When was the last time you update your R and RStudio?
EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing. Download the most recent version of R. The R FAQs and the R Installation and Administration Manual contain detailed instructions for installing R on various platforms (Linux, OS X.
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.
Jul 10, 2019 On July 5, the R Core Group released the source code for the latest update to R, R 3.6.1, and binaries are now available to download for Windows, Linux and Mac from your local CRAN mirror. R 3.6.1 is a minor update to R that fixes a few bugs. As usual with a.
![Mac Mac](/uploads/1/2/6/7/126752465/292130397.png)
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. Mac mail version 4.6 download windows 7.
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
R3.6.1 Download For Mac Windows 10
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) https://evercover195.weebly.com/blog/thunderbird-4580-download-mac.
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
![R3.6.1 Download For Mac R3.6.1 Download For Mac](/uploads/1/2/6/7/126752465/993726912.png)
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)
R3 File Download
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.
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)
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.
References: https://stackoverflow.com/questions/13656699/update-r-using-rstudio
For most users, we recommend installing the official Seurat release from CRAN, using the instructions here
Alternative : Install development version from source
Install the development version of Seurat - directly from Github.
Troubleshooting
If you see the following message: Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).Please reinstall dplyr to avoid random crashes or undefined behavior.Reinstall dplyr from source with the following command:
If you are trying to compile under R >= 3.4 on a Mac, the latest versions of R use Clang 4.0.0 and GNU Fortran 6.1 which you will need to successfully compile and install Seurat. Here’s a link to the official R page that provides some guidance on those.
For older R versions, installing from source causes errors on some standard Mac installs due to R being compiled using gfortran-4.8. They will look something like
To fix this, refer to the following blog post. NOTE: you will need sudo permissions.
Another potential solution to this issue that doesn’t require sudo permission (credit to Michael Steinbaugh) can be found here.
Install from GitHub on Windows
- Install R (v >= 3.2)
- Recommended : Install R Studio
- Install the “devtools” package from Hadley Wickham
- Install Rtools
- Ensure that Java is installed.
- Open CommandPrompt and type
java -version
- If this doesn’t return a version of java >= 1.6, download the latest Java SDK from Oracle and run the installer.
- Restart the R session
- Open CommandPrompt and type
- Install Seurat - directly from Github.