While installing the R package “hdf5r” version 1.3.3, I encountered the error:
fatal error: hdf5.h: No such file or directory #include <hdf5.h> ^~~~~~~~ compilation terminated.
My OS is Debian buster/10.6, and the package “libhdf5-dev” has been installed. It looks R cannot find the path of hdf5 header and library files.
It has been resolved by:
1. Export environment variables for header files
export C_INCLUDE_PATH=/usr/include/hdf5/serial/:$C_INCLUDE_PATH export CPLUS_INCLUDE_PATH=/usr/include/hdf5/serial/:$CPLUS_INCLUDE_PATH
2. Create symbolic links for library files
cd /usr/lib/x86_64-linux-gnu/ sudo ln -s libhdf5_hl_cpp.so.100.1.2 libhdf5_hl.so.100 sudo ln -s libhdf5_cpp.so.103.0.0 libhdf5.so.103
3. Install package “hdf5r”
Now there would be OK.