[Debian-med-packaging] Bug#901562: invesalius: Segmentation fault at startup
Thiago Franco Moraes
totonixsame at gmail.com
Sat Jun 16 21:10:21 BST 2018
Hi Torquil,
I think the problem is with WXPython or VTK. Please, try to run the
code from url https://gitlab.kitware.com/vtk/vtk/raw/5a49848a4978d64eafef825c8c437e9e39bb0ffd/Wrapping/Python/vtk/wx/wxVTKRenderWindowInteractor.py
and see if it runs correctly.
$ wget https://gitlab.kitware.com/vtk/vtk/raw/5a49848a4978d64eafef825c8c437e9e39bb0ffd/Wrapping/Python/vtk/wx/wxVTKRenderWindowInteractor.py
$ python wxVTKRenderWindowInteractor.py
wxVTKRenderWindowInteractor is the class we use in InVesalius3 to use
VTK with WXPython, if you run this code (not import it) it will show a
window with a cone. But I don' t know why, outside of KDE when a
wxVTKRenderWindowInteractor is instantiated a segmentation fault
happens. Also, it' s needed to know if this problem is with libvtk or
python-vtk.
Best regards.
On Fri, Jun 15, 2018 at 6:30 PM Torquil Macdonald Sørensen
<torquil at gmail.com> wrote:
>
> Hi,
>
> I'm using XFCE4, so that would be xfwm4. I did another thing:
> /usr/bin/invesalius3 is a shell script, so I executed those commands
> manuall in my shell. But instead of "python app.py", I ran gdb, and then
> the gdb commands "file python", "set args app.py", "run". When
> invesalius3 then crashed, I could then get a backtrace by running "bt",
> It gave the following output:
>
> (gdb) bt
> #0 0x00007ffff3106202 in ?? () from /usr/lib/x86_64-linux-gnu/libgdk-3.so.0
> #1 0x00007ffff313c47e in gdk_x11_window_get_xid () from
> /usr/lib/x86_64-linux-gnu/libgdk-3.so.0
> #2 0x00007ffff6021251 in ?? () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #3 0x000055555564f874 in PyEval_EvalFrameEx ()
> #4 0x0000555555646c7a in PyEval_EvalCodeEx ()
> #5 0x000055555564edb4 in PyEval_EvalFrameEx ()
> #6 0x000055555564e3e2 in PyEval_EvalFrameEx ()
> #7 0x0000555555646c7a in PyEval_EvalCodeEx ()
> #8 0x0000555555662b09 in ?? ()
> #9 0x000055555567b2be in ?? ()
> #10 0x000055555563290e in PyObject_Call ()
> #11 0x00005555556529f0 in PyEval_CallObjectWithKeywords ()
> #12 0x00007ffff5fa9e99 in wxPyCallback::EventThunker(wxEvent&) () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #13 0x00007ffff44438ce in
> wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&,
> wxEvtHandler*, wxEvent&) () from
> /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #14 0x00007ffff4443cda in
> wxEvtHandler::SearchDynamicEventTable(wxEvent&) () from
> /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #15 0x00007ffff4443d6f in wxEvtHandler::TryHereOnly(wxEvent&) () from
> /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #16 0x00007ffff4443e23 in wxEvtHandler::ProcessEventLocally(wxEvent&) ()
> from /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #17 0x00007ffff4443e85 in wxEvtHandler::ProcessEvent(wxEvent&) () from
> /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #18 0x00007ffff4443be7 in wxEvtHandler::SafelyProcessEvent(wxEvent&) ()
> from /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #19 0x00007ffff4dd4557 in wxWindow::DoSetSize(int, int, int, int, int)
> () from /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #20 0x00007ffff4f6329a in wxBoxSizer::RecalcSizes() () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #21 0x00007ffff4f6111e in wxSizer::Layout() () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #22 0x00007ffff4f60fb5 in wxSizerItem::SetDimension(wxPoint const&,
> wxSize const&) () from /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #23 0x00007ffff4f6329a in wxBoxSizer::RecalcSizes() () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #24 0x00007ffff4f6111e in wxSizer::Layout() () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #25 0x00007ffff4f95436 in wxWindowBase::Layout() () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #26 0x00007ffff4f8fe66 in wxWindowBase::InternalOnSize(wxSizeEvent&) ()
