Upgrading R + Bioconductor

Consider this post as a personal note to my future self

I have just learnt that Bioconductor developers should NOT always use the development version. On the official website it says:

This means that, from mid-October through mid-April, Bioconductor developers should be developing against R-devel. From mid-April to mid-October, developers should use R-release (actually, the R snapshot from the R-x-y-branch) for Bioconductor development.

So I needed to change my R version from development to release and I did. And as it usually happens I got into trouble while trying to use some of the R packages. Luckily I found this nice RStudio post on upgrading R and I used some of the recommendations they provide.

However, then I ran into another problem which was a bit more complicated. When installing some of the packages where C++ compilation was required, my MacOS gcc installation complained that it couldn’t support OpenMP flag. I spent quite a lot of time figuiring out how to solve it until I found this very useful post. By following their recommendations I was able to fix all issues and installed all the necessary packages.

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