GDAL: Library not loaded: /usr/local/opt/hdf5/lib/libhdf5.103.dylib

[palmerj]

• I read
  • [ ] the reporting issues
  • [ ] the troubleshooting
  • [x] I checked the documentation and found no answer
  • [ ] I tried to install after following the suggestions
  • [x] I am running the latest version (brew update twice?)
  • [x] I checked to make sure that this issue has not already been filed
  • [ ] I uploaded logs: brew gist-logs formula

Describe the bug

When running GDAl commands I get a linking error:

$ ogrinfo --version dyld: Library not loaded: /usr/local/opt/hdf5/lib/libhdf5.103.dylib Referenced from: /usr/local/bin/ogrinfo Reason: image not found Abort trap: 6

Additional context

I tried reinstalling both hdf5 and then osgeo-gdal, but it didn't fix the issue

Running catalina

[palmerj]

Here's what installed for hdf:

$ ll /usr/local/opt/hdf5/lib/

drwxr-xr-x  21 user  staff      672 29 Feb 10:52 .
drwxr-xr-x  10 user  staff      320  9 Mar 16:43 ..
lrwxr-xr-x   1 user  staff       25 29 Feb 10:52 libhdf5_fortran.dylib -> libhdf5_fortran.200.dylib
lrwxr-xr-x   1 user  staff       21 29 Feb 10:52 libhdf5_cpp.dylib -> libhdf5_cpp.200.dylib
-rw-r--r--   1 user  staff   168376 29 Feb 10:52 libhdf5hl_fortran.a
-rw-r--r--   1 user  staff   128492  9 Mar 16:43 libhdf5_hl.200.dylib
lrwxr-xr-x   1 user  staff       17 29 Feb 10:52 libhdf5.dylib -> libhdf5.200.dylib
lrwxr-xr-x   1 user  staff       20 29 Feb 10:52 libhdf5_hl.dylib -> libhdf5_hl.200.dylib
-r--r--r--   1 user  staff  5647448 29 Feb 10:52 libhdf5.a
-rw-r--r--   1 user  staff   147032  9 Mar 16:43 libhdf5hl_fortran.200.dylib
-r--r--r--   1 user  staff   405400 29 Feb 10:52 libhdf5_fortran.a
lrwxr-xr-x   1 user  staff       27 29 Feb 10:52 libhdf5hl_fortran.dylib -> libhdf5hl_fortran.200.dylib
-r--r--r--   1 user  staff   298416  9 Mar 16:43 libhdf5_fortran.200.dylib
lrwxr-xr-x   1 user  staff       19 29 Feb 10:52 libhdf5_hl_fortran.a -> libhdf5hl_fortran.a
-r--r--r--   1 user  staff   158168 29 Feb 10:52 libhdf5_hl.a
-r--r--r--   1 user  staff    11184 29 Feb 10:52 libhdf5_hl_cpp.a
-r--r--r--   1 user  staff   639896 29 Feb 10:52 libhdf5_cpp.a
-rw-r--r--   1 user  staff    29324  9 Mar 16:43 libhdf5_hl_cpp.200.dylib
-r--r--r--   1 user  staff   380268  9 Mar 16:43 libhdf5_cpp.200.dylib
-r--r--r--   1 user  staff  3342568  9 Mar 16:43 libhdf5.200.dylib
lrwxr-xr-x   1 user  staff       24 29 Feb 10:52 libhdf5_hl_cpp.dylib -> libhdf5_hl_cpp.200.dylib

[palmerj]

For now the workaround is to symlink the old references:

ln -s /usr/local/opt/hdf5/lib/libhdf5.dylib /usr/local/opt/hdf5/lib/libhdf5.103.dylib
ln -s /usr/local/opt/hdf5/lib/libhdf5_hl.dylib /usr/local/opt/hdf5/lib/libhdf5_hl.100.dylib

[palmerj]

ok that didn't work using using python binding

ImportError: dlopen(/xxx/env/lib/python3.7/site-packages/osgeo/_gdal.cpython-37m-darwin.so, 2): Symbol not found: _H5Literate

[alazarolop]

Hi @palmerj . It's because of an update of hdf5 formula in homebrew/core. The quickest solution would be to rebuild from source gdal and gdal_python (and the rest of formulas you are using and depend on it). As an example, you need to:

brew reinstall osgeo-gdal --build-from-source 

All formulas in OSGeo tap need to be rebuild as well, but next time we'll try to use an stable release so to avoid this kind of issues.

[palmerj]

Ok thanks, I fallen back to building from source.

[alazarolop]

@palmerj Thank you for raising the issue. A small update has already been released.

[palmerj]

Thanks heaps!