Re: [R] compress data on read, decompress on write

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Thu, 28 Feb 2008 19:53:50 +0000 (GMT)

One solution is likely to be the Omegahat package Rcompression.

Otherwise, R does have internal facilities to do internal (gzip) compression and decompression (e.g. see the end of src/main/connections.c), and you could make creative use of serialization to do the compression.

On Thu, 28 Feb 2008, Ramon Diaz-Uriarte wrote:

> Dear All,
>
> I'd like to be able to have R store (in a list component) a compressed
> data set, and then write it out uncompressed. gzcon and gzfile work in
> exactly the opposite direction. What would be a good way to handle
> this?
>
> Details:
> ----------
>
> We have a package that uses C; part of the C output is a large sparse
> matrix. This is never manipulated directly by R, but always by the C
> code. However, we need to store that data somewhere (inside an R
> object) for further calls to the functions in our package. We'd like
> to store that matrix as part of the R object (say, as an element of a
> list). Ideally, it would be stored in as compressed a way as possible.
> Then, when we need to use that information, it would be decompressed
> and passed to the C function.
>
> I guess one way to do it is to have C deal with the compression and
> uncompression (e.g., using zlib or the bzip2 libraries) and then use
> readBin, etc, from R. But, if I can, I'd like to avoid our C code
> having to call zlib, etc, so as to make our package easily portable.

As from R 2.7.0 you will be able to make use of zlib on effectively all platforms, since it has a public interface on Windows.

>
> Thanks,
>
> R.
>
> --
> Ramon Diaz-Uriarte
> Statistical Computing Team
> Structural Biology and Biocomputing Programme
> Spanish National Cancer Centre (CNIO)
> http://ligarto.org/rdiaz

-- 
Brian D. Ripley,                  ripley_at_stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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