Thanks for the remainder. Will be working on that issue on Monday.

can you then update

Tcl_Interp* vtkSlicerCommonInterface::Startup
and
vtkSlicerCommonInterfaceTest1.cxx

accordingly ?
Thanks

I started to refactor the code so that the overall process to execute python from a standalone executable like EMSegmentCommandLine is simplified.

On the other hand, I couldn;t reproduce the error.

Would it be possible to provide me with a stack trace ?

I am trying to run it but all my tests now simply hang :

[14] [11:14am] [sbia-pc82 /software/Slicer4/Slicer4-SuperBuild/Slicer-build/QTModules] >ctest -VV -R vtkSlicerCommonInterfaceStartup
UpdateCTestConfiguration from :/software/Slicer4/Slicer4-SuperBuild/Slicer-build/QTModules/DartConfiguration.tcl
UpdateCTestConfiguration from :/software/Slicer4/Slicer4-SuperBuild/Slicer-build/QTModules/DartConfiguration.tcl
Test project /software/Slicer4/Slicer4-SuperBuild/Slicer-build/QTModules
Constructing a list of tests
Done constructing a list of tests
Checking test dependency graph...
Checking test dependency graph end
test 66
Start 66: vtkSlicerCommonInterfaceStartupTest

66: Test command: /software/Slicer4/Slicer4-SuperBuild/Slicer-build/Slicer "--launcher-no-splash" "--launch" "/software/Slicer4/Slicer4-SuperBuild/Slicer-build/bin/vtkSlicerCommonInterfaceStartupTest"
66: Test timeout computed to be: 9.99988e+06
66: emsegmentModulePythonPath:/software/Slicer4/lib/Slicer-build/qt-loadable-modules/Python

nothing happens afterwards

Could you either provide the version of "vtkSlicerCommonInterfaceStartup" you are using or commit the test into EMSegment repository ?

Adding the test into EMSegment/Testing and updating EMSegment/CMakeLists.txt, after re-configuring and re-compiling, the following tests pass:

jchris@karakoram:~/Projects/Slicer4-Superbuild-Debug/Slicer-build $ ctest -R vtkSlicerCommonInterface
Test project /home/jchris/Projects/Slicer4-Superbuild-Debug/Slicer-build
Start 269: vtkSlicerCommonInterfaceTest1
1/2 Test 0000269: vtkSlicerCommonInterfaceTest1 ......... Passed 1.46 sec
Start 270: vtkSlicerCommonInterfaceStartupTest
2/2 Test 0000270: vtkSlicerCommonInterfaceStartupTest ... Passed 1.22 sec

100% tests passed, 0 tests failed out of 2

Total Test time (real) = 3.23 sec

Following 16910, vtkSlicerCommonInterfaceStartupTest can be simplified. The two "HACK" where mainContext and updatePythonOsEnviron are called can be removed.

See also https://github.com/Slicer/Slicer/commit/72231b6e9880b3ad1ffc93d415e937bcaf192ed6

Now I get to

ctest -VV vtkSlicerCommonInterfaceStartupTest
UpdateCTestConfiguration from :/software/Slicer4/Slicer4-SuperBuild/Slicer-build/QTModules/DartConfiguration.tcl
UpdateCTestConfiguration from :/software/Slicer4/Slicer4-SuperBuild/Slicer-build/QTModules/DartConfiguration.tcl
Test project /software/Slicer4/Slicer4-SuperBuild/Slicer-build/QTModules
Constructing a list of tests
Done constructing a list of tests
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: qSlicerColorsModuleWidgetTest1

1: Test command: /software/Slicer4/Slicer4-SuperBuild/Slicer-build/Slicer "--launcher-no-splash" "--launch" "/software/Slicer4/Slicer4-SuperBuild/Slicer-build/bin/ColorsCxxTests" "qSlicerColorsModuleWidgetTest1"
1: Test timeout computed to be: 9.99988e+06
1: RegisterIO "qSlicerColorsIO"

a window shortly pops up and nothing happens afterwards

How is progress with this?

