Thanks for the ideas, I really like the conflicted package.
I am using RStudio and I think once I load a package I cannot load it again. So typically, I write some code that works, and then if I need to reexecute, it doesn't. Often, I don't know what is the conflicting package, my guess is mainly MASS, because lots of functions I use depend on other functions in MASS. But for example, summarize also stopped working now, and as far as I know, there is no summarize function in MASS.
To sum up, conflicted package seems to work now, I hope this solves my issues in the long turn.
Have a nice day,
Kristof