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Advanced Normalization Tools (ANTs)
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2.0.3 release fails to build against ITK 4.6 #108

Closed yarikoptic closed 9 years ago

yarikoptic commented 10 years ago

On a Debian sid (with ITK 4.6.0-1)

[ 16%] Building CXX object Examples/CMakeFiles/l_CheckTopology.dir/CheckTopology.cxx.o
cd /tmp/buildd/ants-2.0.3/obj-x86_64-linux-gnu/Examples && /usr/bin/c++   -DITK_IO_FACTORY_REGISTER_MANAGER -Dl_CheckTopology_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2   -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -Wno-unused-local-typedefs -fPIC   -Wno-deprecated -fPIC -I/tmp/buildd/ants-2.0.3/Examples/. -I/tmp/buildd/ants-2.0.3/Examples/../Temporary -I/tmp/buildd/ants-2.0.3/Examples/../Tensor -I/tmp/buildd/ants-2.0.3/Examples/../GraphTheory -I/tmp/buildd/ants-2.0.3/Examples/../ImageSegmentation -I/tmp/buildd/ants-2.0.3/Examples/../ImageRegistration -I/tmp/buildd/ants-2.0.3/Examples/../Utilities -I/usr/include/vtk-5.8 -I/tmp/buildd/ants-2.0.3/obj-x86_64-linux-gnu/ITKIOFactoryRegistration -I/tmp/buildd/insighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4 -I/usr/include/ITK-4.6    -o CMakeFiles/l_CheckTopology.dir/CheckTopology.cxx.o -c /tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx
In file included from /tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx:34:0:
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h: In constructor 'BinaryImageToMeshFilter<TImage>::BinaryImageToMeshFilter()':
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:218:18: error: 'class vtkImageMarchingCubes' has no member named 'SetInputData'
     fltMarching->SetInputData(importPipeEnd);
                  ^
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:227:17: error: 'class vtkPolyDataConnectivityFilter' has no member named 'SetInputData'
     fltConnect->SetInputData(meshPipeEnd);
                 ^
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:236:17: error: 'class vtkCleanPolyData' has no member named 'SetInputData'
       fltClean->SetInputData(meshPipeEnd);
                 ^
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:240:20: error: 'class vtkDecimatePro' has no member named 'SetInputData'
       fltDecimate->SetInputData(meshPipeEnd);
                    ^
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:248:19: error: 'class vtkSmoothPolyDataFilter' has no member named 'SetInputData'
     smoothFilter->SetInputData(meshPipeEnd);
                   ^
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:254:18: error: 'class vtkTriangleFilter' has no member named 'SetInputData'
     fltTriangle->SetInputData(meshPipeEnd);
                  ^
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h: In member function 'virtual void BinaryImageToMeshFilter<TImage>::GenerateData()':
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:418:20: error: 'class vtkDecimatePro' has no member named 'SetInputData'
       fltDecimate->SetInputData(fltConnect->GetOutput());
                    ^
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:420:20: error: 'class vtkTriangleFilter' has no member named 'SetInputData'
       fltTriangle->SetInputData(fltDecimate->GetOutput() );
                    ^
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:427:20: error: 'class vtkTriangleFilter' has no member named 'SetInputData'
       fltTriangle->SetInputData(fltConnect->GetOutput());
                    ^
/tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:452:22: error: 'class vtkSmoothPolyDataFilter' has no member named 'SetInputData'
       fltSmoothMesh->SetInputData(m_Result);
                      ^
/tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx: In function 'float ants::ComputeGenus(vtkPolyData*)':
/tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx:61:11: error: 'class vtkExtractEdges' has no member named 'SetInputData'
   edgeex->SetInputData(pd1);
           ^
/tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx: In function 'float ants::vtkComputeTopology(vtkPolyData*)':
/tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx:81:8: error: 'class vtkPolyDataConnectivityFilter' has no member named 'SetInputData'
   con->SetInputData(pd);
        ^
Examples/CMakeFiles/l_CheckTopology.dir/build.make:57: recipe for target 'Examples/CMakeFiles/l_CheckTopology.dir/CheckTopology.cxx.o' failed

didn't try master (yet) -- please advise if master would and if I could cherry-pick some patch or just wait for 2.0.4? Thanks in advance!

stnava commented 10 years ago

that seems right ... it was released to build with ITK 4.5

we can make a 2.1 release to build with 4.6 if you like.

