Check existence of directory and create if doesn't exist

Use showWarnings = FALSE:

dir.create(file.path(mainDir, subDir), showWarnings = FALSE)
setwd(file.path(mainDir, subDir))

dir.create() does not crash if the directory already exists, it just prints out a warning. So if you can live with seeing warnings, there is no problem with just doing this:

dir.create(file.path(mainDir, subDir))
setwd(file.path(mainDir, subDir))

As of April 16, 2015, with the release of R 3.2.0 there's a new function called dir.exists(). To use this function and create the directory if it doesn't exist, you can use:

ifelse(!dir.exists(file.path(mainDir, subDir)), dir.create(file.path(mainDir, subDir)), FALSE)

This will return FALSE if the directory already exists or is uncreatable, and TRUE if it didn't exist but was succesfully created.

Note that to simply check if the directory exists you can use

dir.exists(file.path(mainDir, subDir))

In terms of general architecture I would recommend the following structure with regard to directory creation. This will cover most potential issues and any other issues with directory creation will be detected by the dir.create call.

mainDir <- "~"
subDir <- "outputDirectory"

if (file.exists(paste(mainDir, subDir, "/", sep = "/", collapse = "/"))) {
    cat("subDir exists in mainDir and is a directory")
} else if (file.exists(paste(mainDir, subDir, sep = "/", collapse = "/"))) {
    cat("subDir exists in mainDir but is a file")
    # you will probably want to handle this separately
} else {
    cat("subDir does not exist in mainDir - creating")
    dir.create(file.path(mainDir, subDir))
}

if (file.exists(paste(mainDir, subDir, "/", sep = "/", collapse = "/"))) {
    # By this point, the directory either existed or has been successfully created
    setwd(file.path(mainDir, subDir))
} else {
    cat("subDir does not exist")
    # Handle this error as appropriate
}

Also be aware that if ~/foo doesn't exist then a call to dir.create('~/foo/bar') will fail unless you specify recursive = TRUE.