corpus-viewer, word-cloud etc. not displaying text #877

debojyoti31 · 2022-07-10T17:10:15Z

Describe the bug
On Linux - Ubuntu 22.04 LTS. (with Xorg),
installed orange using pip
In Orange 3.32.0
while using text add-on
corpus-viewer, word-cloud etc. not displaying any text.

To Reproduce
Steps to reproduce the behavior:

select text add on
load a grimm-tales-selected.tab from documantation
connect to corpus-viewer

Expected behavior
Display the text at the right side of corpus-viewer tab (which is not happening)

Orange version:
3.32.0

Text add-on version:
1.10.0

Screenshots

Operating system:
Linux - Ubuntu 22.04 LTS. (with Xorg)

Additional context
Add any other context about the problem here.

ajdapretnar · 2022-07-11T07:36:50Z

You are probably missing WebEngine components.
Try running pip install PyQtWebEngine and see if it helps.

debojyoti31 · 2022-07-11T15:07:51Z

You are probably missing WebEngine components. Try running pip install PyQtWebEngine and see if it helps.

No, I already have it installed (Requirement already satisfied)

ajdapretnar · 2022-07-20T08:59:20Z

Can you run Orange with python -m Orange.canvas -l 4, try to reproduce the error and paste the log here?

ajdapretnar · 2022-08-29T07:05:55Z

Closed due to inactivity.

ahfornitani · 2022-09-16T21:21:00Z

Hi @ajdapretnar !
Unfortunately, this affects me, too.
Config: Arch Linux x86_64 ; Plasma 5.25.5 ; Kernel: 5.19.8-arch1-1 ; X11

Orange 3.32.0, installed via pip (running on its own environment, via pipenv)
Text addon version 1.1.0

❯ pip install PyQtWebEngine
Requirement already satisfied: PyQtWebEngine in /home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages (5.15.5)
Requirement already satisfied: PyQt5>=5.15.4 in /home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages (from PyQtWebEngine) (5.15.6)
Requirement already satisfied: PyQt5-sip<13,>=12.8 in /home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages (from PyQtWebEngine) (12.10.1)
Requirement already satisfied: PyQtWebEngine-Qt5>=5.15.2 in /home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages (from PyQtWebEngine) (5.15.2)
Requirement already satisfied: PyQt5-Qt5>=5.15.2 in /home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages (from PyQt5>=5.15.4->PyQtWebEngine) (5.15.2)

Steps:

Run Orange with python -m Orange.canvas -l 4
Select the Corpus widget, connect its output to the Preprocess Text widget, and its output to Word Cloud
Double click on the Word Cloud widget to visualize its results
No visualization for Word Cloud

Please note this also happens when trying to read documentation for any widget, using F1 (it's been the case for many Orange versions now. Though only now I noticed that it happens for widgets other than "Help"/F1)

The log, when running with python -m Orange.canvas -l 4:

❯ python -m Orange.canvas -l 4
2022-09-16 17:59:33,475:INFO:orangecanvas.registry.base: A category with 'Data' name already exists
2022-09-16 17:59:33,477:INFO:orangecanvas.registry.base: A category with 'Visualize' name already exists
2022-09-16 17:59:33,482:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/Orange/widgets/visualize/owscatterplotgraph.py'.
2022-09-16 17:59:33,482:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/Orange/widgets/visualize/owtreeviewer2d.py'.
2022-09-16 17:59:33,482:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/Orange/widgets/visualize/pythagorastreeviewer.py'.
2022-09-16 17:59:33,482:INFO:orangecanvas.registry.base: A category with 'Model' name already exists
2022-09-16 17:59:33,483:INFO:orangecanvas.registry.base: A category with 'Evaluate' name already exists
2022-09-16 17:59:33,484:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/Orange/widgets/evaluate/contexthandlers.py'.
2022-09-16 17:59:33,484:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/Orange/widgets/evaluate/utils.py'.
2022-09-16 17:59:33,484:INFO:orangecanvas.registry.base: A category with 'Unsupervised' name already exists
2022-09-16 17:59:33,597:WARNING:orangecanvas.registry.discovery: Error while importing 'orangecontrib.bioinformatics.widgets.OWAnnotateProjection'.
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 294, in iter_widget_descriptions
    module = asmodule(name)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 537, in asmodule
    return __import__(module, fromlist=[""])
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/widgets/OWAnnotateProjection.py", line 28, in <module>
    from orangecontrib.bioinformatics.annotation.annotate_samples import (
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/annotation/annotate_samples.py", line 15, in <module>
    from orangecontrib.bioinformatics.ncbi.gene import GeneInfo
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/gene/__init__.py", line 11, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy import species_name_to_taxid
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/__init__.py", line 3, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy.utils import Taxonomy, UnknownSpeciesIdentifier
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/utils.py", line 139, in <module>
    class TaxonomyDB(collections.Mapping):
AttributeError: module 'collections' has no attribute 'Mapping'
2022-09-16 17:59:33,617:WARNING:orangecanvas.registry.discovery: Error while importing 'orangecontrib.bioinformatics.widgets.OWClusterAnalysis'.
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 294, in iter_widget_descriptions
    module = asmodule(name)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 537, in asmodule
    return __import__(module, fromlist=[""])
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/widgets/OWClusterAnalysis.py", line 20, in <module>
    from orangecontrib.bioinformatics.cluster_analysis import DISPLAY_GENE_SETS_COUNT, Cluster, ClusterModel
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/cluster_analysis/__init__.py", line 16, in <module>
    from orangecontrib.bioinformatics.ncbi.gene import Gene
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/gene/__init__.py", line 11, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy import species_name_to_taxid
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/__init__.py", line 3, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy.utils import Taxonomy, UnknownSpeciesIdentifier
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/utils.py", line 139, in <module>
    class TaxonomyDB(collections.Mapping):
AttributeError: module 'collections' has no attribute 'Mapping'
2022-09-16 17:59:33,618:WARNING:orangecanvas.registry.discovery: Error while importing 'orangecontrib.bioinformatics.widgets.OWDatabasesUpdate'.
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 294, in iter_widget_descriptions
    module = asmodule(name)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 537, in asmodule
    return __import__(module, fromlist=[""])
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/widgets/OWDatabasesUpdate.py", line 40, in <module>
    from orangecontrib.bioinformatics.go.config import DOMAIN as gene_ontology_domain
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/go/__init__.py", line 11, in <module>
    from orangecontrib.bioinformatics.ncbi import taxonomy