SuperBuild/External_ITKv4.cmake: set(ITK_VERSION_ID ITK-4.5)

brians-mbp-2:ANTs stnava$ grep GITTAG /_cmake | grep 4

SuperBuild/External_ITKv4.cmake: set(${proj}_GIT_TAG v4.5.0) # 10-Mar-2014

SuperBuild/External_ITKv4.cmake: GIT_TAG ${${proj}_GIT_TAG}

SuperBuild/External_Uncrustify.cmake: set(${proj}_GIT_TAG "60f3681da60462eda539b78e0c6c3eea823481e5")

the other issue looks VTK related:

brians-mbp-2:ANTs stnava$ grep GITTAG /_cmake | grep VTK

SuperBuild/External_VTK.cmake: set(${proj}_GIT_TAG "v6.1.0.rc1")

brian

On Mon, Aug 11, 2014 at 1:00 PM, Yaroslav Halchenko < notifications@github.com> wrote:

On a Debian sid (with ITK 4.6.0-1)

[ 16%] Building CXX object Examples/CMakeFiles/l_CheckTopology.dir/CheckTopology.cxx.o cd /tmp/buildd/ants-2.0.3/obj-x86_64-linux-gnu/Examples && /usr/bin/c++ -DITK_IO_FACTORY_REGISTER_MANAGER -Dl_CheckTopology_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -Wno-unused-local-typedefs -fPIC -Wno-deprecated -fPIC -I/tmp/buildd/ants-2.0.3/Examples/. -I/tmp/buildd/ants-2.0.3/Examples/../Temporary -I/tmp/buildd/ants-2.0.3/Examples/../Tensor -I/tmp/buildd/ants-2.0.3/Examples/../GraphTheory -I/tmp/buildd/ants-2.0.3/Examples/../ImageSegmentation -I/tmp/buildd/ants-2.0.3/Examples/../ImageRegistration -I/tmp/buildd/ants-2.0.3/Examples/../Utilities -I/usr/include/vtk-5.8 -I/tmp/buildd/ants-2.0.3/obj-x86_64-linux-gnu/ITKIOFactoryRegistration -I/tmp/buildd/in sighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4 -I/usr/include/ITK-4.6 -o CMakeFiles/l_CheckTopology.dir/CheckTopology.cxx.o -c /tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx In file included from /tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx:34:0: /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h: In constructor 'BinaryImageToMeshFilter::BinaryImageToMeshFilter()': /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:218:18: error: 'class vtkImageMarchingCubes' has no member named 'SetInputData' fltMarching->SetInputData(importPipeEnd); ^ /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:227:17: error: 'class vtkPolyDataConnectivityFilter' has no member named 'SetInputData' fltConnect->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:236:17: error: 'class vtkCleanPolyData' has no member named 'SetInputData' fltClean->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:240:20: error: 'class vtkDecimatePro' has no member named 'SetInputData' fltDecimate->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:248:19: error: 'class vtkSmoothPolyDataFilter' has no member named 'SetInputData' smoothFilter->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:254:18: error: 'class vtkTriangleFilter' has no member named 'SetInputData' fltTriangle->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h: In member function 'virtual void BinaryImageToMeshFilter::GenerateData()': /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:418:20: error: 'class vtkDecimatePro' has no member named 'SetInputData' fltDecimate->SetInputData(fltConnect->GetOutput()); ^ /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:420:20: error: 'class vtkTriangleFilter' has no member named 'SetInputData' fltTriangle->SetInputData(fltDecimate->GetOutput() ); ^ /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:427:20: error: 'class vtkTriangleFilter' has no member named 'SetInputData' fltTriangle->SetInputData(fltConnect->GetOutput()); ^ /tmp/buildd/ants-2.0.3/Examples/../Utilities/BinaryImageToMeshFilter.h:452:22: error: 'class vtkSmoothPolyDataFilter' has no member named 'SetInputData' fltSmoothMesh->SetInputData(mResult); ^ /tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx: In function 'float ants::ComputeGenus(vtkPolyData)': /tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx:61:11: error: 'class vtkExtractEdges' has no member named 'SetInputData' edgeex->SetInputData(pd1); ^ /tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx: In function 'float ants::vtkComputeTopology(vtkPolyData_)': /tmp/buildd/ants-2.0.3/Examples/CheckTopology.cxx:81:8: error: 'class vtkPolyDataConnectivityFilter' has no member named 'SetInputData' con->SetInputData(pd); ^ Examples/CMakeFiles/l_CheckTopology.dir/build.make:57: recipe for target 'Examples/CMakeFiles/l_CheckTopology.dir/CheckTopology.cxx.o' failed

