conda R environment warnings - error

Question

[marco.barr]

Hello everyone,

I manually copied some R packages from a local directory to the /R/library directory of my conda R_env environment where I installed r-base. However, upon starting R after activating the environment, I receive these warnings:

(/home/user_m/r_env) user_m@login01:~$ R

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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During startup - Warning messages:
1: package 'utils' in options("defaultPackages") was not found
2: package 'grDevices' in options("defaultPackages") was not found
3: package 'graphics' in options("defaultPackages") was not found
4: package 'stats' in options("defaultPackages") was not found.

These packages were and are already present in the directory, and I don't understand what to do. Should I try installing them with conda install -c r r-utils r-grDevices r-graphics r-stats --force-reinstall? Or what do you recommend doing?

Thank you very much for the advice.

[Ram]

How does this pertain to bioinformatics? If this is purely an R problem, please check/ask StackOverflow or similar StackExchange sites.

Answer 1

[ATpoint]

I manually copied some R packages

and I don't understand what to do

Don't randomly copy things. Either stick with conda and let it handle the compilation/installation, or stick entirely to the R machinery to get packages. Don't mix. It messes up dependencies as you see.