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

[Ramon Diaz-Uriarte]

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