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

From: Latchezar Dimitrov <ldimitro_at_wfubmc.edu>
Date: Wed 20 Jul 2005 - 11:48:51 EST


Really sorry for the wrong addressing. It was intended to the list only. I apologize.
Latchezar

> -----Original Message-----
> From: Latchezar Dimitrov
> Sent: Tuesday, July 19, 2005 9:47 PM
> To: Latchezar Dimitrov; 'Prof Brian Ripley'
> Cc: 'r-help@stat.math.ethz.ch'
> Subject: RE: [R] Memory limits using read.table on Windows XP Pro
>
> 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 11:54:58 2005

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