Say you just upgraded from Ubuntu 19.10 to Ubuntu 20.04, as I just did. You may have a number of CRAN packages installed from source in /usr/local/lib/R/site-library. All fine.
But apt and dpkg do not know about them. So it may remove libraries not knowing about these implicit dependencies. Next time you try to load one of the affected packages, it will fail.
Example:
R> library(chshli)
Attaching chshli on ubuntu:20.04
R> checkSharedLibs(db="19.10")
Looking at libxml2.so.2 : libxml2
Looking at libapt-pkg.so.5.90 : libapt-pkg5.90
Looking at libgit2.so.27 : libgit2-27
NULL
R>This identifies libgit2 (likely via package git2r), libapt-pkg (likely via RcppApt and libxml2 (likely via xml2). All three can probably be fixed via a simple reinstallation from source.
Say you experiment with RSPM, for example via this Rocker container which you can pull via docker pull rocker/r-rspm:18.04. And you did install.packages("xml2"). Now you can do (after installing this package, of course)
Example:
R> library(chshli)
Attaching chshli on ubuntu:18.04
R> checkSharedLibs()
Looking at libxml2.so.2 : libxml2
NULL
>and installing (at the system-level, i.e. as root) sudo apt install libxml2 will make your package work. Which is a very nice complement to the nice and fast installation via RSPM.
For now from GitHub via remotes::install_github("eddelbuettel/chshli") or, if you have littler, via installGithub eddelbuettel/chshli.
Dirk Eddelbuettel
GPL (>= 2)