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'`

Question

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'`

goldwind-ting opened this issue 2 years ago · comments

rust:
rustc 1.61.0
rdkit:
rdkit-2022.03.1

Xavier Lange · Answer 1 · Mon Jun 27 2022 00:05:02 GMT+0800 (China Standard Time)

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

goldwind-ting · Answer 2 · Mon Jun 27 2022 13:10:41 GMT+0800 (China Standard Time)

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.

Peter St. John · Answer 3 · Sat Nov 25 2023 02:43:11 GMT+0800 (China Standard Time)

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.

Xavier Lange · Answer 4 · Sat Nov 25 2023 06:12:50 GMT+0800 (China Standard Time)

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.