Could not install R packages about armor

[uqtho10]

Here's my Rout.

Rout.txt

Error in rule pkginstall:
jobid: 1
input: scripts/install_pkgs.R
output: example_data/output/Rout/pkginstall_state.txt
log: example_data/output/Rout/install_pkgs.Rout (check log file(s) for error details)
conda-env: /Users/uqtho10/ARMOR/.snakemake/conda/a4fc58524fec5e8c53450cde04b86ca0_
shell:
R CMD BATCH --no-restore --no-save "--args outtxt='example_data/output/Rout/pkginstall_state.txt' ncores='1' annotation='Ensembl' organism='Homo_sapiens'" scripts/install_pkgs.R example_data/output/Rout/install_pkgs.Rout
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[csoneson]

Hi @uqtho10 - thanks for the report.

There are indeed several error messages in the attached Rout file above - e.g., there seem to be a few timeouts when downloading big packages, and the units package fails to install as the udunits system library is not found.

It looks like you're on a mac, is that correct? May I ask which of the setup approaches for R you are using (1a, 1b, 2)? For macOS, we found approach 1b to be the most reliable.

[uqtho10]

Hi,

Thank you for your response. I'm using MacOS Montery. I'm doing 1a to install.

I would like to try 1b but I'm a little confused how to change the path in Renviron.
What I understand is that:

• I need to change Rbin path in config.yaml to my current R path. I have 2 R paths:
  • /Users/uqtho10/anaconda3/envs/R/bin/R
  • /Users/uqtho10/anaconda3/pkgs/r-base-3.3.1-0/bin/R
    Which one should I use?
    The R lib path in my Mac is :

• /Users/uqtho10/anaconda3/envs/R/lib

How should I change it in Renviron?

#R_LIBS_USER=${R_LIBS_USER-'/R/x86_64-apple-darwin13.4.0-library/4.1'}
R_LIBS_USER=${R_LIBS_USER-'/Library/R/x86_64/4.1/library'}

Sorry as I'm not really familiar with these.

Kind regards,
Thao

[csoneson]

If R is in your path, you can simply set Rbin: R in the yaml file - otherwise, give the full path to the binary you want to use. The second R binary in your list is too old (at least R 4.1.0 is required). If you run into problems with the first binary in your list (as it is installed with conda), I suggest downloading and installing R directly from https://www.r-project.org/.

For the .Renviron file (note that the file name has to start with a dot), just add a line
R_LIBS_USER="/Users/uqtho10/anaconda3/envs/R/lib"
(or any other path where you want to install the packages).

[csoneson]

👋🏻 @uqtho10 - just wanted to check in to see if the suggestions above solved your problem.

[csoneson]

I'm going to close this issue - feel free to reopen if the problem persists.