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/__init__.py", line 3, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy.utils import Taxonomy, UnknownSpeciesIdentifier
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/utils.py", line 139, in <module>
    class TaxonomyDB(collections.Mapping):
AttributeError: module 'collections' has no attribute 'Mapping'
2022-09-16 17:59:33,620:WARNING:orangecanvas.registry.discovery: Error while importing 'orangecontrib.bioinformatics.widgets.OWGOBrowser'.
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 294, in iter_widget_descriptions
    module = asmodule(name)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 537, in asmodule
    return __import__(module, fromlist=[""])
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/widgets/OWGOBrowser.py", line 38, in <module>
    from orangecontrib.bioinformatics import go
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/go/__init__.py", line 11, in <module>
    from orangecontrib.bioinformatics.ncbi import taxonomy
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/__init__.py", line 3, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy.utils import Taxonomy, UnknownSpeciesIdentifier
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/utils.py", line 139, in <module>
    class TaxonomyDB(collections.Mapping):
AttributeError: module 'collections' has no attribute 'Mapping'
2022-09-16 17:59:33,621:WARNING:orangecanvas.registry.discovery: Error while importing 'orangecontrib.bioinformatics.widgets.OWGeneSetEnrichment'.
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 294, in iter_widget_descriptions
    module = asmodule(name)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 537, in asmodule
    return __import__(module, fromlist=[""])
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/widgets/OWGeneSetEnrichment.py", line 30, in <module>
    from orangecontrib.bioinformatics.ncbi.gene import GeneInfo
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/gene/__init__.py", line 11, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy import species_name_to_taxid
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/__init__.py", line 3, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy.utils import Taxonomy, UnknownSpeciesIdentifier
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/utils.py", line 139, in <module>
    class TaxonomyDB(collections.Mapping):
AttributeError: module 'collections' has no attribute 'Mapping'
2022-09-16 17:59:33,622:WARNING:orangecanvas.registry.discovery: Error while importing 'orangecontrib.bioinformatics.widgets.OWGenes'.
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 294, in iter_widget_descriptions
    module = asmodule(name)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 537, in asmodule
    return __import__(module, fromlist=[""])
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/widgets/OWGenes.py", line 32, in <module>
    from orangecontrib.bioinformatics.ncbi import taxonomy
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/__init__.py", line 3, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy.utils import Taxonomy, UnknownSpeciesIdentifier
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/utils.py", line 139, in <module>
    class TaxonomyDB(collections.Mapping):
AttributeError: module 'collections' has no attribute 'Mapping'
2022-09-16 17:59:33,861:WARNING:orangecanvas.registry.discovery: Error while importing 'orangecontrib.bioinformatics.widgets.OWGenialisExpressions'.
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 294, in iter_widget_descriptions
    module = asmodule(name)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 537, in asmodule
    return __import__(module, fromlist=[""])
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/widgets/OWGenialisExpressions.py", line 24, in <module>
    from orangecontrib.bioinformatics.ncbi.gene import GeneMatcher
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/gene/__init__.py", line 11, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy import species_name_to_taxid
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/__init__.py", line 3, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy.utils import Taxonomy, UnknownSpeciesIdentifier
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/utils.py", line 139, in <module>
    class TaxonomyDB(collections.Mapping):
AttributeError: module 'collections' has no attribute 'Mapping'
2022-09-16 17:59:33,862:WARNING:orangecanvas.registry.discovery: Error while importing 'orangecontrib.bioinformatics.widgets.OWHomologs'.
