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angelo-peronio avatar angelo-peronio commented on June 9, 2024

Same issue here:

(base) λ conda pack -n test_env
Collecting packages...
CondaPackError:
Files managed by conda were found to have been deleted/overwritten in the
following packages:

- appdirs='1.4.3'
- attrs='19.1.0'
- black='19.3b0'
- click='7.0'
- toml='0.10.0'

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).

The environment I was trying to pack is just python + black:

(base) λ conda list -n test_env
# packages in environment at C:\Users\angelo.peronio\AppData\Local\Continuum\miniconda3\envs\test_env:
#
# Name                    Version                   Build  Channel
appdirs                   1.4.3                      py_1    conda-forge
attrs                     19.1.0                     py_0    conda-forge
black                     19.3b0                     py_0    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
certifi                   2019.6.16                py37_0    conda-forge
click                     7.0                        py_0    conda-forge
openssl                   1.1.1c               hfa6e2cd_0    conda-forge
pip                       19.1.1                   py37_0    conda-forge
python                    3.7.3                h510b542_1    conda-forge
setuptools                41.0.1                   py37_0    conda-forge
sqlite                    3.29.0               hfa6e2cd_0    conda-forge
toml                      0.10.0                     py_0    conda-forge
vc                        14.1                 h0510ff6_4    defaults
vs2015_runtime            14.15.26706          h3a45250_4    defaults
wheel                     0.33.4                   py37_0    conda-forge
wincertstore              0.2                   py37_1002    conda-forge

My conda installation:

(base) λ conda info

     active environment : base
    active env location : C:\Users\angelo.peronio\AppData\Local\Continuum\miniconda3
            shell level : 1
       user config file : C:\Users\angelo.peronio\.condarc
 populated config files : C:\Users\angelo.peronio\.condarc
          conda version : 4.7.5
    conda-build version : not installed
         python version : 3.7.3.final.0
       virtual packages : __cuda=10.2
       base environment : C:\Users\angelo.peronio\AppData\Local\Continuum\miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/win-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
          package cache : C:\Users\angelo.peronio\AppData\Local\Continuum\miniconda3\pkgs
                          C:\Users\angelo.peronio\.conda\pkgs
                          C:\Users\angelo.peronio\AppData\Local\conda\conda\pkgs
       envs directories : C:\Users\angelo.peronio\AppData\Local\Continuum\miniconda3\envs
                          C:\Users\angelo.peronio\.conda\envs
                          C:\Users\angelo.peronio\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/4.7.5 requests/2.22.0 CPython/3.7.3 Windows/10 Windows/10.0.17763
          administrator : False
             netrc file : None
           offline mode : False
λ conda list conda-pack
# packages in environment at C:\Users\angelo.peronio\AppData\Local\Continuum\miniconda3:
# Name                    Version                   Build  Channel
conda-pack                0.3.1                      py_0    conda-forge
[...]

In another, less minimal environment, I had the same problem involving the packages:

- appdirs='1.4.3'
- asteval='0.9.14'
- attrs='19.1.0'
- backcall='0.1.0'
- black='19.3b0'
- click='7.0'
- cloudpickle='1.2.1'
- colorama='0.4.1'
- cycler='0.10.0'
- decorator='4.4.0'
- flake8-docstrings='1.3.0'
- flake8-polyfill='1.0.2'
- ipython_genutils='0.2.0'
- jupyter_client='5.3.1'
- jupyter_core='4.4.0'
- lmfit='0.9.13'
- mccabe='0.6.1'
[...]
- parso='0.5.0'
- prompt_toolkit='2.0.9'
- pycodestyle='2.5.0'
- pyflakes='2.1.1'
- pygments='2.4.2'
- pyparsing='2.4.0'
- python-dateutil='2.8.0'
- pytz='2019.1'
- rope='0.14.0'
- snowballstemmer='1.9.0'
- toml='0.10.0'
- wcwidth='0.1.7'

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jcrist avatar jcrist commented on June 9, 2024

Apologies for the delay here. I'm unable to reproduce either of these on osx, I wonder if this is a windows specific issue. I'll try to spin up a VM and debug further.

