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opensafely-core / r-docker

Docker image for running R scripts in OpenSAFELY
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Add kableExtra package, please #74

Open ciaranmci opened 2 years ago

ciaranmci commented 2 years ago

I want to produce a publicaiton-ready table using the kableExtra package in R. I previously requested installation of the magick package because the developers of kable libraries mentioned it as a dependency...but of course I never requested installation of kableExtra.

I haven't needed the other dependency (webshot package) to produce the publication-ready table when running a local instance of R (not in the OpenSAFELY docker). Would it be worth installing that too, or is its webpage functionality a No-No for containers?

ciaranmci commented 2 years ago

I've noticed that the kableExtra and webshot packages have been installed. Thank you.

My local OpenSAFELY docker container still fails to save a kable table object using the kableExtra::save_kable(). The guidance on feature dependency notes that the machine might need to run webshot::install_phantomjs(): image

Trying to call webshot::install_phantomjs() obviously throws an error in my local OpenSAFELY docker container (I assume because a call is being made to download something from outside).

Am I correct to assume that my lovely kable tables are probably not possible if kableExtra needs PhantomJS installed in the environment?

Log below: image

bloodearnest commented 2 years ago

Yes, that sounds like the case. We may be able to install it into the docker image, depending on how big it is. I'll look into it.