conda base env not automatically activating in zsh

[shayanhoss]

I recently updated my anaconda and this basically broke my base environment so I switched to miniconda3 4.6.9. Upon installation, miniconda3 did not edit my .zshrc to add miniconda to the path. I had to manually at the snippet below to add conda to the path. Now when I open a new terminal I get an (eval):61 and my conda base env doesnt activate without source .zshrc every time I open a new shell.

 shayan@shayan-macbook  ~  tail -n 15 .zshrc
# >>> conda init >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$(CONDA_REPORT_ERRORS=false '/Users/shayan/miniconda3/bin/conda' shell.bash hook 2> /dev/null)"
if [ $? -eq 0 ]; then
    \eval "$__conda_setup"
else
    if [ -f "/Users/shayan/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/Users/shayan/miniconda3/etc/profile.d/conda.sh"
        CONDA_CHANGEPS1=false conda activate base
    else
        \export PATH="/Users/shayan/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda init <<<

Current Behavior

Steps to Reproduce

Last login: Wed Apr  3 14:20:09 on ttys005
(eval):61: = not found
 shayan@shayan-macbook  ~  conda
usage: conda [-h] [-V] command ...

conda is a tool for managing and deploying applications, environments and packages.

Options:

positional arguments:
  command
    clean        Remove unused packages and caches.
    config       Modify configuration values in .condarc. This is modeled
                 after the git config command. Writes to the user .condarc
                 file (/Users/shayan/.condarc) by default.
    create       Create a new conda environment from a list of specified
                 packages.
    help         Displays a list of available conda commands and their help
                 strings.
    info         Display information about current conda install.
    init         Initialize conda for shell interaction. [Experimental]
    install      Installs a list of packages into a specified conda
                 environment.
    list         List linked packages in a conda environment.
    package      Low-level conda package utility. (EXPERIMENTAL)
    remove       Remove a list of packages from a specified conda environment.
    uninstall    Alias for conda remove.
    run          Run an executable in a conda environment. [Experimental]
    search       Search for packages and display associated information. The
                 input is a MatchSpec, a query language for conda packages.
                 See examples below.
    update       Updates conda packages to the latest compatible version.
    upgrade      Alias for conda update.

optional arguments:
  -h, --help     Show this help message and exit.
  -V, --version  Show the conda version number and exit.

conda commands available from other packages:
  env
 shayan@shayan-macbook  ~  echo $PATH
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
 shayan@shayan-macbook  ~  pip
zsh: command not found: pip
 ✘ shayan@shayan-macbook  ~  source .zshrc
(base)  shayan@shayan-macbook  ~  echo $PATH
/Users/shayan/miniconda3/bin:/Users/shayan/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
(base)  shayan@shayan-macbook  ~ 

Expected Behavior

Last login: Wed Apr  3 14:22:01 on ttys004
 shayan@shayan-macbook  ~ 

Environment Information

`conda info`

 shayan@shayan-macbook  ~  conda info

     active environment : None
            shell level : 0
       user config file : /Users/shayan/.condarc
 populated config files : /Users/shayan/.condarc
          conda version : 4.6.9
    conda-build version : not installed
         python version : 3.7.1.final.0
       base environment : /Users/shayan/miniconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/shayan/miniconda3/pkgs
                          /Users/shayan/.conda/pkgs
       envs directories : /Users/shayan/miniconda3/envs
                          /Users/shayan/.conda/envs
               platform : osx-64
             user-agent : conda/4.6.9 requests/2.21.0 CPython/3.7.1 Darwin/17.7.0 OSX/10.13.6
                UID:GID : 503:20
             netrc file : None
           offline mode : False

`conda config --show-sources`

 shayan@shayan-macbook  ~  conda config --show-sources
==> /Users/shayan/.condarc <==
ssl_verify: True
channels:
  - defaults

