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Error while loading conda entry point: conda-libmamba-solver (libarchive.so.10: cannot open shared object file: No such file or directory) #424

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wjhlang opened this issue Jan 16, 2024 · 5 comments
Closed
2 tasks done

Error while loading conda entry point: conda-libmamba-solver (libarchive.so.10: cannot open shared object file: No such file or directory) #424

wjhlang opened this issue Jan 16, 2024 · 5 comments
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type::bug describes erroneous operation, use severity::* to classify the type

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@wjhlang
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wjhlang commented Jan 16, 2024 •
edited

Checklist

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

What happened?

I was trying to install libmamba to overcome the slow-solving time problem caused by conda-forge. I was initially following this post, without updating the conda version (was previously 23.5.0). I first installed libmamba under my own environment conda install conda-libmamba-solver then conda config --set solver libmamba. After finishing the installation, trying to install another package yields

CondaValueError: You have chosen a non-default solver backend (libmamba) but it was not recognized. Choose one of: classic

I then thought maybe I needed to follow the exact prompt so I did conda install -n base conda-libmamba-solver.

Now this is causing me trouble: every command I make with conda yields:

Error while loading conda entry point: conda-libmamba-solver (libarchive.so.10: cannot open shared object file: No such file or directory).

Installing packages still gives, even i have already set my solver back to classic:

CondaValueError: You have chosen a non-default solver backend (libmamba) but it was not recognized. Choose one of: classic

I have tried reinstalling conda-libmamba-solver, installing libarchive according to this post by conda install -n base libarchive -c main --force-reinstall.
I have also tried removing conda-libmamba-solver, yields:

RemoveError: This operation will remove conda without replacing it with another version of conda.

Nothing helps.
A way to fix this could be appreciated!

Conda Info

Error while loading conda entry point: conda-libmamba-solver (libarchive.so.19: cannot open shared object file: No such file or directory)                      
                                                                                
     active environment : b529
    active env location : /home/wjhlang/miniconda3/envs/b529
            shell level : 1
       user config file : /home/wjhlang/.condarc
 populated config files : /home/wjhlang/.condarc
          conda version : 23.11.0
    conda-build version : not installed
         python version : 3.9.16.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=skylake_avx512
                          __conda=23.11.0=0
                          __glibc=2.28=0
                          __linux=4.18.0=0
                          __unix=0=0
       base environment : /home/wjhlang/miniconda3  (writable)
      conda av data dir : /home/wjhlang/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          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 : /home/wjhlang/miniconda3/pkgs
                          /home/wjhlang/.conda/pkgs
       envs directories : /home/wjhlang/miniconda3/envs
                          /home/wjhlang/.conda/envs
               platform : linux-64
             user-agent : conda/23.11.0 requests/2.31.0 CPython/3.9.16 Linux/4.18.0-372.75.1.el8_6.x86_64 rhel/8.6 glibc/2.28 solver/libmamba
                UID:GID : 114273152:114273152
             netrc file : None
           offline mode : False

Conda Config

Error while loading conda entry point: conda-libmamba-solver (libarchive.so.19: cannot open shared object file: No such file or directory)
==> /home/wjhlang/.condarc <==
auto_activate_base: False
channels:
  - bioconda
  - defaults
always_yes: True
solver: classic


conda config --show-sources
Error while loading conda entry point: conda-libmamba-solver (libarchive.so.19: cannot open shared object file: No such file or directory)
==> /home/wjhlang/.condarc <==
auto_activate_base: False
channels:
  - bioconda
  - defaults
always_yes: True
solver: classic

