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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