Emacs unable to execute shell commands despite them being in the Emacs shell PATH

Question

I am on Ubuntu. I'm trying to run the latex command to run in the Emacs shell. I have done some research, and have already done the following:

I noticed that running env in the Emacs shell gave a different value for PATH than running env in the normal terminal. I installed purcell's exec-path-from-shell to solve this. Following the directions, I copied my current terminal PATH, went to .profile, commented out lines of the kind PATH = something_new:PATH and just replaced it all with PATH=my_whole_copied_path. I then added (exec-path-from-shell-initialize) just after (package-initialize) in my .emacs.

After doing this, running env in Emacs shell gives the same PATH as running env in my terminal. The latex binary lives in /opt/texbin, and my current Emacs PATH reads:

'PATH=/opt/texbin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin'

Still, running latex give command not found. What am I missing?

Update: I have learned that /opt/texbin is actually a symlink to a different location, and I've noticed that I can't cd into it in the Emacs shell. Could this be why this isn't working? Can I get shell to understand symlinks with an option?

Answer 1

Solved it: it was because Emacs was installed as a flatpak. For some reason, this mean the Emacs shell had many differences. I wasn't able to cd into certain folders. Other folders didn't exist: /usr/local, for example.

After uninstalling, and re-installing from the Ubuntu repository, everything works as expected.

I hope this can be helpful to someone. My PATH was setup fine, and I was still running into this problem. I'd love it if someone could explain why installing it as a flatpak caused the Emacs shell to "see" such a different set of directories.