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).