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

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Fri, 29 Feb 2008 18:36:31 +0000 (GMT)

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

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