Question: R Studio memory on Mac
0
19 months ago by
- Just to verify for you that this is where the file is located, while R is running, let’s go ahead and go look in our Mac. 330.7 Inside my finder, if I click on my downloads, I’ll see 2008.csv, and, if I wanna see the full path of that file, I can hold on the command and click on the name of the folder at the top.
- RStudio is currently only available for Mac OS X 10.6 or higher. Click on RStudio for Mac OS X 10.6+. Click on the appropriate file corresponding to Mac OS X. This will again bring up the save file dialog.
- Just to verify for you that this is where the file is located, while R is running, let’s go ahead and go look in our Mac. 330.7 Inside my finder, if I click on my downloads, I’ll see 2008.csv, and, if I wanna see the full path of that file, I can hold on the command and click on the name of the folder at the top.
I am trying to import three really big files (each file size >100GB) to R Studio but it complains of memory. I am using this
version
:I tried increasing the memory limit by using (
.Renviron
) on terminal but it gives the same error.R Download
ADD COMMENT • link • written 19 months ago by evelyn • 130
How much actual memory does your mac have? There is no substitute for not having enough RAM unfortunately.
ADD REPLY • link modified 19 months ago • written 19 months ago by GenoMax ♦ 93k
Run the R‑Studio Agent for Mac and select Connect from the Tools menu 2 Enter the necessary information on the Connect to R‑Studio dialog box and click.
![Rstudio Rstudio](/uploads/1/3/4/2/134237316/159286610.jpg)
My Mac has 16 GB memory.
ADD REPLY • link written 19 months ago by evelyn • 130
I don't think this is going to work as is.
Edit: @zx5784's solution of using virtual memory on disk may work. With such large data set you may need to have patience in equally large amounts.
ADD REPLY • link modified 19 months ago • written 19 months ago by GenoMax ♦ 93k
What kind of data is this? Alternatives:
- HPC with tonnes of memory
- Load data in chunks, do stuff, save results, load another chunk etc.
- Use packages that uses hard drive as memory and 'pretend' to have it as full object in R, e.g.: 'bigmemory' package.
See CRAN TaskView for HPC: Large memory and out-of-memory data
ADD REPLY • link modified 19 months ago • written 19 months ago by zx8754 ♦ 9.7k
These are
vcf
files. ADD REPLY • link written 19 months ago by evelyn • 130
Do you need all the data at once, maybe slim it down first: filter on Samples, on Variants, or split on Chromosomes, etc. See
bcftools
for manipulating VCFs.![How to update r studio on mac How to update r studio on mac](/uploads/1/3/4/2/134237316/297418029.png)
ADD REPLY • link written 19 months ago by zx8754 ♦ 9.7k
What operation are you trying to do with them? Perhaps there are command line alternatives that can be used instead of R. Are these files compressed or not?
ADD REPLY • link written 19 months ago by GenoMax ♦ 93k
I am trying to use them for
Upset
R plot and these are not compressed.ADD REPLY • link written 19 months ago by evelyn • 130
How To R Studio On Mac Desktop
1
Is it to show overlapping Variants or Samples? Again you can get that info using bcftools, then file will be manageable for R.
How To Download R Studio On Mac
ADD REPLY • link written 19 months ago by zx8754 ♦ 9.7k