pyushkevich
commented
2 years ago Hi Agata,
I think you need to turn in C++11 features in your compiler. I believe this means adding -DCMAKE_CXX_FLAGS="-std=c++11" to the CMake command,
Paul
On Mon, Aug 2, 2021 at 7:47 AM Agata @.***> wrote:
Hi Greedy Guys,
I want to compile greedy on linux. I managed to compile itk4.12 with cmake. I cloned greedy from github and now I am trying to build greedy on linux. I stop at some point in this process. I am getting an error like this:
(base) [k ~]$ cd /pst/data/imaging/Agata/greedy/bu ild-greedy-itk4.12 (base) [aga@ build-greedy-itk4.12]$ cmake -B . -S /pst/data/imaging/ Agata/greedy/greedy -D ITK_DIR:PATH=/pst/data/imaging/Agata/greedy/build-itk4.12/ -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 -- Check for working C compiler: /pst/apps/GCC/4.8.4/bin/cc -- Check for working C compiler: /pst/apps/GCC/4.8.4/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /pst/apps/GCC/4.8.4/bin/c++ -- Check for working CXX compiler: /pst/apps/GCC/4.8.4/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- GREEDY Version: 1.0.1 Released Mar 21, 2019 -- GIT Info: -- Branch : master -- SHA : a9fcaac https://github.com/pyushkevich/greedy/commit/a9fcaacc63ce25dc0d0ee2ffced313edab5b1469 -- Date : 2021-02-19 10:13:08 -0500 -- Configuring done -- Generating done -- Build files have been written to: /pst/data/imaging/Agata/greedy/build-greedy-it k4.12 (base) [aga@ build-greedy-itk4.12]$ make Scanning dependencies of target greedyapi [ 4%] Building CXX object CMakeFiles/greedyapi.dir/src/lddmm_data.cxx.o /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In static member function ‘static void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDM MData<TFloat, VDim>::ImageType, double)’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:9: error: ISO C++ for bids declaration of ‘smooth’ with no type [-fpermissive] auto
smooth = fltSmooth->GetOutput(); ^ /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType, double) [with TFloat = float; unsigned int VDim = 2u; LDDMMData<TFlo at, VDim>::ImageType = itk::Image<float, 2u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2124:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<float, 2u> >::OutputImageType {aka itk::Image<float, 2u>}’ to ‘int’ in initialization auto
smooth = fltSmooth->GetOutput(); ^ /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType, double) [with TFloat = float; unsigned int VDim = 3u; LDDMMData<TFlo at, VDim>::ImageType = itk::Image<float, 3u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2125:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<float, 3u> >::OutputImageType {aka itk::Image<float, 3u>}’ to ‘int’ in initialization /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType, double) [with TFloat = float; unsigned int VDim = 4u; LDDMMData<TFlo at, VDim>::ImageType = itk::Image<float, 4u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2126:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<float, 4u> >::OutputImageType {aka itk::Image<float, 4u>}’ to ‘int’ in initialization /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType*, double) [with TFloat = double; unsigned int VDim = 2u; LDDMMData<TFl oat, VDim>::ImageType = itk::Image<double, 2u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2128:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<double, 2u>
::OutputImageType {aka itk::Image<double, 2u>} ’ to ‘int’ in initialization /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType, double) [with TFloat = double; unsigned int VDim = 3u; LDDMMData<TFl oat, VDim>::ImageType = itk::Image<double, 3u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2129:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<double, 3u> ::OutputImageType {aka itk::Image<double, 3u>} ’ to ‘int’ in initialization /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType, double) [with TFloat = double; unsigned int VDim = 4u; LDDMMData<TFl oat, VDim>::ImageType = itk::Image<double, 4u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2130:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<double, 4u> ::OutputImageType {aka itk::Image<double, 4u>} ’ to ‘int*’ in initialization make[2]: [CMakeFiles/greedyapi.dir/src/lddmm_data.cxx.o] Error 1 make[1]: [CMakeFiles/greedyapi.dir/all] Error 2 make: *** [all] Error 2
I would appreciate for any help or advice in this issue.
