Hi Henrik, Thanks for R.matlab and your reply. I cannot find any octave option to save an uncompressed MATLAB-format file. I have just downloaded Rcompression from what I believe is the official website so it should be current. I also think I have the current R version (at least, what is current for Ubuntu), and I will check regarding R.matlab.
Thanks, Stefano On Tue, Dec 21, 2010 at 1:15 PM, Henrik Bengtsson <h...@biostat.ucsf.edu> wrote: > Hi, > > I am using Octave; what does that save options do, more specifically, > is compression taking place when saving that file? > > If compression is done, then the Rcompression package is utilized by > R.matlab (otherwise not). BTW, you don't have to load Rcompression > explicitly; R.matlab will do it for you if needed. So, if you start a > fresh R session and load R.matlab and then try to load your package, > is Rcompression loaded? If so, what version Rcompression do you have > installed, i.e. what does > > sessionInfo() > > report afterward? Duncan TL did Rcompression updates addressing > memory usage about a year ago (I think) and it might be that you are > using an older version of it. You should also update R.matlab et al, > because your using old versions (though I don't think that is the > cause here). > > If Rcompression is the cause here, then it also make sense that you > don't experience the memory hog when reading a text file (which is > never compressed). You could also see if there is an option in Octave > that safes to binary format but without compression. I know Matlab > has such options. > > /Henrik > (author of R.matlab) > > > > > On Mon, Dec 20, 2010 at 7:11 AM, Stefano Ghirlanda > <dr.ghirla...@gmail.com> wrote: >> Hi Ben, >> Thanks for your reply. My data structure is about 20000 x 2000 so one >> order of magnitude the one you tried. I have no problem saving and >> reading smaller data structures (even large ones, just not his large) >> between octave and R using octave's "save -7" (which saves MATLAB v5 >> files) and R.matlab's readMat. And I can save in text format in octave >> and read in R using read.octave (from package foreign) so it's not a >> big deal. I was just surprised that R.matlab needed more memory than I >> have (I have 3GB on this machine). >> >> Thanks, >> Stefano >> >> On Sun, Dec 19, 2010 at 10:54 PM, Ben Bolker <bbol...@gmail.com> wrote: >>> Stefano Ghirlanda <dr.ghirlanda <at> gmail.com> writes: >>> >>>> I am trying to load into R a MATLAB format file (actually, as saved by >>>> octave). The file is about 300kB but R complains with a memory >>>> allocation error: >>>> >>>> > library(Rcompression) >>>> > library(R.matlab) >>>> Loading required package: R.oo >>>> Loading required package: R.methodsS3 >>>> R.methodsS3 v1.2.0 (2010-03-13) successfully loaded. See ?R.methodsS3 for >>>> help. >>>> R.oo v1.7.2 (2010-04-13) successfully loaded. See ?R.oo for help. >>>> R.matlab v1.3.1 (2010-04-20) successfully loaded. See ?R.matlab for help. >>>> > f <- readMat("freq.mat") >>>> Error: cannot allocate vector of size 296.5 Mb >>>> >>>> On the other hand, if I save the same data in ascii format (from >>>> octave: "save -text"), resulting in a 75MB file, then I can load it >>>> without problems with the read.octave() function from package foreign. >>>> Is this a known issue or am I doing something wrong? My R version is: >>> >>> This is not a package I'm particularly familiar with, but: >>> >>> what commands did you use to save the file in octave? Based on >>> 'help save' I think that 'save' by default would get you an octave >>> format file ... you might have to do some careful reading in >>> ?readMat (in R) and 'help save' (in octave) to figure out the >>> correspondence between octave/MATLAB and R/MATLAB. >>> If possible, try saving a small file and see if it works; if >>> you still don't know what's going on, post that file somewhere for >>> people to try. >>> >>> I was able to >>> >>> save -6 "save.mat" in octave and >>> readMat("save.mat") in R successfully, >>> saving a vector of integers from 1 to 1 million (which >>> took about 7.7 Mb) >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >> >> >> >> -- >> Stefano Ghirlanda >> www.intercult.su.se/~stefano - drghirlanda.wordpress.com >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > -- Stefano Ghirlanda www.intercult.su.se/~stefano - drghirlanda.wordpress.com [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.