R devel - Nov 2013 - inflate zlib compressed data using base R or CRAN package?

Hello,

I have a binary file type that includes a zlib compressed data block (ie 
not gzip). Is anyone aware of a way using base R or a CRAN package to 
decompress this kind of data (from disk or memory). So far I have found 
Rcompression::decompress on omegahat, but I would prefer to keep 
dependencies on CRAN (or bioconductor). I am also trying to avoid 
writing yet another C level interface to part of zlib.

Many thanks for any pointers,

Greg.

--
Gregory Jefferis, PhD
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://flybrain.stanford.edu

On 27 November 2013 at 23:49, Dr Gregory Jefferis wrote:
| I have a binary file type that includes a zlib compressed data block (ie 
| not gzip). Is anyone aware of a way using base R or a CRAN package to 
| decompress this kind of data (from disk or memory). So far I have found 
| Rcompression::decompress on omegahat, but I would prefer to keep 
| dependencies on CRAN (or bioconductor). I am also trying to avoid 
| writing yet another C level interface to part of zlib.

Unless I am missing something, this is in base R; see help(connections).

Here is a quick demo:

R> write.csv(trees, file="/tmp/trees.csv")    # data we all have
R> system("gzip -v /tmp/trees.csv")           # as I am lazy here
/tmp/trees.csv:	 50.5% -- replaced with /tmp/trees.csv.gz
R> read.csv(gzfile("/tmp/trees.csv.gz"))      # works out of the
box
    X Girth Height Volume
1   1   8.3     70   10.3
2   2   8.6     65   10.3
3   3   8.8     63   10.2
4   4  10.5     72   16.4
5   5  10.7     81   18.8
6   6  10.8     83   19.7
7   7  11.0     66   15.6
8   8  11.0     75   18.2
9   9  11.1     80   22.6
10 10  11.2     75   19.9
11 11  11.3     79   24.2
12 12  11.4     76   21.0
13 13  11.4     76   21.4
14 14  11.7     69   21.3
15 15  12.0     75   19.1
16 16  12.9     74   22.2
17 17  12.9     85   33.8
18 18  13.3     86   27.4
19 19  13.7     71   25.7
20 20  13.8     64   24.9
21 21  14.0     78   34.5
22 22  14.2     80   31.7
23 23  14.5     74   36.3
24 24  16.0     72   38.3
25 25  16.3     77   42.6
26 26  17.3     81   55.4
27 27  17.5     82   55.7
28 28  17.9     80   58.3
29 29  18.0     80   51.5
30 30  18.0     80   51.0
31 31  20.6     87   77.0
R> 


Hope this helps, Dirk

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com