didn't try master (yet) -- please advise if master would and if I could cherry-pick some patch or just wait for 2.0.4? Thanks in advance!

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTs/issues/108.

yarikoptic commented 10 years ago

if you could cut 2.1 compatible with 4.6 -- that would be awesome! FWIW We have 6.1.0+dfsg-8 VTK in sid/jessie

stnava commented 10 years ago

git tag -a v2.1.0 -m 'with ITK v4.6.0 and VTK 6.1'

this should be compatible w/ the version of ITK you have

brian

On Mon, Aug 11, 2014 at 1:47 PM, Yaroslav Halchenko < notifications@github.com> wrote:

if you could cut 2.1 compatible with 4.6 -- that would be awesome! FWIW We have 6.1.0+dfsg-8 VTK in sid/jessie

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTs/issues/108#issuecomment-51814714.

stnava commented 10 years ago

actually the tag is:

v2.1.0rc1

i will add v2.1.0 if this works for you

brian

On Tue, Aug 12, 2014 at 9:35 AM, brian avants stnava@gmail.com wrote:

git tag -a v2.1.0 -m 'with ITK v4.6.0 and VTK 6.1'

this should be compatible w/ the version of ITK you have

brian

On Mon, Aug 11, 2014 at 1:47 PM, Yaroslav Halchenko < notifications@github.com> wrote:

if you could cut 2.1 compatible with 4.6 -- that would be awesome! FWIW We have 6.1.0+dfsg-8 VTK in sid/jessie

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTs/issues/108#issuecomment-51814714.

yarikoptic commented 10 years ago

not quite yet:

In file included from /tmp/buildd/ants-2.1.0~rc1/Examples/CheckTopology.cxx:34:0:
/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h: In constructor 'BinaryImageToMeshFilter<TImage>::BinaryImageToMeshFilter()':
/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:218:18: error: 'class vtkImageMarchingCubes' has no member named 'SetInputData'                                                                              
     fltMarching->SetInputData(importPipeEnd);                                     
                  ^                                                                
/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:227:17: error: 'class vtkPolyDataConnectivityFilter' has no member named 'SetInputData'                                                                      
     fltConnect->SetInputData(meshPipeEnd);                                        
                 ^                                                                 
/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:236:17: error: 'class vtkCleanPolyData' has no member named 'SetInputData'
       fltClean->SetInputData(meshPipeEnd);                                        
                 ^                                                                 
/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:240:20: error: 'class vtkDecimatePro' has no member named 'SetInputData'
       fltDecimate->SetInputData(meshPipeEnd);                                     
                    ^                                                              
/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:248:19: error: 'class vtkSmoothPolyDataFilter' has no member named 'SetInputData'                                                                            
     smoothFilter->SetInputData(meshPipeEnd);                                      
                   ^                                                               
/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:254:18: error: 'class vtkTriangleFilter' has no member named 'SetInputData'                                                                                  
     fltTriangle->SetInputData(meshPipeEnd);                                       
                  ^                                                                
/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h: In member function 'virtual void BinaryImageToMeshFilter<TImage>::GenerateData()':                                                                          
/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:418:20: error: 'class vtkDecimatePro' has no member named 'SetInputData'
       fltDecimate->SetInputData(fltConnect->GetOutput());                  
...