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 294, in iter_widget_descriptions
    module = asmodule(name)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 537, in asmodule
    return __import__(module, fromlist=[""])
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/widgets/OWHomologs.py", line 12, in <module>
    from orangecontrib.bioinformatics.ncbi.gene import Gene, GeneMatcher, load_gene_summary
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/gene/__init__.py", line 11, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy import species_name_to_taxid
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/__init__.py", line 3, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy.utils import Taxonomy, UnknownSpeciesIdentifier
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/utils.py", line 139, in <module>
    class TaxonomyDB(collections.Mapping):
AttributeError: module 'collections' has no attribute 'Mapping'
2022-09-16 17:59:33,864:INFO:orangecanvas.registry.discovery: Could not import 'orangecontrib.bioinformatics.widgets.OWKEGGPathwayBrowser'.
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/kegg/caching.py", line 21, in <module>
    from UserDict import DictMixin
ModuleNotFoundError: No module named 'UserDict'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 294, in iter_widget_descriptions
    module = asmodule(name)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 537, in asmodule
    return __import__(module, fromlist=[""])
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/widgets/OWKEGGPathwayBrowser.py", line 30, in <module>
    from orangecontrib.bioinformatics import kegg, geneset
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/kegg/__init__.py", line 61, in <module>
    from orangecontrib.bioinformatics.kegg import api, conf, entry, pathway, databases
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/kegg/api.py", line 12, in <module>
    from orangecontrib.bioinformatics.kegg import caching
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/kegg/caching.py", line 23, in <module>
    from collections import MutableMapping as DictMixin
ImportError: cannot import name 'MutableMapping' from 'collections' (/usr/lib/python3.10/collections/__init__.py)
2022-09-16 17:59:33,865:WARNING:orangecanvas.registry.discovery: Error while importing 'orangecontrib.bioinformatics.widgets.OWdictyExpress'.
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 294, in iter_widget_descriptions
    module = asmodule(name)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 537, in asmodule
    return __import__(module, fromlist=[""])
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/widgets/OWdictyExpress.py", line 18, in <module>
    from orangecontrib.bioinformatics.ncbi.gene import ENTREZ_ID, GeneMatcher
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/gene/__init__.py", line 11, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy import species_name_to_taxid
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/__init__.py", line 3, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy.utils import Taxonomy, UnknownSpeciesIdentifier
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/utils.py", line 139, in <module>
    class TaxonomyDB(collections.Mapping):
AttributeError: module 'collections' has no attribute 'Mapping'
2022-09-16 17:59:33,867:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/_textable/widgets/TextableUtils.py'.
2022-09-16 17:59:33,983:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/network/widgets/graphview.py'.
2022-09-16 17:59:33,985:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/single_cell/widgets/contingency_table.py'.
2022-09-16 17:59:33,985:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/single_cell/widgets/load_data.py'.
2022-09-16 17:59:33,985:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/single_cell/widgets/owloaddata.py'.
2022-09-16 17:59:33,987:WARNING:orangecanvas.registry.discovery: Error while importing 'orangecontrib.single_cell.widgets.owscdatasets'.
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 294, in iter_widget_descriptions
    module = asmodule(name)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 537, in asmodule
    return __import__(module, fromlist=[""])
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/single_cell/widgets/owscdatasets.py", line 11, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy import shortname, common_taxids
