maybe reinstall the github packages?

reinstall-CRAN.R

df <- as.data.frame(installed.packages(fields = c("RemoteType", "Repository")))
to_reinstall <- df[df$Repository %in% "CRAN", "Package"]
install.packages(to_reinstall)

reinstall-githubs.R

install.packages("remotes")

packages <- installed.packages(
  fields = c("GithubUsername", "GithubRepo", "GithubSubdir")
)

from_github <- packages[
  !is.na(packages[, "GithubRepo"]), 
  c("GithubUsername", "GithubRepo", "GithubSubdir")
]

repos <- paste0(
  from_github[, 1], "/", 
  from_github[, 2], 
  ifelse(is.na(from_github[, 3]), "", paste0("/", from_github[, 3]))
)

lapply(repos, remotes::install_github,  upgrade = "always", build = FALSE, force = TRUE, type = "binary")