[Bioc-devel] any interest in a BiocMatrix core package?

Gabe Becker becker.gabe at gene.com
Sat Feb 25 01:00:17 CET 2017

On Fri, Feb 24, 2017 at 1:26 PM, Aaron Lun <alun at wehi.edu.au> wrote:

> Hi everyone,
> I was thinking of something that you could supply any supported matrix
> representation to a registered function via .Call; the C++ constructor
> would recognise the type of matrix during class instantiation; and
> operations (row/column/random read access, also possibly various ways of
> writing a matrix) would be overloaded and behave as required for the class.
> Only the implementation of the API would need to care about the nitty
> gritty of each representation, and we would all be free to write code that
> actually does the interesting analytical stuff.

This seems (at least moderately) related to the alternative atomic-vector
representation work I have been doing with R-core. See
and  ALTREP.md in https://svn.r-project.org/R/branches/ALTREP/ (not
necessarily fully up-to-date, you can also look at src/main/altrep.c for

I'd also say there may be a pretty strong impedence mismatch if you want
something customizable at both the R and C levels. That's just a suspicion
at this point, though, I'm writing very quickly and will send out a more
reasoned response later because I don't have the time to do so right this


> Anyway, just throwing some thoughts out there. Any comments appreciated.
> Cheers,
> Aaron
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Gabriel Becker, Ph.D
Associate Scientist
Bioinformatics and Computational Biology
Genentech Research

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