do you need help getting Debian sid environment? do you know/use docker btw?

stnava commented 10 years ago

ok - i added v2.1.0rc2

this just comments out CheckTopology and GetMeshAndTopology which we dont support anymore

they are superseded by antsSurf .....

regarding debian envt - have a virtual box with linux mint on it.

will check out docker.

brian

On Tue, Aug 12, 2014 at 12:01 PM, Yaroslav Halchenko < notifications@github.com> wrote:

not quite yet:

In file included from /tmp/buildd/ants-2.1.0~rc1/Examples/CheckTopology.cxx:34:0: /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h: In constructor 'BinaryImageToMeshFilter::BinaryImageToMeshFilter()': /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:218:18: error: 'class vtkImageMarchingCubes' has no member named 'SetInputData' fltMarching->SetInputData(importPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:227:17: error: 'class vtkPolyDataConnectivityFilter' has no member named 'SetInputData' fltConnect->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:236:17: error: 'class vtkCleanPolyData' has no member named 'SetInputData' fltClean->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:240:20: error: 'class vtkDecimatePro' has no member named 'SetInputData' fltDecimate->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:248:19: error: 'class vtkSmoothPolyDataFilter' has no member named 'SetInputData' smoothFilter->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:254:18: error: 'class vtkTriangleFilter' has no member named 'SetInputData' fltTriangle->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h: In member function 'virtual void BinaryImageToMeshFilter::GenerateData()': /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:418:20: error: 'class vtkDecimatePro' has no member named 'SetInputData' fltDecimate->SetInputData(fltConnect->GetOutput()); ...

do you need help getting Debian sid environment? do you know/use docker btw?

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTs/issues/108#issuecomment-51935640.

stnava commented 10 years ago

docker installed .... though i still havent figured out how it's useful

brian

On Tue, Aug 12, 2014 at 12:12 PM, brian avants stnava@gmail.com wrote:

ok - i added v2.1.0rc2

this just comments out CheckTopology and GetMeshAndTopology which we dont support anymore

they are superseded by antsSurf .....

regarding debian envt - have a virtual box with linux mint on it.

will check out docker.

brian

On Tue, Aug 12, 2014 at 12:01 PM, Yaroslav Halchenko < notifications@github.com> wrote:

not quite yet:

In file included from /tmp/buildd/ants-2.1.0~rc1/Examples/CheckTopology.cxx:34:0: /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h: In constructor 'BinaryImageToMeshFilter::BinaryImageToMeshFilter()': /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:218:18: error: 'class vtkImageMarchingCubes' has no member named 'SetInputData' fltMarching->SetInputData(importPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:227:17: error: 'class vtkPolyDataConnectivityFilter' has no member named 'SetInputData' fltConnect->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:236:17: error: 'class vtkCleanPolyData' has no member named 'SetInputData' fltClean->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:240:20: error: 'class vtkDecimatePro' has no member named 'SetInputData' fltDecimate->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:248:19: error: 'class vtkSmoothPolyDataFilter' has no member named 'SetInputData' smoothFilter->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:254:18: error: 'class vtkTriangleFilter' has no member named 'SetInputData' fltTriangle->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h: In member function 'virtual void BinaryImageToMeshFilter::GenerateData()': /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:418:20: error: 'class vtkDecimatePro' has no member named 'SetInputData' fltDecimate->SetInputData(fltConnect->GetOutput()); ...

do you need help getting Debian sid environment? do you know/use docker btw?

