I’m trying to perform ANCOM-BC in R on Linux, following this tutorial: https://github.com/mortonjt/q2-ancombc, but I’m running into issues with package installation (return code 1; package ‘CVXR’ is not available for this version of R). I realized I need R version 4.1.1., so I upgraded R, but it only works outside of the qiime2 environment. My attempts to upgrade R within the qiime2 environment using conda weren’t successful at all, and creating a new environment doesn’t seem to make sense in my situation.
Do you have any experience or suggestions for upgrading R in the qiime2 environment on Linux? Or maybe you think that that’s not an issue?
[I’m using qiime2-amplicon-2024.5, and currently installed R version is 4.3.3]
Upgrading R within qiime2 is not recommended since it may break many things within the environment and lead to unexpected errors in different plugins. So, installing ANCOM-BC2 into another environment is a better solution than upgrading R within Qiime2.
@joannakolodz, you should not need to use that outdated q2-ancombc plugin - see the note in the README on that page that you're linking to:
This plugin has been replaced with functionality in the q2-composition plugin. You should now access ANCOM-BC in QIIME 2 through the q2-composition plugin that is included in the QIIME 2 amplicon distribution. You do not need to install this plugin to use ANCOM-BC through QIIME 2.
You can find information on using ANCOM-BC through QIIME 2 here. You should also be able to use ANCOM-BC through R directly in a 2024.10 amplicon environment if you want to go that route.