Hello,

in the "setup" script for my project (actually a Dockerfile), I have

apt-get -y install r-base=3.6.3-1bionic
Rscript -e 'install.packages("BiocManager")'
Rscript -e 'BiocManager::install(c("DT", "shiny", "vcfR", "htmlTable", "ggplot2", "tidyverse", "reshape", "dplyr", "jsonlite", "xml2", "biomaRt"), ask = FALSE, version = "3.10")'

I understand that a specific Bioconductor release version should imply that a specific version of each bioconductor is installed. What happens to base R packages? Are these similarly constrained? Or running this installation script now and in 6 months result in differnet package versions being installed?

Thanks! Yannick

It's the latter. You'll get the latest available version of CRAN packages, regardless of the Bioconductor version. There might be constraints if the latest version in 6 months time requires a newer version of R, but otherwise assume you'll get whatever is most recent CRAN at the time.

This is actually true even for Bioconductor packages, in that bug fixes etc can be introduced to the release version, so you might end up with something slightly different, but the intention is for those to be non-breaking changes. So code should continue to work, but you might get different results.

If you really want reproducibility you probably need to build the container image now, and then use that in the future. It's also possible to install archive source tarballs for packages on both Biocondcutor and CRAN, but that would get really hard to maintain.