R/initJava.R

In gMCP: Graph Based Multiple Comparison Procedures

initJava <- function() {
  if (!.jniInitialized) {
    .jinit(parameters=c("-Xrs", "-Xss1m",
                        paste0("-Djava.io.tmpdir=", tempdir())))
    # Remark - rJava 0.9-5: detect support for -Xrs and enable it by default (this prevents
    # Java from killing R process on interrupt)
  }
  .jpackage("gMCP")	
  .jpackage("JavaGD")

  rJava::.jcall("java/lang/System", "S", "setProperty", "log4j1.compatibility", "true")
  rJava::.jcall("java/lang/System", "S", "setProperty", "log4j.configuration", "classpath:org/af/gMCP/gui/commons-logging.properties")

  jars <- c("afcommons", "commons-collections", "commons-lang", 
            "commons-logging", "commons-validator", "jgoodies-common", "forms", 
            "iText", "javax.json", "jhlir.jar", "jlatexmath", "jxlayer", 
            "log4j-1.2-api", "log4j-api", "log4j-core", "swing-worker")
  
  loadJars(jars)
  
  # Some of following lines are based on the code of the rJava .jpackage function
  if (length(grep("64-bit", sessionInfo()$platform))>0) { # Necessary?!
    classes <- system.file("jri/x64", package = "rJava", lib.loc = NULL)
  } else {
    classes <- system.file("jri/i386", package = "rJava", lib.loc = NULL)
  }
  if (nzchar(classes)) {
    .jaddClassPath(classes)
  }
  classes <- system.file("jri", package = "rJava", lib.loc = NULL)
  if (nzchar(classes)) {
    #.jaddClassPath(classes)
    jars <- grep(".*\\.jar", list.files(classes, full.names = TRUE), TRUE, value = TRUE)
    if (length(jars)) { 
      .jaddClassPath(jars)
    }		
  }
  # Adding poi jar files to Classpath:
  classes <- system.file("java", package = "xlsxjars", lib.loc = NULL)
  if (nzchar(classes)) {	  
    jars <- grep(".*\\.jar", list.files(classes, full.names = TRUE), TRUE, value = TRUE)
    if (length(jars)) { 
      .jaddClassPath(jars)
    }		
  }
  
  rJavaVersion <- utils::sessionInfo()$otherPkgs$rJava$Version
  
  # If we have a rJava version < 0.8-3 load JRIEngine.jar and REngine.jar
  if (!is.null(rJavaVersion)) {
    if (rJavaVersion < "0.8-3") {
      classes <- system.file("R28", package = "CommonJavaJars", lib.loc = NULL)
      if (nzchar(classes)) {
        .jaddClassPath(classes) # Necessary?!
        jars <- grep(".*\\.jar", list.files(classes, full.names = TRUE), TRUE, value = TRUE)
        if (length(jars)) { 
          .jaddClassPath(jars)
        }		
      }
    }	
    # If we have a rJava version 0.9-4 load JRIEngine.jar and REngine.jar    
    if (rJavaVersion == "0.9-4") {
      classes <- system.file("JRI", package = "CommonJavaJars", lib.loc = NULL)
      if (nzchar(classes)) {
        .jaddClassPath(classes) # Necessary?!
        jars <- grep(".*\\.jar", list.files(classes, full.names = TRUE), TRUE, value = TRUE)
        if (length(jars)) { 
          .jaddClassPath(jars)
        }		
      }
    }
  }
  
  ## We supply our own JavaGD class
  Sys.setenv("JAVAGD_CLASS_NAME"="org/mutoss/gui/JavaGD")  
  
  # Optional Deducer integration:
  #deducer.addMenuItem <- if (exists("deducer")) get("deducer") else function(...) {}
  #jgr.addMenuSeparator <- if (exists("jgr.addMenuSeparator")) get("jgr.addMenuSeparator") else function(...) {}
  #jgr.addMenuItem <- if (exists("jgr.addMenuItem")) get("jgr.addMenuItem") else function(...) {}
  #deducer.addMenuItem("Multiple Test Graph", NULL, "graphGUI()", "Analysis")
  #jgr.addMenuSeparator("Analysis")
  #jgr.addMenuItem("Analysis", "Multiple Test Graph", "graphGUI()")	
}