           RSQLite_0.11.4      brew_1.0-6          checkmate_1.4       codetools_0.2-9     digest_0.6.4        fail_1.2            foreach_1.4.2       iterators_1.0.7
> [11] parallel_3.2.0      sendmailR_1.1-2     stringr_0.6.2       tools_3.2.0
>
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