From: jim holtman <jholtman_at_gmail.com>

Date: Fri, 29 Feb 2008 19:36:22 -0500

*>
*

Date: Fri, 29 Feb 2008 19:36:22 -0500

You only have 1 row in your matrix, so what you are getting printed out is not an empty matrix, but the header. If you print the transpose you get:

*> head(t(tst))
*

[,1]

[1,] 1 [2,] 2 [3,] 3 [4,] 4 [5,] 5 [6,] 6

The default is to only print out 100000 values. Your data is there, you just have to wait for the headers to print out, or at least make a matrix with more than one row.

On Fri, Feb 29, 2008 at 2:25 PM, Robert Leach <rwleach_at_ccr.buffalo.edu> wrote:

> Hi there,

*>
**> I'm brand new to R, so let me know if this question is not
**> appropriate for this list. I've been reading through the
**> documentation and have tried a number of things, but am pretty much
**> stuck so far. Here's the session info:
**>
**> > sessionInfo()
**> R version 2.6.2 (2008-02-08)
**> i386-apple-darwin8.10.1
**>
**> locale:
**> C
**>
**> attached base packages:
**> [1] stats graphics grDevices utils datasets methods base
**>
**> loaded via a namespace (and not attached):
**> [1] rcompgen_0.1-17
**>
**>
**> So I seem to be hitting a limit on matrix size. First I read in my
**> data into a list and it's OK:
**>
**> > mz <- scan("data.column3.txt", list(0))
**> Read 158991 records
**> >mz
**> > mz
**> [[1]]
**> [1] 0.000000e+00 0.000000e+00 1.003393e+01 3.651888e+00 0.000000e
**> +00
**> [6] 0.000000e+00 3.067042e+00 1.277249e+00 1.984366e+00 3.644203e
**> +01
**> [11] 1.172925e+02 1.933753e+02 2.020940e+02 1.570501e+02 8.990829e
**> +01
**> ...
**>
**> But when I try to put it into a matrix like this, I don't get an
**> error, but the matrix appears empty...
**>
**> > MZ=matrix(mz[[1]],nrow=1)
**> > MZ
**> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,
**> 9] [,10]
**> [,11] [,12] [,13] [,14] [,15] [,16] [,
**> 17] [,18]
**> [,19] [,20] [,21] [,22] [,23] [,24] [,
**> 25] [,26]
**> ...
**>
**> When I did a subset of my data, it was fine. I did a manual binary
**> search and determined the cutoff to be 100000 elements. So if I do
**> just 99,999 elements, it looks as I would expect:
**>
**> > mz <- scan("data.column3.txt", list(0), 99999)
**> Read 99999 records
**> > tst <- matrix(mz[[1]],nrow=1)
**> > tst
**> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,
**> 9] [,10]
**> [1,] 0 0 10.03393 3.651888 0 0 3.067042 1.277249 1.984366
**> 36.44203
**> [,11] [,12] [,13] [,14] [,15] [,16] [,
**> 17] [,18]
**> [1,] 117.2925 193.3753 202.0940 157.0501 89.9083 26.44127 17.05373
**> 53.40315
**> [,19] [,20] [,21] [,22] [,23] [,24] [,
**> 25] [,26]
**> [1,] 65.20086 37.33463 17.71247 27.37268 41.83289 48.46916 58.94969
**> 76.05099
**> ...
**>
**> If I do 100,000, I get the same empty appearance. I've assumed that
**> there must be a limitation on the number of elements in a matrix. Is
**> that right? If so, how do I increase the maximum number of
**> elements? I tried another machine's installation of R and it
**> apparently doesn't have a 99,999 element limit. I've tried using:
**>
**> R --max-mem-size=2G
**> R --max-vsize=200000
**> R --max-nsize=200000
**> R --max-vsize=200000 --max-nsize=200000 --max-ppsize=200000
**> R --max-vsize=10M
**>
**> I still end up with the empty-looking matrix when I try these. How
**> do I get my installation to work like the installation on another
**> computer I tried where I was able to have larger matrices?
**>
**> Oh yeah, I also tried this, just to rule out problems with my data:
**>
**> > tst <- matrix(seq(1,158991),nrow=1,ncol=158991)
**> > tst
**> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
**> [,13] [,14]
**> [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,
**> 25] [,26]
**> [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,
**> 37] [,38]
**> ...
**>
**> Thanks,
**> Rob
**>
**> Robert W. Leach
**> Scientific Programmer
**> Center for Computational Research
**> Center of Excellence in Bioinformatics
**> University at Buffalo
**> http://www.ccr.buffalo.edu/
**>
**> ______________________________________________
**> R-help_at_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.
**>
*

-- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? Tell me what you want to do, not how you want to do it. ______________________________________________ R-help_at_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.Received on Sat 01 Mar 2008 - 00:39:17 GMT

Archive maintained by Robert King, hosted by
the discipline of
statistics at the
University of Newcastle,
Australia.

Archive generated by hypermail 2.2.0, at Sat 01 Mar 2008 - 01:30:17 GMT.

*
Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help.
Please read the posting
guide before posting to the list.
*