[Bioc-devel] BiocParallel-devel error

[Valerie Obenchain]

Hi Michel,

In BiocParallel 0.99.24 .convertToSimpleError() now checks for NULL and 
converts to NA_character_.

I'm testing with BatchJobs 1.4, BiocParallel 0.99.24 and SLURM. I'm 
still not getting an informative error message:

>> xx <- bplapply(1:2, FUN)
> SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
> Waiting [S:2 D:0 E:0 R:0] |+                                 |   0% (00:00:00)
> Error: 2 errors; first error:
>   NA
>
> 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().


Last error:

>> bplasterror()
> 0 / 2 partial results stored. First 2 error messages:
> [1]: NA
> [2]: NA


Valerie


On 09/26/2014 01:44 AM, Michel Lang wrote:
> This was a bug in BatchJobs::waitForJobs(). We now throw an error if
> jobs "disappear" due to a faulty template file. I'd appreciate if you
> could confirm that this is now correctly catched and handled on your
> system. I furthermore suggest to replace NULL with NA_character_ in
> .convertToSimpleError().
>
> I will upload a fixed BatchJobs to CRAN ASAP (but last upload was the
> day before yesterday, thus we have to wait a few days).
>
> Best,
> Michel
>