Issue with seek() on gzipped connections in R-devel

Thanks for the replies. I take the point, although it does seem like a
substantial regression (on non-Windows platforms).

I like to keep the external dependencies of my packages minimal, but I
will look into the mmap package - thanks, Jeff, for the tip.

Aside from that, though, what is the alternative to using seek? If I
want to read something at (original, uncompressed) byte offset 352, as
here, do I have to read and discard everything that comes before it
first? That seems inelegant at best...

Regards,
Jon


On 23 September 2011 16:54, Jeffrey Ryan <jeffrey.ryan at lemnica.com> wrote:

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

--
Jeffrey Ryan
jeffrey.ryan at lemnica.com

www.lemnica.com
www.esotericR.com