`conda list --show-channel-urls`

shayan@shayan-macbook  ~  conda list --show-channel-urls
# packages in environment at /Users/shayan/miniconda3:
#
# Name                    Version                   Build  Channel
aegea                     2.3.2                    pypi_0    pypi
anndata                   0.6.19                   pypi_0    pypi
appnope                   0.1.0                    py37_0    defaults
argcomplete               1.9.5                    pypi_0    pypi
asn1crypto                0.24.0                   py37_0    defaults
attrs                     19.1.0                   py37_1    defaults
awscli                    1.16.138                 pypi_0    pypi
awscli-cwlogs             1.4.5                    pypi_0    pypi
babel                     2.6.0                    pypi_0    pypi
backcall                  0.1.0                    py37_0    defaults
bcrypt                    3.1.6                    pypi_0    pypi
bleach                    3.1.0                    py37_0    defaults
boto3                     1.9.128                  pypi_0    pypi
botocore                  1.12.128                 pypi_0    pypi
ca-certificates           2019.1.23                     0    defaults
certifi                   2019.3.9                 py37_0    defaults
cffi                      1.11.5           py37h6174b99_1    defaults
chardet                   3.0.4                    py37_1    defaults
colorama                  0.3.9                    pypi_0    pypi
conda                     4.6.9                    py37_0    defaults
conda-env                 2.6.0                         1    defaults
cryptography              2.4.2            py37ha12b0ac_0    defaults
cycler                    0.10.0                   pypi_0    pypi
czb-util                  0.4.0                     dev_0    <develop>
dbus                      1.13.6               h90a0687_0    defaults
decorator                 4.4.0                    py37_1    defaults
defusedxml                0.5.0                    py37_1    defaults
dnspython                 1.16.0                   pypi_0    pypi
docutils                  0.14                     pypi_0    pypi
entrypoints               0.3                      py37_0    defaults
expat                     2.2.6                h0a44026_0    defaults
gettext                   0.19.8.1             h15daf44_3    defaults
glib                      2.56.2               hd9629dc_0    defaults
h5py                      2.9.0                    pypi_0    pypi
icu                       58.2                 h4b95b61_1    defaults
idna                      2.8                      py37_0    defaults
ipwhois                   1.1.0                    pypi_0    pypi
ipykernel                 5.1.0            py37h39e3cac_0    defaults
ipython                   7.4.0            py37h39e3cac_0    defaults
ipython_genutils          0.2.0                    py37_0    defaults
ipywidgets                7.4.2                    py37_0    defaults
jedi                      0.13.3                   py37_0    defaults
jinja2                    2.10                     py37_0    defaults
jmespath                  0.9.4                    pypi_0    pypi
joblib                    0.13.2                   pypi_0    pypi
jpeg                      9b                   he5867d9_2    defaults
jsonschema                3.0.1                    py37_0    defaults
jupyter                   1.0.0                    py37_7    defaults
jupyter_client            5.2.4                    py37_0    defaults
jupyter_console           6.0.0                    py37_0    defaults
jupyter_core              4.4.0                    py37_0    defaults
jupyterlab                0.35.4           py37hf63ae98_0    defaults
jupyterlab_server         0.2.0                    py37_0    defaults
keymaker                  1.0.8                    pypi_0    pypi
kiwisolver                1.0.1                    pypi_0    pypi
libcxx                    4.0.1                hcfea43d_1    defaults
libcxxabi                 4.0.1                hcfea43d_1    defaults
libedit                   3.1.20170329         hb402a30_2    defaults
libffi                    3.2.1                h475c297_4    defaults
libiconv                  1.15                 hdd342a3_7    defaults
libpng                    1.6.36               ha441bb4_0    defaults
libsodium                 1.0.16               h3efe00b_0    defaults
llvmlite                  0.28.0                   pypi_0    pypi
markupsafe                1.1.1            py37h1de35cc_0    defaults
matplotlib                3.0.3                    pypi_0    pypi
mistune                   0.8.4            py37h1de35cc_0    defaults
mock                      2.0.0                    pypi_0    pypi
natsort                   6.0.0                    pypi_0    pypi
nbconvert                 5.4.1                    py37_3    defaults
