[vtkusers] Migration to VTK6

David Gobbi david.gobbi at gmail.com
Thu Jan 7 16:17:03 EST 2016 

I apologize for that... I had forgotten that you were using a binary
distribution of VTK rather than building VTK from source.  My recent
thinking was that the only binary piece you were using from Anaconda was
python itself, I didn't go back and re-read our entire conversation.

This means that all of my recent advice to you has been totally irrelevant.
 (It would be very relevant to the Anaconda folks if they plan to put out a
new vtk package soon... they could save people like yourself a lot of
difficulty.)

If you're using a binary vtk, then you'll have to dig into the cmake
exports for VTK and perform some surgical changes to them.  Somewhere in
your Anaconda VTK, there should be a directory called the following:

cmake/vtk-6.3

Once you find that directory, "cd" into it, and it should be full of cmake
files.  These cmake files list the dependencies for your VTK package.  If
you edit these files to remove all references to "AGL" and the problematic
SDK, then your compile difficulties should go away.  For example, use this
to find all the files that reference AGL:

find . -name "*.cmake" -exec fgrep -l AGL {} +

But it might be easier if you find a Mac with OS X 10.9 and Xcode 6.1, and
then re-do your build there.

 - David


On Thu, Jan 7, 2016 at 1:39 PM, Arno Klein <binarybottle at gmail.com> wrote:

