Pyenv shim already exists. Commands constantly timeout in WSL2 environment

[samargy]

What version of Codex is running?

codex-cli 0.36.0

Which model were you using?

gpt-5-codex-medium

What platform is your computer?

Linux 6.6.87.2-microsoft-standard-WSL2 x86_64 x86_64

What steps can reproduce the bug?

Get codex to attempt to run any command.

What is the expected behavior?

Command runs fine.

What do you see instead?

$ rg "class Post" -n my_repo/models -g"*.py"
command timed out after 60285 milliseconds
pyenv: cannot rehash: /home/MY_USER/.pyenv/shims/.pyenv-shim exists
✗ (124) • 1m 00s

Additional information

I have made attempts of deleting pyenv, reinstalling. Rehashing etc.

[Jannchie]

There is the same issue here. However, I noticed that it only gets triggered when running node or python scripts. It always times out and throws an error after one minute:

pyenv: cannot rehash: /home/username/.pyenv/shims/.pyenv-shim exists

[samargy]

Yep this is exactly my experience. Anything that you found that fixes this issue?

Still occuring with codex 0.41.0

[Jannchie]

The solution is to uninstall pyenv. In fact, codex does not depend on pyenv; it simply cannot work in an environment configured with pyenv. If you remove all pyenv-related lines from your ~/.bashrc (or possibly ~/.zshrc), you should be able to bypass this issue.

[hugoJuhel]

Uninstalling pyenv was a bit overkill for me (I still need it for my python stuff), but I added a command to my project Makefile to launch codex without pyenv.

.PHONY: codex-nopyenv

codex-nopyenv:
	@unset PYENV_VERSION PYENV_ROOT; \
		export PATH="$$(printf "%s" "$$PATH" | tr ":" "\n" | grep -vE "^$$HOME/.pyenv|^/mnt/c" | paste -sd: -)"; \
		if ! command -v python >/dev/null 2>&1 && command -v python3 >/dev/null 2>&1; then \
			alias python=python3; \
		fi; \
		exec codex

Sometimes, codex calls bash -lc, so I also added a guard to my .profile to avoid enabling pyenv for non interactive shells :

# Init pyenv only for interactive shells : pyenv will be initialized only if the shell is interactive
if [ -n "$BASH_VERSION" ]; then
  case $- in
    *i*)
      if [ -d "$HOME/.pyenv" ] && command -v pyenv >/dev/null 2>&1; then
        export PYENV_ROOT="$HOME/.pyenv"
        export PATH="$PYENV_ROOT/bin:$PATH"
        eval "$(pyenv init -)"
      fi
      ;;
  esac
fi

[s3d-i]

I met same issue and fixed (validated by prompting codex to search certain lines in codebase) by deleting duplicated pyenv initializing scripts in ~/.bashrc ~/.profile

Environment

• WSL2 Debian 12 (checked via cat /etc/os-release)
• pyenv 2.5.1 (checked via pyenv --version)
• Codex CLI installed via Homebrew
• Was previously initializing pyenv in ~/.zshrc + ~/.bashrc + ~/.profile

Script to detect duplication

#!/usr/bin/env bash

CONFIG_FILES=(
  "$HOME/.zshrc"
  "$HOME/.bashrc"
  "$HOME/.bash_profile"
  "$HOME/.profile"
)

echo "🔍 Scanning for pyenv initialization..."

for file in "${CONFIG_FILES[@]}"; do
  if [ -f "$file" ]; then
    if grep -qE 'pyenv|PYENV_ROOT' "$file"; then
      echo "⚠️  Found pyenv config in: $file"
      grep -nE 'pyenv|PYENV_ROOT' "$file"
      echo
    else
      echo "✅ No pyenv config in: $file"
    fi
  else
    echo "ℹ️  Skipping missing file: $file"
  fi
done

echo "Done."

[mizuikk]

我也遇到了同样的问题，并通过删除 ~/.bashrc 和 ~/.profile 中重复的 pyenv 初始化脚本解决了这个问题（已通过 Codex 搜索代码库中的特定行验证）。

环境

• WSL2 Debian 12（通过 cat /etc/os-release 检查）
• pyenv 2.5.1（通过 pyenv --version 检查）
• 通过 Homebrew 安装的 Codex CLI
• 之前在 ~/.zshrc + ~/.bashrc + ~/.profile 中初始化 pyenv

用于检测重复项的脚本

#!/usr/bin/env bash

CONFIG_FILES=(
  "$HOME/.zshrc"
  "$HOME/.bashrc"
  "$HOME/.bash_profile"
  "$HOME/.profile"
)

echo "🔍 Scanning for pyenv initialization..."

for file in "${CONFIG_FILES[@]}"; do
  if [ -f "$file" ]; then
    if grep -qE 'pyenv|PYENV_ROOT' "$file"; then
      echo "⚠️  Found pyenv config in: $file"
      grep -nE 'pyenv|PYENV_ROOT' "$file"
      echo
    else
      echo "✅ No pyenv config in: $file"
    fi
  else
    echo "ℹ️  Skipping missing file: $file"
  fi
done

echo "Done."

Yes, keeping only one pyenv configuration in ~/.bashrc will fix this issue.

  1. First, add the commands to `~/.bashrc` by running the following in your terminal:

      ```bash
      echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bashrc
      echo '[[ -d $PYENV_ROOT/bin ]] && export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bashrc
      echo 'eval "$(pyenv init - bash)"' >> ~/.bashrc
      ```

[mechanovkirill]

Met the same issue. Codex was way too slow until I removed pyenv initialization from the ~/.profile. Thx a lot!

[vlasky]

The timeout issue has been fixed in pyenv 2.6.16:

https://github.com/pyenv/pyenv/releases/tag/v2.6.16

Easiest way to update pyenv to the latest version is to run the following command from your terminal window:

pyenv update

For more information on the cause and resolution of the issue, see:

• pyenv rehash hangs for 60 seconds in sandboxed environments (Landlock/seccomp) pyenv/pyenv#3365
• rehash: Fix hanging for 60 seconds when shims directory is not writable due to Linux Landlock pyenv/pyenv#3367