A test named qSlicerApplicationTpyclEMSegmentIntegrationTest has been added. See https://github.com/Slicer/Slicer/commit/bb82ef199e72665a4955dc330c39de9dbb3fec20

The test passes on Ubuntu 10.04 / gcc (Ubuntu 4.4.3-4ubuntu5)

Linking issue on windows should now be fixed.
See http://slicer.cdash.org/viewBuildError.php?buildid=6120
and http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=18920

I still have the same issue - how should I debug it ?

Linux sbia-pc82 3.0.0-14-generic 0000023-Ubuntu SMP Mon Nov 21 20:28:43 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux

[5] [9:10pm] [sbia-pc82 /data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build] >ctest -VV -R qSlicerApplicationTpyclEMSegmentIntegrationTest
UpdateCTestConfiguration from :/data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/DartConfiguration.tcl
Parse Config file:/data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/DartConfiguration.tcl
Add coverage exclude regular expressions.
Add coverage exclude: /CMakeFiles/CMakeTmp/
Add coverage exclude: ./moc_.
Add coverage exclude: ./ui_.
Add coverage exclude: ./Testing/.
UpdateCTestConfiguration from :/data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/DartConfiguration.tcl
Parse Config file:/data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/DartConfiguration.tcl
Test project /data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build
Constructing a list of tests
Done constructing a list of tests
Checking test dependency graph...
Checking test dependency graph end
test 466
Start 466: qSlicerApplicationTpyclEMSegmentIntegrationTest

466: Test command: /data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/Slicer "--launcher-no-splash" "--launch" "/data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/bin/SlicerQTCxxTests" "qSlicerApplicationTpyclEMSegmentIntegrationTest" "/data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/lib/Slicer-4.0/cli-modules/EMSegmentCommandLine"
466: Test timeout computed to be: 1500
466: emsegmentModulePythonPath:/data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/lib/Slicer-4.0/qt-loadable-modules/Python
1/1 Test 0000466: qSlicerApplicationTpyclEMSegmentIntegrationTest ...***Timeout 2062.50 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 2063.37 sec

The following tests FAILED:
466 - qSlicerApplicationTpyclEMSegmentIntegrationTest (Timeout)
Errors while running CTest
[6] [9:44pm] [sbia-pc82 /data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build] >

Using the debugger could be useful.
See http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers/Tutorials/Debug_Instructions

We need to find out why the test is timing out

As of Dec 20 2011, the test "qSlicerApplicationTpyclEMSegmentIntegrationTest" passes on the following platform:

• Ubuntu: http://slicer.cdash.org/testDetails.php?test=477270&build=6359
• MacOSX: http://slicer.cdash.org/testDetails.php?test=478121&build=6377
• Win-i386(VS2008): http://slicer.cdash.org/testDetails.php?test=486317&build=6372
• Win-amd64(VS2008): http://slicer.cdash.org/testDetails.php?test=487000&build=6383

I followed the instructions on that web site but it did not help a lot - instead I executed the following :

[12] [9:34pm] [sbia-pc82 /software/Slicer4/Slicer4-SuperBuild/Slicer-build] >gdb /software/Slicer4/Slicer4-SuperBuild/Slicer-build/bin/vtkSlicerCommonInterfaceStartupTest
GNU gdb (Ubuntu/Linaro 7.3-0ubuntu2) 7.3-2011.08
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://bugs.launchpad.net/gdb-linaro/>...
Reading symbols from /software/Slicer4/Slicer4-SuperBuild/Slicer-build/bin/vtkSlicerCommonInterfaceStartupTest...done.
(gdb) run
Starting program: /software/Slicer4/Slicer4-SuperBuild/Slicer-build/bin/vtkSlicerCommonInterfaceStartupTest
[Thread debugging using libthread_db enabled]
[New Thread 0x7fffce7ab700 (LWP 21411)]
[New Thread 0x7fffcdfaa700 (LWP 21412)]
[New Thread 0x7fffc2ee3700 (LWP 21413)]
[New Thread 0x7fffc26e2700 (LWP 21414)]
[New Thread 0x7fffc1ee1700 (LWP 21415)]
[New Thread 0x7fffc16e0700 (LWP 21416)]
emsegmentModulePythonPath:/software/Slicer4/lib/Slicer-build/qt-loadable-modules/Python
[Thread 0x7fffc2ee3700 (LWP 21413) exited]
pure virtual method called
[Thread 0x7fffc26e2700 (LWP 21414) exited]
terminate called without an active exception

