Segmentation fault (core dumped) #4518

Hrovatin · 2020-03-10T07:00:12Z

I am often getting an error Segmentation fault (core dumped) in Orange (3.25.0 Linux). At first the Orange seems to be frozen for a couple of seconds and then it crashes (the window closes on its own). It seems to be happening at random/not always on the same workflow or its part.
The report from when this last happened:

libpng warning: iCCP: known incorrect sRGB profile
QCssParser::parseColorValue: Specified color without alpha value but alpha given: 'rgb 0, 0, 0, 100'
/home/karin/Documents/git/orange-widget-base/orangewidget/widget.py:286: RuntimeWarning: subclassing of widget classes is deprecated and will be disabled in the future.
Extract code from OWGeneSets or explicitly open it.
  RuntimeWarning)
/home/karin/Documents/git/orange-widget-base/orangewidget/widget.py:286: RuntimeWarning: subclassing of widget classes is deprecated and will be disabled in the future.
Extract code from OWPreprocess or explicitly open it.
  RuntimeWarning)
/home/karin/Documents/git/orange3-bioinformatics/orangecontrib/bioinformatics/ncbi/gene/__init__.py:177: OrangeDeprecationWarning: Direct calls to Table's constructor are deprecated and will be removed. Replace this call with Table.from_list
  table = Table(domain, data_x)
/home/karin/Documents/git/orange3/Orange/widgets/settings.py:82: UserWarning: Storing variables as strings in settings is deprecated.
Support for this will be dropped in Orange 3.26.
Change domain_role_hints to store an instance of `Variable`.
  "Storing variables as strings in settings is deprecated.\n"
/home/karin/Documents/git/orange3/Orange/widgets/settings.py:82: UserWarning: Storing variables as strings in settings is deprecated.
Support for this will be dropped in Orange 3.26.
Change domain_role_hints to store an instance of `Variable`.
  "Storing variables as strings in settings is deprecated.\n"
/home/karin/Documents/git/orange3-bioinformatics/orangecontrib/bioinformatics/ncbi/gene/__init__.py:177: OrangeDeprecationWarning: Direct calls to Table's constructor are deprecated and will be removed. Replace this call with Table.from_list
  table = Table(domain, data_x)
/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecontrib/prototypes/widgets/owunique.py:87: OrangeDeprecationWarning: Call to deprecated <function Domain.__iter__ at 0x7f581ae761e0>; Instead, use Domain.variables
  self.model_attrs = (list(data.domain) + list(data.domain.metas), [])
ERROR:orangewidget.workflow.widgetsscheme:Error calling 'set_dataset' of 'Heat Map (1)'
Traceback (most recent call last):
  File "/home/karin/Documents/git/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 826, in process_signals_for_widget
    handler(*args)
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 557, in set_dataset
    self.update_heatmaps()
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 589, in update_heatmaps
    self.construct_heatmaps_scene(parts, self.effective_data)
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 773, in construct_heatmaps_scene
    self.setup_scene(parts, data)
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 796, in setup_scene
    widget.setHeatmaps(parts)
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/utils/heatmap.py", line 450, in setHeatmaps
    data=X_part, span=parts.span, colormap=colormap,
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/utils/heatmap.py", line 953, in __init__
    self.setHeatmapData(data)
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/utils/heatmap.py", line 987, in setHeatmapData
    self.__updatePixmap()
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/utils/heatmap.py", line 1020, in __updatePixmap
    qimage = qimage_from_array(rgb)
  File "/home/karin/Documents/git/orange3/Orange/widgets/utils/image.py", line 33, in qimage_from_array
    buffer = img.bits().asarray(w * h * 4)
AttributeError: 'NoneType' object has no attribute 'asarray'
-------------------------- AttributeError Exception ---------------------------
Traceback (most recent call last):
  File "/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecanvas/scheme/signalmanager.py", line 936, in __process_next
    if self.__process_next_helper(use_max_active=True):
  File "/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecanvas/scheme/signalmanager.py", line 974, in __process_next_helper
    self.process_node(selected_node)
  File "/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecanvas/scheme/signalmanager.py", line 605, in process_node
    self.send_to_node(node, signals_in)
  File "/home/karin/Documents/git/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 792, in send_to_node
    self.process_signals_for_widget(node, widget, signals)
  File "/home/karin/Documents/git/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 826, in process_signals_for_widget
    handler(*args)
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 557, in set_dataset
    self.update_heatmaps()
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 589, in update_heatmaps
    self.construct_heatmaps_scene(parts, self.effective_data)
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 773, in construct_heatmaps_scene
    self.setup_scene(parts, data)
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 796, in setup_scene
    widget.setHeatmaps(parts)
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/utils/heatmap.py", line 450, in setHeatmaps
    data=X_part, span=parts.span, colormap=colormap,
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/utils/heatmap.py", line 953, in __init__
    self.setHeatmapData(data)
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/utils/heatmap.py", line 987, in setHeatmapData
    self.__updatePixmap()
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/utils/heatmap.py", line 1020, in __updatePixmap
    qimage = qimage_from_array(rgb)
  File "/home/karin/Documents/git/orange3/Orange/widgets/utils/image.py", line 33, in qimage_from_array
    buffer = img.bits().asarray(w * h * 4)
AttributeError: 'NoneType' object has no attribute 'asarray'
-------------------------------------------------------------------------------
QLayout: Attempting to add QLayout "" to ErrorReporting "", which already has a layout
Segmentation fault (core dumped)

The text was updated successfully, but these errors were encountered:

janezd · 2020-03-15T18:50:18Z

@Hrovatin, did #4520 fix it? Is the problem common/replicable enough to check?

Hrovatin · 2020-03-16T06:43:58Z

I do not know how to reproduce it. I will add the change to my Orange and see if the issue stops happening.

ales-erjavec · 2020-03-16T07:57:30Z

I do not think #4520 fixed the segmentation fault. I think that happened in the error reporting.

Hrovatin · 2020-04-02T10:04:59Z

Orange was recently crashing on loading of a relatively large workflow (the one I am currently using). - Sometimes it loads and sometimes it crashes.
The error report:

`libpng warning: iCCP: known incorrect sRGB profile
QCssParser::parseColorValue: Specified color without alpha value but alpha given: 'rgb 0, 0, 0, 100'
/home/karin/Documents/git/orange-widget-base/orangewidget/widget.py:286: RuntimeWarning: subclassing of widget classes is deprecated and will be disabled in the future.
Extract code from OWGeneSets or explicitly open it.
  RuntimeWarning)
/home/karin/Documents/git/orange-widget-base/orangewidget/widget.py:979: UserWarning: Storing variables as strings in settings is deprecated.
Support for this will be dropped in Orange 3.26.
Change domain_role_hints to store an instance of `Variable`.
  self.settingsHandler.open_context(self, *a)
/home/karin/Documents/git/orange3/Orange/widgets/data/owselectcolumns.py:310: UserWarning: Storing variables as strings in settings is deprecated.
Support for this will be dropped in Orange 3.26.
Change domain_role_hints to store an instance of `Variable`.
  self.openContext(data)
CRITICAL:orangecanvas.scheme.widgetmanager:
Traceback (most recent call last):
  File "/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecanvas/scheme/widgetmanager.py", line 240, in __add_widget_for_node
    w = self.create_widget_for_node(node)
  File "/home/karin/Documents/git/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 296, in create_widget_for_node
    widget = self.create_widget_instance(node)
  File "/home/karin/Documents/git/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 409, in create_widget_instance
    widget.__init__()
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 239, in __init__
    self.color_cb = gui.palette_combo_box(self.palette_name)
  File "/home/karin/Documents/git/orange3/Orange/widgets/gui.py", line 92, in palette_combo_box
    cb.setCurrentIndex(model.indexOf(initial_palette))
TypeError: setCurrentIndex(self, int): argument 1 has unexpected type 'NoneType'
----------------------------- TypeError Exception -----------------------------
Traceback (most recent call last):
  File "/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecanvas/scheme/widgetmanager.py", line 376, in __process_init_queue
    self.ensure_created(node)
  File "/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecanvas/scheme/widgetmanager.py", line 324, in ensure_created
    self.__add_widget_for_node(node)
  File "/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecanvas/scheme/widgetmanager.py", line 240, in __add_widget_for_node
    w = self.create_widget_for_node(node)
  File "/home/karin/Documents/git/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 296, in create_widget_for_node
    widget = self.create_widget_instance(node)
  File "/home/karin/Documents/git/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 409, in create_widget_instance
    widget.__init__()
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 239, in __init__
    self.color_cb = gui.palette_combo_box(self.palette_name)
  File "/home/karin/Documents/git/orange3/Orange/widgets/gui.py", line 92, in palette_combo_box
    cb.setCurrentIndex(model.indexOf(initial_palette))
TypeError: setCurrentIndex(self, int): argument 1 has unexpected type 'NoneType'
-------------------------------------------------------------------------------
QLayout: Attempting to add QLayout "" to ErrorReporting "", which already has a layout
`

markotoplak · 2020-04-02T10:28:50Z

@Hrovatin, could you try to clear widget settings and see if this is still the case?

Hrovatin · 2020-04-02T10:38:15Z

I did this. However, I still get a similar message after Orange crashed. Now I can not even open the workflow without crashing.

