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

From: Ramon Diaz-Uriarte <rdiaz02_at_gmail.com>
Date: Fri, 29 Feb 2008 22:50:55 +0100

Dear Prof. Ripley,

Thanks for your reply. I think I understand now.

Best,

R.

On Fri, Feb 29, 2008 at 7:36 PM, Prof Brian Ripley <ripley_at_stats.ox.ac.uk> wrote:
> On Fri, 29 Feb 2008, Ramon Diaz-Uriarte wrote:
>
> > 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?
>
> It is only provided on Windows -- that's the only change. On other
> platforms you use configure to find the system copy in the usual way.
> The point is that almost all platforms apart from Windows will have a
> systen copy. What you need to do on Windows is in the CHANGES file.
>
> [You may find entry points in exec/R, but those using shlib R will not.]
>
>
> > In addition, when searching the archives I found the message
> >
> > http://finzi.psych.upenn.edu/R/R-devel/archive/27154.html
> >
> > 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.
>
> Nor implicitly.
>
>
>
> >
> > Thanks,
> >
> > R.
> >
> >
> >
> >
> >
> >
> >
> > 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)
> > 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)
http://ligarto.org/rdiaz

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