Re: [Rd] Issue with seek() on gzipped connections in R-devel

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Fri, 23 Sep 2011 16:28:40 +0100 (BST)

Basically seek with zlib is flaky: we've stumbled on several errors. If it worked for you in the past, count yourself lucky. I'd suggest you avoid relying on it in your packages.

On Fri, 23 Sep 2011, Jon Clayden wrote:

> Dear all,
>
> In R-devel (2011-09-23 r57050), I'm running into a serious problem
> with seek()ing on connections opened with gzfile(). A warning is
> generated and the file position does not seek to the requested
> location. It doesn't seem to occur all the time - I tried to create a
> small example file to illustrate it, but the problem didn't occur.
> However, it can be seen with a file I use for testing my packages,
> which is available through the URL
> <https://github.com/jonclayden/tractor/blob/master/tests/data/nifti/maskedb0_lia.nii.gz?raw=true>:
>
>> con <- gzfile("~/Downloads/maskedb0_lia.nii.gz","rb")
>> seek(con, 352)
> [1] 0
> Warning message:
> In seek.connection(con, 352) :
> seek on a gzfile connection returned an internal error
>> seek(con, NA)
> [1] 190
>
> The same commands with the same file work as expected in R 2.13.1, and
> have worked over many previous versions of R.
>
>> con <- gzfile("~/Downloads/maskedb0_lia.nii.gz","rb")
>> seek(con, 352)
> [1] 0
>> seek(con, NA)
> [1] 352
>
> My sessionInfo() output is:
>
> R Under development (unstable) (2011-09-23 r57050)
> Platform: x86_64-apple-darwin11.1.0 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_US.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] splines stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] tractor.nt_2.0.1 tractor.session_2.0.3 tractor.utils_2.0.0
> [4] tractor.base_2.0.3 reportr_0.2.0
>
> This seems to occur whether or not R is compiled with
> "--with-system-zlib". I see some zlib-related changes mentioned in the
> NEWS, but I don't see any indication that this is expected. Could
> anyone shed any light on it, please?
>
> Thanks and all the best,
> Jon
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
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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Received on Fri 23 Sep 2011 - 15:31:33 GMT

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