FAQs

Below you can find some common error and problems you might face either during installations or during execution of software.

General questions

Contributors: Rui Benfeitas

Where do I find the Zoom links?

----- If you were accepted to the course, you will be able to access the page with all the relevant links (a link to a course discussion).

Computer SVG Vector General installation problems

Contributors: Paulo Czarnewski

Command line developer tools not found (OSX)

If you don't yet have Mac OSX command line developer tools, please install it using: xcode-select --install

Unable to load stringi.so (UNIX/Windows)

You can install stringi in R using: install.packages('stringi')

ERROR: Failed building wheel for gevent / MacOSX10.9.sdk missing (MacOSX)

This is a problem with the MacOSX compiler, in which conda is unable to find it.

#Download MacOSX10.9.sdk from Github 
curl -o MacOSX10.9.sdk.tar.gz "https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.9.sdk.tar.xz" 
#extract
sudo tar -xzf MacOSX10.9.sdk.tar.xz 
#copy 
sudo cp -r MacOSX10.9.sdk /opt/ 
#give executable permissions 
sudo chmod -R a+rX /opt 
#Link the path where conda looks to where the file is 
ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk /opt/MacOSX10.9.sdk

ERROR: option error has NULL value

This error happens when running code inline. One possible solution is to restart Rstudio and type.

if(interactive()) { options(error = utils::recover)}

Please try other solutions listed here: https://github.com/rstudio/rstudio/issues/4723 If none of those work, you can click on the wheel engine symbol and check Chunk output in console

Docker containers

Contributors: Rui Benfeitas

Got


            permission denied

while trying to connect to the Docker:


            ...connect: permission denied. See 'docker run --help'.

----- Make sure you are launching docker commands with


        sudo

. For instance,


        sudo docker run...

I cannot see my folder within a container.

----- Please ensure you are mapping the folders to those inside the container: make sure you set -v /path/to/your/workshop_folder:/home/username/workshop_folder/ .


            WARNING: The requested image's platform ... does not match the detected host platform ... and no specific platform was requested 1e53..9509

----- You need to provide the correct platform in


        docker run... --platform <yourplatform>

. See here Links to an external site. for an example.

Can I use normal bash commands in the containers?

----- Yes, use


        sudo docker run -it ... bash

with any container.

How do I get the container to see a folder in my own computer?

----- When you


        docker run

you can map folders with


        -v host_folder:folder_within_container

. For instance,


        docker run -v $(PWD):/home/username/workshop_folder/

to map your working directory to the folder


        /home/username/workshop_folder/

inside the container.

How do I list containers and their ids?

----- Use docker ps --all.

How do I stop a running container?

----- Use docker stop [container_id].

How do I remove images, containers and volumes?

----- For images docker image rm [container_id], for containers docker container [container_id], for volumes docker volume [container_id].

How do I remove unused images, containers and volumes?

----- For images docker image prune, for containers docker container prune, for volumes docker volume prune.