Specify other R version outside of qiime's conda

[mammerlin]

Before installing Qiime2-2022.8, latest R and many packages I need already installed.
I was wondering if I can change and specify the R outside the qiime2's conda.
By doing that, I don't need to change the environment when I analyze the data with R and qiime at the same thime.

Thanks,
mammer

[Mehrbod_Estaki]

Hi @mammerlin,
While you could technically specify the exact software versions and packages (including R) in the yaml file you use for building the QIIME 2 conda environment, this is not recommended! The whole purpose of conda environments is that they are self-contained and are built with specific versions that the developers have carefully selected and tested. Changing that could lead to other downstream issues that would be extremely hard to troubleshoot. Keep in mind that you can have multiple R versions running at the same time. For example, the R version QIIME 2 calls while you are within its conda environment does not need to be the same one you have installed on your computer, or, in another conda environment. In practice, this is very easy. Simply run your QIIME 2 commands in one terminal that has your QIIME 2 2022.8 conda activated, and open your R/RStudio as you normally do, they will not be using the same R environment.

[mammerlin]

@Mehrbod_Estaki
Thank you for detailed explanation and suggestion. I got it. I think that using different R version would be the good way for troubleshouting.