Updates R and adds back libraries

update_R_chrissy

#Bare bones updater for R version control.
#########################################
# Takes the long way round, by creating an installer script for packages.
# Accounts for weird behaviour where installing packages from within loops or apply commands doesn't handle
# dependencies well an leads to lots of packages failing to install.
# This script contains some code from updateR package, which has never worked for me on its own
# This can take a while but does a much better job of comprehensively rebuilding your catalogue
# Obviously this only works with CRAN packages, but will spit out a list of packages you need
# to manually install at the end.

# updateR package is here if you want to try
# devtools::install_github("AndreaCirilloAC/updateR")


library(dplyr)
library(xml2)
library(rvest)
library(askpass)

####### GET THE USEFUL FUNCTIONS FROM updateR

list_packages <- function() {
  all_pkg <- installed.packages() %>%
    as.data.frame() %>%
    pull(Package)
  base_pkg <- installed.packages() %>%
    as.data.frame() %>%
    filter(Priority == "base") %>%
    pull(Package)
  all_pkg[!all_pkg %in% base_pkg]
}

latest_r_version <- function() {
  cran <- "http://cran.rstudio.com/bin/macosx/"
  version_regex <- "(\\d+)?\\.(\\d+)?\\.(\\d+)?"
  page <- read_html(cran)
  file_url <- page %>%
    html_nodes(xpath = "//td/a") %>% .[1] %>%
    html_attr("href") %>%
    paste(cran, ., sep = "")
  minimal <- page %>%
    html_nodes(xpath = '//table[1]//tr[1]//td[2]') %>%
    html_text() %>%
    trimws() %>%
    regmatches(., regexpr("macOS.*higher.", .)) %>%
    regmatches(., regexpr("\\d+.\\d+", .))
  r_latest <- regmatches(file_url, regexpr(version_regex, file_url))
  r_current <- paste(version$major, version$minor, sep = ".")
  r_latest_numeric <- as.numeric(sub("^(\\d)\\.", "\\1", r_latest))
  r_current_numeric <- as.numeric(sub("^(\\d)\\.", "\\1", r_current))
  
  structure(
    list(update_avail = ifelse(r_latest_numeric > r_current_numeric, T, F),
         latest = r_latest,
         url = file_url),
    current = paste(version$major, version$minor, sep = "."),
    OS_minimal = as.numeric(minimal)
  )
}


ask_password <- function() {
  askpass::askpass(sprintf("Enter password for %s: ", system2("whoami", stdout = TRUE)))
}



#Define Chrissy version of this function


update_R_chrissy<-function(force=FALSE)
{
  check<-latest_r_version()
  
  if(check$update_avail==FALSE){message("Current version is up to date, nothing to be done")}
  
  if(check$update_avail==TRUE | force == TRUE)
  {
    # Make a list of currently installed packages
    packcmds<-NA
    packages<-list_packages()
    
    # Loop through and create an install script
    for (i in 1:length(packages))
    {
      packcmds[i]<-paste("install.packages('",packages[i],"',dependencies = T)",sep = "")
    }
    
    #write installer script to file
    write.table(x = packcmds,file = "packages.install.script.R",quote = F,row.names = F,col.names=FALSE)
    
    admin_password <- ask_password()
    username <- system('whoami', intern = TRUE)
    command <- paste0("echo '", admin_password, "' | sudo -S -l")
    out <- system(command, intern = TRUE)
    if (length(out) == 0) {
      stop(sprintf("current user %s does not have admin privileges", username))
    }
    folderpath <- sprintf("/Users/%s/Downloads/",
                          system2("whoami", stdout = TRUE))
    pkgfile <- regmatches(check$url, regexpr("R.*$", check$url))
    fullpath <- sprintf("%s%s", folderpath, pkgfile)
    # download package, set folder for download
    message("Downloading new version of R")
    download.file(check$url, fullpath)
    
    message("Installinf new version of R")
    {
      message(paste0("Installing R-", check$latest, "...please wait"))
      command <-
        paste0("echo '",
               admin_password,
               "' | sudo -S installer -pkg ",
               "'",
               fullpath,
               "'",
               " -target /")
      system(command, ignore.stdout = TRUE)
      arg <- paste0("--check-signature ", fullpath)
      system2("pkgutil", arg)
    }
    message("Reinstalling packages from source file")
    source("packages.install.script.R")
    
    new.packages<-list_packages()
    needinstall<-packages[packages%in%new.packages==FALSE]
    needinstall<-factor(unique(needinstall))
    
    message(needinstall)
  }
}


update_R_chrissy(force = T)

fixes error that stopped code working on v.4.2.0 update