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/__init__.py", line 3, in <module>
    from orangecontrib.bioinformatics.ncbi.taxonomy.utils import Taxonomy, UnknownSpeciesIdentifier
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/bioinformatics/ncbi/taxonomy/utils.py", line 139, in <module>
    class TaxonomyDB(collections.Mapping):
AttributeError: module 'collections' has no attribute 'Mapping'
2022-09-16 17:59:33,988:ERROR:orangecanvas.registry.discovery: An ImportError occurred while loading entry point 'Associate = orangecontrib.associate.widgets'
Traceback (most recent call last):
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/registry/discovery.py", line 122, in run
    point = entry_point.resolve()
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2477, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/associate/__init__.py", line 1, in <module>
    from .fpgrowth import \
  File "/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/associate/fpgrowth.py", line 152, in <module>
    from collections import defaultdict, Iterator
ImportError: cannot import name 'Iterator' from 'collections' (/usr/lib/python3.10/collections/__init__.py)
2022-09-16 17:59:33,992:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/explain/widgets/owexplainfeaturebase.py'.
2022-09-16 17:59:33,992:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/explain/widgets/shap_debug.py'.
2022-09-16 17:59:34,105:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/timeseries/widgets/_owmodel.py'.
2022-09-16 17:59:34,106:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/timeseries/widgets/_rangeslider.py'.
2022-09-16 17:59:34,106:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/timeseries/widgets/owperiodbase.py'.
2022-09-16 17:59:34,107:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/timeseries/widgets/utils.py'.
2022-09-16 17:59:34,109:INFO:orangecanvas.registry.discovery: Ignoring '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecontrib/geo/widgets/plotutils.py'.
2022-09-16 17:59:34,115:INFO:orangecanvas.main: Adding search path '/home/aug/.local/share/virtualenvs/orange-KjjBmqEd/lib/python3.10/site-packages/orangecanvas/styles/orange' for prefix, 'canvas_icons'
2022-09-16 17:59:43,107:INFO:orangecanvas.scheme.scheme: Added node 'Corpus' to scheme ''.
2022-09-16 17:59:43,125:INFO:orangewidget.workflow.widgetsscheme: WidgetManager: Creating 'orangecontrib.text.widgets.owcorpus.OWCorpus' instance 'Corpus'.
2022-09-16 17:59:53,151:INFO:orangecanvas.scheme.scheme: Added node 'Preprocess Text' to scheme ''.
2022-09-16 17:59:53,164:INFO:orangewidget.workflow.widgetsscheme: WidgetManager: Creating 'orangecontrib.text.widgets.owpreprocess.OWPreprocess' instance 'Preprocess Text'.
2022-09-16 17:59:57,360:INFO:orangecanvas.scheme.scheme: Added node 'Word Cloud' to scheme ''.
2022-09-16 17:59:57,368:INFO:orangewidget.workflow.widgetsscheme: WidgetManager: Creating 'orangecontrib.text.widgets.owwordcloud.OWWordCloud' instance 'Word Cloud'.
2022-09-16 17:59:59,363:INFO:orangecanvas.document.interactions: <orangecanvas.canvas.items.nodeitem.NodeItem object at 0x7faeb3853f40> is the new target.
2022-09-16 17:59:59,660:INFO:orangecanvas.scheme.scheme: Added link 'Corpus' ('Corpus') -> 'Preprocess Text' ('Corpus') to scheme ''.
2022-09-16 17:59:59,660:INFO:orangecanvas.scheme.signalmanager: Scheduling signal data update for 'SchemeLink((Corpus, Corpus) -> (Preprocess Text, Corpus))'.
2022-09-16 17:59:59,827:INFO:gensim.corpora.dictionary: adding document #0 to Dictionary(0 unique tokens: [])
2022-09-16 17:59:59,855:INFO:gensim.corpora.dictionary: built Dictionary(4345 unique tokens: ['!', '!’', '!”', ',', ',--']...) from 54 documents (total 92084 corpus positions)
2022-09-16 17:59:59,858:INFO:gensim.utils: Dictionary lifecycle event {'msg': "built Dictionary(4345 unique tokens: ['!', '!’', '!”', ',', ',--']...) from 54 documents (total 92084 corpus positions)", 'datetime': '2022-09-16T17:59:59.856125', 'gensim': '4.1.2', 'python': '3.10.7 (main, Sep  6 2022, 21:22:27) [GCC 12.2.0]', 'platform': 'Linux-5.19.8-arch1-1-x86_64-with-glibc2.36', 'event': 'created'}
2022-09-16 17:59:59,871:INFO:gensim.corpora.dictionary: adding document #0 to Dictionary(0 unique tokens: [])
2022-09-16 17:59:59,888:INFO:gensim.corpora.dictionary: built Dictionary(4210 unique tokens: ['!', '!’', '!”', ',', ',--']...) from 54 documents (total 48764 corpus positions)
