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.
Too many redirects error in browser
Auth0, which provides the 2FA, can misremembering logins, giving an issue of “too many redirects”. One solution is to clear your cookies. Another solution, to not lose all your cookies, is to go to https://alpha-analytics-moj.eu.auth0.com/v2/logout to properly log out so you can log back in 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.
Note that there are two layers of 2FA in action on the platform:
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.
Your Analytical Platform account has a separate 2FA step. You will be prompted to set this up the first time you access the platform and on subsequent uses, depending on the machine you use and the network it’s connected to:
- From a corporate-networked machine (DOM1 or QUANTUM) or corporate wifi (e.g. MoJDigital) then you will not be challenged for this.
- Otherwise (e.g. working from home on a non-corporate-networked machine) you’ll be challenged to provide the 2FA code during every sign-in to access each part the platform: Control Panel, R Studio, Grafana etc.
This security step lets you log into the platform and use it.
Whilst you may be prompted to enter your platform 2FA frequently (e.g. when working from home), but you will not need to enter your GitHub 2FA because this is remembered for a month.
However, if you have not logged into the platform for more than a month, you will first have to login to GitHub (and enter your GitHub 2FA code), and you will then also be prompted to enter your platform 2FA code.
I’ve lost my platform 2FA
If you’ve lost your platform 2FA code because e.g. you’ve broken or lost your phone, please contact the Analytical Platform team and we will reset it for you.
I have entered my 2FA code, but the platform will not accept it
Smartphone based 2FA apps require the phone’s clock (the time) to be up to date. If your phone’s clock is out of sync by more than 30 seconds or so, this can cause the 2FA codes to be out of sync.
Most phones syncronise their time with the network provider, so this is not a problem. If your time is out of sync, you need to navigate to your clock settings in your phone, and enable the option to sync the time. See e.g. here
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