[Bioc-sig-seq] readAligned error

[Steve Lianoglou]

Hi,

On Mon, Aug 30, 2010 at 12:48 PM, kirti prakash
<kirtiprakash3.14 at gmail.com> wrote:
> Hi,
>
> I am getting this error...
>
> me3 <- readAligned("dirpath", type="Bowtie")
> Error: Input/Output
>  'readAligned' failed to parse files
>  dirPath: 'xxx'
>  pattern: ''
>  type: 'Bowtie'
>  error: Calloc could not allocate (9638489 of 4) memory
>
> I have some six histone modifications files... I didn't got this error
> for the first couple of files that I read.

What do you mean "with the first couple of files you read"?

Did you execute this command before in a different directory or something?

Do you already have some "readAligned" data sets loaded into your workspace?

Is it possible that your machine is simply running out of RAM?

-steve

>
> I read this thread which discussed this problem but I could not follow much...
>
> http://tolstoy.newcastle.edu.au/R/devel/06/01/3641.html
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>  [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915
>  [7] LC_PAPER=en_US.iso885915       LC_NAME=C
>  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] HilbertVis_1.6.0    ShortRead_1.6.2     Rsamtools_1.0.7
> [4] lattice_0.18-8      Biostrings_2.16.9   GenomicRanges_1.0.7
> [7] IRanges_1.6.13      biomaRt_2.4.0
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 hwriter_1.2   RCurl_1.4-3   tools_2.11.1  XML_3.1-0
>
> Best regards,
>
> Kirti Prakash
>
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>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact