Installing packages from RProfile.site file

Question

I asked this question earlier, but am still unable to get it working. I am trying to install custom packages upon starting R. A lot of the code that is written by us right now is available for editing to the users. To try and protect the code, I am packaging the production level code and having the users install it on their machine during start up.

However, when I try to install packages in RProfile.site file, the program goes into a loop and R is constantly launched over and over. I noticed that a lock file for the package is created along with the package in the library folder within R.

Here is the code I have added to the site file:

if(length(grep("customPackage", installed.packages()[,1]))==0) { 
        install.packages("customPackage", repos=NULL, type="source") 
} 

When I try to run this code after starting R (without changing the site file), it installs the package perfectly fine and moves on. However, when I try to do it through the RProfile file, that's when it creates the problems.

Last time I tried resolving this issue (https://stackoverflow.com/questions/10610067/installing-packages-upon-starting-r-session), I thought Justin's suggestion of using the if statement check for packages would fix the problem. But this only seems to solve the problem for packages I install from CRAN and not custom packages.

Any help on this matter would be greatly appreciated!

Answer 1

I don't understand why you'd want to do this. Just have them point their .libPaths to the same place. i.e. instead of install.packages(...), just add a line in Rprofile.site that says

.libPaths('/path/to/common/libraries')
require("commonPackage")

Another thing that you might be able to do is make a system call. I don't know much about installing packages under Windows, but on Unix-alike, instead of using install.packages you could do something like this:

system("R --vanilla CMD INSTALL customPackage")

Among other things, the --vanilla flag causes R to be started without using the Rprofile.site file (Your problem is that the Rprofile.site file is being read when R starts, but the Rprofile.site file tells R to install a package which requires starting R, which in turns reads your Rprofile.site file... etc.). Presumably, R --no-site-file INSTALL customPackage would also work.

Edit

After consulting this SO answer, it looks like you could do something like this on Windows (assuming you have installed Rtools), although I haven't tested it.

system("Rcmd --vanilla INSTALL customPackage")

Answer 2

As GSee said, the problem is that install.packages runs R CMD INSTALL, which starts a new R process that reads the Rprofile.site file, resulting in a loop. Two ways to break the evil loop:

1. Check that R is running interactively:

   if (interactive() && 
       length(grep("customPackage", installed.packages()[,1]))==0) { 
     install.packages("customPackage", repos=NULL, type="source") 
   }
   

   interactive() is FALSE when R CMD is running, so this breaks the loop.

2. Set the R_PROFILE environment variable to an empty or invalid value, so the R session in R CMD won't run yours. Initialization at Start of an R Session says:

   If you want ‘~/.Renviron’ or ‘~/.Rprofile’ to be ignored by child R processes (such as those run by R CMD check and R CMD build), set the appropriate environment variable R_ENVIRON_USER or R_PROFILE_USER to (if possible, which it is not on Windows) "" or to the name of a non-existent file.

   Adapting that for Rprofile.site, you can set R_PROFILE to an empty or nonexistent file, before you call install.packages. For example:

   if (length(grep("customPackage", installed.packages()[,1]))==0) { 
     Sys.setenv(R_PROFILE = "/dev/null")
     install.packages("customPackage", repos=NULL, type="source") 
     Sys.unsetenv("R_PROFILE")
   }
   

   Then when R restarts to install packages, it reads an empty Rprofile.site file, so again you break the loop .

   If the call to install.packages is in .Rprofile, you can set R_PROFILE_USER in the same way.

The first method is simpler, and doesn't require you to worry about maybe overwriting an existing value of R_PROFILE.

Answer 3

You can use the function below to install package(s) without reloading .Rprofile:

surround <- function(x, with) {
  paste0(with, x, with)
}

peq <- function(x, y) paste(x, y, sep = " = ")

install.packages.vanilla <- function(pkgs, ...){

  arguments <- as.list(match.call())[-1]

  if(!"repos" %in% names(arguments)){
    arguments$repos <- getOption("repos")
  }
  names_args <- names(arguments)

  installArgs <- purrr::map_chr(seq_along(arguments),
                                function(i){
                                  value <- arguments[[i]]
                                  peq(names_args[i], ifelse(length(value)<2, deparse(value), as.character(list(value))))
                                })
  installArgs <- stringr::str_replace_all(installArgs, "\"", "'")
  installCmd <- paste0("utils::install.packages(",
                       paste(installArgs, collapse = ", "),
                       ")")
  fullCmd <- paste(
    surround(file.path(R.home("bin"), "R"), with = "\""),
    "--vanilla",
    "--slave",
    "-e",
    surround(installCmd, with = "\"")
  )

  system(fullCmd)
  return(invisible())
}