Re: [R] Memory limits using read.table on Windows XP Pro

From: Latchezar Dimitrov <ldimitro_at_wfubmc.edu>
Date: Wed 20 Jul 2005 - 11:46:50 EST


Hello everyone,

Would you please somebody explain me what my sin is (please see the code and timing bellow)? And how to improve myself and the following piece of R code? BTW, the code works.

This is R 64-bit built by myself on Sun SPARC Solaris 9 with gcc-4.0.1 (64-bit) also built by yours truly. The machine is Sun Fire-V880 with 32GB memory and 8 cpu's. Nobody else was using it.

Thank you very much

Latchezar Dimitrov

PS. Prof. Brian D. Ripley, thank you very much for not wasting your invaluable time responding to the above. I know your answer anyway. Sorry for making you read it though ...

> system.time(

+ haplo[i,2*j-1]<-substr(as.character(geno[i,j]),1,1) + ,TRUE)
[1] 66.27 13.67 80.02 0.00 0.00
> ls()

[1] "P" "geno" "haplo" "i" "j" "lr" "model" "pheno"
> i

[1] 1
> j

[1] 1
> dim(P)

[1] 1 125000
> str(P)

 num [1, 1:125000] 0.6188 0.0533 0.0893 0.8994 0.0316 ...
> str(pheno)

`data.frame': 2500 obs. of 11 variables:

 $ pca    : int  1 1 1 1 1 1 1 1 1 1 ...
 $ her    : int  0 1 0 0 0 0 0 0 0 0 ...
 $ age    : num  67.1 70.4 64.9 60.8 64.3 ...
 $ t      : int  1 3 1 2 1 2 1 3 9 1 ...
 $ n      : int  9 9 9 9 9 9 9 0 9 9 ...
 $ m      : int  0 1 0 0 0 1 9 9 1 9 ...
 $ diffgrd: int  9 9 9 2 9 9 9 9 3 9 ...
 $ gs     : int  6 7 6 7 7 7 5 6 NA 6 ...
 $ psa    : num  13 75 11.3 13 9.1 51 4.3 10.7 NA 93 ...
 $ geo    : int  2 2 1 1 1 1 1 1 1 1 ...
 $ ageg   : int  6 7 5 5 5 5 3 5 4 5 ...

> str(geno)

`data.frame': 2500 obs. of 125000 variables: ^C

>
> dim(geno)

[1] 2500 125000
> dim(haplo)

[1] 2500 250000
> version()

Error: attempt to apply non-function
> version

         _
platform sparc-sun-solaris2.9

arch     sparc               
os       solaris2.9          
system   sparc, solaris2.9   
status   Patched             
major    2                   
minor    1.1                 
year     2005                
month    07                  
day      09                  
language R                   

>

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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Wed Jul 20 11:52:06 2005

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