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metagenlab / zAMP

zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
https://zamp.readthedocs.io/en/latest/
MIT License
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Can't open /miniconda3/622b4111/lib/R/etc/ldpaths #1

Closed valscherz closed 5 years ago

valscherz commented 5 years ago

The following error sometimes occurs near the end of the pipeline, when running the visualizations scripts. A rerun of the same snakemake command usually solves it. 

Activating conda environment: /home/pipeline_user/miniconda3/622b4111
/home/pipeline_user/miniconda3/622b4111/lib/R/bin/R: 238: .: Can't open /home/pipeline_user/miniconda3/622b4111/lib/R/etc/ldpaths
valscherz commented 5 years ago

A rerun of the same snakemake command usually solves it.

And if not, rm of the conda environment and rerun,

valscherz commented 5 years ago

It is actually a conda problem. Hopefully will be solved https://github.com/conda-forge/r-base-feedstock/issues/67#issuecomment-502489475

valscherz commented 5 years ago

Solved by https://github.com/conda-forge/r-base-feedstock/pull/84#issuecomment-503574274