Conda bug: "lib/R/etc/ldpaths: No such file or directory"
Rule visualize_bins
in workflow/rules/Summary/vis_stats.smk
in b534fcaf failed with
Rscript --vanilla <workdir>/.snakemake/scripts/<hash>.visualize_binning.R
Activating conda environment: <smk conda path>
<smk conda path>/lib/R/bin/R: line 238: <smk conda path>/lib/R/etc/ldpaths: No such file or directory
This might be related to the issue describe here.
One solution is to re-install r-base
: find the associated conda
environment in the snakemake
/slurm
log file, activate it and re-install r-base
.
conda activate <smk conda path>/<env name>
conda list | grep "r-base"
# should give you the installed version and the used channel
conda install -c <channel> r-base=<version> --force-reinstall