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project-gemmi / gemmi

macromolecular crystallography library and utilities
https://project-gemmi.github.io/
Mozilla Public License 2.0
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Linking issue using conda-forge package of gemmi on linux #275

Closed agrossfield closed 9 months ago

agrossfield commented 11 months ago

Hi,

I've run into an issue trying to use the package of gemmi distributed via conda-forge. Basically, everything works beautifully on OSX, but on linux I get an error when linking against a c++ library I maintain: lto1: fatal error: bytecode stream in file '/home/alan/miniconda3/envs/loos/lib/libgemmi_cpp.a' generated with LTO version -25390.6 instead of the expected 8.1 compilation terminated.

From what I've read, this issue usually occurs when the toolchains used are incompatible. Since I was building with the conda -forge toolchain, this suggests an issue with the building of the gemmi package (though of course it's possible I'm making an error).

I opened an issue about this on the gemmi-feedstock, but it's been a week and no one responded there. I'm cross-posting it here in hopes of catching a developer's attention.

The relevant issue is: https://github.com/conda-forge/gemmi-feedstock/issues/57

Thanks,

Alan

wojdyr commented 11 months ago

You could try building libgemmi_cpp.a from source.

agrossfield commented 11 months ago

Unfortunately, other than testing (which you’re right, I need to do to nail down the problem 100%), that’s a non-starter for me. My package is distributed via conda-forge, which means I need to pull my dependencies from conda-forge — that’s how they build our binaries to distribute them.

Message ID: @.***>

Has anyone else run into this problem? It seems like it should happen to anyone trying using the libgemmi_cpp on Linux.

wojdyr commented 9 months ago

gemmi-feedstock has not been updated for 6 months and it currently doesn't build on Macos. I'll try to update it myself soon.