Conda list

Error while loading conda entry point: conda-libmamba-solver (libarchive.so.19: cannot open shared object file: No such file or directory)
# packages in environment at /home/wjhlang/miniconda3/envs/b529:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anyio                     4.2.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39hd1e30aa_4    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
attrs                     23.2.0             pyh71513ae_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
brotli                    1.1.0                hd590300_1    conda-forge
brotli-bin                1.1.0                hd590300_1    conda-forge
brotli-python             1.1.0            py39h3d6467e_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
ca-certificates           2023.11.17           hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2023.11.17         pyhd8ed1ab_0    conda-forge
cffi                      1.16.0           py39h7a31438_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
comm                      0.2.1              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.0            py39h7633fee_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
dbus                      1.13.18              hb2f20db_0    defaults
debugpy                   1.8.0            py39h3d6467e_1    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.0              pyhd8ed1ab_0    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonttools                 4.47.0           py39hd1e30aa_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
giflib                    5.2.1                h0b41bf4_3    conda-forge
glib                      2.78.3               hfc55251_0    conda-forge
glib-tools                2.78.3               hfc55251_0    conda-forge
gmp                       6.3.0                h59595ed_0    conda-forge
gst-plugins-base          1.14.1               h6a678d5_1    defaults
gstreamer                 1.14.1               h5eee18b_1    defaults
icu                       58.2              hf484d3e_1000    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
importlib-metadata        7.0.1              pyha770c72_0    conda-forge
importlib-resources       6.1.1              pyhd8ed1ab_0    conda-forge
importlib_metadata        7.0.1                hd8ed1ab_0    conda-forge
importlib_resources       6.1.1              pyhd8ed1ab_0    conda-forge
ipykernel                 6.28.0             pyhd33586a_0    conda-forge
ipython                   8.12.0             pyh41d4057_0    conda-forge
ipywidgets                8.1.1              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
json5                     0.9.14             pyhd8ed1ab_0    conda-forge
jsonpointer               2.4              py39hf3d152e_3    conda-forge
jsonschema                4.20.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.20.0             pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0             pyhd8ed1ab_10    conda-forge
jupyter-lsp               2.2.1              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.0              pyhd8ed1ab_0    conda-forge
jupyter_console           6.6.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.1            py39hf3d152e_0    conda-forge
jupyter_events            0.9.0              pyhd8ed1ab_0    conda-forge
jupyter_server            2.12.3             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.1              pyhd8ed1ab_0    conda-forge
jupyterlab                4.0.10             pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.25.2             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.9              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5            py39h7633fee_1    conda-forge
krb5                      1.20.1               h81ceb04_0    conda-forge
lcms2                     2.12                 h3be6417_0    defaults
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      3.0                  h295c915_0    defaults
libblas                   3.9.0           20_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hd590300_1    conda-forge
libbrotlidec              1.1.0                hd590300_1    conda-forge
libbrotlienc              1.1.0                hd590300_1    conda-forge
libcblas                  3.9.0           20_linux64_openblas    conda-forge
libclang                  10.0.1          default_hb85057a_2    defaults
libdeflate                1.17                 h5eee18b_1    defaults
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_3    conda-forge
libgfortran-ng            13.2.0               h69a702a_3    conda-forge
libgfortran5              13.2.0               ha4646dd_3    conda-forge
libglib                   2.78.3               h783c2da_0    conda-forge
libgomp                   13.2.0               h807b86a_3    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
liblapack                 3.9.0           20_linux64_openblas    conda-forge
libllvm10                 10.0.1               he513fc3_3    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.25          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libpq                     12.15                hdbd6064_1    defaults
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.44.2               h2797004_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_3    conda-forge
libtiff                   4.5.1                h6a678d5_0    defaults
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp                   1.3.2                h11a3e52_0    defaults
libwebp-base              1.3.2                hd590300_0    conda-forge
libxcb                    1.16                 hd590300_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxkbcommon              1.0.1                hfa300c1_0    defaults
libxml2                   2.9.14               h74e7548_0    defaults
libzlib                   1.2.13               hd590300_5    conda-forge
markupsafe                2.1.3            py39hd1e30aa_1    conda-forge
