Conda Doctor Altered Files: Python, in a new install, can't resolve.

[b9Joker108]

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

In Termux, in a Debian proot chroot, I have been having issues with conda. As a result, I have learnt a lot about conda, especially how to keep an install in good health, which I didn't know before. I have tried both miniconda3 and miniforge3. I settled on miniforge3 and I have systematically resolved all issues except for:

(base) root•~» conda update conda                                                          [20:06:17]
Channels:
 - conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): done
Solving environment: done

# All requested packages already installed.

(base) root•~» conda update --all                                                          [20:07:05]
Channels:
 - conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): done
Solving environment: done

# All requested packages already installed.

(base) root•~» conda doctor                                                                [20:07:22]
Environment Health Report for: /root/miniforge3

❌ Altered Files:

python-3.12.7-h5d932e8_0_cpython: 1

✅ The environment is listed in the environments.txt file.

✅ There are no packages with missing files.

I have tried uninstalling all of conda and reinstalling. I have done that five times. Same error. I have tried doing a force reinstall of Python. It doesn't fix it. The curious thing, if I use conda to install a different version of Python, even in the new version, I get the same conda doctor error. Any help resolving this once and for all would be most appreciated.

Installed packages

(base) root•~» conda list                                                                  [20:12:27]
# packages in environment at /root/miniforge3:
#
# Name                    Version                   Build  Channel
_openmp_mutex             4.5                       2_gnu    conda-forge
archspec                  0.2.3              pyhd8ed1ab_0    conda-forge
boltons                   24.0.0             pyhd8ed1ab_0    conda-forge
brotli-python             1.1.0           py312h6f74592_2    conda-forge
bzip2                     1.0.8                h68df207_7    conda-forge
c-ares                    1.34.3               ha64f414_0    conda-forge
ca-certificates           2024.8.30            hcefe29a_0    conda-forge
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py312hac81daf_0    conda-forge
charset-normalizer        3.4.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
conda                     24.9.2          py312h996f985_0    conda-forge
conda-libmamba-solver     24.9.0             pyhd8ed1ab_0    conda-forge
conda-package-handling    2.4.0              pyh7900ff3_0    conda-forge
conda-package-streaming   0.11.0             pyhd8ed1ab_0    conda-forge
distro                    1.9.0              pyhd8ed1ab_0    conda-forge
fmt                       11.0.2               h70be974_0    conda-forge
frozendict                2.4.6           py312hb2c0f52_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       75.1                 hf9b3779_0    conda-forge
idna                      3.10               pyhd8ed1ab_0    conda-forge
jsonpatch                 1.33               pyhd8ed1ab_0    conda-forge
jsonpointer               3.0.0           py312h996f985_1    conda-forge
keyutils                  1.6.1                h4e544f5_0    conda-forge
krb5                      1.21.3               h50a48e9_0    conda-forge
ld_impl_linux-aarch64     2.43                 h80caac9_2    conda-forge
libarchive                3.7.4                h2c0effa_0    conda-forge
libcurl                   8.10.1               h3ec0cbf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h31becfc_2    conda-forge
libexpat                  2.6.4                h5ad3122_0    conda-forge
libffi                    3.4.2                h3557bc0_5    conda-forge
libgcc                    14.2.0               he277a41_1    conda-forge
libgcc-ng                 14.2.0               he9431aa_1    conda-forge
libgomp                   14.2.0               he277a41_1    conda-forge
libiconv                  1.17                 h31becfc_2    conda-forge
libmamba                  1.5.10               h489cd8b_1    conda-forge
libmambapy                1.5.10          py312h33c3f33_1    conda-forge
libnghttp2                1.64.0               hc8609a4_0    conda-forge
libnsl                    2.0.1                h31becfc_0    conda-forge
libsolv                   0.7.30               h62756fc_0    conda-forge
libsqlite                 3.47.0               hc4a20ef_1    conda-forge
libssh2                   1.11.0               h492db2e_0    conda-forge
libstdcxx                 14.2.0               h3f4de04_1    conda-forge
libstdcxx-ng              14.2.0               hf1166c9_1    conda-forge
libuuid                   2.38.1               hb4cce97_0    conda-forge
libxcrypt                 4.4.36               h31becfc_1    conda-forge
libxml2                   2.13.4               hf4efe5d_2    conda-forge
libzlib                   1.3.1                h86ecc28_2    conda-forge
lz4-c                     1.9.4                hd600fc2_0    conda-forge
lzo                       2.10              h31becfc_1001    conda-forge
mamba                     1.5.10          py312hd80a4d2_1    conda-forge
menuinst                  2.2.0           py312h996f985_0    conda-forge
ncurses                   6.5                  hcccb83c_1    conda-forge
openssl                   3.4.0                h86ecc28_0    conda-forge
packaging                 24.2               pyhd8ed1ab_0    conda-forge
pip                       24.3.1             pyh8b19718_0    conda-forge
platformdirs              4.3.6              pyhd8ed1ab_0    conda-forge
pluggy                    1.5.0              pyhd8ed1ab_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.6           py312hdd3e373_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.12.7          h5d932e8_0_cpython    conda-forge
python_abi                3.12                    5_cp312    conda-forge
readline                  8.2                  h8fc344f_1    conda-forge
reproc                    14.2.4.post0         h31becfc_1    conda-forge
reproc-cpp                14.2.4.post0         h2f0025b_1    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.18.6          py312hb2c0f52_1    conda-forge
ruamel.yaml.clib          0.2.8           py312hb2c0f52_1    conda-forge
setuptools                75.3.0             pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h194ca79_0    conda-forge
tqdm                      4.67.0             pyhd8ed1ab_0    conda-forge
truststore                0.10.0             pyhd8ed1ab_0    conda-forge
tzdata                    2024b                hc8b5060_0    conda-forge
urllib3                   2.2.3              pyhd8ed1ab_0    conda-forge
wheel                     0.45.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h9cdd2b7_0    conda-forge
yaml-cpp                  0.8.0                h2f0025b_0    conda-forge
zstandard                 0.23.0          py312hb698573_1    conda-forge
zstd                      1.5.6                h02f22dd_0    conda-forge

