Looks like Spacemacs just added org-roam layer to development branch.
I don’t use Spacemancs but I suppose it’s a good thing for you as a user.
And… I guess when you say “you upgraded org-roam package” you used some Spacemacs way of package updates (?).
Can you change your org layer’s init file and keep the now-standard init in org-roam layer?
There may be someone in this forum who has an experience in removing this warning… If you would like a fix quick, you might like to ask a Spacemacs community for advice.