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 <[email protected]> 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 | [email protected] | http://dirk.eddelbuettel.com
>
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