[Debian-med-packaging] Processed: Re: Bug#909120: camitk FTBFS: tests segfault (Bug #909120)

[Emmanuel Promayon]

Dear Bernhard,

Thank you for your investigation and your time. You are right about 
these double delete and this will have to be fixed.

But I am still puzzled:
1) your patch is absolutely required for handling delete properly (btw 
thanks for the corresponding references!) but unfortunately it can fix 
only some of the tests
2) this bug only appeared recently, no segfault were detected before on 
sid (first trace I found of a failure is in our weekly packaging test 
last Sunday 15 September, everything was fine on Sunday 9 September)
3) the segfaults are generated during testing

This probably means that the problem comes from a deeper (darker, harder 
to find) side of the build.

So I started with the first test on the list that generates a segfaults 
(test #27 named action-editframes-level1-1) and run it through the 
debugger (I run it through the same xvfb-run command line as in the 
debian/control file).

Here is the first outcome:

xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" 
/usr/bin/gdb 
/root/packaging/camitk-debian-ci/camitk-build/bin/camitk-testactions
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Reading symbols from 
/root/packaging/camitk-debian-ci/camitk-build/bin/camitk-testactions...done.
(gdb) r "-i" 
"/root/packaging/camitk-debian-ci/camitk-build/share/camitk-4.2/testdata/brain.mha" 
"-a" 
"/root/packaging/camitk-debian-ci/camitk-build/lib/camitk-4.2/actions/libeditframes.so"
Starting program: 
/root/packaging/camitk-debian-ci/camitk-build/bin/camitk-testactions 
"-i" 
"/root/packaging/camitk-debian-ci/camitk-build/share/camitk-4.2/testdata/brain.mha" 
"-a" 
"/root/packaging/camitk-debian-ci/camitk-build/lib/camitk-4.2/actions/libeditframes.so"
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
camitk-testactions run with arguments:
- action library file: 
"/root/packaging/camitk-debian-ci/camitk-build/lib/camitk-4.2/actions/libeditframes.so"
- input test file: 
"/root/packaging/camitk-debian-ci/camitk-build/share/camitk-4.2/testdata/brain.mha"
Working directory: /root/packaging/camitk-debian-ci/camitk-build
Starting the camitk default application...
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-root'
[New Thread 0x7fffec879700 (LWP 8505)]
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-root'
[New Thread 0x7fffe7f46700 (LWP 8507)]
[OK]
Opening component: 
/root/packaging/camitk-debian-ci/camitk-build/share/camitk-4.2/testdata/brain.mha...
[New Thread 0x7fffda562700 (LWP 8514)]
[New Thread 0x7fffd9d61700 (LWP 8515)]
[New Thread 0x7fffd9560700 (LWP 8516)]
[Thread 0x7fffda562700 (LWP 8514) exited]
[New Thread 0x7fffd8d5f700 (LWP 8517)]
[Thread 0x7fffd9d61700 (LWP 8515) exited]
[New Thread 0x7fffd3fff700 (LWP 8518)]
[New Thread 0x7fffd37fe700 (LWP 8519)]
[New Thread 0x7fffd2ffd700 (LWP 8520)]
[Thread 0x7fffd9560700 (LWP 8516) exited]
[Thread 0x7fffd8d5f700 (LWP 8517) exited]
[Thread 0x7fffd3fff700 (LWP 8518) exited]
[Thread 0x7fffd2ffd700 (LWP 8520) exited]
[Thread 0x7fffd37fe700 (LWP 8519) exited]
[New Thread 0x7fffd2ffd700 (LWP 8521)]
[New Thread 0x7fffd37fe700 (LWP 8522)]
[New Thread 0x7fffd3fff700 (LWP 8523)]
[New Thread 0x7fffd8d5f700 (LWP 8524)]
[New Thread 0x7fffd25c4700 (LWP 8525)]
[New Thread 0x7fffd1dc3700 (LWP 8526)]
[New Thread 0x7fffd15c2700 (LWP 8527)]
[New Thread 0x7fffd0dc1700 (LWP 8528)]

