[Bioc-devel] Bioconductor support for explicit SSE vectorization

Benjamin Callahan benjamin.j.callahan at gmail.com
Tue Oct 10 22:33:11 CEST 2017

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':
Non-portable flags in variable 'PKG_CFLAGS':
Non-portable flags in variable 'PKG_CXXFLAGS':

Two questions: Should I care about this warning or can I just ignore it?
And is there an example Bioconductor package using SSE (or AVX) intrinsics
out there somewhere, or some documentation of best practices?

Benjamin Callahan

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