DEP: ANCOMBC unable to load phyloseq

[cherman2]

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

Comments

1. I was able to get this to work by switching to q2-metagenome-2024.2
2. This error is not reproducible on MAC

Screenshots

Computation Environment

• OS: Linux
• QIIME 2 Release QIIME2-metagenomics-2024.5

[ebolyen]

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.

[lizgehret]

forum xref: https://forum.qiime2.org/t/q2-composition-ancombc-error/31271

[lizgehret]

seems like it's just an issue with the linux environment file. @Oddant1 is testing on his machine today to confirm.

[lizgehret]

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.