From jon.clayden at gmail.com  Fri Sep 23 15:58:32 2011
From: jon.clayden at gmail.com (Jon Clayden)
Date: Fri, 23 Sep 2011 14:58:32 +0100
Subject: [Rd] Issue with seek() on gzipped connections in R-devel
Message-ID: <CAM9CR=0kgvt987jMPU3_N17CLH1aBn1RMi09WES8Z7LSRRYVTg@mail.gmail.com>

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



[Rd] Issue with seek() on gzipped connections in R-devel
Jon Clayden