[Bioc-devel] OpenMP on Mac OS "Mavericks" build server morelia

[Ulrich Bodenhofer]

Dear BioC Core Team members,

As you know, we have submitted a package 'msa' for Bioconductor 3.1 
which has been accepted last week. After having fixed some other 
cross-platform problems, we are still having issues on the Mavericks 
build server morelia (see 
http://bioconductor.org/checkResults/3.1/bioc-LATEST/msa/morelia-buildsrc.html). 
Version 0.99.4 of our package throws an error that the OpenMP include 
file omp.h is not found. Our configure script actually checks for OpenMP 
and our package builds without any errors on all Mac OS systems we have 
tested so far (Yosemite and Mavericks, and it also works on the Snow 
Leopard build server petty). I suppose there are two possible sources of 
the problem: that something is still wrong with our code or that OpenMP 
is ill-configured on morelia. In the meantime, we have checked in 
Version 0.99.5 which explicitly turns off OpenMP for all Mac OS 
platforms, but we would prefer to remove this suboptimal workaround if 
possible. Any help is gratefully appreciated!

Thanks in advance and best regards,
Ulrich

P.S.: If this is a question that should not be discussed on this list, 
but elsewhere, please let us know.
P.P.S.: That the Makefile says "Compilation successful" despite the 
compilation error, has been fixed in 0.99.5.