reinstall-packages.R

# Step 1 ------------------------------------------------------------------
# Before updating R...

`%>%` <- magrittr::`%>%`

# Thanks Chuck Powell - https://ibecav.github.io/update_libraries/
package_source <- function(pkg){
  x <- as.character(packageDescription(pkg)$Repository)
  if (length(x)==0) {
    y <- as.character(packageDescription(pkg)$GithubRepo)
    z <- as.character(packageDescription(pkg)$GithubUsername)
    if (length(y)==0) {
      return("Other")
    } else {
      return(paste0(z, "/", y))
    }
  } else {
    return(x)
  }
}

pkgs <-
  tibble::as_tibble(installed.packages()) %>%
  dplyr::filter(is.na(Priority)) %>%
  dplyr::select(Package, Version, Depends, Imports, NeedsCompilation) %>%
  janitor::clean_names() %>%
  dplyr::mutate(source = purrr::map_chr(package, package_source))

dplyr::count(pkgs, source)
dplyr::filter(pkgs, source == "Other")

r_version <- paste(R.version[c("major", "minor")], collapse = ".")
r_pkgs_csv <- paste0("~/.pkgs_", r_version, ".csv")
readr::write_csv(pkgs, r_pkgs_csv)
message("Wrote installed packages to ", r_pkgs_csv)


# Step 2 ------------------------------------------------------------------
# Download R 4.0.2 from:
# > https://cloud.r-project.org/bin/macosx/R-4.0.2.pkg

install.packages("remotes")

# Step 3 ------------------------------------------------------------------
# restart R session and re-install packages

# r_pkgs_csv <- "SET TO PATH CREATED ABOVE!"

options(install.packages.check.source = "no")

pkgs <- read.csv(r_pkgs_csv) # what, no stringsAsFactor?!?!

# > cran packages ----
cran_pkgs <- pkgs[pkgs$source == "CRAN", ]
cran_pkgs <- cran_pkgs[cran_pkgs$package != "tidycells", ]
remotes::install_cran(cran_pkgs$package, source = "binary")

# > github packages ----
github_pkgs <- subset(pkgs, grepl("/", source))
failed <- c()
lapply(github_pkgs$source, function(repo) {
  tryCatch(
    remotes::install_github(repo, upgrade = "never"),
    error = function(e) failed <<- c(failed, repo)
  )
})

if (length(failed)) {
  message("Failed to install: ", paste(failed, collapse = ", "))
}

# > other ----
# investigate "other" packages and install manually
other_pkgs <- subset(pkgs, source == "Other")
other_pkgs$package