Goal: Introduce ideas and practices to assist in managing the reproducibility of R environments.

1 What Packages Do I Have Installed?
2 Track the R Packages and Versions you have Installed
3 Conda Export and R Packages
4 Track the Building of Your Environments
5 Install R Packages with a Specific Version
6 Suggested Best Practices

What Packages Do I Have Installed?

First step is knowing what your environment is using, and where these packages are installed:

Remember to use .libPaths()

[]$ module load gcc/14.2.0 r/4.4.0
[]$ R
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
...
> .libPaths()
[1] "/cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4"
[2] "/apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R/library"
> quit()

[]$ ls /apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R/library
base  compiler  datasets  graphics  grDevices  grid  methods  parallel  splines  stats  stats4  tcltk  tools  translations  utils

[]$ ls /cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4
class     cli    DBI    e1071  generics  KernSmooth  magrittr  pillar     proxy  R6    rlang  sf       stringr  tidyr       units  vctrs  wk
classInt  cpp11  dplyr  fansi  glue      lifecycle   MASS      pkgconfig  purrr  Rcpp  s2     stringi  tibble   tidyselect  utf8   withr  XML

Anything ARCC has installed will not be updated. We will create a new version of the base R.

Track the R Packages and Versions you have Installed

How can I track the versions of R packages installed? Using plain R:

[salexan5@mblog1 ~]$ R
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
...
> write.table(installed.packages()[,c(1,2,3:4)])
"Package" "LibPath" "Version" "Priority"
"class" "class" "/cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4" "7.3-22" "recommended"
...
"sf" "sf" "/cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4" "1.0-16" NA
"stringi" "stringi" "/cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4" "1.8.4" NA
"stringr" "stringr" "/cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4" "1.5.1" NA
"tibble" "tibble" "/cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4" "3.2.1" NA
...
"tools" "tools" "/apps/u/spack/gcc/14.2.0/r/4.4.0-w7xoohc/rlib/R/library" "4.4.0" "base"
"utils" "utils" "/apps/u/spack/gcc/14.2.0/r/4.4.0-w7xoohc/rlib/R/library" "4.4.0" "base"

Conda Export and R Packages

[]$ module purge
[]$ module load miniconda3/24.3.0
conda activate /cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env
(/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 ~]$
(/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 ~]$ conda list
# packages in environment at /cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env:
#
# Name                    Version                   Build  Channel
...
r-base                    4.3.3                he2d9a6e_3    conda-forge
r-stringi                 1.8.4             r43hbd1cc82_0    conda-forge
...