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Setting 'alias conda="/path/to/miniconda3/bin/conda"' before conda initialized breaks conda #12885

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mulroony opened this issue Jul 13, 2023 · 2 comments
Open
2 tasks done

Setting 'alias conda="/path/to/miniconda3/bin/conda"' before conda initialized breaks conda #12885

mulroony opened this issue Jul 13, 2023 · 2 comments
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severity::4 low; functionality is inconvenient source::community catch-all for issues filed by community members type::bug describes erroneous operation, use severity::* to classify the type

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@mulroony
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mulroony commented Jul 13, 2023 •
edited

Checklist

  • I added a descriptive title
  • I searched open reports and couldn't find a duplicate

What happened?

In bash, haven't tested other shells, if in your .bashrc or .bash_profile before the conda initialize code block you add alias conda="/path/to/miniconda3/bin/conda" it breaks conda. It appears to create a loop that injects '/path/to/miniconda3/bin' over and over into your PATH variable. Tested with a couple different versions of conda on both Mac & Linux and it does the same thing.

For example if in my ~/.bashrc I change it from...

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/pmulrooney/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/pmulrooney/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/home/pmulrooney/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/pmulrooney/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

To...

alias conda="/home/pmulrooney/miniconda3/bin/conda"

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/pmulrooney/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/pmulrooney/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/home/pmulrooney/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/pmulrooney/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

Then launch a new shell. Running echo $PATH will show the repeat injection and conda will be very slow if it works at all.

Conda Info

$ conda info

     active environment : base
    active env location : /home/pmulrooney/miniconda3
            shell level : 1
       user config file : /home/pmulrooney/.condarc
 populated config files : /home/pmulrooney/.condarc
          conda version : 23.3.1
    conda-build version : not installed
         python version : 3.9.7.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.17=0
                          __linux=3.10.0=0
                          __unix=0=0
       base environment : /home/pmulrooney/miniconda3  (writable)
      conda av data dir : /home/pmulrooney/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 : /tmp/pmulrooney/pkgs
                          /home/pmulrooney/miniconda3/pkgs
       envs directories : /home/pmulrooney/miniconda3/envs
                          /home/pmulrooney/.conda/envs
               platform : linux-64
             user-agent : conda/23.3.1 requests/2.27.1 CPython/3.9.7 Linux/3.10.0-1160.92.1.el7.x86_64 rhel/7.9 glibc/2.17
                UID:GID : 927813:10050003
             netrc file : None
           offline mode : False

Conda Config

$ conda config --show-sources
==> /home/pmulrooney/.condarc <==
allow_conda_downgrades: True
default_threads: 12
pkgs_dirs:
  - /tmp/pmulrooney/pkgs
  - /home/pmulrooney/miniconda3/pkgs
ssl_verify: True
channels:
  - defaults

