Computational biology and genomics
I recently found out that when install.packages() fails, it only returns a warning and not an error, i.e., the exit code is 0. R -q -e 'install.packages("thisdoesnotexist!!!")' > install.packages("thisdoesnotexist!!!") Installing package into ‘/home/dtang/R/x86_64-pc-linux-gnu-library/4.3’ (as ‘lib’ is unspecified) Warning message: package ‘thisdoesnotexist!!!’ is not available for this version of R A version of this package for…
A quick post on testing Singularity builds, where I discovered how the %test section of the Singularity Definition File works. If you aren’t familiar, the Definition File is similar to the Dockerfile for Docker; it is used to define and build the image. From the documentation: A SingularityCE Definition File (or “def file” for short)…
For running RStudio Server in a container, I’ve written about how to run RStudio Server with Docker; in the post I also listed out some reasons why you would want to do that instead of simply installing RStudio on your computer. This post demonstrates one way of running RStudio Server with Singularity. I learned that…
Recently I have been learning about Singularity and have been experimenting with building Singularity images. However it seems that there is no layering in Singularity, which exists with Docker and Dockerfiles. This is quite convenient to have because building will resume from the point where the last step failed. However the comment: You can build…