pyenv giving shopt command not found error on macos

Question

I have been using pyenv for managing python versions and virtual environments on my mac for some time now. Recently I reinstalled pyenv and since then on every pyenv command I try to run, I get the following error

/usr/local/bin/pyenv:94: command not found: shopt

My default shell is the latest MacOS's default shell i.e. zsh.
On searching for the fix, I found out it has something to do with bash interfering with the zsh.
My default shell is zsh in settings, the contents of ~/.bash_profile, /etc/profile & /etc/bashrc are all commented out but I am still having the issue.
My OS Verion is: 10.15.4.
I tried reinstalling pyenv as well but I am getting the same error.

I am unable to run ANY pyenv related command.

Edit 1

I already have these lines in my .zshrc as per the documentation, but as you can see, even this run a command pyenv root and this gives me the same shopt error.

export PYENV_ROOT="$HOME/.pyenv"
export PATH="$PYENV_ROOT/bin:$(pyenv root)/shims:$(pyenv root)/completions/pyenv.zsh:$PATH"

Edit 2

Run env and add the output in your question

TMPDIR=/var/folders/gm/t0h6v8jx4bqd6cj73_k27myw0000gp/T/
XPC_FLAGS=0x0
TERM_PROGRAM_VERSION=433
TERM_PROGRAM=Apple_Terminal
XPC_SERVICE_NAME=0
TERM_SESSION_ID=55A65E3A-9B71-4C8A-81B8-0170EEAE3DCE
TERM=xterm-256color
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.j6zkqCw6Of/Listeners
SHELL=/bin/zsh
HOME=/Users/abc
LOGNAME=abc
USER=abc
PATH=/usr/local/opt/openssl@1.1/bin:/Users/saadali/Library/Python/3.7/bin:/usr/local/Cellar/postgresql@9.6/9.6.16/bin/:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/abc/bin:/usr/local/opt/rabbitmq/sbin
SHLVL=1
PYTHONPATH=
LANGUAGE=en_US.UTF-8
port=
LC_NUMERIC=en_US.UTF-8
LC_TIME=en_US.UTF-8
LC_COLLATE=en_US.UTF-8
LC_MONETARY=en_US.UTF-8
LC_PAPER=en_US.UTF-8
LC_NAME=en_US.UTF-8
LC_ADDRESS=en_US.UTF-8
LC_TELEPHONE=en_US.UTF-8
LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=en_US.UTF-8
CPPFLAGS=-I/usr/local/opt/openssl@1.1/include
LDFLAGS=-L/usr/local/opt/openssl@1.1/lib
CFLAGS=-I/usr/local/opt/openssl@1.1/include
LANG=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
LC_ALL=en_US.UTF-8
LC_CTYPE=en_US.UTF-8
_=/usr/bin/env

Edit 3

Please read this chat first before recommending to try something, as I might have already tried it. Chat starts at Apr 29 02:01 UTC +5 and then moves to a thread.

Edit 4

After setting PYENV_DEBUG=1, here the output

(vmds) saadali@A006-00276 ~ :~$ pyenv
+ [:22] enable -f /../libexec/pyenv-realpath.dylib realpath
+ [:29] [ -z '' ']'
+ [:31] READLINK=+ [:31] type -p greadlink readlink
+ [:31] READLINK=+ [:31] head -1
+ [:31] READLINK='greadlink not found' 
+ [:32] [ -n 'greadlink not found' ']'
+ [:57] [ -z '' ']'
+ [:58] PYENV_ROOT=/Users/abc/.pyenv 
+ [:62] export PYENV_ROOT
+ [:65] [ -z '' ']'
+ [:66] [ -n '' ']'
+ [:82] [ -z '' ']'
+ [:83] PYENV_DIR=/Users/abc 
+ [:86] [ ! -d /Users/abc ']'
+ [:86] [ ! -e /Users/abc ']'
+ [:90] PYENV_DIR=+ [:90] cd /Users/abc
+ [:90] echo /Users/abc
+ [:90] PYENV_DIR=/Users/abc 
+ [:91] export PYENV_DIR
+ [:94] shopt -s nullglob
/usr/local/bin/pyenv:94: command not found: shopt

@MarkSetchell first line is `#!/usr/bin/env bash` but this problem happens in bash terminal too. — saadi, May 05 '20 at 20:55
@con-- `shopt` is an internal `bash` command, on `zsh` output of `which shopt` is of course command not found, on `bash` terminal it returns nothing as it's not a command, but if I do simple `shopt`, it shows some shopt related stuff. — saadi, May 05 '20 at 20:56
@saadi Is `/usr/bin/env bash` *really* executing `/usr/bin/bash`? What happens if you change the shebang in your pyenv executable to `#!/usr/bin/bash`? Also, remember you can run *pyenv* with debug output by setting `PYENV_DEBUG=1`. — amain, May 11 '20 at 16:32
@amain added the debug output in question. Also, changing `/usr/bin/env bash` to `/bin/bash` worked for me. But to made it work, I had to change my default terminal shell to `bash` instead of `zsh` and I had been using it with `zsh` and it used to work fine. Also, running `/usr/bin/evn bash` works fine in my `zsh` terminal. — saadi, May 11 '20 at 19:53
So it wasn't working properly, like `pyenv --version` worked but `pyenv ls` did not work, I did `$ which bash` and then seeing the output, I did `ls -l /usr/local/bin/bash` which showed me a symbolic link `/usr/local/bin/bash -> /bin/zsh` should this link be here? Also making the change in the above comment made some commands work and some not, what kind of behaviour is this? — saadi, May 11 '20 at 20:37
@saadi For me, this looks like some broken `bash` command, e.g. some wrong symlinks? That said, *pyenv* should work fine (at least not choke on *shopt*) when you invoke it directly with `/bin/bash /usr/local/bin/pyenv`. — amain, May 11 '20 at 20:38
I THINK it will work if I somehow break that link but I am also scared of the repercussions as it might break many other things. Is there a solution besides reinstalling OS? — saadi, May 11 '20 at 20:54

score 1 · Accepted Answer · answered May 11 '20 at 21:45

According to your info and comments it seems your issue has 3 causes working hand in hand:

pyenv is a bash (and bash-only) script with a shebang line #!/usr/bin/env bash
/usr/local/bin comes before /usr/bin or /bin in your PATH, so executables therein are picked up first by /usr/bin/env (desired behaviour, especially when using homebrew)
/usr/local/bin/bash is symlinked to /bin/zsh!?!

So in the end you are running pyenv with zsh, which, albeit being a close replacement for bash, doesn't know about shopt and therefore chokes. I don't know why the symlink is in place, but it shouldn't, because zsh is not a fully compatible drop-in replacement for bash.

I'd suggest to

(in case you are using homebrew)
Check if you have/had bash installed through homebrew (which was later somehow replaced by a symlink to zsh):
```
# shows only top-level packages (directly installed)
brew leaves        

# shows *all* packages with dependency tree
brew deps --tree --installed
```
And uninstall bash if not required anymore (which should then remove /usr/local/bin/bash).
Either delete or at least rename the culprit:

mv /usr/local/bin/bash /usr/local/bin/bash_link_to_zsh

Or, if some program requires /usr/local/bin/bash to be in place, just have it point to /bin/bash.

According to your observation#2 from comments, I re arranged my `PATH` and now it works fine thanks. — saadi, May 12 '20 at 07:47

pyenv giving shopt command not found error on macos

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