R package or namespace load failed

[igordot]

What to do about R errors such as:

loading package: magrittr
loading package: tibble
loading package: dplyr
installing package: dplyr
Bioconductor version 3.14 (BiocManager 1.30.22), R 4.1.2 (2021-11-01)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'dplyr'
package not available on CRAN or Bioconductor: dplyr
Error: package or namespace load failed for ‘dplyr’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace ‘vctrs’ 0.6.3 is already loaded, but >= 0.6.4 is required
Execution halted

[igordot]

This is likely caused by conflicting package versions across multiple R libraries. R checks both your personal and the system-wide shared library. You can get namespace conflicts if different versions of the same package exists in both. Even if you recently haven't changed anything in your personal library, HPC admins may update packages in the global library, creating a mismatch.

To confirm that the problem is with R, load the relevant R module, launch R, and try loading the problematic package.

To diagnose the problem, start R and run:

.libPaths()
find.package("packagename")
packageVersion("packagename")

The .libPaths() command typically returns two paths: the shared one starts with /gpfs/share/apps/R/ and the other is your personal one. The other commands will show you which version of the conflicting package are found.

If you don't need specific versions in your personal library, you can remove the conflicting packages from there. Navigate to your personal path in the terminal and you will see all the libraries installed there. You can delete the directory corresponding to the offending package. If you prefer to be cautious, you can simply rename the directories to hide them from R and R will fall back to the system library versions.