R: what's the proper way to overwrite a function from a package?
There are lots of different cases here.
If it's a bug in someone else's package
Then the best practice is to contact the package maintainer and persuade them to fix it. That way everyone gets the fix, not just you.
If it's a bug while developing your own package
Then you need to find a workflow where rebuilding packages is easy. Like using the devtools package and typing build(mypackage), or clicking a button ("Build & Reload" in RStudio; "R CMD build" in Architect).
If you just want different behaviour to an existing package
If it isn't a bug as such, or the package maintainer won't make the fix that you want, then you'll have to maintain you own copy of f1. Using assignInNamespace to override it in the existing package is OK for exploring, but it's a bit hacky so it isn't really suitable for a permanent solution.
Your best bet is to create your own package containing copies of f1 and f2. This is less effort than it sounds, since you can just define f2 <- existingpackage::f2.
In response to the comment:
Second and third cases makes sense if you are alone but they require to build and install the packages which is tricky in the case of my organisation as the packages are deployed on dozens of computer and I need root access to update the packages.
So take a copy of the existing package source, apply your patch, and host it on your company network or github or Bitbucket. Then the updated package can be installed programmatically via
install.packages("//some/network/path/mypackage_0.0-1.tar.gz", repos = NULL)
or
library(devtools)
install_github("mypackage", "mygithubusername")
Since the installation is just a line of code, you can easily push it to as many machines as you like. You don't need root access either - just install the package to a library folder that doesn't require root access to write to. (Read the Startup and .libPaths help pages for how to define a new library.) You'll need network access to those machines, but I can't help you with that. Speak to your network administrator or your boss or whoever can get you permission.
In case the function has no explicit binding within the package:
rlang::env_unlock(env = asNamespace('mypackage'))
rlang::env_binding_unlock(env = asNamespace('mypackage'))
assign('f1', f1, envir = asNamespace('mypackage'))
rlang::env_binding_lock(env = asNamespace('mypackage'))
rlang::env_lock(asNamespace('mypackage'))