[Bioc-devel] error related to kmp_runtime.cpp(6480)

Hervé Pagès hpages at fredhutch.org
Tue Apr 25 01:47:26 CEST 2017

Hi Vlad,

veracruz2 uses clang 4.0.0 instead of the compilers shipped with Xcode.


About 1 month ago the CRAN folks decided to use El Capitan + clang
4.0.0 for building the R and package binaries distributed on CRAN. So
we're just following their lead on this. We installed clang 4.0.0 on
veracruz2 by extracting the tarball provided here:


My understanding is that one of the motivations for them to use
clang 4.0.0 is that it has built-in support for OpenMP.

I don't know how you are set up on your laptop but if you install
packages from source then make sure to use clang 4.0.0 if you want
to increase your chances to reproduce this error. In particular,
make sure that mzR and MSnbase have been compiled with clang 4.0.0.
You also want to make sure that you're using the official CRAN binary
for R 3.4:


Thanks for looking into this.


On 04/24/2017 01:43 PM, Vladislav Petyuk wrote:
> My package passes all the builds except OS X.
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_checkResults_devel_bioc-2DLATEST_MSnID_veracruz2-2Dbuildsrc.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=OPWgCqsx47iwIB3NpYwWet16UFW8gVYtAhsTwiBNMd0&s=4_qAn837g-e8T6YpPM_KA6V73MrtoDd0E-NTiisSl8M&e=
> 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?
> Thanks,
> Vlad
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=OPWgCqsx47iwIB3NpYwWet16UFW8gVYtAhsTwiBNMd0&s=8uuqR-nZvvgUqZ1Di0WLso-7ap9VByOdbS8gRVZzCTI&e=

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioc-devel mailing list