[BioC] snpMatrix: read.plink() allocMatrix: too many elements specified

[Benilton Carvalho]

The issue is that R has this internal limit of 2^31-1 elements per
object... and, guess what, 796384*2989 is bigger than 2^31-1.

So you probably want to split your BED file in two and try from there...

b

On 24 September 2010 17:49, Jim Moon <moonja at ohsu.edu> wrote:
> Hello.  Might someone have a solution to this problem?
>
>> aricAffy6<-read.plink('ARIC_CARe_Affy6_FINAL_2989.bed')
> Number of SNPs:  796384
> SNP_A-8282315 SNP_A-8282317 SNP_A-8289954 SNP_A-8289982 SNP_A-8289994 SNP_A-8338
> 245  ...
> Number of samples:  2989
> 1I5D8C DLAJ5B 3OW97U S4EL8O 8N5Z18 7AXAF7 ...
> Error in read.plink("ARIC_CARe_Affy6_FINAL_2989.bed") :
>  allocMatrix: too many elements specified
>
>> mem.limits()
> nsize vsize
>   NA    NA
>
> $ free -m
>             total       used       free     shared    buffers     cached
> Mem:         64396      48317      16079          0        397      46126
> -/+ buffers/cache:       1793      62603
> Swap:         1983          0       1983
>
>
> Thanks,
> Jim
>
> ------------------------------------------------------
>> R.Version()
> $platform
> [1] "x86_64-redhat-linux-gnu"
> $arch
> [1] "x86_64"
> $os
> [1] "linux-gnu"
> $system
> [1] "x86_64, linux-gnu"
> $status
> [1] ""
> $major
> [1] "2"
> $minor
> [1] "8.1"
> $year
> [1] "2008"
> $month
> [1] "12"
> $day
> [1] "22"
> $`svn rev`
> [1] "47281"
> $language
> [1] "R"
> $version.string
> [1] "R version 2.8.1 (2008-12-22)"
>
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>
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