How to deal with R Code execution error

r

#1

Hello,

While using the biocLite package from bi0conductor in R I am getting an error whenever I am trying to execute a function from the package.


The error is cannot allocate memory size of 3.9Gb.Does R not have the functionality to allocate such a big package??How do I deal with this?
I want to use the EBImage package in biocLite package for some image analysis but not able to do so because of this error.
Can somebody kindly help me in this regard.


#2

About the error message “cannot allocate…”: My best guess is that you don’t have enough computer memory available. R stores all objects in memory, so you might quickly run out if you create several big objects. Possible solutions (next to buying more computer memory): delete objects you no longer need, save intermediate steps and keep working from there instead of always re-running computational intensive tasks, use data.table instead of data.frame, work with a database instead of a data.frame/data.table,… I hope this is helpful, Thomas


#3

Looking at the error, it looks like a memory constraint.

As @Thomase said, you can work with a Database or increase your RAM or spin up a virtual machine on AWS.

You can also look at some of the suggestions in this thread:

http://discuss.analyticsvidhya.com/t/what-are-the-ways-to-handle-huge-data-in-r/141

Hope this helps.

Kunal


#4