Check for needed R packages, optionally installing them.

ensurePackages.R

hasPackage <- function( package ) {
	suppressWarnings( suppressMessages(
		require( package, quietly= TRUE, warn.conflicts= FALSE, character.only= TRUE )
	))
}

# Set progress=FALSE to hide progress messages. Install messages always
# displayed as they are changing the system.
ensurePackages <- function( packages, installOk= FALSE, progress= TRUE,
							exitOnError= installOk ) {
	
	# First package must be "BiocManager" as that is used.
	# Second package will be "remotes" if any package name includes "/",
	# e.g. is installed from github
	packages <- packages[ packages != "BiocManager" ]
	if (any( grepl( pattern = "/", packages, fixed= TRUE ))) {
		packages <- packages[ packages != "remotes" ]
		packages <- c( "remotes", packages )
	}
	packages <- c( "BiocManager", packages )
	
	if ( progress ) {
		message( "Verifying required R packages..." )
	}
    for (package in packages) {
    	
		if ( progress ) {
			message( paste0( "\t", package, "..." ))
		}
        if ( ! hasPackage( package )) {
            if ( ! installOk ) {
            	errMsg <- paste0(
            		"Required package '", package, "' not found.",
	                " Auto-install is not enabled;",
	                " you'll have to install it yourself."
        		)
            	if (exitOnError) {
	                stop( errMsg )
            	}
        		else {
        			warning( errMsg )
        		}
            } else {
                message( "Installing '", package, "' and dependencies...")
            	if (package == "BiocManager") {
            		install.packages( "BiocManager", character.only= TRUE,
            						  quiet= TRUE, verbose= FALSE )
            	}
            	else {
            		BiocManager::install( package, update=FALSE, ask=FALSE )
            	}
		        if ( ! hasPackage( package )) {
		       		errMsg <- paste0(
		       			"Installing ", package, " seems to have failed.",
		       			" Please try installing manually."
		       		)
		        	if (exitOnError) {
		                stop( errMsg )
		        	}
		    		else {
		    			warning( errMsg )
		    		}
		        }
            }
        }
    }
}

checkBioconductor <- function( biocVersion ) {
	# No need to validate the version, it
	# will fail in the comparison if not formatted correctly.
    version <- BiocManager::version()
    if ( version != numeric_version( biocVersion )) {
        warning( paste0(
    		"This is intended to work with BioConductor ", biocVersion,
            ". May not work with the currently installed BioConductor (",
        	version, ")."
		))
    }
}

# Use like
# myPackages <- c("someCranPackage", "someBioconductorPackage", "author/githubRepoPackage", "author/repo@tag_or_branch")
# ensurePackages( myPackages, installOk= TRUE )