search

conda-forge / vmd-feedstock

A conda-smithy repository for vmd.
BSD 3-Clause "New" or "Revised" License
1 stars 2 forks source link

VMD breaks jupyter notebooks due to clobber with sqlite3 #4

Open RubenChM opened 1 day ago

RubenChM commented 1 day ago

Solution to issue cannot be found in the documentation.

Issue

After installing vmd in an enviroment with jupyter, the notebooks stop working due to a shared path. This warning is shown when installing with conda create -n test2 -c conda-forge vmd jupyter:

ClobberWarning: This transaction has incompatible packages due to a shared path.                                                                      
  packages: conda-forge/linux-64::libsqlite-3.47.0-hadc24fc_1, conda-forge/linux-64::vmd-1.9.3-hf484d3e_1                                             
  path: 'lib/libsqlite3.so.0'                                                                                                                         

ClobberWarning: Conda was asked to clobber an existing path.                                                                                          
  source path: /home/rchaves/miniforge3/pkgs/vmd-1.9.3-hf484d3e_1/lib/libsqlite3.so.0                                                                 
  target path: /home/rchaves/miniforge3/envs/test2/lib/libsqlite3.so.0

And this one when trying to launch jupyter notebook:

/home/rchaves/miniforge3/envs/test2/bin/jupyter-notebook:6: DeprecationWarning: Parsing dates involving a day of month without a year specified is ambiguious
and fails to parse leap day. The default behavior will change in Python 3.15
to either always raise an exception or to use a different default year (TBD).
To avoid trouble, add a specific year to the input & format.
See https://github.com/python/cpython/issues/70647.
  from notebook.notebookapp import main
Traceback (most recent call last):
  File "/home/rchaves/miniforge3/envs/test2/lib/python3.13/site-packages/notebook/services/sessions/sessionmanager.py", line 9, in <module>
    import sqlite3
  File "/home/rchaves/miniforge3/envs/test2/lib/python3.13/sqlite3/__init__.py", line 57, in <module>
    from sqlite3.dbapi2 import *
  File "/home/rchaves/miniforge3/envs/test2/lib/python3.13/sqlite3/dbapi2.py", line 27, in <module>
    from _sqlite3 import *
ImportError: /home/rchaves/miniforge3/envs/test2/lib/python3.13/lib-dynload/_sqlite3.cpython-313-x86_64-linux-gnu.so: undefined symbol: sqlite3_trace_v2

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/rchaves/miniforge3/envs/test2/bin/jupyter-notebook", line 6, in <module>
    from notebook.notebookapp import main
  File "/home/rchaves/miniforge3/envs/test2/lib/python3.13/site-packages/notebook/notebookapp.py", line 83, in <module>
    from .services.sessions.sessionmanager import SessionManager
  File "/home/rchaves/miniforge3/envs/test2/lib/python3.13/site-packages/notebook/services/sessions/sessionmanager.py", line 12, in <module>
    from pysqlite2 import dbapi2 as sqlite3
ModuleNotFoundError: No module named 'pysqlite2'

Jupyter notebooks can be launch again after using conda install libsqlite --force-reinstall.

