I am using RStudio ver 4.1.0 on Ubuntu 20.04 LTS and are having almost exactly the same issue.
Previously (24 days ago), I was able to PUSH & PULL correctly usin RStudio and Github with SSH_Keys. The only variable that has changed is the changeover at Github from PASSWDs to SSH_Keys. Could this be related?
Although I am getting a specific SSH message:
>>> /usr/bin/git push origin HEAD:refs/heads/main
ssh: connect to host github.com port 7913: Connection timed out
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
I have no idea why the SSH would be attempting to connect to Github Port 7913. However I do use Port 7913 on all of my sshd_configs, for both this machine and remote Debian-based ones. Coincidence?
In the meantime, I am going to revoke all SSH_Keys, Passwds and Personal Access Tokens, then start again.