Conda list

$ conda list --show-channel-urls
# packages in environment at /home/pmulrooney/miniconda3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
bash-completion           2.11                          0    conda-forge
boltons                   23.0.0           py39h06a4308_0    defaults
brotlipy                  0.7.0           py39h27cfd23_1003    defaults
bzip2                     1.0.8                h7b6447c_0    defaults
c-ares                    1.18.1               h7f8727e_0    defaults
ca-certificates           2022.12.7            ha878542_0    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.0           py39hd667e15_1    defaults
chardet                   4.0.0           py39h06a4308_1003    defaults
charset-normalizer        2.0.4              pyhd3eb1b0_0    defaults
conda                     23.3.1           py39hf3d152e_0    conda-forge
conda-bash-completion     1.5                           1    conda-forge
conda-package-handling    1.7.3            py39h27cfd23_1    defaults
cryptography              36.0.0           py39h9ce1e76_0    defaults
curl                      7.80.0               h7f8727e_0    defaults
icu                       68.1                 h2531618_0    defaults
idna                      3.3                pyhd3eb1b0_0    defaults
jq                        1.6               h27cfd23_1000    defaults
jsonpatch                 1.32               pyhd3eb1b0_0    defaults
jsonpointer               2.1                pyhd3eb1b0_0    defaults
krb5                      1.19.2               hcc1bbae_0    conda-forge
ld_impl_linux-64          2.35.1               h7274673_9    defaults
libarchive                3.5.2                hccf745f_1    conda-forge
libcurl                   7.80.0               h0b77cf5_0    defaults
libedit                   3.1.20210910         h7f8727e_0    defaults
libev                     4.33                 h7f8727e_1    defaults
libffi                    3.3                  he6710b0_2    defaults
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libmamba                  0.19.1               h3985d26_0    conda-forge
libmambapy                0.19.1           py39h8bfa403_0    conda-forge
libnghttp2                1.46.0               hce63b2e_0    defaults
libsolv                   0.7.19               h780b84a_5    conda-forge
libssh2                   1.9.0                h1ba5d50_1    defaults
libstdcxx-ng              11.2.0              he4da1e4_11    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
llvm-openmp               12.0.1               h4bd325d_1    conda-forge
lz4-c                     1.9.3                h295c915_1    defaults
lzo                       2.10                 h7b6447c_2    defaults
mamba                     0.19.1           py39hfa8f2c8_0    conda-forge
mamba-bash-completion     1.0                  ha770c72_0    conda-forge
micromamba                1.4.2                         1    conda-forge
ncdu                      1.16                 h46c0cb4_0    conda-forge
ncurses                   6.3                  h7f8727e_2    defaults
oniguruma                 6.9.7.1              h27cfd23_0    defaults
openssl                   1.1.1t               h0b41bf4_0    conda-forge
packaging                 23.0             py39h06a4308_0    defaults
pip                       21.2.4           py39h06a4308_0    defaults
pluggy                    1.0.0            py39h06a4308_1    defaults
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.3            py39h27cfd23_0    defaults
pycparser                 2.21               pyhd3eb1b0_0    defaults
pyopenssl                 21.0.0             pyhd3eb1b0_1    defaults
pysocks                   1.7.1            py39h06a4308_0    defaults
python                    3.9.7                h12debd9_1    defaults
python_abi                3.9                      2_cp39    conda-forge
readline                  8.1.2                h7f8727e_1    defaults
reproc                    14.2.3               h7f98852_0    conda-forge
reproc-cpp                14.2.3               h9c3ff4c_0    conda-forge
requests                  2.27.1             pyhd3eb1b0_0    defaults
ruamel.yaml               0.17.21          py39h5eee18b_0    defaults
ruamel.yaml.clib          0.2.6            py39h5eee18b_1    defaults
ruamel_yaml               0.15.100         py39h27cfd23_0    defaults
setuptools                58.0.4           py39h06a4308_0    defaults
six                       1.16.0             pyhd3eb1b0_0    defaults
sqlite                    3.37.0               hc218d9a_0    defaults
tk                        8.6.11               h1ccaba5_0    defaults
toolz                     0.12.0           py39h06a4308_0    defaults
tqdm                      4.62.3             pyhd3eb1b0_1    defaults
tzdata                    2021e                hda174b7_0    defaults
urllib3                   1.26.7             pyhd3eb1b0_0    defaults
wheel                     0.37.1             pyhd3eb1b0_0    defaults
xz                        5.2.5                h7b6447c_0    defaults
yaml                      0.2.5                h7b6447c_0    defaults
yaml-cpp                  0.6.3                he1b5a44_4    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstd                      1.5.0                ha4553b6_1    defaults

Additional Context

No response
@mulroony mulroony added the type::bug describes erroneous operation, use severity::* to classify the type label Jul 13, 2023
@travishathaway
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Hi @mulroony,

Thanks for reporting this. This is definitely good information to know, but I also think this is a pretty low priority bug given the work around is relatively straightforward and simple.

I'll be happy to leave this bug issue open though if others want to chime in, but I would not expect that the maintainers would get around to working on this anytime soon given our current workload.

@travishathaway travishathaway added source::community catch-all for issues filed by community members severity::4 low; functionality is inconvenient labels Jul 18, 2023
@mulroony
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@travishathaway Completely understand. Figured I would report and see if it was an easy check / fix for someone that knows the code base better than I do.

@beeankha beeankha changed the title Setting 'alias conda="/path/to/miniconda3/bin/conda"' before conda initialized breaks conda Setting 'alias conda="/path/to/miniconda3/bin/conda"' before conda initialized breaks conda Jul 21, 2023
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severity::4 low; functionality is inconvenient source::community catch-all for issues filed by community members type::bug describes erroneous operation, use severity::* to classify the type
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