Conda-pack: CondaPackError: files managed by conda were

[waveskimmer]

So, I have a python project where all my tests run but then I do:

conda install -y conda-pack

which succeeds and when I run:

conda-pack

I get a lengthy complaint:

`Collecting packages...
CondaPackError:
Files managed by conda were found to have been deleted/overwritten in the
following packages:

• conda-pack 0.6.0:
  lib/python3.1/site-packages/conda_pack-0.6.0.dist-info/INSTALLER
  lib/python3.1/site-packages/conda_pack-0.6.0.dist-info/LICENSE.txt
  lib/python3.1/site-packages/conda_pack-0.6.0.dist-info/METADATA
  • 19 others
• types-requests 2.26.0:
  lib/python3.1/site-packages/requests-stubs/METADATA.toml
  lib/python3.1/site-packages/requests-stubs/init.pyi
  lib/python3.1/site-packages/requests-stubs/adapters.pyi
  • 41 others
• jsonschema 4.2.1:
  lib/python3.1/site-packages/jsonschema-4.2.1.dist-info/COPYING
  lib/python3.1/site-packages/jsonschema-4.2.1.dist-info/INSTALLER
  lib/python3.1/site-packages/jsonschema-4.2.1.dist-info/METADATA
  • 39 others
• types-setuptools 57.4.2:
  lib/python3.1/site-packages/pkg_resources-stubs/METADATA.toml
  lib/python3.1/site-packages/pkg_resources-stubs/init.pyi
  lib/python3.1/site-packages/pkg_resources-stubs/py31compat.pyi
  • 56 others
    `

I see no issues in conda list and I can still run my tests. I see no issues with my environment.

Any Ideas?

[waveskimmer]

I've been struggling with this the last 24 hours or so. I'm using python 3.9.7 on a Mac. Here are a few more findings:

First, if I install it into the base environment on a fresh install, I get this error:

(base) ➜  vl-headlands-file git:(make_conda) ✗ conda-pack
Collecting packages...
CondaPackError: 
Files managed by conda were found to have been deleted/overwritten in the
following packages:

- python.app 3:
    pythonapp/Contents/Info.plist
    pythonapp/Contents/MacOS/python
    pythonapp/Contents/PkgInfo
    + 4 others

This is usually due to `pip` uninstalling or clobbering conda managed files,
resulting in an inconsistent environment. Please check your environment for
conda/pip conflicts using `conda list`, and fix the environment by ensuring
only one version of each package is installed (conda preferred).

Second, If try to create an environment with anything else, then I see my original error. For example,

name: testenv
channels:
  - conda-forge

dependencies:
  - conda-pack
  - fastapi

And, I get.

(base) ➜  vl-headlands-file git:(make_conda) ✗ conda env create -f test-env.yaml 
Collecting package metadata (repodata.json): done
Solving environment: done
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate testenv
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) ➜  vl-headlands-file git:(make_conda) ✗ conda activate testenv
(testenv) ➜  vl-headlands-file git:(make_conda) ✗ conda-pack 
Collecting packages...
CondaPackError: 
Files managed by conda were found to have been deleted/overwritten in the
following packages:

- wheel 0.37.0:
    lib/python3.1/site-packages/wheel-0.37.0-py3.9.egg-info/PKG-INFO
    lib/python3.1/site-packages/wheel-0.37.0-py3.9.egg-info/SOURCES.txt
    lib/python3.1/site-packages/wheel-0.37.0-py3.9.egg-info/dependency_links.txt
    + 20 others
- pip 21.3.1:
    lib/python3.1/site-packages/pip-21.3.1-py3.9.egg-info/PKG-INFO
    lib/python3.1/site-packages/pip-21.3.1-py3.9.egg-info/SOURCES.txt
    lib/python3.1/site-packages/pip-21.3.1-py3.9.egg-info/dependency_links.txt
    + 412 others
- conda-pack 0.6.0:
    lib/python3.1/site-packages/conda_pack-0.6.0.dist-info/INSTALLER
    lib/python3.1/site-packages/conda_pack-0.6.0.dist-info/LICENSE.txt
    lib/python3.1/site-packages/conda_pack-0.6.0.dist-info/METADATA
    + 19 others
- starlette 0.16.0:
    lib/python3.1/site-packages/starlette-0.16.0.dist-info/INSTALLER
    lib/python3.1/site-packages/starlette-0.16.0.dist-info/LICENSE.md
    lib/python3.1/site-packages/starlette-0.16.0.dist-info/METADATA
    + 37 others
- fastapi 0.70.0:
    lib/python3.1/site-packages/fastapi-0.70.0.dist-info/INSTALLER
    lib/python3.1/site-packages/fastapi-0.70.0.dist-info/LICENSE
    lib/python3.1/site-packages/fastapi-0.70.0.dist-info/METADATA
    + 46 others
- idna 3.1:
    lib/python3.1/site-packages/idna-3.1.dist-info/INSTALLER
    lib/python3.1/site-packages/idna-3.1.dist-info/LICENSE.md
    lib/python3.1/site-packages/idna-3.1.dist-info/METADATA
    + 13 others
- typing_extensions 3.10.0.2:
    lib/python3.1/site-packages/typing_extensions-3.10.0.2.dist-info/INSTALLER
    lib/python3.1/site-packages/typing_extensions-3.10.0.2.dist-info/LICENSE
    lib/python3.1/site-packages/typing_extensions-3.10.0.2.dist-info/METADATA
    + 6 others

This is usually due to `pip` uninstalling or clobbering conda managed files,
resulting in an inconsistent environment. Please check your environment for
conda/pip conflicts using `conda list`, and fix the environment by ensuring
only one version of each package is installed (conda preferred).

Third, if I install conda-pack in a new environment with nothing else installed, I get the expected results:

✗ conda-pack Collecting packages... Packing environment at '/Users/kurt.guenther.ext/miniconda3/envs/debug-env' to 'debug-env.tar.gz' [########################################] | 100% Completed | 41.2s

I think I can work this this as I can pass in an env from the command-line.

[waveskimmer]

Wow! I think I finally nailed it. The lib/python3.1 was actually symlinked to a lib/python3.10, so the whole python3.1 was a red herring. If I added python=3.9 to my environment, it works as designed. Almost too much for a conda newbie, but I did learn a lot on the journey.

I still think there is something wrong above.

[geoHeil]

#197 might be related.

I am facing a similar problem.

And can confirm that pinning the python version in the environment.yml file like i.e. python=3.8 is working.

[dbast]

This got fixed by #199 ... which is part of the released conda-pack version 0.7.0 (currently available via conda-forge).

The above commands as one liner to test run successful here:

conda create --name testenv -c conda-forge conda-pack fastapi -y && conda activate testenv && conda-pack

See also #200

[orsk-moscow]

Hello!

I still have the same bug. Simple check with @dbast's cmd:
conda create --name testenv -c conda-forge conda-pack fastapi -y && conda activate testenv && conda-pack got me the error:

CondaPackError:
Files managed by conda were found to have been deleted/overwritten in the
following packages: ...

conda-pack --version
conda-pack 0.7.0

UPD
simple modification cmd to conda create -y -n testenv -c conda-forge conda-pack fastapi python=3.9 && conda activate testenv && conda-pack helped, but looks like fix doesn't handle the bug