nbformat                  4.4.0                    py37_0    defaults
ncurses                   6.1                  h0a44026_1    defaults
networkx                  2.2                      pypi_0    pypi
notebook                  5.7.8                    py37_0    defaults
numba                     0.43.1                   pypi_0    pypi
numexpr                   2.6.9                    pypi_0    pypi
numpy                     1.16.2                   pypi_0    pypi
openssl                   1.1.1b               h1de35cc_1    defaults
pandas                    0.24.2                   pypi_0    pypi
pandoc                    2.2.3.2                       0    defaults
pandocfilters             1.4.2                    py37_1    defaults
paramiko                  2.4.2                    pypi_0    pypi
parso                     0.3.4                    py37_0    defaults
patsy                     0.5.1                    pypi_0    pypi
pbr                       5.1.3                    pypi_0    pypi
pcre                      8.43                 h0a44026_0    defaults
pexpect                   4.6.0                    py37_0    defaults
pickleshare               0.7.5                    py37_0    defaults
pip                       18.1                     py37_0    defaults
prometheus_client         0.6.0                    py37_0    defaults
prompt_toolkit            2.0.9                    py37_0    defaults
ptyprocess                0.6.0                    py37_0    defaults
pyasn1                    0.4.5                    pypi_0    pypi
pycosat                   0.6.3            py37h1de35cc_0    defaults
pycparser                 2.19                     py37_0    defaults
pygments                  2.3.1                    py37_0    defaults
pynacl                    1.3.0                    pypi_0    pypi
pyopenssl                 18.0.0                   py37_0    defaults
pyparsing                 2.3.1                    pypi_0    pypi
pyqt                      5.9.2            py37h655552a_2    defaults
pyrsistent                0.14.11          py37h1de35cc_0    defaults
pysocks                   1.6.8                    py37_0    defaults
python                    3.7.1                haf84260_7    defaults
python-dateutil           2.8.0                    py37_0    defaults
python.app                2                        py37_9    defaults
pytz                      2018.9                   pypi_0    pypi
pyyaml                    3.13                     pypi_0    pypi
pyzmq                     18.0.0           py37h0a44026_0    defaults
qt                        5.9.7                h468cd18_1    defaults
qtconsole                 4.4.3                    py37_0    defaults
readline                  7.0                  h1de35cc_5    defaults
requests                  2.21.0                   py37_0    defaults
rsa                       3.4.2                    pypi_0    pypi
ruamel_yaml               0.15.46          py37h1de35cc_0    defaults
s3transfer                0.2.0                    pypi_0    pypi
scanpy                    1.4+226.gfc24dfc           dev_0    <develop>
scikit-learn              0.20.3                   pypi_0    pypi
scipy                     1.2.1                    pypi_0    pypi
seaborn                   0.9.0                    pypi_0    pypi
send2trash                1.5.0                    py37_0    defaults
setuptools                40.6.3                   py37_0    defaults
sip                       4.19.8           py37h0a44026_0    defaults
six                       1.12.0                   py37_0    defaults
sqlite                    3.26.0               ha441bb4_0    defaults
statsmodels               0.9.0                    pypi_0    pypi
tables                    3.5.1                    pypi_0    pypi
terminado                 0.8.1                    py37_1    defaults
testpath                  0.4.2                    py37_0    defaults
tk                        8.6.8                ha441bb4_0    defaults
tornado                   6.0.2            py37h1de35cc_0    defaults
traitlets                 4.3.2                    py37_0    defaults
tweak                     1.0.2                    pypi_0    pypi
uritemplate               3.0.0                    pypi_0    pypi
urllib3                   1.24.1                   py37_0    defaults
wcwidth                   0.1.7                    py37_0    defaults
webencodings              0.5.1                    py37_1    defaults
wheel                     0.32.3                   py37_0    defaults
widgetsnbextension        3.4.2                    py37_0    defaults
xz                        5.2.4                h1de35cc_4    defaults
yaml                      0.1.7                hc338f04_2    defaults
zeromq                    4.3.1                h0a44026_3    defaults
zlib                      1.2.11               h1de35cc_3    defaults

