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

Ankush Sharma ankush.sak at gmail.com
Fri Feb 3 12:19:12 CET 2017

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.


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),
​nstitute of Clinical Physiology
​- National Research Council, ​
 Siena (IT)

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