Missing "commands" and other plugins at starts

giammi56 · November 19, 2022, 12:05pm

Hi all,
I just compiled from source the Openchemistry suite on a Ubuntu 20.04 x86 64bit machine.
Running avogadro2 from terminal I get the following error:

qt5ct: using qt5ct plugin
Using locale:  "en_US"
Extension plugins dynamically found… 46
OBProcess::executeObabel: Running "obabel" "-L formats read"
OBProcess::executeObabel: Running "obabel" "-L formats write"
OBProcess::executeObabel: Running "obabel" "-L forcefields"
OBProcess::executeObabel: Running "obabel" "-L charges"
OBProcess::executeObabel: Running "obabel" "-V"
"obabel"  found:  "obabel: Open Babel 3.0.0 -- Mar 11 2020 -- 11:52:36"
Checking for  "commands"  scripts in "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/share/ubuntu/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/home/giammi56/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/local/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/home/giammi56/Documents/openchemistry-build/avogadroapp/bin/../lib/avogadro2/scripts/commands"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-build-ase/mx2.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-build-ase/mx2.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-build-ase/mx2.py\", line 14, in <module>\n    import ase.io\nModuleNotFoundError: No module named 'ase'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-build-ase/ribbon.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-build-ase/ribbon.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-build-ase/ribbon.py\", line 14, in <module>\n    import ase.io\nModuleNotFoundError: No module named 'ase'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/centroid.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/centroid.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nAdd Centroid for Selection\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/centroid.py\", line 86, in <module>\n    elif args['run_workflow']:\nKeyError: 'run_workflow'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/scale.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/scale.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nScale Coords...\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/scale.py\", line 92, in <module>\n    elif args['run_workflow']:\nKeyError: 'run_workflow'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-genice/genice.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-genice/genice.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-genice/genice.py\", line 10, in <module>\n    from genice2.genice import GenIce\nModuleNotFoundError: No module named 'genice2'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/etkdg.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/etkdg.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\n/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/etkdg.py:41: SyntaxWarning: \"is\" with a literal. Did you mean \"==\"?\n  if opts['ff'] is 'UFF':\n/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/etkdg.py:43: SyntaxWarning: \"is\" with a literal. Did you mean \"==\"?\n  elif opts['ff'] is 'MMFF94':\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/etkdg.py\", line 13, in <module>\n    from rdkit import Chem\nModuleNotFoundError: No module named 'rdkit'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/uff.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/uff.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/uff.py\", line 9, in <module>\n    from rdkit import Chem\nModuleNotFoundError: No module named 'rdkit'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/mmff94.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/mmff94.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/mmff94.py\", line 9, in <module>\n    from rdkit import Chem\nModuleNotFoundError: No module named 'rdkit'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/tautomer.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/tautomer.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-rdkit/tautomer.py\", line 9, in <module>\n    from rdkit import Chem\nModuleNotFoundError: No module named 'rdkit'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-scikit-nano/swnt.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-scikit-nano/swnt.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-scikit-nano/swnt.py\", line 14, in <module>\n    from sknano.generators import SWNTGenerator\nModuleNotFoundError: No module named 'sknano'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-scikit-nano/mwnt.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-scikit-nano/mwnt.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-scikit-nano/mwnt.py\", line 13, in <module>\n    from sknano.generators import MWNTGenerator\nModuleNotFoundError: No module named 'sknano'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/add_chassis.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/add_chassis.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/add_chassis.py\", line 12, in <module>\n    from angstrom import Molecule\nModuleNotFoundError: No module named 'angstrom'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/connect_wheel.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/connect_wheel.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/connect_wheel.py\", line 12, in <module>\n    from angstrom import Molecule\nModuleNotFoundError: No module named 'angstrom'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/lammps_setup.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/lammps_setup.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/lammps_setup.py\", line 13, in <module>\n    from angstrom import Molecule\nModuleNotFoundError: No module named 'angstrom'\n"
Checking for  "inputGenerators"  scripts in "/home/giammi56/.local/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/share/ubuntu/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/home/giammi56/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/local/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/home/giammi56/Documents/openchemistry-build/avogadroapp/bin/../lib/avogadro2/scripts/inputGenerators"
Checking for  "formatScripts"  scripts in "/home/giammi56/.local/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/share/ubuntu/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/home/giammi56/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/local/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/home/giammi56/Documents/openchemistry-build/avogadroapp/bin/../lib/avogadro2/scripts/formatScripts"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/formatScripts/avogadro-cclib/cclibScript.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/formatScripts/avogadro-cclib/cclibScript.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/formatScripts/avogadro-cclib/cclibScript.py\", line 20, in <module>\n    import cclib\nModuleNotFoundError: No module named 'cclib'\n"
Checking for  "charges"  scripts in "/home/giammi56/.local/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/usr/share/ubuntu/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/home/giammi56/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/usr/local/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/usr/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/home/giammi56/Documents/openchemistry-build/avogadroapp/bin/../lib/avogadro2/scripts/charges"
qt5ct: D-Bus global menu: no
Open Babel formats ready:  145

any idea how to fix it?
Maybe another clue: when started from .desktop icon, the app is not shown on the dock and doesn´t close properly upon exiting (i.e., the process keep running, although the GUI is closed).

