library(tidyverse): timedatectl: no version information available (required by /lib64/

In order to work around the following error for xml2 we found that Anaconda Python has We're using RHEL 8 on a a HPC cluster with R 4.1.0.

> library(xml2)
Error: package or namespace load failed for ‘xml2’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/path/to/me/R/x86_64-pc-linux-gnu-library/4.1/xml2/libs/': cannot open shared object file: No such file or directory

So we've been using export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/anaconda/lib after loading Anaconda Python.

However with tidyverse we're now seeing these errors:

> library(tidyverse)
timedatectl: /path/to/anaconda3-2022.05/lib/ no version information available (required by /lib64/
timedatectl: /path/to/anaconda3-2022.05/lib/ no version information available (required by /lib64/
── Attaching core tidyverse packages ─────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.2     ✔ readr     2.1.4
✔ forcats   1.0.0     ✔ stringr   1.5.0
✔ ggplot2   3.4.2     ✔ tibble    3.2.1
✔ lubridate 1.9.2     ✔ tidyr     1.3.0
✔ purrr     1.0.1     
── Conflicts ───────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<>) to force all conflicts to become errors

I believe the conflicts are expected. But these timedatectl errors are new. The closest thread I found was about rmarkdown with reticulate.

Anyone else seeing these errors and/or a fix?

In my experience mixing the Anaconda libraries with the R system libraries often does not work correctly. If you are using Anaconda, then I think your best bet is to install everything, including R and R packages from (Ana)conda.

We make Anaconda Python and R available as modules ad hoc. I did find a clumsy work-around. is also in /usr/lib64. So I exported LD_LIBRARY_PATH and placed /usr/lib64 first and put that Anaconda lib last.

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