[Bioc-devel] timeout on perceval server macos snow leopard

Obenchain, Valerie Valerie.Obenchain at roswellpark.org
Fri Sep 4 18:52:50 CEST 2015


I've taken a quick look at LowMACA. It looks like you're doing more work
than you need to with 'applyfun'. BiocParallel automatically detects the
OS and will use SnowParam, MulticoreParam or SerialParam as needed.

The more important problem is that you have several nested layers of
parallel evaluation, each requesting maximum cores. That doesn't explain
why the package only fails only on perceval but it probably points to
requesting more resources than are available. I can help you work
through this offline (valerie.obenchain at roswellpark.org) or here on the

I would start by making these changes:

- replace 'applyfun' with bplapply()

- remove "Parallel Options" section in code files

- expose the BPPARAM arg to users so they can select the back-end and
number of cores

- modify allPfamAnalysis.R

Inside the allPfamAnalysis() function you have another function with the
same name and allPfamanalysis is also used as a variable name. This
makes the code difficult to read and hard to determine the number of
time the function is called.

It looks like inside allPfamAnalysis() you create another
allPfamAnalysis() that calls lfmSingleSequence() (2 nested layers of
bplaply with max cores). The same goes for singleSequence() which calls
lfmSingleSequence() (2 nested layers again).

BiocParallel does not manage the number of cores used so you need to be
careful of nesting layers too deep. The best approach is to expose
BPPARAM to the user so they can manage resources. By 'expose' I mean
allow the argument to be passed to the function and used in bplapply().

Let me know if you have questions.

On 09/04/2015 03:22 AM, Giorgio Melloni wrote:
> I recently enhanced my package LowMACA on Bioconductor and I finally obtained the OK on build and check from linux and windows. On MacOS, the build get stuck at some point of the vignette during building but I don't know how to spot what is the function that is taking so long. 
> Here is the result of the build report. http://bioconductor.org/checkResults/devel/bioc-LATEST/LowMACA/perceval-buildsrc.html
> Do you know how to figure it out?
> thanks,
> Giorgio
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> Bioc-devel at r-project.org mailing list
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