installr does not copy over packages to new version of R

Question

I recently used the installr package to update my version of R (from 3.6.2 to 4.0.0). The update was successful, and I have confirmed using print(R.version). However, my packages from the old version of R have not copied over to the new version, despite me following these steps to the letter. I have also tried to run copy.packages.between.libraries(ask = T) to copy the packages over. Both times returned No packages to copy. Goodbye :), despite me being unable to load any of the packages previously installed on the old version.

Answer 1

This is because updating from R 3.6.x to 4.x requires that you reinstall all packages (see the news).

The best way I found of doing this is:

1. get your old packages

   old_packages <- installed.packages(lib.loc = "/home/johannes/R/x86_64-pc-linux-gnu-library/3.6/")
   

Of course, you have to change the path to the one where your packages live. Simply use .libPaths() and if you've already installed the new R version, replace the 4.0 with 3.6.

2. check the old against the already installed packages:

   new_packages <- installed.packages()
   missing_df <- as.data.frame(old_packages[
     !old_packages[, "Package"] %in% new_packages[, "Package"], 
     ])
   

3. install missing packages (use multiple cores for extra speed)

   install.packages(missing_df$Package, Ncpus = 3)

I wrote this up on my blog some time ago here, but these are the essential steps and you should be good to go.

Answer 2

If you have a look at the source code of copy.packages.between.libraries (just type F2 when your mouse pointer is on the function name), you find the following commands :

library(installr)

(installed_R_folders <- get.installed.R.folders())
#>                   4.0.3                   4.0.2 
#> "C:/PROGRA~1/R/R-4.0.3" "C:/PROGRA~1/R/R-4.0.2"
(installed_R_folders_TABLE <- data.frame(R_version = names(installed_R_folders), 
                                        Folder = installed_R_folders))
#>       R_version                Folder
#> 4.0.3     4.0.3 C:/PROGRA~1/R/R-4.0.3
#> 4.0.2     4.0.2 C:/PROGRA~1/R/R-4.0.2
(from <- installed_R_folders[2])
#>                   4.0.2 
#> "C:/PROGRA~1/R/R-4.0.2"
(to <- installed_R_folders[1])
#>                   4.0.3 
#> "C:/PROGRA~1/R/R-4.0.3"
(from_library <- file.path(from, "library"))
#> [1] "C:/PROGRA~1/R/R-4.0.2/library"
(to_library <- file.path(to, "library"))
#> [1] "C:/PROGRA~1/R/R-4.0.3/library"
(packages_in_the_from_library <- list.files(from_library))
#>  [1] "base"         "boot"         "class"        "cluster"      "codetools"   
#>  [6] "compiler"     "datasets"     "foreign"      "graphics"     "grDevices"   
#> [11] "grid"         "KernSmooth"   "lattice"      "MASS"         "Matrix"      
#> [16] "methods"      "mgcv"         "nlme"         "nnet"         "parallel"    
#> [21] "rpart"        "spatial"      "splines"      "stats"        "stats4"      
#> [26] "survival"     "tcltk"        "tools"        "translations" "utils"
(packages_in_the_to_library <- list.files(to_library))
#>  [1] "base"         "boot"         "class"        "cluster"      "codetools"   
#>  [6] "compiler"     "datasets"     "foreign"      "graphics"     "grDevices"   
#> [11] "grid"         "KernSmooth"   "lattice"      "MASS"         "Matrix"      
#> [16] "methods"      "mgcv"         "nlme"         "nnet"         "parallel"    
#> [21] "rpart"        "spatial"      "splines"      "stats"        "stats4"      
#> [26] "survival"     "tcltk"        "tools"        "translations" "utils"
(packages_to_NOT_move <- unname(installed.packages(priority = "high")[,"Package"]))
#>  [1] "codetools"  "base"       "boot"       "class"      "cluster"   
#>  [6] "codetools"  "compiler"   "datasets"   "foreign"    "graphics"  
#> [11] "grDevices"  "grid"       "KernSmooth" "lattice"    "MASS"      
#> [16] "Matrix"     "methods"    "mgcv"       "nlme"       "nnet"      
#> [21] "parallel"   "rpart"      "spatial"    "splines"    "stats"     
#> [26] "stats4"     "survival"   "tcltk"      "tools"      "utils"
(packages_to_NOT_move <- c(packages_to_NOT_move, packages_in_the_to_library))
#>  [1] "codetools"    "base"         "boot"         "class"        "cluster"     
#>  [6] "codetools"    "compiler"     "datasets"     "foreign"      "graphics"    
#> [11] "grDevices"    "grid"         "KernSmooth"   "lattice"      "MASS"        
#> [16] "Matrix"       "methods"      "mgcv"         "nlme"         "nnet"        
#> [21] "parallel"     "rpart"        "spatial"      "splines"      "stats"       
#> [26] "stats4"       "survival"     "tcltk"        "tools"        "utils"       
#> [31] "base"         "boot"         "class"        "cluster"      "codetools"   
#> [36] "compiler"     "datasets"     "foreign"      "graphics"     "grDevices"   
#> [41] "grid"         "KernSmooth"   "lattice"      "MASS"         "Matrix"      
#> [46] "methods"      "mgcv"         "nlme"         "nnet"         "parallel"    
#> [51] "rpart"        "spatial"      "splines"      "stats"        "stats4"      
#> [56] "survival"     "tcltk"        "tools"        "translations" "utils"
(ss_packages_to_NOT_move_from <- packages_in_the_from_library %in% 
  packages_to_NOT_move)
#>  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#> [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
(ss_packages_to_YES_move_from <- !ss_packages_to_NOT_move_from)
#>  [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [25] FALSE FALSE FALSE FALSE FALSE FALSE
(packages_to_YES_move_from <- packages_in_the_from_library[ss_packages_to_YES_move_from])
#> character(0)

Which comes to the conclusion there's no difference between the packages of the different R installations and leads to:

No packages to copy. Goodbye :)

However, if you look at .libPaths(), you see that get.installed.R.folders is missing the packages you installed on your own user's library:

.libPaths()
[1] "C:/Users/User/Documents/R/win-library/4.0"
[2] "C:/Program Files/R/R-4.0.3/library"

So default behaviour of installr is missing all the packages you installed after R installation :

packages <- as.data.frame(utils::installed.packages())
head(packages[is.na(packages$Priority),c("Package","LibPath")])

arrow                               arrow C:/Users/User/Documents/R/win-library/4.0
arules                             arules C:/Users/User/Documents/R/win-library/4.0
arulesViz                       arulesViz C:/User/User/Documents/R/win-library/4.0
ash                                   ash C:/Users/User/Documents/R/win-library/4.0
askpass                           askpass C:/Users/User/Documents/R/win-library/4.0
assertive                       assertive C:/Users/User/Documents/R/win-library/4.0
...