Elegant way to check for missing packages and inst

Question

I seem to be sharing a lot of code with coauthors these days. Many of them are novice/intermediate R users and don't realize that they have to install packages they don't already have.

Is there an elegant way to call installed.packages(), compare that to the ones I am loading and install if missing?

Answer 1

I use the following which will check if package is installed and if dependencies are updated, then loads the package.

p<-c('ggplot2','Rcpp')
install_package<-function(pack)
{if(!(pack %in% row.names(installed.packages())))
{
  update.packages(ask=F)
  install.packages(pack,dependencies=T)
}
 require(pack,character.only=TRUE)
}
for(pack in p) {install_package(pack)}

completeFun <- function(data, desiredCols) {
  completeVec <- complete.cases(data[, desiredCols])
  return(data[completeVec, ])
}

Answer 2

You can just use the return value of require:

if(!require(somepackage)){
    install.packages("somepackage")
    library(somepackage)
}

I use library after the install because it will throw an exception if the install wasn't successful or the package can't be loaded for some other reason. You make this more robust and reuseable:

dynamic_require <- function(package){
  if(eval(parse(text=paste("require(",package,")")))) return True

  install.packages(package)
  return eval(parse(text=paste("require(",package,")")))
}

The downside to this method is that you have to pass the package name in quotes, which you don't do for the real require.

Answer 3

A lot of the answers above (and on duplicates of this question) rely on installed.packages which is bad form. From the documentation:

This can be slow when thousands of packages are installed, so do not use this to find out if a named package is installed (use system.file or find.package) nor to find out if a package is usable (call require and check the return value) nor to find details of a small number of packages (use packageDescription). It needs to read several files per installed package, which will be slow on Windows and on some network-mounted file systems.

So, a better approach is to attempt to load the package using require and and install if loading fails (require will return FALSE if it isn't found). I prefer this implementation:

using<-function(...) {
    libs<-unlist(list(...))
    req<-unlist(lapply(libs,require,character.only=TRUE))
    need<-libs[req==FALSE]
    if(length(need)>0){ 
        install.packages(need)
        lapply(need,require,character.only=TRUE)
    }
}

which can be used like this:

using("RCurl","ggplot2","jsonlite","magrittr")

This way it loads all the packages, then goes back and installs all the missing packages (which if you want, is a handy place to insert a prompt to ask if the user wants to install packages). Instead of calling install.packages separately for each package it passes the whole vector of uninstalled packages just once.

Here's the same function but with a windows dialog that asks if the user wants to install the missing packages

using<-function(...) {
    libs<-unlist(list(...))
    req<-unlist(lapply(libs,require,character.only=TRUE))
    need<-libs[req==FALSE]
    n<-length(need)
    if(n>0){
        libsmsg<-if(n>2) paste(paste(need[1:(n-1)],collapse=", "),",",sep="") else need[1]
        print(libsmsg)
        if(n>1){
            libsmsg<-paste(libsmsg," and ", need[n],sep="")
        }
        libsmsg<-paste("The following packages could not be found: ",libsmsg,"\n\r\n\rInstall missing packages?",collapse="")
        if(winDialog(type = c("yesno"), libsmsg)=="YES"){       
            install.packages(need)
            lapply(need,require,character.only=TRUE)
        }
    }
}

Answer 4

You can simply use the setdiff function to get the packages that aren't installed and then install them. In the sample below, we check if the ggplot2 and Rcpp packages are installed before installing them.

unavailable <- setdiff(c("ggplot2", "Rcpp"), rownames(installed.packages()))
install.packages(unavailable)

In one line, the above can be written as:

install.packages(setdiff(c("ggplot2", "Rcpp"), rownames(installed.packages())))

Answer 5

Yes. If you have your list of packages, compare it to the output from installed.packages()[,"Package"] and install the missing packages. Something like this:

list.of.packages <- c("ggplot2", "Rcpp")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

Otherwise:

If you put your code in a package and make them dependencies, then they will automatically be installed when you install your package.

Answer 6

In my case, I wanted a one liner that I could run from the commandline (actually via a Makefile). Here is an example installing "VGAM" and "feather" if they are not already installed:

R -e 'for (p in c("VGAM", "feather")) if (!require(p, character.only=TRUE)) install.packages(p, repos="http://cran.us.r-project.org")'

From within R it would just be:

for (p in c("VGAM", "feather")) if (!require(p, character.only=TRUE)) install.packages(p, repos="http://cran.us.r-project.org")

There is nothing here beyond the previous solutions except that:

• I keep it to a single line
• I hard code the repos parameter (to avoid any popups asking about the mirror to use)
• I don't bother to define a function to be used elsewhere

Also note the important character.only=TRUE (without it, the require would try to load the package p).