Error: vector memory exhausted (limit reached?)
1
0
Entering edit mode
rina • 0
@rina-16738
Last seen 25 days ago
Toulouse

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

 

tcgabiolinks tcga cnv mac os x gaia • 1.5k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
rreck ▴ 20
@rreck-12488
Last seen 2.8 years ago
Fairfax County, VA

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 COMMENT

Login before adding your answer.

Traffic: 436 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6