[R] using zlib (was compress data on read, decompress on write)

From: Ramon Diaz-Uriarte <rdiaz02_at_gmail.com>
Date: Fri, 29 Feb 2008 19:16:52 +0100

Dear All,

I think I am confused about how I'd be able to use zlib starting with R 2.7.0. I just downloaded the latest development version, built it, etc, but I am not able to find the zlib.h that, I believe, R should place somewhere under "where/you/want/R/to/go" (from --prefix=/where/you/want/R/to/go). There seem to be entry points for zlib in the binary (e.g., grep -r gzopen ./ Binary file ./lib64/R/bin/exec/R matches; etc). What is the appropriate way (if any) to tell my package where to look for the R-provided zlib.h?

In addition, when searching the archives I found the message


which seems to suggest that I'd be better off including my own copies of zlib.h, although I understand that the message is not referring explicitly to the new R 2.7.0.



On Thu, Feb 28, 2008 at 8:53 PM, Prof Brian Ripley <ripley_at_stats.ox.ac.uk> wrote:
> 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

Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)

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