Yes, inelegant would be a good description. Sadly a fact we have to put up with I guess.
FWIW, I too don't like dependencies. mmap has none, and is cross platform, but I get the idea. Good luck, Jeff On Fri, Sep 23, 2011 at 11:13 AM, Jon Clayden <jon.clay...@gmail.com> wrote: > 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.r...@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.clay...@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@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >> >> >> >> -- >> Jeffrey Ryan >> jeffrey.r...@lemnica.com >> >> www.lemnica.com >> www.esotericR.com >> > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Jeffrey Ryan jeffrey.r...@lemnica.com www.lemnica.com www.esotericR.com ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
