BUG: libstdc++.so.6 linkage issue #253
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We have also run into this issue over on RMG-Py, see here. |
JacksonBurns
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as reported at conda-forge/julia-feedstock#253 the latest release of julia (1.9.0) is brokey, don't use it (put !=1.9.0 in the environment file)
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Can someone generate a minimum working example (MWE)? |
rwest
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This is a combination of 12 commits, as we tried everything under the sun to debug the CI. But they all cancelled out when merged (apart from fixing a typo in a comment) - This is the 1st commit message: CI: trying to force ubuntu-20.04 instead of ubuntu-latest (temporary) While we figure out what's happening, let's try an older ubuntu. - This is commit message #2: fixup! CI: trying to force ubuntu-20.04 instead of ubuntu-latest (temporary) - This is the commit message #3: Switch back to ubuntu-latest But leave a 20.04 in the matrix build - This is the commit message #4: Trying libstdcxx-ng < 13 in Conda environment. Trying to debug. If this works it should be put in docker file too. Or, better, the real cause found and fixed. - This is the commit message #5: fix typo in env, undo ubuntu os changes, set gcc version in CI to 6 this system object of this version is being provided by gcc, and the runners no longer come prepackaged with it since its old (?) - This is the commit message #6: it wasn't the gcc version - This is the commit message #7: it was the julia version, 1.9.0 is brokey as reported at conda-forge/julia-feedstock#253 the latest release of julia (1.9.0) is brokey, don't use it (put !=1.9.0 in the environment file) - This is the commit message #8: make mac and ubuntu use the same cxx library - This is the commit message #9: but what if it was rdkit all along? - This is the commit message #10: Revert "but what if it was rdkit all along?" because it wasn't - This is the commit message #11: Revert "make mac and ubuntu use the same cxx library" cos it didn't work - This is the commit message #12: Revert "it was the julia version, 1.9.0 is brokey" but it wasn't
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Maybe we should try rebuilding Julia with USE_SYSTEM_CSL=1 ? |
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Should I close it since we fixed the Conda.jl issue? |
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This has been resolved for us with that change. |
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The Conda.jl fix you mean? Or limiting libstdcxx-ng<13? |
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Closing since JuliaPy/Conda.jl#241 resolves the issue. |
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All of my CI tests on Ubuntu + Conda seem to be failing with a library linkage issue:
Here is an example run: https://github.com/MilesCranmer/PySR/actions/runs/5171734252
I had initially thought this was a scipy issue from the pathname, but the error message actually looks to be from this line in the Julia source: https://github.com/JuliaLang/julia/blob/f407a4cac3d1c660d1f8f1a9b367eec108d98178/cli/loader_lib.c#L456, so now I'm not so sure.
A strange thing is that I have actually successfully run the unit tests on Julia 1.9 in the past: https://github.com/MilesCranmer/PySR/actions/runs/5163099602. It's only the past day where they started to break.
Here are the dependencies that changed from 2 days ago (working) to 1 day ago (broken across all Python versions):
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