Program received signal SIGABRT, Aborted.
0x00007ffff51ef3a5 in raise () from /lib/x86_64-linux-gnu/libc.so.6

(gdb) backtrace
#0 0x00007ffff51ef3a5 in raise () from /lib/x86_64-linux-gnu/libc.so.6
0000001 0x00007ffff51f2b0b in abort () from /lib/x86_64-linux-gnu/libc.so.6
0000002 0x00007ffff5829d7d in gnu_cxx::__verbose_terminate_handler() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
0000003 0x00007ffff5827f26 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
0000004 0x00007ffff5827f53 in std::terminate() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
0000005 0x00007ffff582896f in cxa_pure_virtual () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
0000006 0x00007fffb8c1ab96 in OFCondition::~OFCondition (this=0x7fffb9c7cb90, __in_chrg=<optimized out>)
at /software/Slicer4/Slicer4-SuperBuild/CTK-build/CMakeExternals/Install/include/dcmtk/ofstd/ofcond.h:346
0000007 0x00007ffff51f4821 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
0000008 0x00007ffff51f48a5 in exit () from /lib/x86_64-linux-gnu/libc.so.6
0000009 0x00007ffff51da314 in __libc_start_main () from /lib/x86_64-linux-gnu/libc.so.6
0000010 0x0000000000401eb9 in _start ()

Any help ?

http://forum.dcmtk.org/viewtopic.php?t=1119
http://forum.dcmtk.org/viewtopic.php?t=503

Somewhere in your test, you might want to add "OFCondition cond = EC_Normal;"

After preventing the DICOM related modules from loading, it resumes the issue is related to FD message handler.

The following backtrace has been obtained by attaching gdb to the SlicerQTCxxTests.

