Hello,
I have fresh nightly build of Avogadro and I tried to download all plugins. However, some downloads failed, and I am looking for a way to fix it. Please help…
Downloading avo_xtb.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/avo_xtb.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands/
Finished 42 files
Extraction successful
Downloading Turtle Molecule Builder.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/Turtle Molecule Builder.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands/
Finished 135 files
Extraction successful
Downloading nanocar-avogadro.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/nanocar-avogadro.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands/
Finished 84 files
Extraction successful
Defaulting to user installation because normal site-packages is not writeable
Collecting angstrom (from -r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//nanocar-avogadro/requirements.txt (line 4))
Cloning git://github.com/kbsezginel/angstrom (to revision master) to c:\users\miroi\appdata\local\temp\pip-install-awuvoow2\angstrom_948c6f5e3b234120b182e4533307203f
Running command git clone --filter=blob:none --quiet git://github.com/kbsezginel/angstrom 'C:\Users\miroi\AppData\Local\Temp\pip-install-awuvoow2\angstrom_948c6f5e3b234120b182e4533307203f'
fatal: unable to connect to github.com:
github.com[0: 140.82.121.4]: errno=Connection timed out
error: subprocess-exited-with-error
git clone --filter=blob:none --quiet git://github.com/kbsezginel/angstrom 'C:\Users\miroi\AppData\Local\Temp\pip-install-awuvoow2\angstrom_948c6f5e3b234120b182e4533307203f' did not run successfully.
exit code: 128
See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
[notice] A new release of pip is available: 24.3.1 -> 25.0.1
[notice] To update, run: C:\Users\miroi\AppData\Local\Microsoft\WindowsApps\PythonSoftwareFoundation.Python.3.12_qbz5n2kfra8p0\python.exe -m pip install --upgrade pip
error: subprocess-exited-with-error
git clone --filter=blob:none --quiet git://github.com/kbsezginel/angstrom 'C:\Users\miroi\AppData\Local\Temp\pip-install-awuvoow2\angstrom_948c6f5e3b234120b182e4533307203f' did not run successfully.
exit code: 128
See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
Downloading commands.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands/
Finished 6 files
Extraction successful
Defaulting to user installation because normal site-packages is not writeable
Collecting glyles==0.5.11 (from -r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Glycans_to_SMILES_script/requirements.txt (line 1))
Using cached glyles-0.5.11-py3-none-any.whl.metadata (5.3 kB)
Collecting antlr4-python3-runtime==4.9.3 (from glyles==0.5.11->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Glycans_to_SMILES_script/requirements.txt (line 1))
Using cached antlr4-python3-runtime-4.9.3.tar.gz (117 kB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting joblib<2.0.0,>=1.2.0 (from glyles==0.5.11->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Glycans_to_SMILES_script/requirements.txt (line 1))
Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
Collecting networkx>=2.6.3 (from glyles==0.5.11->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Glycans_to_SMILES_script/requirements.txt (line 1))
Using cached networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)
Collecting numpy<2.0.0,>=1.21.4 (from glyles==0.5.11->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Glycans_to_SMILES_script/requirements.txt (line 1))
Using cached numpy-1.26.4-cp312-cp312-win_amd64.whl.metadata (61 kB)
Collecting pydot<2.0.0,>=1.4.2 (from glyles==0.5.11->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Glycans_to_SMILES_script/requirements.txt (line 1))
Using cached pydot-1.4.2-py2.py3-none-any.whl.metadata (8.0 kB)
INFO: pip is looking at multiple versions of glyles to determine which version is compatible with other requirements. This could take a while.
