[vtkusers] Migration to VTK6

Arno Klein binarybottle at gmail.com
Fri Dec 11 01:57:16 EST 2015 

I forgot to mention that the other reason for not explicitly setting the
version of OSX in the CMakeLists.txt file is because when I do set it
appropriately (as you suggested), compilation inexplicably raises the
following error, suggesting that outdated SDKs are required:

make[2]: *** No rule to make target
`/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/AGL.framework',
needed by `travel_depth/TravelDepthMain'.  Stop.

Cheers,
@rno

On Thu, Dec 10, 2015 at 10:46 PM, Arno Klein <binarybottle at gmail.com> wrote:

> I built VTK 6 through the Anaconda Python distribution ("conda install
> vtk" installed 6.3).
>
> I placed the three lines you recommended in the top-level CMakeLists.txt
> file in my library:
> SET(CMAKE_OSX_DEPLOYMENT_TARGET "10.11")
> SET(CMAKE_OSX_ARCHITECTURES "x86_64")
> SET(CMAKE_OSX_SYSROOT "macosx10.11")
>
> This enabled the make command to compile farther than I have been able to
> get so far.  However, it requires someone to explicitly specify which
> version of MacOSX, which I was hoping to avoid.  Previously, I was using:
>
> #https://forums.developer.apple.com/thread/17334
> SET(CMAKE_OSX_DEPLOYMENT_TARGET "")
> SET(CMAKE_OSX_SYSROOT /)
>
> or:
>
> # https://cmake.org/Bug/view.php?id=14695
> SET(MACOSX_DEPLOYMENT_TARGET
> ${DARWIN_MAJOR_SDK_VERSION}.${DARWIN_MINOR_SDK_VERSION})
> SET(CMAKE_CXX_FLAGS "--sysroot ${CMAKE_OSX_SYSROOT} ${CMAKE_CXX_FLAGS}")
>
>
>
> Cheers,
> @rno
>
> On Thu, Dec 10, 2015 at 10:14 PM, David Gobbi <david.gobbi at gmail.com>
> wrote:
>
>> Actually I might have misunderstood your issue.  Did you build VTK 6
>> yourself, or did you download a binary package?  In either case, the three
>> cmake variables that I mentioned above should be set the same in your own
>> project as they are in the VTK that you are building against.
>>
>> On Thu, Dec 10, 2015 at 11:00 PM, David Gobbi <david.gobbi at gmail.com>
>> wrote:
>>
>>> You can try setting the SDK info in the CMakeCache.txt:
>>>
>>> CMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.11
>>> CMAKE_OSX_ARCHITECTURES:STRING=x86_64
>>> CMAKE_OSX_SYSROOT:STRING=macosx10.11
>>>
>>> I recommend deleting your entire build directory, creating a new
>>> CMakeCache.txt that has only these three lines, and then re-running cmake.
>>>
>>>  - David
>>>
>>>
>>> On Thu, Dec 10, 2015 at 10:49 PM, Arno Klein <binarybottle at gmail.com>
>>> wrote:
>>>
>>>> 'gcc tmp.cpp' created an 'a.out' file, and I have been able to compile
>>>> other things, so I guess my Xcode installation is fine.  What do you
>>>> recommend I try next?
>>>>
>>>> Cheers,
>>>> @rno
>>>>
>>>> On Thu, Dec 10, 2015 at 7:52 PM, David Gobbi <david.gobbi at gmail.com>
>>>> wrote:
>>>>
>>>>> The header unistd.h is posix standard and comes with every Xcode SDK.
>>>>> Try compiling the following trivial program.  If it doesn't compile, then
>>>>> there must be something awry with your Xcode installation:
>>>>>
>>>>> #include <unistd.h>
>>>>> int main()
>>>>> {
>>>>>   return 0;
>>>>> }
>>>>>
>>>>>  - David
>>>>>
>>>>> On Thu, Dec 10, 2015 at 7:39 PM, Arno Klein <binarybottle at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Thank you for your help!
>>>>>>
>>>>>> I am now able to compile with cmake on linux, but get the following
>>>>>> error on macosx 10.11, even though there is no "unistd.h" anywhere in my
>>>>>> github repo (https://github.com/nipy/mindboggle/issues/69):
>>>>>>
>>>>>> Scanning dependencies of target FsSurfaceReader
>>>>>> [ 3%] Building CXX object
>>>>>> CMakeFiles/FsSurfaceReader.dir/FsSurfaceReader.cpp.o
>>>>>> In file included from
>>>>>> /software/mindboggle/surface_cpp_tools/FsSurfaceReader.cpp:13:
>>>>>> In file included from
