R Conda Environments and Installed Packages
- Simon Alexander
Goal: Understand R environments build with Conda.
Note: There is a known vulnerability with R versions less than 4.4.0.
This page uses R version 4.3.3. This page is purely for example since as of the date of creating this page there were issues using an r-base/4.4.1.
I am hoping in a few weeks/months the 4.4.x base will be stable and I’ll update the examples.
- 1 Basic R Conda Environment
- 2 Where are Packages Installed?
- 3 Try Installing vctrs Package
- 4 Where was this installed?
- 5 But What about the R_LIBS_USER Environment Variable?
- 6 Can I Create this Folder?
- 7 Should I Create this Folder?
- 8 Try Installing stringi Package
- 9 Conda Install stringi Package: Search
- 10 Conda Install stringi Package
- 11 Where was this installed?
- 12 Anaconda: R Essentials
Basic R Conda Environment
General Process:
[]$ cd /project/<project-name>/software/conda-envs/
[]$ module purge
[]$ module load miniconda3/24.3.0
[]$ conda search r-base
Loading channels: done
# Name Version Build Channel
...
r-base 4.3.3 hf0d99cb_1 conda-forge
...
r-base 4.4.1 h1dca405_0 conda-forge
[]$ conda create -p r_4.3.3_env r-base=4.3.3
[]$ 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) []$ R --version
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
...Note: The conda environment was created using the -p option, so it was installed under the current working directory, which in the case was: /project/arcc/software/conda-envs
Where are Packages Installed?
Lets look at the environment variables:
(/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env) []$ R -e 'Sys.getenv(c("R_PLATFORM", "R_HOME", "R_LIBS_USER", "R_LIBS", "R_LIBS_SITE"))'
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
...
> Sys.getenv(c("R_PLATFORM", "R_HOME", "R_LIBS_USER"))
R_PLATFORM "x86_64-conda-linux-gnu"
R_HOME "/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env/lib/R"
R_LIBS_USER "/cluster/medbow/home/<username>/R/x86_64-conda-linux-gnu-library/4.3"
R_LIBS ""
R_LIBS_SITE "/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env/lib/R/site-library"
Note: The platform string value is different: x86_64-conda-linux-gnu
Try Installing vctrs Package
# Within R:
> install.packages("vctrs")
...
also installing the dependencies ‘cli’, ‘glue’, ‘lifecycle’, ‘rlang’
...
* DONE (vctrs)Where was this installed?
Check .libPaths():
(/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 ~]$ R
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
...
> .libPaths()
[1] "/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library"Since I own this Conda environment, I have permission to install under: /project/arcc/software/conda-envs/r_4.3.3_env/lib/R.
Lets check:
[]$ ls /project/<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library/
base cli compiler datasets glue graphics grDevices grid lifecycle methods
parallel rlang splines stats stats4 tcltk tools translations utils vctrsBut What about the R_LIBS_USER Environment Variable?
Remember our environment variables:
R_LIBS_USER "/cluster/medbow/home/<username>/R/x86_64-conda-linux-gnu-library/4.3"
R_HOME "/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env/lib/R"[]$ ls /home/<username>/R/x86_64-conda-linux-gnu-library/4.3
ls: cannot access '/home/<username>/R/x86_64-conda-linux-gnu-library/4.3': No such file or directory
[]$ ls /home/<username>/R/
x86_64-pc-linux-gnu-librarySince this folder is missing, it is not being picked up and used by the .libPaths() command.
Can I Create this Folder?
If you manually create this folder then .libPaths() does pick it up.
(/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env) []$ mkdir -p x86_64-conda-linux-gnu-library/4.3
(/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env) []$ R
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
...
> .libPaths()
[1] "/cluster/medbow/home/<username>/R/x86_64-conda-linux-gnu-library/4.3"
[2] "/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library"Using the install.packages() command within R will now look/install packages into this folder that could be shared across multiple Conda environments using this version of R.
Should I Create this Folder?
Question: Should you manually create the ~/R/x86_64-conda-linux-gnu-library/X.Y/ folder?
First, we would suggest that unless you are confident in self-managing your Conda/R environments then do not.
If this is not in your .libPaths(), then it will force all R package installs to be contained under the Conda environment.
If this path IS in your .libPaths(), across multiple conda environments, then all the environments will install into and look/share this folder.
You can run into dependency/version issues if you want to use version X of a package in one Conda environment, but version Y in another. You can only have one version in this folder.
We have observed that some times this folder have been automatically created.
Best thing is to always check and set the .libPaths() to you necessary needs.
Try Installing stringi Package
# Within R:
> install.packages("stringi")
...
configure: error: in `/tmp/RtmpVm7ias/R.INSTALL2ad60710733cd2/stringi':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘stringi’
* removing ‘/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library/stringi’
The downloaded source packages are in
‘/tmp/Rtmpio5YFH/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("stringi") :
installation of package ‘stringi’ had non-zero exit statusConda environments are not the same as the System/compute nodes - libraries and behavior can be different.
Conda Install stringi Package: Search
(/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env) []$ conda search stringi
Loading channels: done
No match found for: stringi. Search: *stringi*
# Name Version Build Channel
r-stringi 0.4_1 r3.1.3_0 pkgs/r
...
r-stringi 1.8.4 r43hbd1cc82_0 conda-forge
(/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env) []$ conda search r-stringi
Loading channels: done
# Name Version Build Channel
r-stringi 0.4_1 r3.1.3_0 pkgs/r
...
r-stringi 1.8.4 r43hbd1cc82_0 conda-forgeRemember: Conda r packages use the naming convention: r-<package-name>
Conda Install stringi Package
(/cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env) []$ conda install r-stringi
Channels:
- conda-forge
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /cluster/medbow/project/<project-name>/software/conda-envs/r_4.3.3_env
added / updated specs:
- r-stringi
The following NEW packages will be INSTALLED:
r-stringi conda-forge/linux-64::r-stringi-1.8.4-r43hbd1cc82_0
...
Executing transaction: doneWhere was this installed?
The conda install command (whatever the type of package/library) installs within the conda environment .
[salexan5@mblog2 ~]$ ls /project/<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library/
base cli compiler datasets glue graphics grDevices grid lifecycle methods parallel
rlang splines stats stats4 stringi tcltk tools translations utils vctrsAnaconda: R Essentials
Although we do not recommend installing Anaconda (unless you are comfortable with how it works and modifies your home environment), it does provide an R Essentials bundle which “includes approximately 80 of the most popular scientific packages for the R programming language.“
conda install -c r r-essentials