I have a script that works perfectly when I'm not using Renv. However, when running it in a project with Renv enabled, the last command line returns the following message:
> r5r_core <- setup_r5(data_path = data_path, verbose = FALSE)
Error in rJava::.jinit() : Unable to create a Java class loader.
Just run the code below inside a renv project to have a reproducible example:
options(java.parameters = "-Xmx2G")
library(r5r)
library(rJava)
data_path <- system.file("extdata/poa", package = "r5r")
list.files(data_path)
poi <- fread(file.path(data_path, "poa_points_of_interest.csv"))
head(poi)
points <- fread(file.path(data_path, "poa_hexgrid.csv"))
points <- points[ c(sample(1:nrow(points), 10, replace=TRUE)), ]
head(points)
# Indicate the path where OSM and GTFS data are stored
r5r_core <- setup_r5(data_path = data_path, verbose = FALSE)
My Java version is compatible with the one used in this package, but it looks like R is having a hard time communicating with Java in Renv. Could anyone tell me?
I have a class in Java which looks like this:
package com.charandeepmatta.keywords;
import org.robotframework.javalib.annotation.RobotKeyword;
import org.robotframework.javalib.annotation.RobotKeywords;
#RobotKeywords
public class SampleKeywords {
#RobotKeyword
public void printToErrorStream() {
System.err.println("!!! Hello from keyword developed in java ...");
}
}
And my test case looks like this
*** Settings ***
Library org.robotframework.javalib.library.AnnotationLibrary /**.class
*** Test Cases ***
Keyword defined in java class can print to error stream
Print To Error Stream
When I try to run it on RIDE it gives me the following error
[ ERROR ] Error in file 'C:\Users\BFerreira\git\robotframework-maven-project\src\main\robot\suite\OwnDevelopedKeywordTestCase.txt':
Importing test library 'org.robotframework.javalib.library.AnnotationLibrary' failed:
ImportError: No module named org.robotframework.javalib.library
Traceback (most recent call last):
None
PYTHONPATH:
C:\Python27\lib\site-packages\robot\libraries
C:\Python27\lib\site-packages
C:\Windows\system32\python27.zip
C:\Python27\DLLs
C:\Python27\lib
C:\Python27\lib\plat-win
C:\Python27\lib\lib-tk
C:\Python27
C:\Python27\lib\site-packages\wx-2.8-msw-unicode
.
C:\Users\user1\git\robotframework-maven-project\src\main\robot\suite
Everything is in the same classpath, can anyone help?
From the looks of your output, you are not executing with jybot/Jython. Jython is required to load Java classes in a Python interpreter. Here is what the output would look like if you were:
PYTHONPATH:
C:\apps\Python27\Lib\site-packages
C:\apps\jython2.5.3\Lib\site-packages\setuptools-0.6c11-py2.5.egg
C:\apps\jython2.5.3\Lib\site-packages\pip-1.2.1-py2.5.egg
C:\apps\jython2.5.3\Lib
__classpath__
__pyclasspath__/
C:\apps\jython2.5.3\Lib\site-packages
.
c:\ws\local
CLASSPATH:
C:\apps\jython2.5.3\jython.jar
A word of caution: if you run the Robot Framework jar (e.g. java -jar robotframework-2.5.3.jar ...) as some examples suggest, all classpath settings are ignored. You would have to put all your dependencies in one jar for that way to work...
While Compiling an Scala 2.10 Project, I got an error I cannot even understand
java.lang.NoClassDefFoundError: no Java class corresponding to MongoPersistable.this.type found
at scala.reflect.runtime.JavaMirrors$JavaMirror.typeToJavaClass(JavaMirrors.scala:1218) ~[scala-reflect-2.10.0.jar:na]
at scala.reflect.runtime.JavaMirrors$JavaMirror.runtimeClass(JavaMirrors.scala:202) ~[scala-reflect-2.10.0.jar:na]
at scala.reflect.runtime.JavaMirrors$JavaMirror.runtimeClass(JavaMirrors.scala:65) ~[scala-reflect-2.10.0.jar:na]
...
How is this even possible to get such a error message if the code got well in eclipse in first place?
Following line of Code produces this error:
trait MongoPersistable {
def save() {
val dao : MongoDAO[MongoPersistable.this.type] = MongoDAO[this.type];
....
I would upload more code if I know where to search
Hello I have a main method in a Java class and I would like to access and run my clojure functions from my java classes, is that possible right?
Help please
If you just want to call a function which you have defined in a Clojure script the following code might help you getting the job done:
test.clj:
(ns test)
(defn hello [name]
(println (str "Hi " name "!")))
TestRun.java:
import clojure.lang.RT;
public class TestRun {
public static void main(String[] args) throws Exception {
RT.loadResourceScript("test.clj");
// var(namespace, function name).invoke(parameters..)
RT.var("test", "hello").invoke("Daisy Duck");
}
}
Output:
Hi Daisy Duck!
Make sure you have the Clojure jar on your classpath
Do you have your Clojure code compiled and packaged in a jar? Do you have the jar in your classpath? If so, you should be able to use the classes in the jar just as if there were written in Java.
see the accepted answer to this question: Calling clojure from java
in short you add the mothods you want to expose to your namespace:
(ns com.domain.tiny
(:gen-class
:name com.domain.tiny
:methods [ [binomial [int int] double]]))
then write the functions. compile your class file with maven/leiningen
then call them from java:
System.out.println("(binomial 5 3): " + tiny.binomial(5, 3));
This is just an excerpt. take a look as the origional question.
