[Debian-med-packaging] Bug#901562: invesalius: Segmentation fault at startup
Torquil Macdonald Sørensen
torquil at gmail.com
Fri Jun 15 22:30:47 BST 2018
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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