Conda exception on start of vscode, exceptinon reported inside of vscode terminal

Users conda
1

Not sure what to do. I have been using vscode for quite a while now with no issues.

exec summary
When I started vscode today, with base env activated I get an exception (see below) in the vscode terminal. It only happens if I start vscode in base env. If I start in another env I can get the exception by deactivating and falling into base env.

I have ripped out all my env, ripped out miniconda, ripped out vscode, put in updated versions of both, and get the same issue. So that is, I see the problem with a completely fresh install of both, that is with base env only and a new clean install of vscode without any extensions added.

Would be very interested how to fix this.

LONG STORY

Today when it starts I get the following conda exception in the terminal within vscode:


# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/exception_handler.py", line 18, in __call__
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/main.py", line 87, in main_sourced
        print(activator.execute(), end="")
              ^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/activate.py", line 238, in execute
        response = getattr(self, self.command)()
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/activate.py", line 200, in activate
        builder_result = self.build_activate(self.env_name_or_prefix)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/activate.py", line 367, in build_activate
        return self._build_activate_stack(env_name_or_prefix, False)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/activate.py", line 391, in _build_activate_stack
        return self.build_reactivate()
               ^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/activate.py", line 578, in build_reactivate
        self._replace_prefix_in_path(conda_prefix, conda_prefix)
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/activate.py", line 724, in _replace_prefix_in_path
        if path_list[last_idx + 1] == library_bin_dir:
           ~~~~~~~~~^^^^^^^^^^^^^^
    IndexError: list index out of range

`$ /opt/miniconda3/bin/conda shell.posix activate base`

 environment variables:
        AMENT_PREFIX_PATH=/opt/ros/iron
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/opt/miniconda3/bin/conda
             CONDA_PREFIX=/opt/miniconda3
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
               CONDA_ROOT=/opt/miniconda3
              CONDA_SHLVL=1
           CURL_CA_BUNDLE=<not set>
          LD_LIBRARY_PATH=/opt/ros/iron/opt/rviz_ogre_vendor/lib:/opt/ros/iron/lib/x86_64-linux-
                          gnu:/opt/ros/iron/lib
               LD_PRELOAD=<not set>
                     PATH=/opt/ros/iron/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/s
                          bin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin:/opt/minicond
                          a3/condabin:/opt/miniconda3/bin
               PYTHONPATH=/opt/ros/iron/lib/python3.10/site-packages
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>
               WINDOWPATH=2

     active environment : base
    active env location : /opt/miniconda3
            shell level : 1
       user config file : /home/asterion/.condarc
 populated config files : /opt/miniconda3/.condarc
                          /home/asterion/.condarc
          conda version : 24.11.1
    conda-build version : not installed
         python version : 3.12.8.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=zen3
                          __conda=24.11.1=0
                          __cuda=12.7=0
                          __glibc=2.35=0
                          __linux=6.8.0=0
                          __unix=0=0
       base environment : /opt/miniconda3  (writable)
      conda av data dir : /opt/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/miniconda3/pkgs
                          /home/asterion/.conda/pkgs
       envs directories : /opt/miniconda3/envs
                          /home/asterion/.conda/envs
               platform : linux-64
             user-agent : conda/24.11.1 requests/2.32.3 CPython/3.12.8 Linux/6.8.0-51-generic ubuntu/22.04.5 glibc/2.35 solver/libmamba conda-libmamba-solver/24.9.0 libmambapy/1.5.11
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.
If you suspect this error is being caused by a malfunctioning plugin,
consider using the --no-plugins option to turn off plugins.

Example: conda --no-plugins install <package>

Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
the command line to run the command without plugins enabled.

Example: CONDA_NO_PLUGINS=true conda install <package>


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The problem was weird because it only seemed to be a problem for the “base”. If I started code in another env other than base, I didn’t get the exception. Then eventually I seemed to be able to start two windows in code with one call to code?!?! Both would have a different env set in the vscode terminal (not necessarily the one code was started in). If code was started in something other that base, I could cause the exception by deactivating the env in the vscode terminal to return to base env.

2

Can you run conda init --reverse and then conda init?

3

Yep. If I close vscode and do it in the bash shell (closing and opening shells for changes to take effect), then open vscode again, I get 2 vscode windows open, both with the exception in the vscode terminal.

4

@jaimergp so I created base2 with:

conda create -n base2
conda activate base2

If I start vscode in base2, vscode starts with no exception in its terminal but it’s terminal is reporting (base).

In the vscode terminal I use conda deactivate, conda changes to (base2).

If I use conda deactivate again inside vscode terminal, it drops out of conda envs, with no exception.

If I close vscode, use conda deactivate to drop from (base2) to (base) and start vscode, the exception is back.

5

This is so strange because you are on a Linux machine (judging by the paths) and is somehow trying to get rid of a Windows-only PATH entry. If I were you, I’d go to the section of the code mentioned in the traceback (“/opt/miniconda3/lib/python3.12/site-packages/conda/activate.py”, line 724) and comment it out so it looks like this:

                # if path_list[last_idx + 1] == library_bin_dir:
                #     last_idx += 1
6

@jaimergp Weird?! I’ll say weird.

Hmmm.

I can’t even put my finger on when it started happening. As mentioned, I had a number of env that I was using and wasn’t ever really dropping into (base) when using vscode.

I’ll try your suggestion report once I poke around a little with that, thanks.

7

DOH!

I thought I might try installing again, but now I am getting:

asterion@MonstaPC:~$ conda activate base
Command '' not found, but can be installed with:
sudo apt install mailutils-mh  # version 1:3.14-1, or
sudo apt install mmh           # version 0.4-4
sudo apt install nmh           # version 1.7.1-11
sudo apt install termtris      # version 1.3-1ubuntu1

Happens against init, create yadda.

Seems to be fixed if I run:
source ~/miniconda3/bin/activate

That is I opted out of installing into /opt.

Now when I start vscode no exception but vscode is not picking up conda (so I still need to re-config the vscode to pick up the conda). As an experiment I sourced activate inside of vscode and no exception, that is I got the (base) prompt in the terminal.

I very VERY bravely typed conda deactivate, it dropped out of (base) into normal shell MITT NO, I SAY NO EXCEPTION!

So, I will fiddle now with vscode config.

8

Okay, I hazard to say I have got my vscode sorted now.

But, no clue really why the error apparently started up, why it persisted after ripping out conda and vscode (including hidden nuggets) and reinstalling later versions.

The conda I now have running was the latest conda that saw the problem with the exception.

Where as with the first couple of attempts conda init et al ran, for whatever reason, this latest install failed such that the source->activate brought the env up.

Now the chore if rebuilding my other env.

Thanks @jaimergp but the mystery of why my install was “thinking” it twas on a windows machine, who knows.

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