ghutchis · November 19, 2022, 5:32pm

There’s no particular problem. You have installed a bunch of Python extensions, but not the relevant Python libraries (e.g., rdkit, genice, etc.).

If you want to use those scripts, you’ll need to install the appropriate packages, e.g.

pip3 install rdkit
pip3 install ase

giammi56 · November 21, 2022, 5:09pm

Thank you,
after installing rdkit, scikit-nano and ase I get a cleaner out put:

qt5ct: using qt5ct plugin
Using locale:  "en_US"
Extension plugins dynamically found… 46
OBProcess::executeObabel: Running "obabel" "-L formats read"
OBProcess::executeObabel: Running "obabel" "-L formats write"
OBProcess::executeObabel: Running "obabel" "-L forcefields"
OBProcess::executeObabel: Running "obabel" "-L charges"
OBProcess::executeObabel: Running "obabel" "-V"
"obabel"  found:  "obabel: Open Babel 3.0.0 -- Mar 11 2020 -- 11:52:36"
Checking for  "commands"  scripts in "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/share/ubuntu/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/home/giammi56/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/local/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/home/giammi56/Documents/openchemistry-build/avogadroapp/bin/../lib/avogadro2/scripts/commands"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/centroid.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/centroid.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nAdd Centroid for Selection\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/centroid.py\", line 86, in <module>\n    elif args['run_workflow']:\nKeyError: 'run_workflow'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/scale.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/scale.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nScale Coords...\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-commands/scale.py\", line 92, in <module>\n    elif args['run_workflow']:\nKeyError: 'run_workflow'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-genice/genice.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-genice/genice.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/avogadro-genice/genice.py\", line 10, in <module>\n    from genice2.genice import GenIce\nModuleNotFoundError: No module named 'genice2'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/add_chassis.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/add_chassis.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/add_chassis.py\", line 12, in <module>\n    from angstrom import Molecule\nModuleNotFoundError: No module named 'angstrom'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/connect_wheel.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/connect_wheel.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/connect_wheel.py\", line 12, in <module>\n    from angstrom import Molecule\nModuleNotFoundError: No module named 'angstrom'\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/lammps_setup.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/lammps_setup.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/commands/nanocar-avogadro/lammps_setup.py\", line 13, in <module>\n    from angstrom import Molecule\nModuleNotFoundError: No module named 'angstrom'\n"
Checking for  "inputGenerators"  scripts in "/home/giammi56/.local/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/share/ubuntu/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/home/giammi56/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/local/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/home/giammi56/Documents/openchemistry-build/avogadroapp/bin/../lib/avogadro2/scripts/inputGenerators"
Checking for  "formatScripts"  scripts in "/home/giammi56/.local/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/share/ubuntu/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/home/giammi56/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/local/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/home/giammi56/Documents/openchemistry-build/avogadroapp/bin/../lib/avogadro2/scripts/formatScripts"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/home/giammi56/.local/share/OpenChemistry/Avogadro/formatScripts/avogadro-cclib/cclibScript.py" ; "Error running script '/usr/bin/python3 /home/giammi56/.local/share/OpenChemistry/Avogadro/formatScripts/avogadro-cclib/cclibScript.py --display-name --lang en_US': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/home/giammi56/.local/share/OpenChemistry/Avogadro/formatScripts/avogadro-cclib/cclibScript.py\", line 20, in <module>\n    import cclib\nModuleNotFoundError: No module named 'cclib'\n"
Checking for  "charges"  scripts in "/home/giammi56/.local/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/usr/share/ubuntu/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/home/giammi56/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/usr/local/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/usr/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/home/giammi56/Documents/openchemistry-build/avogadroapp/bin/../lib/avogadro2/scripts/charges"
qt5ct: D-Bus global menu: no
Error starting RPC server: "QLocalServer::listen: Address in use"
Starting new server.
Open Babel formats ready:  145

but, due to what appears to be a coding error inside rdkit, I get this interesting effect on the top menu bar:

it is reversible upon uninstalling rdkit.