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sephib avatar sephib commented on June 9, 2024

Hi,
This be similar to #63 (which is closed)
We are running on OS :

openSUSE Leap 42.3

setting up environment with

conda create -n test-pack python=3.6 -y -c conda-forge
conda activate test-pack
conda install -c conda-forge pandas-profiling

We get an error

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

  • statsmodels='0.10.0'

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angelo-peronio avatar angelo-peronio commented on June 9, 2024

@jcrist , thank you. Let me know if I can help.

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jcrist avatar jcrist commented on June 9, 2024

With #82 and #81 the following environments now work:

  • The one with tomopy posted here: #78 (comment). Tomopy packages its LICENSE file in the root directory for some reason, which was causing issues.
  • The one with black posted here: #78 (comment). This was due to an issue with conda and .nonadmin files.

The one posted by @sephib above doesn't fail for me on osx, but I can't currently test on linux. If it still fails after the next release, please raise a new issue.

I'm going to finish a few cleanups and push a release out today. Thanks everyone for being patient. Closing.

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carterbox avatar carterbox commented on June 9, 2024

Thanks, @jcrist.

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angelo-peronio avatar angelo-peronio commented on June 9, 2024

@jcrist , thank you! It works perfectly.

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sephib avatar sephib commented on June 9, 2024

@jcrist - I've updated to version 0.4.0 but still getting the same error

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

  • statsmodels='0.10.1'

Is there any log that I can supply ?

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jcrist avatar jcrist commented on June 9, 2024

I spun up a linux env to debug, and am unable to reproduce:

$ conda create -n test-pack python=3.6 pandas-profiling conda-pack -y -c conda-forge
...
$ conda activate test-pack
$ conda pack --version
conda-pack 0.4.0
$ conda pack
Collecting packages...
Packing environment at '/opt/miniconda/envs/test-pack' to 'test-pack.tar.gz'
[########################################] | 100% Completed | 33.9s

If you could reproduce, then create a new issue with the results of conda list --export for the failing environment that would be helpful.

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sephib avatar sephib commented on June 9, 2024

Hi,
I ran the code again with --force-reinstall and still got an error.
Here is the results of conda list --export:

