From jeffrey.ryan at lemnica.com  Fri Sep 23 17:54:07 2011
From: jeffrey.ryan at lemnica.com (Jeffrey Ryan)
Date: Fri, 23 Sep 2011 10:54:07 -0500
Subject: [Rd] Issue with seek() on gzipped connections in R-devel
In-Reply-To: <CAM9CR=0kgvt987jMPU3_N17CLH1aBn1RMi09WES8Z7LSRRYVTg@mail.gmail.com>
References: <CAM9CR=0kgvt987jMPU3_N17CLH1aBn1RMi09WES8Z7LSRRYVTg@mail.gmail.com>
Message-ID: <CABDUZc-hG9DAv8T+FNn0y8n8L1Z0=n5QqWkoHO594t96Q3m5FA@mail.gmail.com>

seek() in general is a bad idea IMO if you are writing cross-platform code.

?seek

Warning:

     Use of ?seek? on Windows is discouraged.  We have found so many
     errors in the Windows implementation of file positioning that
     users are advised to use it only at their own risk, and asked not
     to waste the R developers' time with bug reports on Windows'
     deficiencies.

Aside from making me laugh, the above highlights the core reason to not use IMO.

For not zipped files, you can try the mmap package.  ?mmap and ?types
are good starting points.  Allows for accessing binary data on disk
with very simple R-like semantics, and is very fast.  Not as fast as a
sequential read... but fast.  At present this is 'little endian' only
though, but that describes most of the world today.

Best,
Jeff

On Fri, Sep 23, 2011 at 8:58 AM, Jon Clayden <jon.clayden at gmail.com> 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
>



-- 
Jeffrey Ryan
jeffrey.ryan at lemnica.com

www.lemnica.com
www.esotericR.com



[Rd] Issue with seek() on gzipped connections in R-devel
Jeffrey Ryan