Thread 1 "camitk-testacti" received signal SIGSEGV, Segmentation fault.
0x00007ffff5718f15 in vtkTextProperty::ShallowCopy(vtkTextProperty*) () 
from /lib/x86_64-linux-gnu/libvtkRenderingCore-6.3.so.6.3
(gdb) where
#0  0x00007ffff5718f15 in vtkTextProperty::ShallowCopy(vtkTextProperty*) 
() from /lib/x86_64-linux-gnu/libvtkRenderingCore-6.3.so.6.3
#1  0x00007ffff7f457d7 in 
camitk::RendererWidget::RendererWidget(QWidget*, 
camitk::RendererWidget::ControlMode) () at 
/usr/include/vtk-6.3/vtkSmartPointer.h:77
#2  0x00007ffff7f31d42 in 
camitk::InteractiveViewer::InteractiveViewer(QString&, 
camitk::InteractiveViewer::ViewerType) ()
     at ./sdk/libraries/core/viewer/InteractiveViewer.cpp:192
#3  0x00007ffff7f33533 in 
camitk::InteractiveViewer::getNewViewer(QString, 
camitk::InteractiveViewer::ViewerType) ()
     at ./sdk/libraries/core/viewer/InteractiveViewer.cpp:90
#4  0x00007ffff7f337c5 in camitk::InteractiveViewer::getViewer(QString) 
() at /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:953
#5  0x00007ffff7f33b25 in camitk::InteractiveViewer::getAxialViewer() () 
at /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:953
#6  0x00007ffff7efea2f in 
camitk::SingleImageComponent::initRepresentation() () at 
./sdk/libraries/core/component/image/SingleImageComponent.cpp:94
#7  0x00007ffff7efeb67 in 
camitk::SingleImageComponent::SingleImageComponent(camitk::Component*, 
camitk::Slice::SliceOrientation, QString const&, 
vtkSmartPointer<vtkWindowLevelLookupTable>) () at 
./sdk/libraries/core/component/image/SingleImageComponent.cpp:58
#8  0x00007ffff7ef5fbf in camitk::ImageComponent::buildImageComponents() 
() at /usr/include/vtk-6.3/vtkSmartPointer.h:26
#9  0x00007ffff7ef8b4d in 
camitk::ImageComponent::setImageData(vtkSmartPointer<vtkImageData>, 
bool, camitk::ImageOrientationHelper::PossibleImageOrientations, 
vtkSmartPointer<vtkMatrix4x4>) () at 
./sdk/libraries/core/component/image/ImageComponent.cpp:313
#10 0x00007fffdb5f1df9 in VtkImageComponent::createComponent(QString 
const&) () at /usr/include/vtk-6.3/vtkSmartPointer.h:26
#11 0x00007fffdb5f2905 in VtkImageComponent::VtkImageComponent(QString 
const&) () at ./sdk/components/vtkimage/VtkImageComponent.cpp:53
#12 0x00007fffdb5f2f3a in VtkImageComponentExtension::open(QString 
const&) () at ./sdk/components/vtkimage/VtkImageComponentExtension.cpp:76
#13 0x00007ffff7ec6c24 in camitk::Application::open(QString const&) () 
at ./sdk/libraries/core/application/Application.cpp:470
#14 0x000055555555b3df in main () at 
/usr/include/c++/8/bits/basic_string.h:2293
#15 0x00007ffff6e90b17 in __libc_start_main (main=0x55555555ae80 <main>, 
argc=5, argv=0x7fffffffeb58, init=<optimized out>, fini=<optimized out>,
     rtld_fini=<optimized out>, stack_end=0x7fffffffeb48) at 
../csu/libc-start.c:310
#16 0x000055555555c1aa in _start () at 
./sdk/applications/testactions/main.cpp:189

It is very strange as this specific call to vtkTextProperty::ShallowCopy 
never generated a segfault in any version of the code. Is this a problem 
linked with X11/OpenGL?

This is where I am at the moment, nothing solved at all, but I wanted to 
let you know of this findings.

I suspect something changed in one of the dependencies that generates 
this. I tried to check which package was modified recently and might 
have influence this. I found that xvfb might changed recently and I am 
currently rebuilding with an older version installed to checked (but 
that looks like groping my way along!)

Andreas, do you have any smart way to check the list of packages that 
have changed/been uploaded in sid in the dependencies of a package 
during a period of time (here from 9 Sep to 15 Sep)? This might help me 
finding how to solve this.

Thanks for your help again and hopefully this will be tackled down soon!

Mahnu

On 20/09/2018 21:03, Debian Bug Tracking System wrote:
> Processing control commands:
>
>> tags -1 upstream
> Bug #909120 [src:camitk] camitk FTBFS: tests segfault
> Added tag(s) upstream.
>