Question: Error: vector memory exhausted (limit reached?)
0
gravatar for rina
16 months ago by
rina0
rina0 wrote:

Hi everyone!

I am new to the bioinformatics world and I would much appreciate your help. I am following the TCGA Workflow tutorial and at the Genomic Analysis part, specifically on the CNV analysis I get this error Error: vector memory exhausted (limit reached?), when trying to load the information about the abberant regions into a form of matrix(through the load_cnv function of gaia package). In contrast to the tutorial I am using the whole data set from the TCGA COAD project and not limited samples. 

Any ideas on how I could solve it?

Session info:

R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

 

ADD COMMENTlink modified 16 months ago by rreck20 • written 16 months ago by rina0

If you can, try to install 64 bit version of R. 

ADD REPLYlink written 16 months ago by mario.zanfardino150
Answer: Error: vector memory exhausted (limit reached?)
0
gravatar for rreck
16 months ago by
rreck20
Fairfax County, VA
rreck20 wrote:

I would consider whether adding RAM or virtual memory in the form of swap space might make a difference. I am familiar with the process under Linux and UNIX but not under MacOS.

ADD COMMENTlink written 16 months ago by rreck20
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