Fix: pip Still Points to Global Path After Activating a Conda Environment

Symptoms

Even after verifying with which python / which pip that both resolve to the current conda environment, running pip install still installs packages into /usr/local/lib/.

How to check whether this problem exists:

which pip
which python3

Solution

Update (May 19)

The fix is simple — use python -m pip install instead of pip install.

Other approaches such as upgrading pip, clearing caches, etc. (including suggestions from the web and GPT) are all ineffective.

---

Update (Jun 21)

This workaround breaks again when python is invoked inside a .sh script.

Step 1: In ~/.zshrc, comment out the following line:

# . "$HOME/.local/bin/env"

Step 2: Make sure the conda initialization block appears last in ~/.zshrc:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/chang/anaconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/chang/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/home/chang/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/chang/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

Fix for SSH servers

When logging in via SSH, the system loads ~/.profile in addition to ~/.bashrc, so you must check both files.

Make sure ~/.bashrc is sourced after the PATH assignments in ~/.profile, otherwise the change to ~/.bashrc will be overridden and PATH will revert to "$HOME/.local/bin:$PATH".

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/bin" ] ; then
    PATH="$HOME/bin:$PATH"
fi

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/.local/bin" ] ; then
    PATH="$HOME/.local/bin:$PATH"
fi

# if running bash
if [ -n "$BASH_VERSION" ]; then
    # include .bashrc if it exists
    if [ -f "$HOME/.bashrc" ]; then
        . "$HOME/.bashrc"
    fi
fi

---

Update (Jun 25)

Another root cause: conda does not automatically install pip when creating a new environment. If pip and python are missing from the environment's bin/ directory, pip will naturally fall back to the global one.

ls -l /home/chang/anaconda3/envs/test5/bin/pip
# ls: cannot access '/home/chang/anaconda3/envs/test5/bin/pip': No such file or directory

conda install pip