I think none of these examples describe a zlib compressed data block inside
a binary file that the OP asked about, as all of your examples are e.g.
prepending gzip or zip headers.

Greg, is memDecompress what you are looking for?

          - Murray



On Wed, Nov 27, 2013 at 5:22 PM, Dirk Eddelbuettel <edd@debian.org> wrote:

>
> On 27 November 2013 at 18:38, Dirk Eddelbuettel wrote:
> |
> | 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
>
> Oh, and in case you meant zip file containing a data file, that also works.
>
> First converting what I did last
>
> edd@max:/tmp$ gunzip trees.csv.gz
> edd@max:/tmp$ zip trees.zip trees.csv
>   adding: trees.csv (deflated 50%)
> edd@max:/tmp$
>
> Then reading the csv from inside the zip file:
>
> R> read.csv(unz("/tmp/trees.zip", "trees.csv"))
>     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>
>
> Regards, Dirk
>
> --
> Dirk Eddelbuettel | edd@debian.org | http://dirk.eddelbuettel.com
>
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>

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