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
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Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
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