(gdb) backtrace
#0 0x00007f6ed489004c in pthread_cond_wait@@GLIBC_2.3.2 () from /lib/x86_64-linux-gnu/libpthread.so.0
0000001 0x00007f6ed4b271ab in QWaitCondition::wait(QMutex*, unsigned long) () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4
0000002 0x00007f6ed4b26a4c in QThread::wait(unsigned long) () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4
0000003 0x00007f6ed5c79b4d in ctkFDHandler::setEnabled (this=0x210dcf0, value=false) at /software/Slicer4/Slicer4-SuperBuild/CTK/Libs/Core/ctkErrorLogFDMessageHandler.cpp:133
0000004 0x00007f6ed5c7a111 in ctkErrorLogFDMessageHandler::setEnabledInternal (this=0x210d5d0, value=false) at /software/Slicer4/Slicer4-SuperBuild/CTK/Libs/Core/ctkErrorLogFDMessageHandler.cpp:254
0000005 0x00007f6ed5c76139 in ctkErrorLogAbstractMessageHandler::setEnabled (this=0x210d5d0, value=false) at /software/Slicer4/Slicer4-SuperBuild/CTK/Libs/Core/ctkErrorLogModel.cpp:734
0000006 0x00007f6ed5c72d5f in ctkErrorLogModelPrivate::~ctkErrorLogModelPrivate (this=0x2115fb0, in_chrg=<optimized out>) at /software/Slicer4/Slicer4-SuperBuild/CTK/Libs/Core/ctkErrorLogModel.cpp:231
0000007 0x00007f6ed5c787a9 in QScopedPointerDeleter<ctkErrorLogModelPrivate>::cleanup (pointer=0x2115fb0) at /usr/include/qt4/QtCore/qscopedpointer.h:62
0000008 0x00007f6ed5c77556 in QScopedPointer<ctkErrorLogModelPrivate, QScopedPointerDeleter<ctkErrorLogModelPrivate> >::~QScopedPointer (this=0x2149ef0, __in_chrg=<optimized out>) at /usr/include/qt4/QtCore/qscopedpointer.h:100
0000009 0x00007f6ed5c73348 in ctkErrorLogModel::~ctkErrorLogModel (this=0x2149ee0, in_chrg=<optimized out>) at /software/Slicer4/Slicer4-SuperBuild/CTK/Libs/Core/ctkErrorLogModel.cpp:287
0000010 0x00007f6ed5c733cb in ctkErrorLogModel::~ctkErrorLogModel (this=0x2149ee0, in_chrg=<optimized out>) at /software/Slicer4/Slicer4-SuperBuild/CTK/Libs/Core/ctkErrorLogModel.cpp:289
0000011 0x00007f6ed66704fb in QtSharedPointer::ExternalRefCount<ctkErrorLogModel>::deref (d=0x214fb90, value=0x2149ee0) at /usr/include/qt4/QtCore/qsharedpointer_impl.h:344
0000012 0x00007f6ed666f927 in QtSharedPointer::ExternalRefCount<ctkErrorLogModel>::deref (this=0x1e980b8) at /usr/include/qt4/QtCore/qsharedpointer_impl.h:338
0000013 0x00007f6ed666e39f in QtSharedPointer::ExternalRefCount<ctkErrorLogModel>::~ExternalRefCount (this=0x1e980b8, in_chrg=<optimized out>) at /usr/include/qt4/QtCore/qsharedpointer_impl.h:403
0000014 0x00007f6ed666dd2d in QSharedPointer<ctkErrorLogModel>::~QSharedPointer (this=0x1e980b8, in_chrg=<optimized out>) at /usr/include/qt4/QtCore/qsharedpointer_impl.h:461
0000015 0x00007f6ed6666666 in qSlicerCoreApplicationPrivate::~qSlicerCoreApplicationPrivate (this=0x1e98010, __in_chrg=<optimized out>) at /software/Slicer4/Slicer4/Base/QTCore/qSlicerCoreApplication.cxx:99
0000016 0x00007f6ed6b6d29c in qSlicerApplicationPrivate::~qSlicerApplicationPrivate (this=0x1e98010, in_chrg=<optimized out>) at /software/Slicer4/Slicer4/Base/QTGUI/qSlicerApplication.cxx:96
0000017 0x00007f6ed6b6d329 in qSlicerApplicationPrivate::~qSlicerApplicationPrivate (this=0x1e98010, in_chrg=<optimized out>) at /software/Slicer4/Slicer4/Base/QTGUI/qSlicerApplication.cxx:100
0000018 0x00007f6ed666fe0e in QScopedPointerDeleter<qSlicerCoreApplicationPrivate>::cleanup (pointer=0x1e98010) at /usr/include/qt4/QtCore/qscopedpointer.h:62
0000019 0x00007f6ed666eba6 in QScopedPointer<qSlicerCoreApplicationPrivate, QScopedPointerDeleter<qSlicerCoreApplicationPrivate> >::~QScopedPointer (this=0x1d235f8, __in_chrg=<optimized out>) at /usr/include/qt4/QtCore/qscopedpointer.h:100
0000020 0x00007f6ed6669a64 in qSlicerCoreApplication::~qSlicerCoreApplication (this=0x1d235d0, in_chrg=<optimized out>) at /software/Slicer4/Slicer4/Base/QTCore/qSlicerCoreApplication.cxx:562
0000021 0x00007f6ed6b6d90f in qSlicerApplication::~qSlicerApplication (this=0x1d235d0, __in_chrg=<optimized out>) at /software/Slicer4/Slicer4/Base/QTGUI/qSlicerApplication.cxx:173
0000022 0x00007f6ed6b6d965 in qSlicerApplication::~qSlicerApplication (this=0x1d235d0, __in_chrg=<optimized out>) at /software/Slicer4/Slicer4/Base/QTGUI/qSlicerApplication.cxx:175
0000023 0x00000000004080d7 in qSlicerApplicationTpyclEMSegmentIntegrationTest (argc=2, argv=0x7ffff9b8bc80) at /software/Slicer4/Slicer4/Applications/SlicerQT/Testing/Cpp/qSlicerApplicationTpyclEMSegmentIntegrationTest.cxx:54
0000024 0x0000000000404cdb in main (ac=2, av=0x7ffff9b8bc80) at /software/Slicer4/Slicer4-SuperBuild/Slicer-build/Applications/SlicerQT/Testing/Cpp/SlicerQTCxxTests.cxx:171