> from /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #27 0x00007ffff44438ce in
> wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&,
> wxEvtHandler*, wxEvent&) () from
> /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #28 0x00007ffff44439d3 in wxEventHashTable::HandleEvent(wxEvent&,
> wxEvtHandler*) () from /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #29 0x00007ffff4443d9b in wxEvtHandler::TryHereOnly(wxEvent&) () from
> /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #30 0x00007ffff4443e23 in wxEvtHandler::ProcessEventLocally(wxEvent&) ()
> from /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #31 0x00007ffff4443e85 in wxEvtHandler::ProcessEvent(wxEvent&) () from
> /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #32 0x00007ffff4443be7 in wxEvtHandler::SafelyProcessEvent(wxEvent&) ()
> from /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #33 0x00007ffff4dd4557 in wxWindow::DoSetSize(int, int, int, int, int)
> () from /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #34 0x00007ffff4dd661d in wxWindow::DoSetClientSize(int, int) () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #35 0x00007ffff4f649a7 in wxSizer::Fit(wxWindow*) () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #36 0x00007ffff6043941 in ?? () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #37 0x000055555564f874 in PyEval_EvalFrameEx ()
> #38 0x0000555555646c7a in PyEval_EvalCodeEx ()
> #39 0x000055555564edb4 in PyEval_EvalFrameEx ()
> #40 0x000055555564e3e2 in PyEval_EvalFrameEx ()
> #41 0x0000555555646c7a in PyEval_EvalCodeEx ()
> #42 0x0000555555662b09 in ?? ()
> #43 0x000055555567b2be in ?? ()
> #44 0x000055555567aeca in ?? ()
> #45 0x0000555555637afb in ?? ()
> #46 0x000055555564e5d0 in PyEval_EvalFrameEx ()
> #47 0x000055555564e3e2 in PyEval_EvalFrameEx ()
> #48 0x0000555555646c7a in PyEval_EvalCodeEx ()
> #49 0x0000555555662b09 in ?? ()
> #50 0x000055555567b2be in ?? ()
> #51 0x000055555567aeca in ?? ()
> #52 0x0000555555637afb in ?? ()
> #53 0x000055555564e5d0 in PyEval_EvalFrameEx ()
> #54 0x000055555564e3e2 in PyEval_EvalFrameEx ()
> #55 0x0000555555646c7a in PyEval_EvalCodeEx ()
> #56 0x0000555555662b09 in ?? ()
> #57 0x000055555567b2be in ?? ()
> #58 0x000055555567aeca in ?? ()
> #59 0x0000555555637afb in ?? ()
> #60 0x000055555564e5d0 in PyEval_EvalFrameEx ()
> #61 0x0000555555646c7a in PyEval_EvalCodeEx ()
> #62 0x0000555555662d9d in ?? ()
> #63 0x000055555563290e in PyObject_Call ()
> #64 0x000055555564b6d3 in PyEval_EvalFrameEx ()
> #65 0x000055555564e3e2 in PyEval_EvalFrameEx ()
> #66 0x0000555555646c7a in PyEval_EvalCodeEx ()
> #67 0x0000555555662b09 in ?? ()
> #68 0x000055555567b2be in ?? ()
> #69 0x000055555563290e in PyObject_Call ()
> #70 0x00005555556529f0 in PyEval_CallObjectWithKeywords ()
> #71 0x00007ffff5fa915e in wxPyCallbackHelper::callCallbackObj(_object*)
> const () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #72 0x00007ffff5fa91cd in wxPyCallbackHelper::callCallback(_object*)
> const () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #73 0x00007fffe8a05f03 in wxPyTimer::Notify() () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_misc_.x86_64-linux-gnu.so
> #74 0x00007ffff4dcc2c1 in ?? () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #75 0x00007ffff241bb73 in ?? () from
> /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
> #76 0x00007ffff241b0f5 in g_main_context_dispatch () from
> /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
> #77 0x00007ffff241b4c0 in ?? () from
