R-Studio Agent for Mac is installed on computers where files are to be recovered over network. R-Studio Agent for Mac supports the TCP/IP protocol. R-Studio Agent for Mac Universal for Power PC and Intel based computers; R-Studio Agent Emergency ISO Image is used to create R-Studio Agent Emergency startup CD. RStudio is available in open source and commercial editions and runs on the desktop (Windows, Mac, and Linux) or in a browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, Red Hat/CentOS, and SUSE Linux). New in RStudio 1.3. From spell check to a new tutorial pane, there is a lot to love. Now connect remote sessions between. This video shows the user how to download, install, and configure R and R studio (on the Macintosh platform) to be ready to work through almost everything I'll ask them to do. I'll also walk them. Installing R & RStudio on a Mac The installation on a Mac is simple and straight forward. There are 2 installations that are required, the R language and the RStudio front end. You can install a desktop or server version, however I find for personal use the desktop install and user experience easier to manage.
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.
How much actual memory does your mac have? There is no substitute for not having enough RAM unfortunately.
My Mac has 16 GB memory.
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.
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
These are vcf files.
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.
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?
I am trying to use them for Upset R plot and these are not compressed.
Is it to show overlapping Variants or Samples? Again you can get that info using bcftools, then file will be manageable for R.
When was the last time you update your R and RStudio?
I installed RStudio and R a year ago, and never update it since then. Today I just noticed I cannot install new R packages because of my old R version. So I explore some ways to update R and would like to share with someone who is also looking to update R on RStudio.
The problem
RStudio and R cannot update on their own because some packages may not work after switching to the new version (You can still downgrade R version in RStudio if something went wrong though). After you install the new version, the previously installed packages will not go to next version. So it is required extra procedures to move the packages.
Here are 3 ways you can update R version in RStudio. Note that we need to move the install R packages, which I will show how at the end.
3 Solutions to update R on RStudio
Solution 1) Manually install (Recommended if you don't care about the old packages)
The first method is to download a new version of R from R website > CRAN. Then restart your RStudio. The new R version will be loaded automatically.
The new R version appear right after I install R and restart RStudio
Update 29/05/2019: For Mac users, solution 3 is too painful and not working well for me. This method is fast and working well. I would recommend to save your time from headache and use this method. Take note of your previous packages so you can install them again as needed.
Solution 2) Windows only – use installr
installr is the R package which helps install and update software.
The R code you will need for updating R is: (credit goes to Cara Wogsland for the code)
install.packages('installr')
library(installr)
updateR()
You can find the tutorial on how to use installr to update RStudio on R-Statistics website.
Solution 3) Mac only – use updateR
Similar to installr, updateR is the package to help updating R on Mac OS.
The R code you will need is these 5 lines: (credit goes to jroberayalas for the code)
install.packages('devtools') #assuming it is not already installed
library(devtools)
install_github('andreacirilloac/updateR')
library(updateR)
updateR(admin_password = 'Admin user password')
You can find in-depth tutorial on how to use updateR package on this blog.
How to move the previously installed R packages
This is the instructions for Mac OS user (who used solution 1 or 3 above). For Windows user, installr package will do this for you
(credit goes to RyanStochastic and micstr):
1. Move all folders from your old R version to new R version.
/Library/Frameworks/R.framework/Versions/x.xx/Resources/library
Replace x.xx with the old and new R version at a time.
How To R Studio On Mac Desktop
Note that you have to move only the packages that are not currently in the destination folder (because those are the base packages, and you don’t want to ruin them). But if you already did replaced everything, the next step will solve this for you.
If you cannot find the proper path, you can run this command to check: installed.packages()
2. Update the moved packages
Run the following command in R. Type ‘y’ for every question that popped up.
update.packages(checkBuilt=TRUE)
How To Open Rstudio On Mac
3. Type the following command in R to check if everything went well
version
packageStatus()
That’s it! Hope you guys success in updating R. If not, please check in the reference link below.
How To Use Rstudio On Mac
References: https://stackoverflow.com/questions/13656699/update-r-using-rstudio