matplotlib                3.8.2            py39hf3d152e_0    conda-forge
matplotlib-base           3.8.2            py39he9076e7_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge
nbconvert                 7.14.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.14.0             pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.14.0             pyhd8ed1ab_0    conda-forge
nbformat                  5.9.2              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
nest-asyncio              1.5.8              pyhd8ed1ab_0    conda-forge
notebook                  7.0.6              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
nspr                      4.35                 h27087fc_0    conda-forge
nss                       3.96                 h1d7d5a4_0    conda-forge
numpy                     1.26.3           py39h474f0d3_0    conda-forge
openjpeg                  2.5.0                hfec8fc6_2    conda-forge
openssl                   3.2.0                hd590300_1    conda-forge
overrides                 7.4.0              pyhd8ed1ab_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pandas                    2.1.4            py39hddac248_0    conda-forge
pandoc                    3.1.3                h32600fe_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.42                hcad00b1_0    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.0.1           py39ha6cbd5a_0    defaults
pip                       23.3.2             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.1.0              pyhd8ed1ab_0    conda-forge
ply                       3.11                       py_1    conda-forge
prometheus_client         0.19.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.42             pyha770c72_0    conda-forge
prompt_toolkit            3.0.42               hd8ed1ab_0    conda-forge
psutil                    5.9.7            py39hd1e30aa_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.17.2             pyhd8ed1ab_0    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.10          py39h6a678d5_0    defaults
pyqt5-sip                 12.13.0          py39h5eee18b_0    defaults
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.9.18          h0755675_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.19.1             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.4             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      4_cp39    conda-forge
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1            py39hd1e30aa_1    conda-forge
pyzmq                     25.1.2           py39h8c080ef_0    conda-forge
qt-main                   5.15.2               h327a75a_7    defaults
qtconsole-base            5.5.1              pyha770c72_0    conda-forge
qtpy                      2.4.1              pyhd8ed1ab_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.32.1             pyhd8ed1ab_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.16.2           py39h9fdd4d6_0    conda-forge
scipy                     1.11.4           py39h474f0d3_0    conda-forge
send2trash                1.8.2              pyh41d4057_0    conda-forge
setuptools                69.0.3             pyhd8ed1ab_0    conda-forge
sip                       6.7.12           py39h3d6467e_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sqlite                    3.44.2               h2c6b66d_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
terminado                 0.18.0             pyh0d859eb_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.3.3            py39hd1e30aa_1    conda-forge
traitlets                 5.14.1             pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.8.19.20240106    pyhd8ed1ab_0    conda-forge
typing-extensions         4.9.0                hd8ed1ab_0    conda-forge
typing_extensions         4.9.0              pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2023d                h0c530f3_0    conda-forge
unicodedata2              15.1.0           py39hd1e30aa_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.1.0              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.7.0              pyhd8ed1ab_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.9              pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xz                        5.4.5                h5eee18b_0    defaults
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.5                h59595ed_0    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Additional Context

No response
@wjhlang wjhlang added the type::bug describes erroneous operation, use severity::* to classify the type label Jan 16, 2024
@jaimergp
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You are experiencing one of the known issues, stemming from mixing defaults and conda-forge. See pinned issues for details.

@schymans
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schymans commented Feb 1, 2024

I had exactly the same problem. @jaimergp Could you point us to the pinned issue you had in mind and how to solve it?
Anyway, the solution for me was to install mamba from scratch, as described here and here:

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

@jaimergp
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jaimergp commented Feb 1, 2024

Yes, sorry. It's the first item at #283

@noahlibby17
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I'm also experiencing this issue where none of the conda commands are working now. Any tips to resolve it?

@wjhlang
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wjhlang commented Feb 16, 2024

I nuked my anaconda3/miniconda3 and started fresh, then updating conda to the newest version(24. something) solved it for me.

I'm also experiencing this issue where none of the conda commands are working now. Any tips to resolve it?

@wjhlang wjhlang closed this as completed Feb 16, 2024
@wjhlang wjhlang reopened this Feb 16, 2024
@wjhlang wjhlang closed this as completed Feb 16, 2024
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@jaimergp @schymans @noahlibby17 @wjhlang