[parano]

I'm having the exact issue under zsh(OS X, oh-my-zsh based configuration), and seeing the error when initializing a new shell: (eval):61: = not found

Noticed that when I run the conda shell.zsh hook code under zsh directly, everything works fine. And the error only seems to occur when initializing zsh:

[soapy1]

This should be fixed in the latest conda. Updating conda and then running init should resolve the issue

$ conda update conda
$ conda init zsh
WARNING: The conda.compat module is deprecated and will be removed in a future release.
no change     /Users/scastellarin/miniconda3/condabin/conda
no change     /Users/scastellarin/miniconda3/bin/conda
no change     /Users/scastellarin/miniconda3/bin/conda-env
no change     /Users/scastellarin/miniconda3/bin/activate
no change     /Users/scastellarin/miniconda3/bin/deactivate
no change     /Users/scastellarin/miniconda3/etc/profile.d/conda.sh
no change     /Users/scastellarin/miniconda3/etc/fish/conf.d/conda.fish
no change     /Users/scastellarin/miniconda3/shell/condabin/Conda.psm1
no change     /Users/scastellarin/miniconda3/shell/condabin/conda-hook.ps1
no change     /Users/scastellarin/miniconda3/lib/python3.7/site-packages/xonsh/conda.xsh
no change     /Users/scastellarin/miniconda3/etc/profile.d/conda.csh
modified      /Users/scastellarin/.zshrc

[shayanhoss]

That did the trick! Thanks for resolving this so quickly.

[parano]

Thanks for the quick reply! Looks like #8476 has fixed this issue.

[soapy1]

It is not recommended to just add conda to path, conda really does need to be initialized and activated to work as expected. Instead of adding conda to path you can add the initialization bit that would have been added to your shell

# >>> conda initialize >>>
__conda_setup="$('PATH_TO_CONDA_INSTALL/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "PATH_TO_CONDA_INSTALL/etc/profile.d/conda.sh" ]; then
        . "PATH_TO_CONDA_INSTALL/etc/profile.d/conda.sh"
    else
        export PATH="PATH_TO_CONDA_INSTALL/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

[raytanIO]

Thank you soapy1. I had deleted my comment so not to confuse anyone. Just adding the conda path defeats the purpose of conda. I just added >>>changeps1: False to ~/.condarc to remove the (base) on the ZSH prompt.

[ashutoshjv661]

thanks a ton ^_^

[ElArkk]

Conda works as expected and activates the base env on every new login when I run conda init zsh in my zsh shell. However, if I replace all occurences of

"/Users/username/anaconda.. (my conda install path)

with

"$HOME/anaconda..

in the conda init block in my .zshrc, it does not activate the base env anymore at new logins, even though $HOME evaluates to /Users/username. The command conda itself still works though.

What could cause this strange behaviour? I'm using conda 4.8.3 on macOS Mojave 10.14.6

[AllieUbisse]

This should be fixed in the latest conda. Updating conda and then running init should resolve the issue

$ conda update conda
$ conda init zsh
WARNING: The conda.compat module is deprecated and will be removed in a future release.
no change     /Users/scastellarin/miniconda3/condabin/conda
no change     /Users/scastellarin/miniconda3/bin/conda
no change     /Users/scastellarin/miniconda3/bin/conda-env
no change     /Users/scastellarin/miniconda3/bin/activate
no change     /Users/scastellarin/miniconda3/bin/deactivate
no change     /Users/scastellarin/miniconda3/etc/profile.d/conda.sh
no change     /Users/scastellarin/miniconda3/etc/fish/conf.d/conda.fish
no change     /Users/scastellarin/miniconda3/shell/condabin/Conda.psm1
no change     /Users/scastellarin/miniconda3/shell/condabin/conda-hook.ps1
no change     /Users/scastellarin/miniconda3/lib/python3.7/site-packages/xonsh/conda.xsh
no change     /Users/scastellarin/miniconda3/etc/profile.d/conda.csh
modified      /Users/scastellarin/.zshrc

---

Before

---

solution

Now

Thank you! @soapy1 [ Sophia Castellarin]

[github-actions]

Hi there, thank you for your contribution to Conda!

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