> (test-pack) ds@linux-vnlc:~> conda list --export > This file may be used to create an environment using: > $ conda create --name --file > platform: linux-64 > _libgcc_mutex=0.1=main > asn1crypto=0.24.0=py36_1003 > astroid=2.2.5=py36_0 > astropy=3.2.1=py36h516909a_0 > atomicwrites=1.3.0=py_0 > attrs=19.1.0=py_0 > bleach=3.1.0=py_0 > ca-certificates=2019.6.16=hecc5488_0 > certifi=2019.6.16=py36_1 > cffi=1.12.3=py36h8022711_0 > chardet=3.0.4=py36_1003 > conda-pack=0.4.0=py_0 > confuse=1.0.0=py_0 > cryptography=2.7=py36h72c5cf5_0 > cycler=0.10.0=py_1 > dbus=1.13.6=he372182_0 > decorator=4.4.0=py_0 > defusedxml=0.5.0=py_1 > entrypoints=0.3=py36_1000 > expat=2.2.5=he1b5a44_1003 > fontconfig=2.13.1=h86ecdb6_1001 > freetype=2.10.0=he983fc9_0 > gettext=0.19.8.1=hc5be6a0_1002 > glib=2.58.3=h6f030ca_1002 > gst-plugins-base=1.14.5=h0935bb2_0 > gstreamer=1.14.5=h36ae1b5_0 > htmlmin=0.1.12=py_1 > icu=64.2=he1b5a44_0 > idna=2.8=py36_1000 > importlib_metadata=0.18=py36_0 > ipython_genutils=0.2.0=py_1 > isort=4.3.21=py36_0 > jinja2=2.10.1=py_0 > jpeg=9c=h14c3975_1001 > jsonschema=3.0.1=py36_0 > jupyter_client=5.3.1=py_0 > jupyter_core=4.4.0=py_0 > kiwisolver=1.1.0=py36hc9558a2_0 > lazy-object-proxy=1.4.1=py36h516909a_0 > libblas=3.8.0=10_openblas > libcblas=3.8.0=10_openblas > libffi=3.2.1=he1b5a44_1006 > libgcc-ng=9.1.0=hdf63c60_0 > libgfortran-ng=7.3.0=hdf63c60_0 > libiconv=1.15=h516909a_1005 > liblapack=3.8.0=10_openblas > libopenblas=0.3.6=h6e990d7_5 > libpng=1.6.37=hed695b0_0 > libsodium=1.0.17=h516909a_0 > libstdcxx-ng=9.1.0=hdf63c60_0 > libuuid=2.32.1=h14c3975_1000 > libxcb=1.13=h14c3975_1002 > libxml2=2.9.9=hee79883_2 > llvmlite=0.29.0=py36hfd453ef_1 > markupsafe=1.1.1=py36h14c3975_0 > matplotlib=3.1.1=py36_1 > matplotlib-base=3.1.1=py36he7580a8_1 > mccabe=0.6.1=py_1 > missingno=0.4.2=py_0 > mistune=0.8.4=py36h14c3975_1000 > more-itertools=7.1.0=py_0 > nbconvert=5.5.0=py_0 > nbformat=4.4.0=py_1 > ncurses=6.1=hf484d3e_1002 > numba=0.45.0=py36hb3f55d8_0 > numpy=1.16.4=py36h95a1406_0 > openblas=0.3.6=h6e990d7_5 > openssl=1.1.1c=h516909a_0 > packaging=19.0=py_0 > pandas=0.25.0=py36hb3f55d8_0 > pandas-profiling=2.2.0=py_0 > pandoc=2.7.3=0 > pandocfilters=1.4.2=py_1 > patsy=0.5.1=py_0 > pcre=8.41=hf484d3e_1003 > phik=0.9.8=py_0 > pip=19.2.1=py36_0 > pluggy=0.12.0=py_0 > psutil=5.6.3=py36h516909a_0 > pthread-stubs=0.4=h14c3975_1001 > py=1.8.0=py_0 > pycparser=2.19=py36_1 > pygments=2.4.2=py_0 > pylint=2.3.1=py36_0 > pyopenssl=19.0.0=py36_0 > pyparsing=2.4.1=py_0 > pyqt=5.9.2=py36hcca6a23_0 > pyrsistent=0.15.3=py36h516909a_0 > pysocks=1.7.0=py36_0 > pytest=5.0.1=py36_1 > pytest-arraydiff=0.3=py_0 > pytest-astropy=0.5.0=py_0 > pytest-doctestplus=0.3.0=py_0 > pytest-openfiles=0.3.1=py_0 > pytest-pylint=0.14.0=py_0 > pytest-remotedata=0.3.1=py_0 > pytest-runner=5.1=py_0 > python=3.6.7=h357f687_1005 > python-dateutil=2.8.0=py_0 > pytz=2019.1=py_0 > pyyaml=5.1.1=py36h516909a_0 > pyzmq=18.0.2=py36h1768529_2 > qt=5.9.7=h0c104cb_3 > readline=8.0=hf8c457e_0 > requests=2.22.0=py36_1 > scipy=1.3.0=py36h921218d_0 > seaborn=0.9.0=py_1 > setuptools=41.0.1=py36_0 > sip=4.19.8=py36hf484d3e_1000 > six=1.12.0=py36_1000 > sqlite=3.29.0=hcee41ef_0 > statsmodels=0.10.1=py36hc1659b7_0 > testpath=0.4.2=py_1001 > tk=8.6.9=hed695b0_1002 > tornado=6.0.3=py36h516909a_0 > traitlets=4.3.2=py36_1000 > typed-ast=1.4.0=py36h516909a_0 > urllib3=1.25.3=py36_0 > wcwidth=0.1.7=py_1 > webencodings=0.5.1=py_1 > wheel=0.33.4=py36_0 > wrapt=1.11.2=py36h516909a_0 > xorg-libxau=1.0.9=h14c3975_0 > xorg-libxdmcp=1.1.3=h516909a_0 > xz=5.2.4=h14c3975_1001 > yaml=0.1.7=h14c3975_1001 > zeromq=4.3.2=he1b5a44_2 > zipp=0.5.1=py_0 > zlib=1.2.11=h516909a_1005

I won't be able to recheck until next week.
Thx for all your time and great work!

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jcrist avatar jcrist commented on June 9, 2024

Can you please open a new issue with that information?

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github-actions avatar github-actions commented on June 9, 2024

Hi there, thank you for your contribution!

This issue has been automatically locked because it has not had recent activity after being closed.

Please open a new issue if needed.

Thanks!

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