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Creating a Custom R Library

1. Make a local directory to store your packages:

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   $ mkdir -p ~/R/library

   
   

2. Tell R where the directory is by creating an environment file:

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   $ echo 'R_LIBS=~/R/library/' >> ~/.Renviron

   
   

3. That's it! Now you can install packages normally. For example, to install and load the package "ggplot2":

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   $ module load R $ R > install.packages("ggplot2") > library(ggplot2)

   
   

Switching Between Custom Libraries

If you're using different versions of R, we recommend you use different libraries. See Common Problems below for more information. When creating a library, consider including pertinent information in the name such as R version. For example:

If you start by using R version 4.0, following the instructions provided above:

$ mkdir -p ~/R/library_R_v4.0
$ echo 'R_LIBS=~/R/library_R_v4.0/' >> ~/.Renviron

If you later decide to switch to R version 4.1, instead of using your existing library, create a new one:

$ mkdir -p ~/R/library_R_v4.1

To use your new library, edit your .Renviron file:

$ nano ~/.Renviron                # opens the R environment file for editing
> R_LIBS=~/R/library_R_v4.1       # delete ~/R/library_R_v4.0 and enter the new directory
> CONTROL + X                     # exits (remember to save at the prompt)

Now you can go about your business and install as you normally would.

Common Problems

Working on a cluster without root privileges can lead to complications. Some are listed below with suggested solutions:

1. General Installation Questions
   
   Solution: Check out http://www.r-bloggers.com/installing-r-packages/ for more information.
   
   
   
2. A Corrupted Environment: One of the most common reasons R packages won't install is an altered environment. Most frequently this is caused by the presence anaconda (or miniconda) installed locally.
   
   Solution: If Anaconda is present, follow the instructions in the Resolving Anaconda Issues section below. Otherwise:
   
   Look for any of the file types listed below on your account. If you find them, remove them (make a backup somewhere if you need them) and try the installation again.
   
   1. Saved R sessions. If this is the case, after starting a session, you will get the message "[Previously saved workspace restored]". Old sessions are saved as a hidden file .RData in your home directory. 
   2. Gnu compilers
   3. Windows files
      
      
      

3. Library Issues 
   
   Solution: Double-check that you have an .Renviron file. This is a hidden file located in your home directory and should set the path to your custom R library. If you do not have a custom library name set up, R will create one for you saved as something like:

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   ~/R/x86_64-pc-linux-gnu-library

   This directory can lead to unwanted behavior. For example, if you're trying to use a new custom library (such as when switching R version), R will still search x86_64-pc-linux-gnu-library for package dependencies and may cause installs to fail. To fix this, rename these types of folders something unique and descriptive.
   
   To set up/switch custom libraries, follow the instructions in the Creating a Custom R Library section above.
   
   
   

4. Mixing R Versions: Because HPC is a cluster where multiple versions of R are available, users should take care to avoid mixing and matching. Because packages often depend on one another, libraries using different versions of R can turn into a tangled mess.  Common errors that can crop up include: "Error: package or namespace load failed."
   
   Solution: If you're switching R versions, we recommend creating a new library.
   
   
   

5. OOD RStudio Issues: OOD RStudio is a great tool! Sometimes though, because it's a different environment than working directly from the terminal, you may run into problems. Specifically, these typically arise for installs or when using packages that rely on software modules.
   
   Solution: 

   Package Installations: If you're trying to install a package in an OOD RStudio session and you've tried all the troubleshooting advice above without luck, try starting R in the terminal and give the installation another try. You can start an R session in the terminal using:
   
   

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   $ module load R/<version> $ R > install.packages("package_name")

   Remember that when you log into HPC, you're on a login node so you'll want to start up an interactive session to access R and for the installation.
   
   Accessing Modules: RStudio does not have access to module load commands. This means that if you have a package that relies on a system module, the easiest option is to work through an interactive terminal session. The alternative is to to modify your RStudio environment. For example, the library hdf5r relies on Ocelote's hdf5 software module. If you try to load hdf5r, you will get an error complaining about a shared object file. To get around this, you will need to manually add that shared object to your environment using dyn.load(). For example:
   
   

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   > library("hdf5r") # without using dyn.load() Error:: package or namespace load failed for 'hdf5r'‘hdf5r’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/path/to/home/u21/sarawillis/R/lib_4.0/hdf5r/libs/hdf5r.so': libhdf5_hl.so.10100: cannot open shared object file: No such file or directory > dyn.load("/opt/ohpc/cmpub/sharedlibs/uaappsgnu8/hdf5/1.810.185/lib/libhdf5_hl.so.10100") # adds shared object file to your environment > library("hdf5r") # success! >

   
   

   This requires that you know the location of the relevant file(s). These can usually be tracked down by looking at your system path variables (e.g. LD_LIBRARY_PATH) after loading the relevant module in a terminal. It should be noted that modifying your system paths from RStudio will not help since RStudio has its own configuration file that overrides these. 
   
   

6. Software Installed in Non-Standard Locations: When packages are dependent on 3rd party software, particularly when the software is installed locally, R can have trouble finding it. This can usually be fixed by changing your environment paths but can sometimes be challenging. 
   
   

   Solution:

   1. Packages that require 3rd party software should be installed in a terminal session and not through an OOD RStudio session.
   2. Check whether the software you need is installed as a module using the module avail command.
   3. If you know which paths need to be changed, point them to the correct location. 
   4. Search online help forums such as R-Bloggers, Stack Exchange, Stack Overflow, etc. for your specific error. It's likely others have experienced the same problem you're encountering and know where the trouble spots are.
   5. If you're in too deep, reach out to the consultants with a support ticket.
   6. Sometimes it can't be helped and you need the software installed globally. Submit a software installation request to get things up and running. Note: there is no expected timeframe for software requests.

Resolving Anaconda Issues

When Anaconda is initialized, your .bashrc file is edited so that it becomes the first thing in your PATH variable. This can cause all sorts of mayhem. To get around this, you can either remove anaconda from your PATH and deactivate your environment, or comment out/delete the initialization in your ~/.bashrc if you want the change to be permanent.

Turn off Auto-activation

Anaconda's initialization will tell it to automatically activate itself when you log in (when anaconda is active, you will see a "(conda)" preceding your command prompt). To disable this behavior, run the following from the command line in an interactive terminal session:

conda config --set auto_activate_base false

This will suppress anaconda's activation until you explicitly call conda activate and is a handy way to have more control over your environment. Once you run this, you will either need to log out and log back in again to make the changes live, or you can follow the instructions in the section below. 

Temporary Removal

You can either use the command conda deactivate and then manually edit your PATH variable to remove all instances of anaconda/miniconda or copy the following and run it in your terminal:

conda deactivate > /dev/null 2>&1
IFS=':' read -ra PATHAR <<< "$PATH"
for i in "${PATHAR[@]}"
    do if [[ $i == *"conda"* ]]
        then echo "removing $i from PATH"
    else NEWPATH=$i:$NEWPATH
    fi
done
export PATH=$NEWPATH
module unload gnu8 && module load gnu8
unset NEWPATH
echo "Successfully removed conda" 

Permanent Removal

Note: this change will remove anaconda from all future terminal sessions but will not make the changes live right away. To make the changes live, either follow the instructions above for removing anaconda from your PATH, or log out and back in again.

$ nano ~/.bashrc # opens your bashrc file to edit

Then comment out or delete the following lines and the text in between:

# >>> conda initialize >>>
...
# <<< conda initialize <<<

To exit and save, use control+x and follow the prompts.