shows `error while loading shared libraries: libRDKitDataStructs.so.1: cannot open shared object file: No such file or directory error: test failed, to rerun pass '--test test_descriptors'`

rdkit-rs / rdkit

RDKit Made Idiomatic for Rust

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shows `error while loading shared libraries: libRDKitDataStructs.so.1: cannot open shared object file: No such file or directory error: test failed, to rerun pass '--test test_descriptors'` #1

Closed goldwind-ting closed 2 years ago

goldwind-ting commented 2 years ago

rust: rustc 1.61.0 rdkit: rdkit-2022.03.1

xrl commented 2 years ago

Interesting, I would have thought that library is on all recent installs. Can you give a listing of all your *.so files.

goldwind-ting commented 2 years ago

I have resolved the issue, I used ubuntu, the library rdkit is installed in /usr/local, but the library_root in the build.rs(in library rdkit_sys) is /usr. So could you change the library_root to /usr/local for linux in the library rdkit_sys? or use an ENV variable.

pstjohn commented 7 months ago

I also encountered this issue when using dynamic-linking-from-conda under WSL2. Setting export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH let rust find the rdkit libraries at runtime.

xrl commented 7 months ago

There's been a regression in conda support in CI so it's not a big surprise to me that it stopped working. For whatever reason the conda registry doesn't trust our CI and we can no longer pull down prebuilt rdkit.

This coincides with a bit of refactoring on the flakey build.rs that makes rdkit-sys tick. I would be happy to accept PRs that fix CI -- we don't use conda but maybe we should.