On 04/24/2017 04:43 PM, Vladislav Petyuk wrote:
My package passes all the builds except OS X.
http://www.bioconductor.org/checkResults/devel/bioc-LATEST/MSnID/veracruz2-buildsrc.html
Interestingly, the build goes just fine (with the same arguments) on my
laptop, which is OS X 10.12.3.
Given that kmp_runtime.cpp is from OpenMP and chunk 25 in the vignette
indirectly engages `mclapply`, my hunch is that this is something to do
with parallel processing. Is multithreading not allowed on this OS X
machine? Is simply forcing mc.cores = 1 going to solve the problem? Any
other suggestions on what is this error about and how to handle it?
is this nested parallelism -- mclapply() (forked process) then in the
parallel chunks invoking OpenMP code? This probably at least partly
defeats the parallelism, since threads are competing with one another
for forked resources.
Just a guess,
Martin
Thanks,
Vlad
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