Environment info

(base) root•~» conda info                                                                  [20:13:40]

     active environment : base
    active env location : /root/miniforge3
            shell level : 1
       user config file : /root/.condarc
 populated config files : /root/miniforge3/.condarc
          conda version : 24.9.2
    conda-build version : not installed
         python version : 3.12.7.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=neoverse_n1
                          __conda=24.9.2=0
                          __glibc=2.36=0
                          __linux=6.2.1=0
                          __unix=0=0
       base environment : /root/miniforge3  (writable)
      conda av data dir : /root/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-aarch64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /root/miniforge3/pkgs
                          /root/.conda/pkgs
       envs directories : /root/miniforge3/envs
                          /root/.conda/envs
               platform : linux-aarch64
             user-agent : conda/24.9.2 requests/2.32.3 CPython/3.12.7 Linux/6.2.1-PRoot-Distro debian/12.8 glibc/2.36 solver/libmamba conda-libmamba-solver/24.9.0 libmambapy/1.5.10
                UID:GID : 0:0
             netrc file : None
           offline mode : False

[b9Joker108]

I have found the forum, which is prolly a more appropriate place for this issue than in the repo. But, I have left this issue open until I am in receipt of assistance on the forum:

https://conda-forge.zulipchat.com/#narrow/channel/457337-general/topic/Conda.20Doctor.20Altered.20File.3A.20Python.20-.20Can't.20Fix

If and when the situation is resolved, I will remember to close this issue.

[b9Joker108]

It was determined in the forum that this is a minor inoffensive packaging bug, as another forum member had the direct analogue of the doctor notification in their Anaconda base environment

[jakirkham]

From that thread this is the file changed:

(base) ~ conda doctor -v
Environment Health Report for: /root/miniforge3

❌ Altered Files:

python-3.12.7-h5d932e8_0_cpython:
  lib/python3.12/__pycache__/_sysconfigdata__linux_aarch64-linux-gnu.cpython-312.pyc

✅ The environment is listed in the environments.txt file.

✅ There are no packages with missing files.

[jakirkham]

Moving to the python feedstock as that is the package that has the modified file