R/onLoad.R

In DEIB-GECO/RGMQL: GenoMetric Query Language for R/Bioconductor

#' @importFrom rJava .jpackage .jinit
#' @import RGMQLlib
#' 
.onLoad <- function(libname, pkgname) {
    .jpackage(pkgname, lib.loc = libname)
    initGMQLscalaAPI()
}

.onAttach <- function(libname, pkgname) {
    packageStartupMessage("GMQL successfully loaded")
}

.onDetach <- function(libpath) { } 

.onUnload <- function(libpath) { }


#' @importFrom rJava .jinit .jaddClassPath
#' 
initGMQLscalaAPI <- function(libLoc, mem = "12G") {
    # Check if library directory is missing
    
    # Starting the java engine
    .jinit(force.init = TRUE)
    if (missing(libLoc)) {
        libLoc = system.file("extdata", "java", package = "RGMQLlib")
    }
    
    path = Sys.glob(paste0(libLoc, "/*.jar"))
    available_local_files <- list.files(
        libLoc, 
        full.names = FALSE, 
        pattern = "\\.jar$"
    )
    
    # Check if all the files are there
    if (!"GMQL.jar" %in% available_local_files) {
        stop("GMQL jar not available")
    }
    
    if (length(path) > 0) {
        rJava::.jaddClassPath(path)
    }
    
    rJava::.jaddClassPath(dirname(path))
}