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

Dan Tenenbaum dtenenba at fredhutch.org
Mon Apr 13 19:22:38 CEST 2015

Hi Ulrich,

----- Original Message -----
> From: "Ulrich Bodenhofer" <bodenhofer at bioinf.jku.at>
> To: bioc-devel at r-project.org
> Cc: "Hervé Pagès" <hpages at fhcrc.org>, msa at bioinf.jku.at, "Johannes Palme" <jpalme at aon.at>
> Sent: Monday, April 13, 2015 3:37:37 AM
> Subject: [Bioc-devel] OpenMP on Mac OS "Mavericks" build server morelia
> 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

How did you set up OpenMP on your Mavericks machine?

> 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.
> _______________________________________________
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