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

Bert Gunter bgunter.4567 at gmail.com
Fri Feb 3 16:31:33 CET 2017


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]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



More information about the R-help mailing list