I have noticed that creating computational environments on Terra/AnVIL is taking much longer than usual. Using the same start up script which installs packages using BiocManager::install() , last year it would take about 8 minutes to finish and now it is taking ~25 minutes. I’ve noticed this with a number of start up scripts installing different packages so I don’t think it is due to a specific package in R. Do you have any thoughts on this? Thanks!
This is directly related to a change in personnel that has affected the ability of the Bioconductor team to keep producing precompiled binaries for terra/anvil cloud environments. A short term solution can be achieved by a) running the 20 minute installation process in an AnVIL Rstudio cloud env, b) collecting the compiled images of all the necessary packages from the .libPaths() folder where they were installed, and making a tar.gz of these, c) placing the tarball in accessible cloud storage, d) writing a startup script that retrieves the tarball and untars it into the .libPaths destination. The environment that runs that script will have R with all the packages installed.
We are at work on producing appropriate container images and binaries for current Bioconductor, based on the new sudo-enabled container. Once this is completed the workaround noted above will be unnecessary.