When executing

make SlicerQTCxxTests && ctest -VV -R EMSegmentInt

with
int qSlicerApplicationTpyclEMSegmentIntegrationTest(int argc, char argv[])
{
// qSlicerApplication::setAttribute(qSlicerApplication::AA_DisablePython, true);
qSlicerApplication app = new qSlicerApplication(argc, argv);
delete app;
return EXIT_SUCCESS;
}

then the test passes. if we include
SlicerApplication::setAttribute(qSlicerApplication::AA_DisablePython, true);

then the test crashes

481: pure virtual method called
481: terminate called without an active exception
481: error: [/software/Slicer4/Slicer4-SuperBuild/Slicer-build/bin/SlicerQTCxxTests] exit abnormally - Report the problem.
1/1 Test 0000481: qSlicerApplicationTpyclEMSegmentIntegrationTest ...***Failed 1.61 sec

with the following backtrace:

Program received signal SIGABRT, Aborted.
0x00007ffff410d3a5 in raise () from /lib/x86_64-linux-gnu/libc.so.6
(gdb) backtrace
#0 0x00007ffff410d3a5 in raise () from /lib/x86_64-linux-gnu/libc.so.6
0000001 0x00007ffff4110b0b in abort () from /lib/x86_64-linux-gnu/libc.so.6
0000002 0x00007ffff4747d7d in gnu_cxx::__verbose_terminate_handler() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
0000003 0x00007ffff4745f26 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
0000004 0x00007ffff4745f53 in std::terminate() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
0000005 0x00007ffff474696f in cxa_pure_virtual () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
0000006 0x00007fffbabc6b96 in OFCondition::~OFCondition (this=0x7fffbbc28b90, __in_chrg=<optimized out>) at /software/Slicer4/Slicer4-SuperBuild/CTK-build/CMakeExternals/Install/include/dcmtk/ofstd/ofcond.h:346
0000007 0x00007ffff4112821 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
0000008 0x00007ffff41128a5 in exit () from /lib/x86_64-linux-gnu/libc.so.6
0000009 0x00007ffff40f8314 in __libc_start_main () from /lib/x86_64-linux-gnu/libc.so.6
0000010 0x00000000004043b9 in _start ()

which is due to dcmtk

To pass it disable DICOM (temporary solution)
Step 1) Remove form CTK

• go to CTK-build
• ccmake . and disable all entries with DICOM on the top level -> make
  Step 2) Remove from Slicer 4
• Comment out dicom entry from /software/Slicer4/Slicer4/Base/QTCore/CMakeLists.txt
• recompile slicer
• remove in Slicer-build/lib/Slicer-4.0/qt-scripted-modules/
  DICOM2FullBrainTractography.py and DICOM.py

then the above test passes

if comment out

//this->ErrorLogModel->registerMsgHandler(new ctkErrorLogFDMessageHandler);

in

Slicer4/Base/QTCore/qSlicerCoreApplication.cxx

then the entire test passes

If I execute the test in release mode same bug comes up

test 481
Start 481: qSlicerApplicationTpyclEMSegmentIntegrationTest

481: Test command: /data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/Slicer "--launcher-no-splash" "--launch" "/data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/bin/SlicerQTCxxTests" "qSlicerApplicationTpyclEMSegmentIntegrationTest" "/data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/lib/Slicer-4.0/cli-modules/EMSegmentCommandLine"
481: Test timeout computed to be: 1500
481: emsegmentModulePythonPath:/data/software/Slicer4-2011-12-15-18938/Slicer4-SuperBuild/Slicer-build/lib/Slicer-4.0/qt-loadable-modules/Python

now it hangs

The OFCondition crash at exit is due to:
import ctk
in slicerqt.py (loaded at startup)

I tried to reproduce the error in CTK only by running:
$ ./bin/CTKScriptingPythonWidgetsCppTests ctkPythonConsoleTest1 -I

import ctk
ImportError: No module named ctk

I do not understand the entry completely - it does not seem to replicate the bug - correct ?

