I changed the path in our extension by changing
DESTINATION_DIR ${CMAKE_CURRENT_BINARY_DIR}/${Slicer_QTSCRIPTEDMODULES_LIB_DIR}
to
DESTINATION_DIR ${CMAKE_BINARY_DIR}/${Slicer_QTSCRIPTEDMODULES_LIB_DIR}
in the ctkMacroCompilePythonScript call in the module CMakeLists.txt file.

Maybe if the same change is made in the templates, it'd be enough.

I couldn't reproduce that problem on Linux. Is this issue specific to Windows ?

I checked the following structure and they seem to be valid:
1) Linux - build tree
2) Linux - package tree
3) windows - package tree

Could you provide more context ? Are we talking about the tree structure after installing on extension or may be the tree structure associated with windows build tree ?

Thanks

// ---------------------
1) Linux - build tree:

jchris@karakoram:~/Projects/SlicerRt-build/inner-build $ ls lib/Slicer-4.1/*
lib/Slicer-4.1/qt-loadable-modules:
libqSlicerContoursModule.so libvtkSlicerDoseAccumulationModuleLogicPythonD.so Python
libqSlicerDicomRtImportModule.so libvtkSlicerDoseAccumulationModuleLogic.so vtkSlicerDicomRtImportModuleLogicPython.so
libqSlicerDoseAccumulationModule.so libvtkSlicerDoseComparisonModuleLogicPythonD.so vtkSlicerDoseAccumulationModuleLogicPython.so
libqSlicerDoseComparisonModule.so libvtkSlicerDoseComparisonModuleLogic.so vtkSlicerDoseComparisonModuleLogicPython.so
libqSlicerDoseVolumeHistogramModule.so libvtkSlicerDoseVolumeHistogramModuleLogicPythonD.so vtkSlicerDoseVolumeHistogramModuleLogicPython.so
libqSlicerIsodoseModule.so libvtkSlicerDoseVolumeHistogramModuleLogic.so vtkSlicerIsodoseModuleLogicPython.so
libvtkSlicerDicomRtImportModuleLogicPythonD.so libvtkSlicerIsodoseModuleLogicPythonD.so
libvtkSlicerDicomRtImportModuleLogic.so libvtkSlicerIsodoseModuleLogic.so

lib/Slicer-4.1/qt-scripted-modules:
DicomRtImportPlugin.py DicomRtImportPlugin.pyc DicomRtImportSelfTest.py DicomRtImportSelfTest.pyc

// ---------------------
2) Linux - package tree:

jchris@karakoram:~/Projects/SlicerRt-build/inner-build/_CPack_Packages/Linux/TGZ/21184-linux-amd64-SlicerRT-svn356-2012-10-15 $ ls lib/Slicer-4.1/*
lib/Slicer-4.1/qt-loadable-modules:
libqSlicerContoursModule.so libvtkSlicerDoseAccumulationModuleLogicPythonD.so Python
libqSlicerDicomRtImportModule.so libvtkSlicerDoseAccumulationModuleLogic.so vtkSlicerDicomRtImportModuleLogicPython.so
libqSlicerDoseAccumulationModule.so libvtkSlicerDoseComparisonModuleLogicPythonD.so vtkSlicerDoseAccumulationModuleLogicPython.so
libqSlicerDoseComparisonModule.so libvtkSlicerDoseComparisonModuleLogic.so vtkSlicerDoseComparisonModuleLogicPython.so
libqSlicerDoseVolumeHistogramModule.so libvtkSlicerDoseVolumeHistogramModuleLogicPythonD.so vtkSlicerDoseVolumeHistogramModuleLogicPython.so
libqSlicerIsodoseModule.so libvtkSlicerDoseVolumeHistogramModuleLogic.so vtkSlicerIsodoseModuleLogicPython.so
libvtkSlicerDicomRtImportModuleLogicPythonD.so libvtkSlicerIsodoseModuleLogicPythonD.so
libvtkSlicerDicomRtImportModuleLogic.so libvtkSlicerIsodoseModuleLogic.so

lib/Slicer-4.1/qt-scripted-modules:
DicomRtImportPlugin.py DicomRtImportPlugin.pyc DicomRtImportSelfTest.py DicomRtImportSelfTest.pyc