2022-09-16 17:59:59,888:INFO:gensim.utils: Dictionary lifecycle event {'msg': "built Dictionary(4210 unique tokens: ['!', '!’', '!”', ',', ',--']...) from 54 documents (total 48764 corpus positions)", 'datetime': '2022-09-16T17:59:59.888975', 'gensim': '4.1.2', 'python': '3.10.7 (main, Sep  6 2022, 21:22:27) [GCC 12.2.0]', 'platform': 'Linux-5.19.8-arch1-1-x86_64-with-glibc2.36', 'event': 'created'}
2022-09-16 17:59:59,900:INFO:gensim.corpora.dictionary: adding document #0 to Dictionary(0 unique tokens: [])
2022-09-16 17:59:59,917:INFO:gensim.corpora.dictionary: built Dictionary(4210 unique tokens: ['!', '!’', '!”', ',', ',--']...) from 54 documents (total 48764 corpus positions)
2022-09-16 17:59:59,917:INFO:gensim.utils: Dictionary lifecycle event {'msg': "built Dictionary(4210 unique tokens: ['!', '!’', '!”', ',', ',--']...) from 54 documents (total 48764 corpus positions)", 'datetime': '2022-09-16T17:59:59.917847', 'gensim': '4.1.2', 'python': '3.10.7 (main, Sep  6 2022, 21:22:27) [GCC 12.2.0]', 'platform': 'Linux-5.19.8-arch1-1-x86_64-with-glibc2.36', 'event': 'created'}
2022-09-16 17:59:59,930:INFO:gensim.corpora.dictionary: adding document #0 to Dictionary(0 unique tokens: [])
2022-09-16 17:59:59,945:INFO:gensim.corpora.dictionary: built Dictionary(4167 unique tokens: ['able', 'accord', 'actually', 'afraid', 'ago']...) from 54 documents (total 34388 corpus positions)
2022-09-16 17:59:59,945:INFO:gensim.utils: Dictionary lifecycle event {'msg': "built Dictionary(4167 unique tokens: ['able', 'accord', 'actually', 'afraid', 'ago']...) from 54 documents (total 34388 corpus positions)", 'datetime': '2022-09-16T17:59:59.945909', 'gensim': '4.1.2', 'python': '3.10.7 (main, Sep  6 2022, 21:22:27) [GCC 12.2.0]', 'platform': 'Linux-5.19.8-arch1-1-x86_64-with-glibc2.36', 'event': 'created'}
2022-09-16 17:59:59,946:INFO:gensim.corpora.dictionary: adding document #0 to Dictionary(0 unique tokens: [])
2022-09-16 17:59:59,961:INFO:gensim.corpora.dictionary: built Dictionary(4167 unique tokens: ['able', 'accord', 'actually', 'afraid', 'ago']...) from 54 documents (total 34388 corpus positions)
2022-09-16 17:59:59,961:INFO:gensim.utils: Dictionary lifecycle event {'msg': "built Dictionary(4167 unique tokens: ['able', 'accord', 'actually', 'afraid', 'ago']...) from 54 documents (total 34388 corpus positions)", 'datetime': '2022-09-16T17:59:59.961871', 'gensim': '4.1.2', 'python': '3.10.7 (main, Sep  6 2022, 21:22:27) [GCC 12.2.0]', 'platform': 'Linux-5.19.8-arch1-1-x86_64-with-glibc2.36', 'event': 'created'}
2022-09-16 17:59:59,964:INFO:gensim.corpora.dictionary: discarding 4067 tokens: [('able', 18), ('accord', 2), ('actually', 3), ('afraid', 14), ('ago', 4), ('ah', 20), ('air', 12), ('alive', 8), ('allow', 3), ('allowed', 8)]...
2022-09-16 17:59:59,964:INFO:gensim.corpora.dictionary: keeping 100 tokens which were in no less than 0 and no more than 54 (=100.0%) documents
2022-09-16 17:59:59,964:INFO:gensim.corpora.dictionary: resulting dictionary: Dictionary(100 unique tokens: ['another', 'answered', 'asked', 'away', 'back']...)
2022-09-16 18:00:01,138:INFO:orangecanvas.document.interactions: <orangecanvas.canvas.items.nodeitem.NodeItem object at 0x7faeb36f9ab0> is the new target.
2022-09-16 18:00:01,396:INFO:orangecanvas.scheme.scheme: Added link 'Preprocess Text' ('Corpus') -> 'Word Cloud' ('Corpus') to scheme ''.
2022-09-16 18:00:01,396:INFO:orangecanvas.scheme.signalmanager: Scheduling signal data update for 'SchemeLink((Preprocess Text, Corpus) -> (Word Cloud, Corpus))'.
2022-09-16 18:05:17,688:INFO:orangecanvas.help.manager: Created <class 'orangecanvas.help.provider.HtmlIndexProvider'> provider for Orange3-Text 1.11.0
2022-09-16 18:05:17,689:INFO:orangecanvas.application.canvasmain: Setting help to url: PyQt5.QtCore.QUrl('file:///home/aug/.local/share/virtualenvs/orange-KjjBmqEd/help/orange3-text/widgets/corpus-widget.html')
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
2022-09-16 18:05:29,229:INFO:orangecanvas.scheme.scheme: Added node 'CSV File Import' to scheme ''.
2022-09-16 18:05:29,250:INFO:orangewidget.workflow.widgetsscheme: WidgetManager: Creating 'Orange.widgets.data.owcsvimport.OWCSVFileImport' instance 'CSV File Import'.
2022-09-16 18:05:31,092:INFO:orangecanvas.help.manager: Created <class 'orangecanvas.help.provider.HtmlIndexProvider'> provider for Orange3 3.32.0
2022-09-16 18:05:31,093:INFO:orangecanvas.application.canvasmain: Setting help to url: PyQt5.QtCore.QUrl('file:///home/aug/.local/share/virtualenvs/orange-KjjBmqEd/share/help/en/orange3/htmlhelp/widgets/data/csvfileimport.html')