Best, Agata
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-- Paul A. Yushkevich, Ph.D. Professor of Radiology Penn Image Computing and Science Laboratory University of Pennsylvania Perelman School of Medicine
agatadefr
Hi Greedy Guys,
I want to compile greedy on linux. I managed to compile itk4.12 with cmake. I cloned greedy from github and now I am trying to build greedy on linux. I stop at some point in this process. I am getting an error like this:
(base) [k ~]$ cd /pst/data/imaging/Agata/greedy/bu ild-greedy-itk4.12 (base) [aga@ build-greedy-itk4.12]$ cmake -B . -S /pst/data/imaging/ Agata/greedy/greedy -D ITK_DIR:PATH=/pst/data/imaging/Agata/greedy/build-itk4.12/ -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 -- Check for working C compiler: /pst/apps/GCC/4.8.4/bin/cc -- Check for working C compiler: /pst/apps/GCC/4.8.4/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /pst/apps/GCC/4.8.4/bin/c++ -- Check for working CXX compiler: /pst/apps/GCC/4.8.4/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- GREEDY Version: 1.0.1 Released Mar 21, 2019 -- GIT Info: -- Branch : master -- SHA : a9fcaacc63ce25dc0d0ee2ffced313edab5b1469 -- Date : 2021-02-19 10:13:08 -0500 -- Configuring done -- Generating done -- Build files have been written to: /pst/data/imaging/Agata/greedy/build-greedy-it k4.12 (base) [aga@ build-greedy-itk4.12]$ make Scanning dependencies of target greedyapi [ 4%] Building CXX object CMakeFiles/greedyapi.dir/src/lddmm_data.cxx.o /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In static member function ‘static void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDM MData<TFloat, VDim>::ImageType, double)’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:9: error: ISO C++ for bids declaration of ‘smooth’ with no type [-fpermissive] auto smooth = fltSmooth->GetOutput(); ^ /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType, double) [with TFloat = float; unsigned int VDim = 2u; LDDMMData<TFlo at, VDim>::ImageType = itk::Image<float, 2u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2124:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<float, 2u> >::OutputImageType {aka itk::Image<float, 2u>}’ to ‘int’ in initialization auto smooth = fltSmooth->GetOutput(); ^ /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType, double) [with TFloat = float; unsigned int VDim = 3u; LDDMMData<TFlo at, VDim>::ImageType = itk::Image<float, 3u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2125:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<float, 3u> >::OutputImageType {aka itk::Image<float, 3u>}’ to ‘int’ in initialization /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType, double) [with TFloat = float; unsigned int VDim = 4u; LDDMMData<TFlo at, VDim>::ImageType = itk::Image<float, 4u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2126:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<float, 4u> >::OutputImageType {aka itk::Image<float, 4u>}’ to ‘int’ in initialization /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType, double) [with TFloat = double; unsigned int VDim = 2u; LDDMMData<TFl oat, VDim>::ImageType = itk::Image<double, 2u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2128:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<double, 2u> >::OutputImageType {aka itk::Image<double, 2u>} ’ to ‘int’ in initialization /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType, double) [with TFloat = double; unsigned int VDim = 3u; LDDMMData<TFl oat, VDim>::ImageType = itk::Image<double, 3u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2129:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<double, 3u> >::OutputImageType {aka itk::Image<double, 3u>} ’ to ‘int’ in initialization /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx: In instantiation of ‘stat ic void LDDMMData<TFloat, VDim>::img_downsample(LDDMMData<TFloat, VDim>::ImageType, LDDMMData< TFloat, VDim>::ImageType, double) [with TFloat = double; unsigned int VDim = 4u; LDDMMData<TFl oat, VDim>::ImageType = itk::Image<double, 4u>]’: /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:2130:16: required from h ere /pst/data/imaging/Agata/greedy/greedy/src/lddmm_data.cxx:1689:39: error: cannot con vert ‘itk::ImageSource<itk::Image<double, 4u> >::OutputImageType {aka itk::Image<double, 4u>} ’ to ‘int’ in initialization make[2]: ** [CMakeFiles/greedyapi.dir/src/lddmm_data.cxx.o] Error 1 make[1]: [CMakeFiles/greedyapi.dir/all] Error 2 make: *** [all] Error 2
I would appreciate for any help or advice in this issue.
Best, Agata