In CTK, ctkSimplePythonShell reproduces the OFCondition crash at exit (pure virtual method called).
Preventing CTKDICOMWidgetsPythonQt from being loaded in init.py doesn't produce the error.
More specifically, removing all the registerClass() from PythonQt_init_org_commontk_CTKDICOMWidgets prevents the error from occuring.
Jc, any idea on what could go wrong ?

Ok, I can now reproduce in CTK without the need of using python.
Just running the ctkDICOM app is enough to reproduce the crash. An email has been sent to the offis (dcmtk) team.

From Julien:

With what test do you have the crash ?

When I fix the DICOM error, I don't have the msghandler problem:
from a clean slicer repo:
edit the file: Slicer-Superbuild/CTK/Libs/Scripting/Python/Core/Python/ctk/init.py.in :
...
if kit != 'DICOMWidgets' :
exec "from CTK%sPythonQt import *" % (kit)
...
cd CTK-build/CTK-build; make;
cd ../../Slicer-build; make
ctest -R EMSeg

then all the tests but 2 pass.

so I checked out Slicer

edited Slicer-Superbuild/CTK/Libs/Scripting/Python/Core/Python/ctk/init.py.in

I changed

try:
exec "from CTK%sPythonQt import *" % (kit)

to
try:
if kit != 'DICOMWidgets' :
exec "from CTK%sPythonQt import *" % (kit)

build CTK and SLICER

and executed ctest -VV -R qSlicerApplicationTpyclEMSegmentIntegrationTest

The test still gets stuck - nothing has changed. Is that also true for you ?

If yours is passing do you have the 32 or 64 bit version of ubuntu installed ?
Here is mine

Linux sbia-pc82 3.0.0-15-generic 0000026-Ubuntu SMP Fri Jan 20 17:23:00 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

Could you make sure the file "CTK-build/CTK-build/bin/Python/ctk/init.py" still contains the modification after rebuilding ?

If not, I would suggest to directly update the file "CTK-build/CTK-build/bin/Python/ctk/init.py"

it does

The problem with ctkErrorLogFDMessageHandler seems to be resolved thanks to JC . We now still have the issue with DCMTK. So If we run Slicer without DCMTK by
1) removing DICOMWidgets' and 'DICOMCore' from CTK-build/CTK-build/bin/Python/ctk/init.py
2) remove DICOM2FullBrainTractography.py and DICOM.py in Slicer-build/lib/Slicer-4.0/qt-scripted-modules/
then ctest qSlicerApplicationTpyclEMSegmentIntegrationTest passes

Additional notes from JC:
No recompilation of CTK / Slicer should be required to disable DICOM related module.

Each time you will update EMSegment code, make sure to either just rebuild the corresponding target in Slicer or remove the DICOM2FullBrainTractography.py and DICOM.py again.

Now when I

1) removing DICOMWidgets' and 'DICOMCore' from CTK-build/CTK-build/bin/Python/ctk/init.py
2) remove DICOM2FullBrainTractography.py and DICOM.py in Slicer-build/lib/Slicer-4.1/qt-scripted-modules/

ctest qSlicerApplicationTpyclEMSegmentIntegrationTest fails

If the stack trace still mention OFCondition .. it means you failed to remove / rebuild without DCMTK. Could you check which stack trace you obtain ?

See http://www.na-mic.org/Bug/view.php?id=1537#c3527

FYI - Few days ago, an option named Slicer_BUILD_DICOM_SUPPORT has been added. You could probably do a clean build in a different folder disabling this option.

I confirm that the test does not fail anymore after performing a clean build with Slicer_BUILD_DICOM_SUPPORT disabled

Either
a) fix the linking with Static DCMTK or
b) change to loadable DCMTK

This should be fixed with the recent update made at the AHM2013 when working on the ITKv4 integration. See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=21602