[Bioc-devel] EXTERNAL: Bioconductor support for explicit SSE vectorization

Martin Morgan martin.morgan at roswellpark.org
Tue Oct 10 22:45:06 CEST 2017

On 10/10/2017 04:33 PM, Benjamin Callahan wrote:
> Hi,
> In the BioC 3.6 release of the dada2 package, I've added sections of C code
> that are explicitly vectorized using Intel SSE2 intrinsics. I've finally
> got the package building on all three platforms, but to get WIndows/MinGW
> building, I've had to add the -msse2 to the PKG_CXXFLAGS (etc) which is now
> causing the following warning:
> * checking compilation flags in Makevars ... WARNING
> Non-portable flags in variable 'PKG_CPPFLAGS':
>    -msse2
> Non-portable flags in variable 'PKG_CFLAGS':
>    -msse2
> Non-portable flags in variable 'PKG_CXXFLAGS':
>    -msse2
> Two questions: Should I care about this warning or can I just ignore it?

Use a Makevars.win (same content as Makevars, but windows-specific, 
freeing up Makevars to be non-Windows specific) file to specify the flag 
only Windows.

Not sure about other packages using SSE / AVX.


> And is there an example Bioconductor package using SSE (or AVX) intrinsics
> out there somewhere, or some documentation of best practices?
> Regards,
> Benjamin Callahan
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

This email message may contain legally privileged and/or...{{dropped:2}}

More information about the Bioc-devel mailing list