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTs/issues/108#issuecomment-51935640.

yarikoptic commented 10 years ago

On Tue, 12 Aug 2014, stnava wrote:

docker installed .... though i still havent figured out how it's useful

e.g.

docker.io pull debian

will fetch all (just in case if you have enough disc space, otherwise say "debian:sid") stock basic debian images. Then in the directory with your ants sources:

docker.io run -i -t --rm=true -v $PWD:/tmp/ants debian:sid /bin/bash

would give you the core Debian sid environment (which will be removed after you are done with it! you might want to use docker.io commit command to create an explicit version of the one with everything needed pre-installed after you do that), where you could do

echo 'deb-src http://http.debian.net/debian sid main' >> /etc/apt/sources.list apt-get update apt-get upgrade # upgrade the beast apt-get build-dep ants # fetch all build-depends for ants apt-get install libhdf5-dev # just to overcome current problem apt-get clean # just tidy up

At this point you might like to save this state for future reuse: run docker.io ps to see what is your CONTAINER ID , in my case 990409a5dd1f so I would do

docker.io commit -m "sid with all build-deps for ants pre-installed" 990409a5dd1f sid-ants-alpha

so now you would have docker.io images list sid-ants-alpha

and later do

docker.io run -i -t --rm=true -v $PWD:$PWD sid-ants-alpha /bin/bash

do get to that state within a second or two ;)

anyways, now just

cd /tmp/ants

and do whatever you like e.g. try to build/run tests ;)

Yaroslav O. Halchenko, Ph.D. http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org Research Scientist, Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik

yarikoptic commented 10 years ago

got further but

[ 91%] Building CXX object Examples/CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o
cd "/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu/Examples" && /usr/bin/c++   -DITK_IO_FACTORY_REGISTER_MANAGER -Dl_antsSurf_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2   -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -fPIC   -Wno-deprecated -fPIC -I"/tmp/buildd/ants-2.1.0~rc1/Examples/." -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../Temporary" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../Tensor" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../GraphTheory" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../ImageSegmentation" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../ImageRegistration" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities" -I/usr/include/vtk-5.8 -I"/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu/ITKIOFactoryRegistration" -I/tmp/buildd/insighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4 -I/usr/include/ITK-4.6    -o CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o -c "/tmp/buildd/ants-2.1.0~rc1/Examples/antsSurf.cxx"
/tmp/buildd/ants-2.1.0~rc1/Examples/antsSurf.cxx:13:38: fatal error: itkImageToVTKImageFilter.h: No such file or directory
 #include "itkImageToVTKImageFilter.h"
                                      ^
compilation terminated.
Examples/CMakeFiles/l_antsSurf.dir/build.make:57: recipe for target 'Examples/CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o' failed
make[4]: *** [Examples/CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o] Error 1
make[4]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu'
CMakeFiles/Makefile2:6771: recipe for target 'Examples/CMakeFiles/l_antsSurf.dir/all' failed
make[3]: *** [Examples/CMakeFiles/l_antsSurf.dir/all] Error 2
make[3]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu'
Makefile:146: recipe for target 'all' failed
make[2]: *** [all] Error 2
make[2]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu'
dh_auto_build: make -j1 returned exit code 2
debian/rules:51: recipe for target 'override_dh_auto_build' failed
make[1]: *** [override_dh_auto_build] Error 2
make[1]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1'
debian/rules:30: recipe for target 'binary' failed
make: *** [binary] Error 2
Chaircrusher commented 10 years ago

You are linking against ITK that hasn’t built the VTK support.

Are you using the ANTs SuperBuild, or trying to build by specifying VTK_DIR and ITK_DIR on the command line?