/home/karin/Documents/git/orange-widget-base/orangewidget/widget.py:286: RuntimeWarning: subclassing of widget classes is deprecated and will be disabled in the future.
Extract code from OWGeneSets or explicitly open it.
  RuntimeWarning)
CRITICAL:orangecanvas.scheme.widgetmanager:
Traceback (most recent call last):
  File "/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecanvas/scheme/widgetmanager.py", line 240, in __add_widget_for_node
    w = self.create_widget_for_node(node)
  File "/home/karin/Documents/git/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 296, in create_widget_for_node
    widget = self.create_widget_instance(node)
  File "/home/karin/Documents/git/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 409, in create_widget_instance
    widget.__init__()
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 239, in __init__
    self.color_cb = gui.palette_combo_box(self.palette_name)
  File "/home/karin/Documents/git/orange3/Orange/widgets/gui.py", line 92, in palette_combo_box
    cb.setCurrentIndex(model.indexOf(initial_palette))
TypeError: setCurrentIndex(self, int): argument 1 has unexpected type 'NoneType'
----------------------------- TypeError Exception -----------------------------
Traceback (most recent call last):
  File "/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecanvas/scheme/widgetmanager.py", line 376, in __process_init_queue
    self.ensure_created(node)
  File "/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecanvas/scheme/widgetmanager.py", line 324, in ensure_created
    self.__add_widget_for_node(node)
  File "/home/karin/Documents/git/orange3venv/lib/python3.6/site-packages/orangecanvas/scheme/widgetmanager.py", line 240, in __add_widget_for_node
    w = self.create_widget_for_node(node)
  File "/home/karin/Documents/git/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 296, in create_widget_for_node
    widget = self.create_widget_instance(node)
  File "/home/karin/Documents/git/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 409, in create_widget_instance
    widget.__init__()
  File "/home/karin/Documents/git/orange3/Orange/widgets/visualize/owheatmap.py", line 239, in __init__
    self.color_cb = gui.palette_combo_box(self.palette_name)
  File "/home/karin/Documents/git/orange3/Orange/widgets/gui.py", line 92, in palette_combo_box
    cb.setCurrentIndex(model.indexOf(initial_palette))
TypeError: setCurrentIndex(self, int): argument 1 has unexpected type 'NoneType'
QLayout: Attempting to add QLayout "" to ErrorReporting "", which already has a layout

[1]+  Killed                  orange-canvas```

ajdapretnar · 2020-04-02T12:23:04Z

@Hrovatin Please consider editing your comments. It is much easier to inspect the log if it is formatted as code.

Hrovatin · 2020-04-02T14:37:47Z

@ajdapretnar I spent quite some time trying to get it out of this bold format into code before posting, but I did no manage to do it. if you know why how to solve it please let me know, so that I can correct them.
Edit: I have now figured out the issue: the bold was somehow created by long ----------------- in the error report and the code was not working seemingly because there was an empty line in the middle of the error report.

Hrovatin added the bug report Bug is reported by user, not yet confirmed by the core team label Mar 10, 2020

ales-erjavec mentioned this issue Mar 10, 2020

[FIX] utils/image: Return early when image is empty #4520

Merged

3 tasks

janezd assigned ales-erjavec Mar 15, 2020

janezd added bug A bug confirmed by the core team and removed bug report Bug is reported by user, not yet confirmed by the core team labels Mar 15, 2020

janezd closed this as completed Sep 4, 2020

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Segmentation fault (core dumped) #4518

Segmentation fault (core dumped) #4518

Hrovatin commented Mar 10, 2020 •

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janezd commented Mar 15, 2020

Hrovatin commented Mar 16, 2020

ales-erjavec commented Mar 16, 2020

Hrovatin commented Apr 2, 2020 •

edited by ajdapretnar

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markotoplak commented Apr 2, 2020

Hrovatin commented Apr 2, 2020 •

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ajdapretnar commented Apr 2, 2020

Hrovatin commented Apr 2, 2020 •

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Segmentation fault (core dumped) #4518

Segmentation fault (core dumped) #4518

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Hrovatin commented Mar 10, 2020 • edited Loading

janezd commented Mar 15, 2020

Hrovatin commented Mar 16, 2020

ales-erjavec commented Mar 16, 2020

Hrovatin commented Apr 2, 2020 • edited by ajdapretnar Loading

markotoplak commented Apr 2, 2020

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Hrovatin commented Mar 10, 2020 •

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Hrovatin commented Apr 2, 2020 •

edited by ajdapretnar

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Hrovatin commented Apr 2, 2020 •

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Hrovatin commented Apr 2, 2020 •

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