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nickjer / singularity-rstudio

RStudio Server in a Singularity container
https://singularity-hub.org/collections/463
MIT License
54 stars 41 forks source link

Linked libRpack/libRblas, added dependencies for cairo, added libssl #5

Closed alexiswl closed 5 years ago

alexiswl commented 5 years ago

Added a few installations that allow the installation of packages such as 'Cairo' and 'survival' which many packages rely on.

nickjer commented 5 years ago

Thanks, but if these will benefit R as a whole and not necessarily RStudio Server, then maybe these should instead be added to:

https://github.com/nickjer/singularity-r

Since this RStudio Server Singularity image is built from the above image, it will have these dependencies included after I rebuild everything.

alexiswl commented 5 years ago

No worries, did you want to make a pull request there instead?

nickjer commented 5 years ago

Yeah, I can add these to the R Singularity image.

What are the R packages that you are attempting to install that require these dependencies? That way I can test that the dependencies are installed and working.

alexiswl commented 5 years ago

'survival' from CRAN and 'arrayQualityMetrics' from bioconductor

alexiswl commented 5 years ago

To install the package 'rJava' I also needed default-jdk installed (via apt-get, oracle java not required).

nickjer commented 5 years ago

Thanks I can look into adding them. Not sure I want to include Java as it can be fairly heavy and has constant updates. But I believe you can just bind mount a local copy of Java into the container and it should work out-of-the-box.

nickjer commented 5 years ago

I updated the container with the dependencies necessary to get arrayQualityMetrics installed. Can you download the latest container and try again.

If there are still missing dependencies feel free to list the packages you are attempting to install. Although for rJava I wonder if you can get away with a precompiled binary of jdk (e.g., https://jdk.java.net/11/), and just point to it in your home directory during install.

nickjer commented 5 years ago

Closing this as some of the dependencies are now included in the base Singularity R repo which bubble up to this repo.