I have just updated to macOS Big Sur. Though the upgrade seems to have gone well, I seem to have some problems with permissions.

I am logged in as the same user, no other users on the system, and my ~/.bash_profile seems intact, but it does not see python3.7 when I type python at the terminal and it goes to default 2.7, or when I click on anaconda-navigator it says you do not have permission to open this app.

I have not found this problem with anything else at the moment. This is my bash_profile listing:

MacBook-4:~ k$ vi ~/.bash_profile

#added to open jupyter notebook
export BROWSER=open

[[ -s "$HOME/.rvm/scripts/rvm" ]] && source "$HOME/.rvm/scripts/rvm" # Load RVM into a shell session *as a function*
# added by Anaconda3 5.3.0 installer
# >>> conda init >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$(CONDA_REPORT_ERRORS=false '/anaconda3/bin/conda' shell.bash hook 2> /dev/null)"
if [ $? -eq 0 ]; then
    \eval "$__conda_setup"
    if [ -f "/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/anaconda3/etc/profile.d/conda.sh"
        CONDA_CHANGEPS1=false conda activate base
        \export PATH="/anaconda3/bin:$PATH"
unset __conda_setup
# <<< conda init <<<
  • 1
    You may have been switched to zsh, which means it wouldn't reach the bash_profile. Can you type echo $0 and see if it says zsh or bash?
    – Ezekiel
    Commented Oct 22, 2021 at 0:40
  • He wasn't. Existing accounts do not have their shells changed. Further, that's the default bash prompt there. Commented Oct 22, 2021 at 1:49
  • echo $0 uses bash.
    – kevbuntu
    Commented Oct 22, 2021 at 14:28
  • When I open a new terminal it does say that default shell is zsh and to update my account I should run 'chsh -s /bin/zsh', but I want to make sure I will cause no additional harm if I was to do that.
    – kevbuntu
    Commented Oct 22, 2021 at 19:29
  • There is no reason to switch to zsh unless you want to. Follow the link the alert gives and you can stop bash from producing that message. Commented Oct 22, 2021 at 20:39

1 Answer 1


Your directories off the root like that have been removed. Those are not allowed under Big Sur (or Catalina).

I can't believe Anaconda is that broken on the Mac, so did you make that choice when you originally installed it?

Good information on this topic is here: Where does the upgrade to macOS Catalina and Big Sur move root "/" directory files?

  • I made no choices, simply downloaded the file and opened it and ran all the way through.
    – kevbuntu
    Commented Oct 22, 2021 at 14:17
  • Also none of the files in root are missing. Seems to have picked on python related path. And on maybe unrelated topic my cnbc.com web site has stopped working properly just text displayed and no quotes!? But it does work on my phone. Maybe just a coincidence!
    – kevbuntu
    Commented Oct 22, 2021 at 15:40
  • The directory /anaconda that your bash configuration calls out is still there? Commented Oct 22, 2021 at 20:40
  • No there is no /anaconda3, does this mean it has got rid of all my installations for anaconda as well as python 3 and libraries like pandas? I guess I have to pip install everything again, but even pip is gone when I run the command. I guess maybe jupyter notebook was part of anaconda package which is not recognized either!
    – kevbuntu
    Commented Oct 23, 2021 at 17:00
  • Actually I can see python3.9 and pip on /usr/local/bin so I think I should just change the path?
    – kevbuntu
    Commented Oct 23, 2021 at 17:37

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