Hi, 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.obench...@roswellpark.org) or here on the list. 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. Valerie 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 > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
