installr不会将软件包复制到R的新版本

Question

我最近使用installr包更新了我的R版本(从3.6.2升级到4.0.0)。更新成功了，我已经确认使用了print(R.version)。然而，尽管我严格遵循了these的步骤，但我的R旧版本的包并没有复制到新版本中。我还尝试运行copy.packages.between.libraries(ask = T)来复制这些包。这两次都返回了No packages to copy. Goodbye :)，尽管我无法加载以前安装在旧版本上的任何包。

Answer 1

这是因为从R 3.6.x更新到4.x需要重新安装所有软件包(请参阅news)。

我找到的最好的方法是：

获取您的旧软件包old_packages <- installed.packages(lib.loc = "/home/johannes/R/x86_64-pc-linux-gnu-library/3.6/")

当然，您必须将路径更改为包所在的路径。只需使用.libPaths()，如果您已经安装了新的R版本，请将4.0替换为3.6。

1. 根据已安装的包检查旧包：

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

1. 安装缺少的软件包(使用多核以获得额外的速度)

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

前段时间我在我的博客here上写了这篇文章，但这些都是必要的步骤，你应该可以开始了。

Answer 2

如果您查看了copy.packages.between.libraries的源代码(当鼠标指针位于函数名称上时，只需键入F2 )，您会发现以下命令：

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)

得出的结论是，不同R安装的软件包之间没有区别，并导致：

没有要复制的包。再见:)

但是，如果您查看.libPaths()，您会发现get.installed.R.folders缺少您在自己的用户库中安装的包：

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

因此，installr的默认行为是缺少R安装后安装的所有软件包：

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
...