Installed packages

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anyio                     4.6.2.post1        pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py313h536fd9c_5    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                     24.2.0             pyh71513ae_0    conda-forge
babel                     2.16.0             pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
bleach                    6.2.0              pyhd8ed1ab_0    conda-forge
brotli-python             1.1.0           py313h46c70d0_2    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
ca-certificates           2024.8.30            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py313hfab6e84_0    conda-forge
charset-normalizer        3.4.0              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
debugpy                   1.8.9           py313h46c70d0_0    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            1.2.2              pyhd8ed1ab_0    conda-forge
executing                 2.1.0              pyhd8ed1ab_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.7              pyh29332c3_1    conda-forge
httpx                     0.27.2             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
idna                      3.10               pyhd8ed1ab_0    conda-forge
importlib-metadata        8.5.0              pyha770c72_0    conda-forge
importlib_resources       6.4.5              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.5             pyh3099207_0    conda-forge
ipython                   8.29.0             pyh707e725_0    conda-forge
ipython_genutils          0.2.0              pyhd8ed1ab_1    conda-forge
ipywidgets                8.1.5              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.2             pyhff2d567_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
json5                     0.10.0             pyhd8ed1ab_0    conda-forge
jsonpointer               3.0.0           py313h78bf25f_1    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2024.10.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.23.0               hd8ed1ab_0    conda-forge
jupyter                   1.1.1              pyhd8ed1ab_0    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
jupyter_client            7.4.9              pyhd8ed1ab_0    conda-forge
jupyter_console           6.6.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2              pyh31011fe_1    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.14.2             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.3.1              pyhff2d567_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.27.3             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.13             pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
ld_impl_linux-64          2.43                 h712a8e2_2    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libexpat                  2.6.4                h5888daf_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc                    14.2.0               h77fa898_1    conda-forge
libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgomp                   14.2.0               h77fa898_1    conda-forge
libmpdec                  4.0.0                h4bc722e_0    conda-forge
libsodium                 1.0.20               h4ab18f5_0    conda-forge
libsqlite                 3.47.0               hadc24fc_1    conda-forge
libstdcxx                 14.2.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              14.2.0               h4852527_1    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcb                    1.17.0               h8a09558_0    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    conda-forge
markupsafe                3.0.2           py313h8060acc_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
nbclassic                 1.1.0              pyhd8ed1ab_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.5                  he02047a_1    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
notebook                  6.5.7              pyha770c72_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
openssl                   3.4.0                hb9d3cd8_0    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.2               pyhff2d567_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       24.3.1             pyh145f28c_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.3.6              pyhd8ed1ab_0    conda-forge
prometheus_client         0.21.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.48             pyha770c72_0    conda-forge
prompt_toolkit            3.0.48               hd8ed1ab_0    conda-forge
psutil                    6.1.0           py313h536fd9c_0    conda-forge
pthread-stubs             0.4               hb9d3cd8_1002    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.13.0          h9ebbce0_101_cp313    conda-forge
python-dateutil           2.9.0.post0        pyhff2d567_0    conda-forge
python-fastjsonschema     2.20.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.13                    5_cp313    conda-forge
pytz                      2024.2             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.2           py313h536fd9c_1    conda-forge
pyzmq                     26.2.0          py313h8e95178_3    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.21.0          py313h920b4c0_0    conda-forge
send2trash                1.8.3              pyh0d859eb_0    conda-forge
setuptools                75.6.0             pyhff2d567_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
terminado                 0.18.1             pyh0d859eb_0    conda-forge
tinycss2                  1.4.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.1.0              pyhff2d567_0    conda-forge
tornado                   6.4.2           py313h536fd9c_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20241003     pyhff2d567_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024b                hc8b5060_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.3              pyhd8ed1ab_0    conda-forge
vmd                       1.9.3                hf484d3e_1    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.8.0             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.13             pyhd8ed1ab_0    conda-forge
xorg-libx11               1.8.10               h4f16b4b_0    conda-forge
xorg-libxau               1.0.11               hb9d3cd8_1    conda-forge
xorg-libxdmcp             1.1.5                hb9d3cd8_0    conda-forge
xorg-libxext              1.3.6                hb9d3cd8_0    conda-forge
xorg-libxfixes            6.0.1                hb9d3cd8_0    conda-forge
xorg-libxi                1.8.2                hb9d3cd8_0    conda-forge
xorg-libxinerama          1.1.5                h5888daf_1    conda-forge
xorg-xorgproto            2024.1               hb9d3cd8_1    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.5                h3b0a872_7    conda-forge
zipp                      3.21.0             pyhd8ed1ab_0    conda-forge
zstandard                 0.23.0          py313h80202fe_1    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

Environment info

active environment : test2
    active env location : /home/rchaves/miniforge3/envs/test2
            shell level : 1
       user config file : /home/rchaves/.condarc
 populated config files : /home/rchaves/miniforge3/.condarc
                          /home/rchaves/.condarc
          conda version : 24.11.0
    conda-build version : not installed
         python version : 3.12.5.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=skylake
                          __conda=24.11.0=0
                          __glibc=2.35=0
                          __linux=6.8.0=0
                          __unix=0=0
       base environment : /home/rchaves/miniforge3  (writable)
      conda av data dir : /home/rchaves/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/rchaves/miniforge3/pkgs
                          /home/rchaves/.conda/pkgs
       envs directories : /home/rchaves/miniforge3/envs
                          /home/rchaves/.conda/envs
               platform : linux-64
             user-agent : conda/24.11.0 requests/2.32.3 CPython/3.12.5 Linux/6.8.0-48-generic ubuntu/22.04.5 glibc/2.35 solver/libmamba conda-libmamba-solver/24.7.0 libmambapy/1.5.9
                UID:GID : 17871:500
             netrc file : None
           offline mode : False
njzjz commented 1 day ago

To resolve the issue, the package has to be built from source instead of using a pre-built package. But it seems very hard, though.