From: Yaroslav Halchenko notifications@github.com<mailto:notifications@github.com> Reply-To: stnava/ANTs reply@reply.github.com<mailto:reply@reply.github.com> Date: Tuesday, August 12, 2014 at 1:19 PM To: stnava/ANTs ANTs@noreply.github.com<mailto:ANTs@noreply.github.com> Subject: Re: [ANTs] 2.0.3 release fails to build against ITK 4.6 (#108)

got further but

[ 91%] Building CXX object Examples/CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o cd "/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu/Examples" && /usr/bin/c++ -DITK_IO_FACTORY_REGISTER_MANAGER -Dl_antsSurf_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -fPIC -Wno-deprecated -fPIC -I"/tmp/buildd/ants-2.1.0~rc1/Examples/." -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../Temporary" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../Tensor" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../GraphTheory" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../ImageSegmentation" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../ImageRegistration" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities" -I/usr/include/vtk-5.8 -I"/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu/ITKIOFactor! yRegistra tion" -I/tmp/buildd/insighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4 -I/usr/include/ITK-4.6 -o CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o -c "/tmp/buildd/ants-2.1.0~rc1/Examples/antsSurf.cxx" /tmp/buildd/ants-2.1.0~rc1/Examples/antsSurf.cxx:13:38: fatal error: itkImageToVTKImageFilter.h: No such file or directory

include "itkImageToVTKImageFilter.h"

                                  ^

compilation terminated. Examples/CMakeFiles/l_antsSurf.dir/build.make:57: recipe for target 'Examples/CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o' failed make[4]: * [Examples/CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o] Error 1 make[4]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu' CMakeFiles/Makefile2:6771: recipe for target 'Examples/CMakeFiles/l_antsSurf.dir/all' failed make[3]: * [Examples/CMakeFiles/l_antsSurf.dir/all] Error 2 make[3]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu' Makefile:146: recipe for target 'all' failed make[2]: * [all] Error 2 make[2]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu' dh_auto_build: make -j1 returned exit code 2 debian/rules:51: recipe for target 'override_dh_auto_build' failed make[1]: * [override_dh_auto_build] Error 2 make[1]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1' debian/rules:30: recipe for target 'binary' failed make: *\ [binary] Error 2

— Reply to this email directly or view it on GitHubhttps://github.com/stnava/ANTs/issues/108#issuecomment-51954937.


Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.


Chaircrusher commented 10 years ago

The errors below are actually VTK issues, not ITK issues.

Specifically, VTK 6 replaced SetInput with SetInputData and SetInputConnection.

You need to build and link VTK6

From: stnava notifications@github.com<mailto:notifications@github.com> Reply-To: stnava/ANTs reply@reply.github.com<mailto:reply@reply.github.com> Date: Tuesday, August 12, 2014 at 11:12 AM To: stnava/ANTs ANTs@noreply.github.com<mailto:ANTs@noreply.github.com> Subject: Re: [ANTs] 2.0.3 release fails to build against ITK 4.6 (#108)

ok - i added v2.1.0rc2

this just comments out CheckTopology and GetMeshAndTopology which we dont support anymore

they are superseded by antsSurf .....

regarding debian envt - have a virtual box with linux mint on it.

will check out docker.

brian

On Tue, Aug 12, 2014 at 12:01 PM, Yaroslav Halchenko < notifications@github.commailto:notifications@github.com> wrote:

not quite yet:

In file included from /tmp/buildd/ants-2.1.0~rc1/Examples/CheckTopology.cxx:34:0: /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h: In constructor 'BinaryImageToMeshFilter::BinaryImageToMeshFilter()': /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:218:18: error: 'class vtkImageMarchingCubes' has no member named 'SetInputData' fltMarching->SetInputData(importPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:227:17: error: 'class vtkPolyDataConnectivityFilter' has no member named 'SetInputData' fltConnect->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:236:17: error: 'class vtkCleanPolyData' has no member named 'SetInputData' fltClean->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:240:20: error: 'class vtkDecimatePro' has no member named 'SetInputData' fltDecimate->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:248:19: error: 'class vtkSmoothPolyDataFilter' has no member named 'SetInputData' smoothFilter->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:254:18: error: 'class vtkTriangleFilter' has no member named 'SetInputData' fltTriangle->SetInputData(meshPipeEnd); ^ /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h: In member function 'virtual void BinaryImageToMeshFilter::GenerateData()': /tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities/BinaryImageToMeshFilter.h:418:20: error: 'class vtkDecimatePro' has no member named 'SetInputData' fltDecimate->SetInputData(fltConnect->GetOutput()); ...

do you need help getting Debian sid environment? do you know/use docker btw?

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTs/issues/108#issuecomment-51935640.

— Reply to this email directly or view it on GitHubhttps://github.com/stnava/ANTs/issues/108#issuecomment-51937259.


Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.


stnava commented 10 years ago

yes - kent is correct ....

you might compile the rc2 w/o VTK

or make sure that ITK is compiled w/VTK support on.

either way.

brian

On Tue, Aug 12, 2014 at 2:23 PM, Kent Williams notifications@github.com wrote:

You are linking against ITK that hasn’t built the VTK support.

Are you using the ANTs SuperBuild, or trying to build by specifying VTK_DIR and ITK_DIR on the command line?

From: Yaroslav Halchenko <notifications@github.com<mailto: notifications@github.com>> Reply-To: stnava/ANTs <reply@reply.github.com<mailto: reply@reply.github.com>> Date: Tuesday, August 12, 2014 at 1:19 PM To: stnava/ANTs ANTs@noreply.github.com<mailto:ANTs@noreply.github.com> Subject: Re: [ANTs] 2.0.3 release fails to build against ITK 4.6 (#108)

got further but

[ 91%] Building CXX object Examples/CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o cd "/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu/Examples" && /usr/bin/c++ -DITK_IO_FACTORY_REGISTER_MANAGER -Dl_antsSurf_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -fPIC -Wno-deprecated -fPIC -I"/tmp/buildd/ants-2.1.0~rc1/Examples/." -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../Temporary" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../Tensor" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../GraphTheory" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../ImageSegmentation" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../ImageRegistration" -I"/tmp/buildd/ants-2.1.0~rc1/Examples/../Utilities" -I/usr/include/vtk-5.8 -I"/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu/ITKIOFactor! yRegistra tion" -I/tmp/buildd/insighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4 -I/usr/include/ITK-4.6 -o CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o -c "/tmp/buildd/ants-2.1.0~rc1/Examples/antsSurf.cxx" /tmp/buildd/ants-2.1.0~rc1/Examples/antsSurf.cxx:13:38: fatal error: itkImageToVTKImageFilter.h: No such file or directory

include "itkImageToVTKImageFilter.h"

^ compilation terminated. Examples/CMakeFiles/l_antsSurf.dir/build.make:57: recipe for target 'Examples/CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o' failed make[4]: * [Examples/CMakeFiles/l_antsSurf.dir/antsSurf.cxx.o] Error 1 make[4]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu' CMakeFiles/Makefile2:6771: recipe for target 'Examples/CMakeFiles/l_antsSurf.dir/all' failed make[3]: * [Examples/CMakeFiles/l_antsSurf.dir/all] Error 2 make[3]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu' Makefile:146: recipe for target 'all' failed make[2]: * [all] Error 2 make[2]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1/obj-x86_64-linux-gnu' dh_auto_build: make -j1 returned exit code 2 debian/rules:51: recipe for target 'override_dh_auto_build' failed make[1]: * [override_dh_auto_build] Error 2 make[1]: Leaving directory '/tmp/buildd/ants-2.1.0~rc1' debian/rules:30: recipe for target 'binary' failed make: *\ [binary] Error 2

— Reply to this email directly or view it on GitHub< https://github.com/stnava/ANTs/issues/108#issuecomment-51954937>.


Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.


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yarikoptic commented 10 years ago

I am building against system wide itk and vtk:

override_dh_auto_configure:
        dh_auto_configure -- \
                -DANTS_SUPERBUILD:BOOL=OFF \
                -DANTS_USE_GIT_PROTOC:BOOL=OFF \
                -DCOPY_SCRIPT_FILES_TO_BIN_DIR:BOOL=OFF \
                -DCMAKE_SKIP_RPATH:BOOL=OFF \
                -DUSE_SYSTEM_ITK:BOOL=ON \
                -DUSE_VTK:BOOL=ON \
                -DBUILD_SHARED_LIBS:BOOL=ON \
                -DRUN_SHORT_TESTS:BOOL=ON \
                -DRUN_LONG_TESTS:BOOL=OFF \
                -DEXECUTABLE_OUTPUT_PATH:PATH=$(DESTBINDIR) \
                --debug-output

ITK in Debian build with support to VTK (build depends on vtk5) I think... although I do not see any of ITK libraries being linked against vtk : see log https://buildd.debian.org/status/fetch.php\?pkg\=insighttoolkit4\&arch\=i386\&ver\=4.6.0-1\&stamp\=1407289091 So you are suggesting disabling USE_VTK? (BEWARE -- it is large -- better wget instead of opening in the browser)

stnava commented 10 years ago

yes - i would turn vtk off

the ants vtk dependencies use vtk6.x ( major changes from vtk5.x or less )

brian

On Tue, Aug 12, 2014 at 3:16 PM, Yaroslav Halchenko < notifications@github.com> wrote:

I am building against system wide itk and vtk:

override_dh_auto_configure: dh_auto_configure -- \ -DANTS_SUPERBUILD:BOOL=OFF \ -DANTS_USE_GIT_PROTOC:BOOL=OFF \ -DCOPY_SCRIPT_FILES_TO_BIN_DIR:BOOL=OFF \ -DCMAKE_SKIP_RPATH:BOOL=OFF \ -DUSE_SYSTEM_ITK:BOOL=ON \ -DUSE_VTK:BOOL=ON \ -DBUILD_SHARED_LIBS:BOOL=ON \ -DRUN_SHORT_TESTS:BOOL=ON \ -DRUN_LONG_TESTS:BOOL=OFF \ -DEXECUTABLE_OUTPUT_PATH:PATH=$(DESTBINDIR) \ --debug-output

ITK in Debian build with support to VTK (build depends on vtk5) I think... although I do not see any of ITK libraries being linked against vtk : see log

https://buildd.debian.org/status/fetch.php\?pkg\=insighttoolkit4\&arch\=i386\&ver\=4.6.0-1\&stamp\=1407289091 So you are suggesting disabling USE_VTK? (BEWARE -- it is large -- better wget instead of opening in the browser)

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTs/issues/108#issuecomment-51963136.

yarikoptic commented 10 years ago

or should I just try building against vtk6? (forgot that we have it) or it would bring chaos since itk was built with vtk5?

stnava commented 10 years ago

i would guess that problems would occur if you mixed vtk versions ...

so either itk+vtk6+ants or just itk+ants

the only thing that's missing if you dont compile ants w/vtk is antssurf

which very few people know about or use ...

brian

On Tue, Aug 12, 2014 at 4:45 PM, Yaroslav Halchenko < notifications@github.com> wrote:

or should I just try building against vtk6? (forgot that we have it) or it would bring chaos since itk was built with vtk5?

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTs/issues/108#issuecomment-51974574.

stnava commented 9 years ago

I think that Nick finally fixed this by explicitly specifying the VTK modules that are needed. We are trying to get ANTSV2.1 going this week hopefully. Closing this issue for now.