Closed cherman2 closed 10 hours ago
I'm able to reproduce this on my linux machine as well.
We've found that all of the library objects are loaded from within the conda environment, so it's not a case of escaping the env.
Rather it appears that there's an unknown-to-conda conflict in libcxx here. This will take some investigation into the original recipes.
seems like it's just an issue with the linux environment file. @Oddant1 is testing on his machine today to confirm.
okay so this is a confirmed issue with the linux environment files for 2024.5 (both metagenome and amplicon are affected). @Oddant1 confirmed that creating a fresh environment from the 2024.5 seed environment resolved the issue, so I'm re-minting the 2024.5 environment files and we'll make sure that fixes the issue before merging.
Bug Description ruuning ancombc on QIIME2-metagenomics-2024.5 on Linux.
Error: package or namespace load failed for ‘phyloseq’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/scratch/crh423/conda2/envs/qiime2-metagenome-2024.5/lib/R/library/ade4/libs/ade4.so': /scratch/crh423/conda2/envs/qiime2-metagenome-2024.5/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.15' not found (required by /scratch/crh423/conda2/envs/qiime2-metagenome-2024.5/lib/R/library/ade4/libs/ade4.so)
Command qiime composition ancombc --i-table end-all-taxa-5-metaphlan-table-freq-filt.qza --m-metadata-file ../../../metadata-current.tsv --p-formula "Type" --o-differentials type-diff
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