ichorCNA can't find packages

[fjgassner]

I get the following error when running ichorCNA.snakefile from this repo:

Error in library(optparse) : there is no package called ‘optparse’ Execution halted in logs/ichorCNA/tumor_sample_1.log

Additional info:

• OSX with Linux
• R version 3.6.1
• ichorCNA R package version 0.3.2
• ichorCNA.R from the cloned broadinstitute/ichorCNA GitHub repo
• optparse version 1.6.2
• console command:

  snakemake -s ~/Documents/programs/TitanCNA/scripts/snakemake/ichorCNA.snakefile --cores 4

config.yaml parameters:

• ichorCNA_rscript: /Users/[UserName]/Documents/programs/ichorCNA/scripts/runIchorCNA.R
• ichorCNA_libdir: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ichorCNA/R/

[fjgassner]

Solved. I downloaded the packages in RStudio, which saves them to a different folder than the one the Script command looks in.