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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"
else
    if [ -f "/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/anaconda3/etc/profile.d/conda.sh"
        CONDA_CHANGEPS1=false conda activate base
    else
        \export PATH="/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup


<<< conda init <<<
jaume
  • 15,010
kevbuntu
  • 101
  • 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 Oct 22 '21 at 00:40
  • He wasn't. Existing accounts do not have their shells changed. Further, that's the default bash prompt there. – Marc Wilson Oct 22 '21 at 01:49
  • echo $0 uses bash. – kevbuntu Oct 22 '21 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 Oct 22 '21 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. – Marc Wilson Oct 22 '21 at 20:39
  • I changed it to zsh, see if anything might change, no harm but nothing changed. – kevbuntu Oct 23 '21 at 16:46

1 Answers1

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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?

Marc Wilson
  • 5,920
  • I made no choices, simply downloaded the file and opened it and ran all the way through. – kevbuntu Oct 22 '21 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 Oct 22 '21 at 15:40
  • The directory /anaconda that your bash configuration calls out is still there? – Marc Wilson Oct 22 '21 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 Oct 23 '21 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 Oct 23 '21 at 17:37
  • @kevbuntu Did you not read the link in the answer for some particular reason? For everyone's clarity, what OS did you upgrade from? – Marc Wilson Oct 23 '21 at 23:44
  • I did read the link but /anaconda3 does not exist so can't see how to mount it and there are no files except system directory inside /Users/Shared/Previously Relocated Items. My previous macOS was Sierra. Though added the path for python3 which comes with big spur. At the end of installation it did ask me to remove some items that will damage the computer but they were some names not like remove anaconda. – kevbuntu Oct 24 '21 at 14:54