// ---------------------
3) windows - package tree:

jchris@karakoram:~/Downloads/21176-win-amd64-SlicerRT-svn352-2012-10-14 $ ls lib/Slicer-4.1/*
lib/Slicer-4.1/qt-loadable-modules:
Python vtkSlicerDicomRtImportModuleLogic.dll vtkSlicerDoseComparisonModuleLogicPythonD.lib
qSlicerContoursModule.dll vtkSlicerDicomRtImportModuleLogic.lib vtkSlicerDoseComparisonModuleLogicPython.pyd
qSlicerContoursModule.lib vtkSlicerDicomRtImportModuleLogicPythonD.dll vtkSlicerDoseVolumeHistogramModuleLogic.dll
qSlicerDicomRtImportModule.dll vtkSlicerDicomRtImportModuleLogicPythonD.lib vtkSlicerDoseVolumeHistogramModuleLogic.lib
qSlicerDicomRtImportModule.lib vtkSlicerDicomRtImportModuleLogicPython.pyd vtkSlicerDoseVolumeHistogramModuleLogicPythonD.dll
qSlicerDoseAccumulationModule.dll vtkSlicerDoseAccumulationModuleLogic.dll vtkSlicerDoseVolumeHistogramModuleLogicPythonD.lib
qSlicerDoseAccumulationModule.lib vtkSlicerDoseAccumulationModuleLogic.lib vtkSlicerDoseVolumeHistogramModuleLogicPython.pyd
qSlicerDoseComparisonModule.dll vtkSlicerDoseAccumulationModuleLogicPythonD.dll vtkSlicerIsodoseModuleLogic.dll
qSlicerDoseComparisonModule.lib vtkSlicerDoseAccumulationModuleLogicPythonD.lib vtkSlicerIsodoseModuleLogic.lib
qSlicerDoseVolumeHistogramModule.dll vtkSlicerDoseAccumulationModuleLogicPython.pyd vtkSlicerIsodoseModuleLogicPythonD.dll
qSlicerDoseVolumeHistogramModule.lib vtkSlicerDoseComparisonModuleLogic.dll vtkSlicerIsodoseModuleLogicPythonD.lib
qSlicerIsodoseModule.dll vtkSlicerDoseComparisonModuleLogic.lib vtkSlicerIsodoseModuleLogicPython.pyd
qSlicerIsodoseModule.lib vtkSlicerDoseComparisonModuleLogicPythonD.dll

lib/Slicer-4.1/qt-scripted-modules:
DicomRtImportPlugin.py DicomRtImportPlugin.pyc

The issue Andras described is that by default, the DLLs coming from C++ source were deployed in the ${CMAKE_BINARY_DIR}/lib/Slicer-4.1/qt-loadable-modules/[Configuration], but the compiled python scripts (py and pyc files) were deployed in the ${CMAKE_CURRENT_BINARY_DIR}/${Slicer_QTSCRIPTEDMODULES_LIB_DIR}, which is a completely different location and different from module to module.

Looking at the template Extensions\Testing\ScriptedLoadableExtensionTemplate\CMakeLists.txt it seems that this has changed, so that the destination directory is now ${CMAKE_BINARY_DIR}/${Slicer_QTSCRIPTEDMODULES_LIB_DIR} (just like I did recently in case of our python module).

Andras, I think the issue has been resolved, but not sooner than we used the template for our module, this is why it was inconsistent in our case. If you agree, we can close the issue.

The template is fixed, so I agree that this issue can be closed now.

I don't have rights to change the status from the current "feedback" to "closed", so someone with dev or admin rights have to do it.

Re-open if there are still issues.

I also created an issue to track the fact a macro named "slicerMacroBuildScriptedModule" should be added. See 0002647