[R] Error: long vectors (argument 1) are not supported in .Fortran

[Bert Gunter]

Probably wrong list. Try the Bioconductor list instead.

Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Fri, Feb 3, 2017 at 3:19 AM, Ankush Sharma <ankush.sak at gmail.com> wrote:
> Hi all ,
>
> I'm working on WGCNA on  R-3.3.1 version to reconstruct gene -gene
> coexpression networks of 54000 probes in 230 samples on Load Sharing
> facility (Remote computing cluster). Despite memory at dispose, I'm
> encountering a error of allocation of memory at soft thresholding step or
>  at TOM Similarity step.  The problem of memory allocation at soft
> thresholding step  was corrected by allocating the required memory using [bsub
> -R "rusage[mem=40000]".
>
> Error Message
>  > # Turn adjacency into topological overlap
>
>> TOM = TOMsimilarity(adjacency);
>
> Error in TOMsimilarity(adjacency) :
>
>   long vectors (argument 1) are not supported in .Fortran
>
> Calls: TOMsimilarity -> .C
>
> Execution halted
>
> Warning message:
>
> system call failed: Cannot allocate memory
>
>
> Is there a way to run build this TOMsimilarity matrix.
>
>
> Thanks
>
>
>
>
>
>
> Best Regards,
> Ankush Sharma,PhD
> Visiting CASyM Postdoctoral Research fellow (CASyM Consortium, EU-FP7)
> LISM, Institute of Clinical Physiology, Siena (Italy)
> Experimental Oncology Unit (UOS),
> I
> nstitute of Clinical Physiology
> - National Research Council,
>  Siena (IT)
>
>         [[alternative HTML version deleted]]
>
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