> /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
> #78 0x00007ffff241b7d2 in g_main_loop_run () from
> /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
> #79 0x00007ffff35e3e85 in gtk_main () from
> /usr/lib/x86_64-linux-gnu/libgtk-3.so.0
> #80 0x00007ffff4db9cc5 in wxGUIEventLoop::DoRun() () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #81 0x00007ffff42ffea3 in wxEventLoopBase::Run() () from
> /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #82 0x00007ffff42c74b6 in wxAppConsoleBase::MainLoop() () from
> /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #83 0x00007ffff5faf027 in wxPyApp::MainLoop() () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #84 0x00007ffff600ad45 in ?? () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #85 0x000055555564f874 in PyEval_EvalFrameEx ()
> #86 0x0000555555646c7a in PyEval_EvalCodeEx ()
> #87 0x0000555555662b09 in ?? ()
> #88 0x000055555567b2be in ?? ()
> #89 0x000055555564e5d0 in PyEval_EvalFrameEx ()
> #90 0x000055555564e3e2 in PyEval_EvalFrameEx ()
> #91 0x000055555564e3e2 in PyEval_EvalFrameEx ()
> #92 0x0000555555646c7a in PyEval_EvalCodeEx ()
> #93 0x0000555555646709 in PyEval_EvalCode ()
> #94 0x000055555567771f in ?? ()
> #95 0x0000555555672472 in PyRun_FileExFlags ()
> #96 0x00005555556718ed in PyRun_SimpleFileExFlags ()
> #97 0x0000555555620a2b in Py_Main ()
> #98 0x00007ffff6e69a87 in __libc_start_main () from
> /lib/x86_64-linux-gnu/libc.so.6
> #99 0x00005555556202aa in _start ()
> (gdb) quit
>
> if this is useful...
>
> Best regards,
> Torquil Sørensen
>
> On 15/06/18 23:19, Thiago Franco Moraes wrote:
> > Hi,
> >
> > What window manager are your using? I don't why yet, but this error
> > doesn't happen if you use KDE as window manager. It's happening also
> > with the git version (https://github.com/invesalius/invesalius3). If
> > you use the WXPython4 this doesn't happen, but you need to use the git
> > version.
> >
> > Thanks for the bug report.
> > On Thu, Jun 14, 2018 at 3:27 PM Torquil Macdonald Sørensen
> > <torquil at gmail.com> wrote:
> >> Package: invesalius
> >> Version: 3.1.1-3
> >> Severity: grave
> >> Justification: renders package unusable
> >>
> >> When trying to run invesalius, I get this segmentation fault:
> >>
> >> torquil at lenovo-p51:~$ invesalius3
> >> /usr/share/invesalius/invesalius/data/transformations.py:1899: UserWarning: failed to import module _transformations
> >> warnings.warn("failed to import module %s" % name)
> >> session mode: 0
> >> Segmentation fault
> >> torquil at lenovo-p51:~$
> >>
> >> Best regards,
> >> Torquil Sørensen
> >>
> >> -- System Information:
> >> Debian Release: buster/sid
> >> APT prefers unstable
> >> APT policy: (500, 'unstable')
> >> Architecture: amd64 (x86_64)
> >>
> >> Kernel: Linux 4.16.0-2-amd64 (SMP w/8 CPU cores)
> >> Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), LANGUAGE=en_GB:en (charmap=UTF-8)
> >> Shell: /bin/sh linked to /bin/dash
> >> Init: systemd (via /run/systemd/system)
> >>
> >> Versions of packages invesalius depends on:
> >> ii invesalius-bin 3.1.1-3
> >> ii python 2.7.15-3
> >> ii python-concurrent.futures 3.2.0-1
> >> ii python-configparser 3.5.0-1
> >> ii python-gdcm 2.8.6-2
> >> ii python-nibabel 2.3.0-1
> >> ii python-numpy 1:1.14.5-1
> >> ii python-pil 5.1.0-1
> >> ii python-psutil 5.4.6-1
> >> ii python-scipy 0.19.1-2
> >> ii python-serial 3.4-3
> >> ii python-skimage 0.13.1-3
> >> ii python-vtk6 6.3.0+dfsg2-2+b2
> >> ii python-vtkgdcm 2.8.6-2
> >> ii python-wxgtk3.0 3.0.2.0+dfsg-8
> >> ii python2.7 2.7.15-1
> >>
> >> invesalius recommends no packages.
> >>
> >> invesalius suggests no packages.
> >>
> >> -- no debconf information
>
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