Please let me know if this is useful information, and if there's any additional info I can provide.
Thanks!

Albert5861 · 2023-01-03T15:45:01Z

This bug affects me too.

Ubuntu 22.04 with Xorg
Orange 3.34.1 installed with conda
text add-on version 1.2 installed
PyQtWebEngine installed

corpus viewer, word cloud etc. not displaying any text.
It doesn't even show the help for me.

Every time I launch orange with the command "orange-canvas" and not with the command "python -m Orange.canvas" I get this error message: "QMainWindowLayout::tabPosition called with out-of-bounds value '0'"

Can anyone help me?
Thank you

PrimozGodec · 2023-01-07T19:12:00Z

@ahfornitani and @Albert5861 thank you for the additional details. I also notice some weird behaviour on Ubuntu 22.04 while switching CI to newer Ubuntu (through our CI - automatic tests) #917. I will try to reproduce it to see what is wrong soon (I just need to prepare an Ubuntu VM).

Albert5861 · 2023-01-07T20:13:13Z

@PrimozGodec and @ahfornitani thank you for your help.
I want to add that the data I provided above relate to a machine installed a week ago from scratch to do this test.
The machine is clean with the configuration I told you.
I also have another Ubuntu 22.04.1 machine installed over six months ago (ubuntu 22.04.1 just came out) and there Orange data mining (installed with pip) works and doesn't have these problems.
Whenever I install Ubuntu 22.04.1 on a new machine now it gives me these problems. The test machine I made for you to report this bug is a machine with an AMD Ryzen processor, but it gives the same error on an Intel Celeron (always with Ubuntu 22.04.1). Before writing to you I tried two other installations (Linux MInt 22.1 based on Ubuntu 22.04 and KUbuntu 22.04.1) and either it had the same error or it didn't start.
Summary I tried 3 Ubuntu based distributions on two different hardware, even if I'm mainly interested in Ubuntu LTS 22.04
In my humble opinion one of the latest Ubuntu updates causes these errors.
Thanks

Albert5861 · 2023-01-10T19:33:20Z

@PrimozGodec @ahfornitani

I did one more test.
I installed on a Virtualbox 6.1.40 virtual machine the same configuration:

Ubuntu 22.04.1 with Xorg
miniconda version 22.11.1 installed
conda config --add channels conda-forge
conda config --set channel_priority strict
pyqt installed
PyQtWebEngine installed
Orange 3.34.1 (installed with conda)
text-add-on version 1.2 installed

Here too I have the same errors:
corpus viewer, word cloud etc. not displaying any text.
It doesn't even show the help for me.

Thanks

PrimozGodec · 2023-01-17T14:41:50Z

@ales-erjavec, do you maybe know what the reason for this error is? I would like to know if you have seen something like this before I start installing Ubuntu somewhere to debug. It happens only on Ubuntu 22.04; it works fine on other OSs and at older Ubuntus.

ales-erjavec · 2023-01-18T12:04:24Z

Can you try running

QTWEBENGINE_CHROMIUM_FLAGS="--disable-gpu --no-sandbox" python -m Orange.canvas -l 4

Albert5861 · 2023-01-18T19:02:18Z

@ales-erjavec @PrimozGodec @ahfornitani
It works, thank you very much.
With this workaround Orange finally displays the help, corpus viewer, word cloud, etc. 👍
What exactly does it depend on?
Will this be fixed as a bug as well?
Thanks

ahfornitani · 2023-01-18T20:41:42Z

Sorry if it counts as a duplicate / unnecessary comnent, but adding screenshots showing that it works for me, too:

Running with python -m Orange.canvas &>/dev/null:

Running with QTWEBENGINE_CHROMIUM_FLAGS="--disable-gpu --no-sandbox" python -m Orange.canvas -l 4

Thank you!

PrimozGodec · 2023-01-20T08:18:45Z

@ales-erjavec, thank you for the solution. Do you think it can be somehow included in WebView that users do not need to set environment variables?

PrimozGodec · 2023-08-07T12:04:07Z

@ales-erjavec, can those flags be somehow implemented in Orange so that users do not need to set them themselves?

ales-erjavec · 2023-08-08T10:04:57Z

No.

PrimozGodec · 2023-08-11T12:30:08Z

Ok then we can't do anything here. Closing

uelramon · 2024-10-01T17:50:38Z

Hey guys,

I have the same problem here, with installation on MacOS, version Orange 3.37. Any tips to resolve?

ajdapretnar closed this as completed Aug 29, 2022

PrimozGodec reopened this Jan 7, 2023

PrimozGodec closed this as completed Aug 11, 2023

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