> Thank you!  I am afraid I still don't know where it goes, given the conda
> installation of vtk doesn't have a CMake subdirectory (miniconda2/pkgs/vtk-6.3.0-py27_1/).
> Any suggestions how to proceed?
>
> On Thu, Jan 7, 2016 at 3:16 PM David Gobbi <david.gobbi at gmail.com> wrote:
>
>> It is not the same directory.  FindOpenGL.cmake is part of cmake, but
>> vtkOpenGL.cmake is part of VTK.
>>
>> On Thu, Jan 7, 2016 at 12:50 PM, Arno Klein <binarybottle at gmail.com>
>> wrote:
>>
>>> If that is the same directory that FindOpenGL.cmake is in, then the path
>>> I sent should be correct, yes?  I installed cmake using Anaconda: "conda
>>> install --yes cmake"
>>>
>>> On Thu, Jan 7, 2016 at 12:15 PM David Gobbi <david.gobbi at gmail.com>
>>> wrote:
>>>
>>>> Hi Arno,
>>>>
>>>> My fault, I should have mentioned that it needs to be in
>>>> <vtk-source>/CMake/vtkOpenGL.cmake in order be used during the VTK build.
>>>>
>>>>  - David
>>>>
>>>> On Thu, Jan 7, 2016 at 9:59 AM, Arno Klein <binarybottle at gmail.com>
>>>> wrote:
>>>>
>>>>> Thank you for the suggestion, David.  I placed the vtkOpenGL.cmake
>>>>> file in
>>>>>
>>>>> /Users/arno/Software/install/miniconda2/pkgs/cmake-3.3.1-0/share/cmake-3.3/Modules
>>>>> but still receive the same error.
>>>>>
>>>>> On Thu, Jan 7, 2016 at 11:44 AM David Gobbi <david.gobbi at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> There's also this patch to vtkOpenGL.cmake that you can try:
>>>>>>
>>>>>> https://gitlab.kitware.com/vtk/vtk/commit/4a1fbefe
>>>>>>
>>>>>>  - David
>>>>>>
>>>>>>
>>>>>> On Thu, Jan 7, 2016 at 7:11 AM, Arno Klein <binarybottle at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> That was an excellent suggestion, but alas, even after replacing
>>>>>>> that file with the newer one from the link you shared I am still getting
>>>>>>> the same error!
>>>>>>>
>>>>>>> On Thu, Jan 7, 2016 at 8:34 AM David Gobbi <david.gobbi at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Arno,
>>>>>>>>
>>>>>>>> You can try replacing FindOpenGL.cmake with the latest one from the
>>>>>>>> cmake master branch:
>>>>>>>>
>>>>>>>> https://cmake.org/gitweb?p=cmake.git;a=blob_plain;f=Modules/FindOpenGL.cmake
>>>>>>>> On my machine, for example, the file is located here:
>>>>>>>>
>>>>>>>> /Applications/CMake.app/Contents/share/cmake-3.4/Modules/FindOpenGL.cmake
>>>>>>>> That might help with AGL.
>>>>>>>>
>>>>>>>>  - David
>>>>>>>>
>>>>>>>>
>>>>>>>> On Thu, Jan 7, 2016 at 5:37 AM, Arno Klein <binarybottle at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Yes, it should be building from miniconda2.  However, I can't find
>>>>>>>>> any instance of "AGL" or of "10.7" anywhere in the code base  (only within
>>>>>>>>> the bin directory after running cmake).  I am baffled and stuck.
>>>>>>>>>
>>>>>>>>> On Wed, Jan 6, 2016 at 9:36 PM David Gobbi <david.gobbi at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Arno,
>>>>>>>>>>
>>>>>>>>>> Are you still building against the Anaconda python?  The build
>>>>>>>>>> has to be picking up the AGL and the 10.7 SDK from somewhere, and if it
>>>>>>>>>> isn't in your CMakeCache.txt, then it must be coming from somewhere.
>>>>>>>>>>
>>>>>>>>>>  - David
>>>>>>>>>>
>>>>>>>>>> On Wed, Jan 6, 2016 at 7:19 PM, Arno Klein <
>>>>>>>>>> binarybottle at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Dear David,
>>>>>>>>>>>
>>>>>>>>>>> When I clear the bin directory, then run "cmake .." and "make" I
>>>>>>>>>>> don't find any instance of 10.7 mentioned in any file, but still get
>>>>>>>>>>> "AGL.framework" in every subdirectory's build.make file.  The
>>>>>>>>>>> CMakeCache.txt file contains the following line:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> CMAKE_OSX_SYSROOT:PATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk
>>>>>>>>>>>
>>>>>>>>>>> And yet I am still receiving the following error:
>>>>>>>>>>>
>>>>>>>>>>> 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 Wed, Jan 6, 2016 at 8:48 PM, David Gobbi <
>>>>>>>>>>> david.gobbi at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Arno,
>>>>>>>>>>>>
>>>>>>>>>>>> It could be a stale dependency.  Remove everything after the
>>>>>>>>>>>> "INTERNAL cache entries" comment in your CMakeCache.txt, and also search
>>>>>>>>>>>> your cache to make sure that 10.7 does not appear anywhere.
>>>>>>>>>>>>
>>>>>>>>>>>> Also do an "ls -l /System/Library/Frameworks/" to make sure
>>>>>>>>>>>> that the OpenGL framework isn't a link to a non-existent 10.7 SDK (though I
>>>>>>>>>>>> don't see how that could happen).
>>>>>>>>>>>>
>>>>>>>>>>>>  - David
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Jan 6, 2016 at 5:34 PM, Arno Klein <
>>>>>>>>>>>> binarybottle at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> David --
>>>>>>>>>>>>>
>>>>>>>>>>>>> There was no instance of "AGL" in CMakeCache.txt, but I
>>>>>>>>>>>>> replaced every instance of "AGL" with OpenGL" in all of the build.make
>>>>>>>>>>>>> files.  Without cmake, but with make I got the following error:
>>>>>>>>>>>>>
>>>>>>>>>>>>> make[2]: *** No rule to make target
>>>>>>>>>>>>> `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/OpenGL.framework',
>>>>>>>>>>>>> needed by `travel_depth/TravelDepthMain'.  Stop.
>>>>>>>>>>>>>
>>>>>>>>>>>>> It still calls 10.7 even though I have 10.11 installed on my
>>>>>>>>>>>>> Mac.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>> @rno
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Wed, Jan 6, 2016 at 7:02 PM, David Gobbi <
>>>>>>>>>>>>> david.gobbi at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Arno,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Look for the following line in your CMakeCache.txt:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> OPENGL_glu_LIBRARY:FILEPATH=/System/Library/Frameworks/AGL.framework
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Change it to the following and then recompile:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> OPENGL_glu_LIBRARY:FILEPATH=/System/Library/Frameworks/OpenGL.framework
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> That should keep the problematic AGL library out of your
>>>>>>>>>>>>>> build.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Please let me know if this works.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>  - David
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Wed, Jan 6, 2016 at 4:45 PM, Arno Klein <
>>>>>>>>>>>>>> binarybottle at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thank you all so much for your kind help.  Unfortunately, I
>>>>>>>>>>>>>>> am still unable to compile the C++ code in my project on MacOSX, even after
>>>>>>>>>>>>>>> setting the following in my top-level CMakeLists.txt file:
