error during make install while trying to install on new macbook

[lgazdzin]

Hi,

I'm running into the following error while trying to install minc-toolkit-v2 on my new macbook (M2).

minc-toolkit-v2-build/HDF5/src/H5Fsuper.c:1397:16: error: call to undeclared function 'H5O__fsinfo_set_version'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
1397 | if(H5O__fsinfo_set_version(f, &fsinfo) < 0)
| ^
1 error generated.
make[5]: *** [src/CMakeFiles/hdf5-static.dir/H5Fsuper.c.o] Error 1
make[4]: *** [src/CMakeFiles/hdf5-static.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [HDF5-prefix/src/HDF5-stamp/HDF5-build] Error 2
make[1]: *** [CMakeFiles/HDF5.dir/all] Error 2
make: *** [all] Error 2

My cmake call is this:

cmake ../minc-toolkit-v2/ -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.18 -DMT_BUILD_ABC:BOOL=ON -DMT_BUILD_ANTS:BOOL=ON -DMT_BUILD_C3D:BOOL=ON -DMT_BUILD_ELASTIX:BOOL=ON -DMT_BUILD_IM:BOOL=OFF -DMT_BUILD_ITK_TOOLS:BOOL=ON -DMT_BUILD_LITE:BOOL=OFF -DMT_BUILD_SHARED_LIBS:BOOL=ON -DMT_BUILD_VISUAL_TOOLS:BOOL=ON -DMT_USE_OPENMP:BOOL=ON -DUSE_SYSTEM_FFTW3D:BOOL=OFF -DUSE_SYSTEM_FFTW3F:BOOL=OFF -DUSE_SYSTEM_GLUT:BOOL=OFF -DUSE_SYSTEM_GSL:BOOL=ON -DUSE_SYSTEM_HDF5:BOOL=OFF -DUSE_SYSTEM_ITK:BOOL=OFF -DUSE_SYSTEM_NETCDF:BOOL=OFF -DUSE_SYSTEM_NIFTI:BOOL=OFF -DUSE_SYSTEM_PCRE:BOOL=OFF -DUSE_SYSTEM_ZLIB:BOOL=OFF -DBISON_EXECUTABLE=/usr/local/opt/bison/bin/bison -DHDF5_ROOT=$(brew --prefix hdf5)

The HDF5 version that I think it's using is 1.14.5 (I've tried the above command with -DUSE_SYSTEM_HDF5:BOOL=ON as well, but this didn't help.

Thanks!

[lgazdzin]

Hi -- I submitted this question a couple of weeks ago and haven't received a response ... Just wanted to follow up to see if anyone has any advice. Thanks!

[vfonov]

try with older version of HDF5, i have tried with 1.12 so far. And use develop branch.

[lgazdzin]

Thanks for your reply. I'll try to figure out how to get an older version of HDF5 and will let you know if I need help! Do you mean the develop branch for minctools?

[vfonov]

develop branch of minc-toolkit-v2 , i.e develop-1.9.18

[vfonov]

although, on MacOS Silicone, ITK4 will not compile, so better try https://github.com/BIC-MNI/minc-toolkit-v2/tree/develop-1.9.19

[lgazdzin]

Looks like I'm still having trouble, unfortunately. I installed hdf5 version 1.10.11 using brew and ensured it was in my path:

brew install [email protected]
export LDFLAGS="-L/usr/local/opt/[email protected]/lib"
export CPPFLAGS="-I/usr/local/opt/[email protected]/include"
brew unlink hdf5 && brew link hdf5
echo 'export PATH="/usr/local/opt/[email protected]/bin:$PATH"' >> /Users/Lisa/.bash_profile

h5cc -showconfig | grep "HDF5 Version"
HDF5 Version: 1.10.11

Downloaded minc toolkit from the develop branch like this:

git clone --recursive --branch develop-1.9.19-ITKv5.4 https://github.com/BIC-MNI/minc-toolkit-v2.git minc-toolkit-v2

And then ran cmake as shown here, followed by make && make install, but then ran into the error below yet again.

cmake ../minc-toolkit-v2/ -DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.19 -DMT_BUILD_ABC:BOOL=ON -DMT_BUILD_ANTS:BOOL=ON -DMT_BUILD_C3D:BOOL=ON -DMT_BUILD_ELASTIX:BOOL=ON -DMT_BUILD_IM:BOOL=OFF -DMT_BUILD_ITK_TOOLS:BOOL=ON -DMT_BUILD_LITE:BOOL=OFF -DMT_BUILD_SHARED_LIBS:BOOL=ON -DMT_BUILD_VISUAL_TOOLS:BOOL=ON -DMT_USE_OPENMP:BOOL=ON -DUSE_SYSTEM_FFTW3D:BOOL=OFF -DUSE_SYSTEM_FFTW3F:BOOL=OFF -DUSE_SYSTEM_GLUT:BOOL=OFF -DUSE_SYSTEM_GSL:BOOL=ON -DUSE_SYSTEM_HDF5:BOOL=OFF -DUSE_SYSTEM_ITK:BOOL=OFF -DUSE_SYSTEM_NETCDF:BOOL=OFF -DUSE_SYSTEM_NIFTI:BOOL=OFF -DUSE_SYSTEM_PCRE:BOOL=OFF -DUSE_SYSTEM_ZLIB:BOOL=OFF -DBISON_EXECUTABLE=/usr/local/opt/bison/bin/bison

The error:
[ 12%] Building C object src/CMakeFiles/hdf5-static.dir/H5Fspace.c.o
[ 12%] Building C object src/CMakeFiles/hdf5-static.dir/H5Fsuper.c.o
/Users/Lisa/minctoolkit-build/HDF5/src/H5Fsuper.c:1397:16: error: call to undeclared function 'H5O__fsinfo_set_version'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
1397 | if(H5O__fsinfo_set_version(f, &fsinfo) < 0)
| ^
1 error generated.
make[5]: *** [src/CMakeFiles/hdf5-static.dir/H5Fsuper.c.o] Error 1
make[4]: *** [src/CMakeFiles/hdf5-static.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [HDF5-prefix/src/HDF5-stamp/HDF5-build] Error 2
make[1]: *** [CMakeFiles/HDF5.dir/all] Error 2
make: *** [all] Error 2

[vfonov]

so, the fact that it's finding an error in HDF5-prefix/src/HDF5-stamp/HDF5-build means that it doesn't use system provided HDF5 library, but rather builds it's own (also indicated by DUSE_SYSTEM_HDF5:BOOL=OFF) . And it looks like the compiler is more strict that it used to be and insists on using C99 standard.

[lgazdzin]

Hm ok, that makes sense. I'm not sure what the implications if the C99 standard are. But if I set DUSE_SYSTEM_HDF5:BOOL=OFF, then it can't find HDF5, so fails very quickly. Is there something else I can try?