Common Errors and Solutions
Failed to lock directory
This error is typically encountered after a failed package install.
Error
ERROR: failed to lock directory ‘/home/robinl/R/library’ for modifying
Try removing ‘/home/robinl/R/library/00LOCK-readr’
Solution
Run the following:
install.packages('pacman')
pacman::p_unlock()
If that does not work, or if you have trouble installing the pacman package, try the following:
Go to Tools -> Shell and type:
rm -rf /home/robinl/R/library/00LOCK-readr
See here for more details. Be careful with the rm command!
rsession-username ERROR session hadabend
Errors like the following can typically be ignored:
[rsession-aidanmews] ERROR session hadabend; LOGGED FROM: rstudio::core::Error {anonymous}::rInit(const rstudio::r::session::RInitInfo&) /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:1934
They seem to occur when R Studio has been unable to restore your session following a crash. Note the items in your R environment will no longer be there following a crash, and you’ll need to re-run your scripts to bring your data back into memory.
Crashes often occur when you run out of memory. For more information about tracking and reducing memory usage in RStudio, see the RStudio memory issues section.
Status Code 502 error message
R Studio Server is single-cpu (single thread), which means it can’t ‘do two things at once’.
If you ask it to, sometimes one of the operations will timeout. The ‘Status code 502’ message is basically a timeout message.
Usually this doesn’t cause anything to crash. You just need to wait for the currently-running code to finish executing and try again.
One example of when this can happen is if you attempt to save a file whilst a long-running script is running. R Studio has to wait until the script has finished running to attempt to save the file. However, sometimes the wait is too long, causing a timeout. In this case, you just need to wait for the code to finish running, and then press save again.
Two-factor authentication problems
Two-factor authentication (2FA) is critical to the security of the platform. We have opted to use smartphone-based authentication apps as hardware tokens, like the RSA device you use to log in to DOM1, are expensive and SMS codes are susceptible to interception.
There is now only one layer of 2FA:
- Your GitHub account must have 2FA enabled. When you log in to GitHub, your session will stay active for a month before you need to re-enter your 2FA code. Your GitHub username identifies you to the platform, and we use this identity to control access to data and other resources once you’ve logged into the platform. You therefore must be logged into GitHub to use the platform.
I’m having problems deploying a Shiny app
For help resolving deployment problems, see the advanced deployment section of the docs.
Geospatial data package problems
Some conda environments may prevent you from installing some packages relating to geospatial data, such as sf and rgeos. In order to get access to these packages, you need to create and activate a brand new conda environment, which will allow you to install the required packages.
To create a new conda environment, go to the terminal and enter
conda create --name myenv
Replacing myenv with the environment name.
conda deactivate
conda activate myenv
Will set this environment to be your currently active environment. From here, install packages as you would normally, with
conda install packagename
Don’t forget to add this new environment to your currently active .libPath(), which is done in the console.
s3tools::s3_path_to_full_df() fails on Excel file
Note that s3tools has now been deprecated in favour of Rs3tools. We are retaining this information here in case of similar errors in Rs3tools as the general advice may be relevant. More information is available in this ADR Record
s3tools::s3_path_to_full_df attempts to read in data from various filetypes, including Excel, but this sometimes fails.
If it does, you have two options:
Option 1: Use s3tools::read_using()
This allows you to specify what function you want to use to attempt to read the file. So, for example you can do:
s3tools::read_using(openxlsx::readWorkbook, path = "alpha-everyone/my_excel.xlsx") to attempt to read the file alpha-everyone/my_excel.xlsx using openxlsx::readWorkbook
Option 2: Save the file to your project directory and load it from there, rather than from S3
s3tools::get_credentials()
aws.s3::save_object("my_excel.xlsx", "alpha-everyone", "file_name_to_save_to_in_home_directory.xlsx")
and then read it in using e.g.
openxlsx::readWorkbook("file_name_to_save_to_in_home_directory.xlsx")
Note, it’s best to avoid using aws.s3 directly, see here
Error when switching branches: fatal: index file smaller than expected.
This occurs when the index file gets corrupted, and can be fixed with:
$ rm .git/index
$ git add .
$ git reset HEAD