>>>>>>>>>>>>>>> SET(CMAKE_OSX_DEPLOYMENT_TARGET "10.7")
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> When I type:
>>>>>>>>>>>>>>> $ export VERBOSE=1
>>>>>>>>>>>>>>> $ make
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I get the following even though I don't have
>>>>>>>>>>>>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/
>>>>>>>>>>>>>>> but instead have
>>>>>>>>>>>>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/
>>>>>>>>>>>>>>> on my computer:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ------------------
>>>>>>>>>>>>>>> ...
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> *Scanning dependencies of target TravelDepthMain*
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> /Applications/Xcode.app/Contents/Developer/usr/bin/make -f
>>>>>>>>>>>>>>> travel_depth/CMakeFiles/TravelDepthMain.dir/build.make
>>>>>>>>>>>>>>> travel_depth/CMakeFiles/TravelDepthMain.dir/build
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [ 57%] Building CXX object
>>>>>>>>>>>>>>> travel_depth/CMakeFiles/TravelDepthMain.dir/TravelDepthMain.cpp.o
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> cd
>>>>>>>>>>>>>>> /software/install/mindboggle/surface_cpp_tools/bin/travel_depth &&
>>>>>>>>>>>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
>>>>>>>>>>>>>>>   -DvtkRenderingContext2D_AUTOINIT="1(vtkRenderingContextOpenGL)"
>>>>>>>>>>>>>>> -DvtkRenderingCore_AUTOINIT="3(vtkInteractionStyle,vtkRenderingFreeType,vtkRenderingOpenGL)"
>>>>>>>>>>>>>>> -DvtkRenderingFreeType_AUTOINIT="1(vtkRenderingMatplotlib)"
>>>>>>>>>>>>>>> -DvtkRenderingVolume_AUTOINIT="1(vtkRenderingVolumeOpenGL)"
>>>>>>>>>>>>>>> -I/software/install/miniconda2/include/vtk-6.3
>>>>>>>>>>>>>>> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
>>>>>>>>>>>>>>> -isystem /software/install/miniconda2/include  -isysroot
>>>>>>>>>>>>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk
>>>>>>>>>>>>>>>   -o CMakeFiles/TravelDepthMain.dir/TravelDepthMain.cpp.o -c
>>>>>>>>>>>>>>> /software/install/mindboggle/surface_cpp_tools/travel_depth/TravelDepthMain.cpp
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> make[1]: ***
>>>>>>>>>>>>>>> [travel_depth/CMakeFiles/TravelDepthMain.dir/all] Error 2
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> make: *** [all] Error 2
>>>>>>>>>>>>>>> -------------------
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>> @rno
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Fri, Dec 11, 2015 at 9:36 PM, David Gobbi <
>>>>>>>>>>>>>>> david.gobbi at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Arno,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I think that I've found out where the AGL link is coming
>>>>>>>>>>>>>>>> from.  It isn't via Carbon, it looks like it was linked directly into the
>>>>>>>>>>>>>>>> VTK that you're using.  And it looks like a bug within CMake itself.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> CMake has a module called FindOpenGL.cmake that VTK uses to
>>>>>>>>>>>>>>>> find OpenGL.  It looks for both the OpenGL.framework and for the obsolete
>>>>>>>>>>>>>>>> AGL.framework (which is only for Carbon, and is deprecated by Apple).  If
>>>>>>>>>>>>>>>> it finds both (e.g. with an older SDK and XCode 6 or earlier), then it uses
>>>>>>>>>>>>>>>> both, even though AGL.framework is really not needed for any modern
>>>>>>>>>>>>>>>> software.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> This means that a VTK that is built with (for example)
>>>>>>>>>>>>>>>> Xcode 6 and its SDKs becomes linked to AGL, because AGL.framework is
>>>>>>>>>>>>>>>> present in those older SDKs.  It's a private link, though, so I'm surprised
>>>>>>>>>>>>>>>> that it would cause the error.  But you are building with Xcode 7 and you
>>>>>>>>>>>>>>>> are seeing an error... that much is indisputable.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I suggest that you enable verbose error reporting so that
>>>>>>>>>>>>>>>> you can see exactly what is being linked when the error occurs:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> export VERBOSE=1
>>>>>>>>>>>>>>>> make
>>>>>>>>>>>>>>>> ...
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Use "unset VERBOSE" to turn off the verbosity.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>  - David
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Fri, Dec 11, 2015 at 3:57 PM, Arno Klein <
>>>>>>>>>>>>>>>> binarybottle at gmail.com> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I tried again, and am still getting the AGL.framework
>>>>>>>>>>>>>>>>> error even when I set to 10.9 and the SDK to 10.11 (see:
>>>>>>>>>>>>>>>>> https://github.com/nipy/mindboggle/blob/master/surface_cpp_tools/CMakeLists.txt
>>>>>>>>>>>>>>>>> ):
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> > [ 57%] Building CXX object
>>>>>>>>>>>>>>>>> travel_depth/CMakeFiles/TravelDepthMain.dir/TravelDepthMain.cpp.o
>>>>>>>>>>>>>>>>> > 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.
>>>>>>>>>>>>>>>>> > make[1]: ***
>>>>>>>>>>>>>>>>> [travel_depth/CMakeFiles/TravelDepthMain.dir/all] Error 2
>>>>>>>>>>>>>>>>> > make: *** [all] Error 2
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Could you please tell me how to ensure that there are no
>>>>>>>>>>>>>>>>> calls to Carbon APIs?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> By the way, I am tracking this as an issue on Github:
>>>>>>>>>>>>>>>>> https://github.com/nipy/mindboggle/issues/69
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>> @rno
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Fri, Dec 11, 2015 at 5:27 AM, David Gobbi <
>>>>>>>>>>>>>>>>> david.gobbi at gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Arno,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Using the macosx10.11 SDK is fine as long as it allows
>>>>>>>>>>>>>>>>>> you to set this desired deployment target.  So if you are able to compile
>>>>>>>>>>>>>>>>>> with the following settings, then the result should run on OS X 10.7:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> CMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.7
>>>>>>>>>>>>>>>>>> CMAKE_OSX_SYSROOT:STRING=macosx10.11
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> I'm not sure how far back you can set the deployment
>>>>>>>>>>>>>>>>>> target with this SDK, but if the 10.7 target doesn't compile, you can try
>>>>>>>>>>>>>>>>>> 10.8 or 10.9.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> If if gives errors for the AGL.framework, then make sure
>>>>>>>>>>>>>>>>>> that your code has no calls to Carbon APIs.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>  - David
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>>
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