>>>>>> /software/mindboggle/surface_cpp_tools/FsSurfaceReader.h:16:
>>>>>> In file included from /usr/local/include/vtk-6.0/vtkPolyData.h:58:
>>>>>> In file included from /usr/local/include/vtk-6.0/vtkPointSet.h:30:
>>>>>> In file included from /usr/local/include/vtk-6.0/vtkDataSet.h:41:
>>>>>> In file included from /usr/local/include/vtk-6.0/vtkDataObject.h:36:
>>>>>> In file included from /usr/local/include/vtk-6.0/vtkObject.h:42:
>>>>>> In file included from /usr/local/include/vtk-6.0/vtkObjectBase.h:44:
>>>>>> In file included from /usr/local/include/vtk-6.0/vtkIndent.h:25:
>>>>>> In file included from
>>>>>> /usr/local/include/vtk-6.0/vtkSystemIncludes.h:36:
>>>>>> In file included from /usr/local/include/vtk-6.0/vtkIOStream.h:33:
>>>>>> In file included from
>>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/iostream:37:
>>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:23:10:
>>>>>> fatal error:
>>>>>> 'unistd.h' file not found
>>>>>> #include
>>>>>> ^
>>>>>> 1 error generated.
>>>>>> make[2]: *** [CMakeFiles/FsSurfaceReader.dir/FsSurfaceReader.cpp.o]
>>>>>> Error 1
>>>>>> make[1]: *** [CMakeFiles/FsSurfaceReader.dir/all] Error 2
>>>>>> make: *** [all] Error 2
>>>>>>
>>>>>> Cheers,
>>>>>> @rno
>>>>>>
>>>>>> On Thu, Dec 3, 2015 at 6:25 AM, David E DeMarle <
>>>>>> dave.demarle at kitware.com> wrote:
>>>>>>
>>>>>>> I agree with Cory on Update() being redundant before the Write().
>>>>>>>
>>>>>>> >    vtkDataObject* dobj = someAlgorithm->GetOutput(1);
>>>>>>> >    dobj->Update();
>>>>>>>
>>>>>>> should become:
>>>>>>>
>>>>>>>   someAlgorithm->Update(1); //to make sure there is something valid
>>>>>>>   vtkDataObject* dobj = someAlgorithm->GetOutput(1); //keep the
>>>>>>> output for later use
>>>>>>>
>>>>>>> Because since vtk6, dobj no longer has any connection to the
>>>>>>> algorithm, so updating it (which used to update the algorithm for you) no
>>>>>>> longer has any meaning.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> David E DeMarle
>>>>>>> Kitware, Inc.
>>>>>>> R&D Engineer
>>>>>>> 21 Corporate Drive
>>>>>>> Clifton Park, NY 12065-8662
>>>>>>> Phone: 518-881-4909
>>>>>>>
>>>>>>> On Thu, Dec 3, 2015 at 9:09 AM, Cory Quammen <
>>>>>>> cory.quammen at kitware.com> wrote:
>>>>>>>
>>>>>>>> Arno,
>>>>>>>>
>>>>>>>> That pattern should be valid in VTK6. Are you getting compile
>>>>>>>> errors?
>>>>>>>>
>>>>>>>> I believe the Update() and Write() calls to the writer are
>>>>>>>> redundant - you should need only one.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Cory
>>>>>>>>
>>>>>>>> On Wed, Dec 2, 2015 at 5:56 PM, Arno Klein <binarybottle at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> I am trying to update my code to migrate to VTK6 according to:
>>>>>>>>>
>>>>>>>>> http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Update
>>>>>>>>>
>>>>>>>>> According to the examples on that site, I understand that:
>>>>>>>>>
>>>>>>>>>     vtkDataObject* dobj = someAlgorithm->GetOutput(1);
>>>>>>>>>     dobj->Update();
>>>>>>>>>
>>>>>>>>> should become:
>>>>>>>>>
>>>>>>>>>     someAlgorithm->Update(1);
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> However, I don’t know how to deal with the following pattern:
>>>>>>>>>
>>>>>>>>> void PointAreaComputer::WriteIntoFile(char *fileName)
>>>>>>>>> {
>>>>>>>>>     vtkPolyDataWriter* writer=vtkPolyDataWriter::New();
>>>>>>>>>     writer->SetFileName(fileName);
>>>>>>>>>     m_mesh->GetPointData()->SetScalars(m_pointsArea);
>>>>>>>>>     writer->SetInputData(m_mesh);
>>>>>>>>>     writer->Update();
>>>>>>>>>     writer->Write();
>>>>>>>>>     writer->Delete();
>>>>>>>>> }
>>>>>>>>>
>>>>>>>>> What should I do to make this compatible with VTK6?
>>>>>>>>>
>>>>>>>>> Cheers,
>>>>>>>>> @rno
>>>>>>>>>
>>>>>>>>
>>>>>
>>>>
>>>
>>
>
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