ERROR: Ignored the following versions that require a different python version: 0.0.1 Requires-Python >=3.7,<3.11; 0.0.2 Requires-Python >=3.7,<3.11; 0.0.3 Requires-Python >=3.7,<3.11; 0.0.4 Requires-Python >=3.7,<3.11; 0.1.0 Requires-Python >=3.7,<3.11; 0.1.1 Requires-Python >=3.7,<3.11; 0.1.2 Requires-Python >=3.7,<3.11; 0.2.0 Requires-Python >=3.7,<3.11; 0.2.1 Requires-Python >=3.7,<3.11; 0.3.0 Requires-Python >=3.7,<3.11; 0.3.1 Requires-Python >=3.7,<3.11; 0.4.0 Requires-Python >=3.7,<3.11; 0.4.1 Requires-Python >=3.7,<3.11; 0.4.2 Requires-Python >=3.7,<3.11; 0.5.0 Requires-Python >=3.7,<3.11; 0.5.1 Requires-Python >=3.7,<3.11; 0.5.2 Requires-Python >=3.7,<3.11; 0.5.3 Requires-Python >=3.7,<3.11; 0.5.4 Requires-Python >=3.7,<3.11; 0.5.7 Requires-Python >=3.7,<3.11; 0.5.8 Requires-Python >=3.7,<3.11; 0.5.9 Requires-Python >=3.7,<3.11; 1.21.2 Requires-Python >=3.7,<3.11; 1.21.3 Requires-Python >=3.7,<3.11; 1.21.4 Requires-Python >=3.7,<3.11; 1.21.5 Requires-Python >=3.7,<3.11; 1.21.6 Requires-Python >=3.7,<3.11
ERROR: Could not find a version that satisfies the requirement rdkit-pypi>=2021.9.2 (from glyles) (from versions: none)
[notice] A new release of pip is available: 24.3.1 -> 25.0.1
[notice] To update, run: C:\Users\miroi\AppData\Local\Microsoft\WindowsApps\PythonSoftwareFoundation.Python.3.12_qbz5n2kfra8p0\python.exe -m pip install --upgrade pip
ERROR: No matching distribution found for rdkit-pypi>=2021.9.2
Downloading commands.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands/
Finished 37 files
Extraction successful
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: rdkit>=2022.03.1 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from -r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 1)) (2024.9.5)
Requirement already satisfied: numpy>=1.22.2 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from -r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 2)) (2.2.2)
Requirement already satisfied: pandas>=1.4.1 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from -r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 3)) (2.2.3)
Requirement already satisfied: requests>=2.27.1 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from -r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 4)) (2.32.3)
Requirement already satisfied: igraph>=0.9.10 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from -r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 5)) (0.11.8)
Requirement already satisfied: biopython>=1.79 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from -r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 6)) (1.85)
Requirement already satisfied: Pillow in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from rdkit>=2022.03.1->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 1)) (11.1.0)
Requirement already satisfied: python-dateutil>=2.8.2 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from pandas>=1.4.1->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 3)) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from pandas>=1.4.1->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 3)) (2025.1)
Requirement already satisfied: tzdata>=2022.7 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from pandas>=1.4.1->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 3)) (2025.1)
Requirement already satisfied: charset-normalizer<4,>=2 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from requests>=2.27.1->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 4)) (3.4.1)
Requirement already satisfied: idna<4,>=2.5 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from requests>=2.27.1->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 4)) (3.10)
Requirement already satisfied: urllib3<3,>=1.21.1 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from requests>=2.27.1->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 4)) (2.3.0)
Requirement already satisfied: certifi>=2017.4.17 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from requests>=2.27.1->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 4)) (2025.1.31)
Requirement already satisfied: texttable>=1.6.2 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from igraph>=0.9.10->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 5)) (1.7.0)
Requirement already satisfied: six>=1.5 in c:\users\miroi\appdata\local\packages\pythonsoftwarefoundation.python.3.12_qbz5n2kfra8p0\localcache\local-packages\python312\site-packages (from python-dateutil>=2.8.2->pandas>=1.4.1->-r C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands//Peptide_generation_script/requirements.txt (line 3)) (1.17.0)
[notice] A new release of pip is available: 24.3.1 -> 25.0.1
[notice] To update, run: C:\Users\miroi\AppData\Local\Microsoft\WindowsApps\PythonSoftwareFoundation.Python.3.12_qbz5n2kfra8p0\python.exe -m pip install --upgrade pip
Downloading scikit-nano.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/scikit-nano.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands/
Finished 8 files
Extraction successful
Downloading genice.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/genice.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands/
Finished 7 files
Extraction successful
Downloading rdkit.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/rdkit.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands/
Finished 14 files
Extraction successful
Downloading build-ase.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/build-ase.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands/
Finished 8 files
Extraction successful
Downloading commands.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/commands/
Finished 9 files
Extraction successful
Downloading cclib.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/cclib.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/formatScripts/
Finished 11 files
Extraction successful
Downloading i18n.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/i18n.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/i18n/
Finished 124 files
Extraction successful
Downloading crystals.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/crystals.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/data/
Finished 1050 files
Extraction successful
Downloading molecules.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/molecules.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/data/
Finished 899 files
Extraction successful
Downloading avogenerators.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro
Extracting C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/avogenerators.zip to C:/Users/miroi/AppData/Local/OpenChemistry/Avogadro/inputGenerators/
Finished 24 files
Extraction successful