Check the Java Scripting API for calling functions in script files:
http://download.oracle.com/javase/6/docs/technotes/guides/scripting/programmer_guide/index.html
Most of the top google hits for "calling clojure from java" are outdated and recommend using clojure.lang.RT to compile the source code. Could you help with a clear explanation of how to call Clojure from Java assuming you have already built a jar from the Clojure project and included it in the classpath?
Update: Since this answer was posted, some of the tools available have changed. After the original answer, there is an update including information on how to build the example with current tools.
It isn't quite as simple as compiling to a jar and calling the internal methods. There do seem to be a few tricks to make it all work though. Here's an example of a simple Clojure file that can be compiled to a jar:
(ns com.domain.tiny
(:gen-class
:name com.domain.tiny
:methods [#^{:static true} [binomial [int int] double]]))
(defn binomial
"Calculate the binomial coefficient."
[n k]
(let [a (inc n)]
(loop [b 1
c 1]
(if (> b k)
c
(recur (inc b) (* (/ (- a b) b) c))))))
(defn -binomial
"A Java-callable wrapper around the 'binomial' function."
[n k]
(binomial n k))
(defn -main []
(println (str "(binomial 5 3): " (binomial 5 3)))
(println (str "(binomial 10042 111): " (binomial 10042 111)))
)
If you run it, you should see something like:
(binomial 5 3): 10
(binomial 10042 111): 49068389575068144946633777...
And here's a Java program that calls the -binomial function in the tiny.jar.
import com.domain.tiny;
public class Main {
public static void main(String[] args) {
System.out.println("(binomial 5 3): " + tiny.binomial(5, 3));
System.out.println("(binomial 10042, 111): " + tiny.binomial(10042, 111));
}
}
It's output is:
(binomial 5 3): 10.0
(binomial 10042, 111): 4.9068389575068143E263
The first piece of magic is using the :methods keyword in the gen-class statement. That seems to be required to let you access the Clojure function something like static methods in Java.
The second thing is to create a wrapper function that can be called by Java. Notice that the second version of -binomial has a dash in front of it.
And of course the Clojure jar itself must be on the class path. This example used the Clojure-1.1.0 jar.
Update: This answer has been re-tested using the following tools:
Clojure 1.5.1
Leiningen 2.1.3
JDK 1.7.0 Update 25
The Clojure Part
First create a project and associated directory structure using Leiningen:
C:\projects>lein new com.domain.tiny
Now, change to the project directory.
C:\projects>cd com.domain.tiny
In the project directory, open the project.clj file and edit it such that the contents are as shown below.
(defproject com.domain.tiny "0.1.0-SNAPSHOT"
:description "An example of stand alone Clojure-Java interop"
:url "http://clarkonium.net/2013/06/java-clojure-interop-an-update/"
:license {:name "Eclipse Public License"
:url "http://www.eclipse.org/legal/epl-v10.html"}
:dependencies [[org.clojure/clojure "1.5.1"]]
:aot :all
:main com.domain.tiny)
Now, make sure all of the dependencies (Clojure) are available.
C:\projects\com.domain.tiny>lein deps
You may see a message about downloading the Clojure jar at this point.
Now edit the Clojure file C:\projects\com.domain.tiny\src\com\domain\tiny.clj such that it contains the Clojure program shown in the original answer. (This file was created when Leiningen created the project.)
Much of the magic here is in the namespace declaration. The :gen-class tells the system to create a class named com.domain.tiny with a single static method called binomial, a function taking two integer arguments and returning a double. There are two similarly named functions binomial, a traditional Clojure function, and -binomial and wrapper accessible from Java. Note the hyphen in the function name -binomial. The default prefix is a hyphen, but it can be changed to something else if desired. The -main function just makes a couple of calls to the binomial function to assure that we are getting the correct results. To do that, compile the class and run the program.
C:\projects\com.domain.tiny>lein run
You should see output shown in the original answer.
Now package it up in a jar and put it someplace convenient. Copy the Clojure jar there too.
C:\projects\com.domain.tiny>lein jar
Created C:\projects\com.domain.tiny\target\com.domain.tiny-0.1.0-SNAPSHOT.jar
C:\projects\com.domain.tiny>mkdir \target\lib
C:\projects\com.domain.tiny>copy target\com.domain.tiny-0.1.0-SNAPSHOT.jar target\lib\
1 file(s) copied.
C:\projects\com.domain.tiny>copy "C:<path to clojure jar>\clojure-1.5.1.jar" target\lib\
1 file(s) copied.
The Java Part
Leiningen has a built-in task, lein-javac, that should be able to help with the Java compilation. Unfortunately, it seems to be broken in version 2.1.3. It can't find the installed JDK and it can't find the Maven repository. The paths to both have embedded spaces on my system. I assume that is the problem. Any Java IDE could handle the compilation and packaging too. But for this post, we're going old school and doing it at the command line.
First create the file Main.java with the contents shown in the original answer.
To compile java part
javac -g -cp target\com.domain.tiny-0.1.0-SNAPSHOT.jar -d target\src\com\domain\Main.java
Now create a file with some meta-information to add to the jar we want to build. In Manifest.txt, add the following text
Class-Path: lib\com.domain.tiny-0.1.0-SNAPSHOT.jar lib\clojure-1.5.1.jar
Main-Class: Main
Now package it all up into one big jar file, including our Clojure program and the Clojure jar.
C:\projects\com.domain.tiny\target>jar cfm Interop.jar Manifest.txt Main.class lib\com.domain.tiny-0.1.0-SNAPSHOT.jar lib\clojure-1.5.1.jar
To run the program:
C:\projects\com.domain.tiny\target>java -jar Interop.jar
(binomial 5 3): 10.0
(binomial 10042, 111): 4.9068389575068143E263
The output is essentially identical to that produced by Clojure alone, but the result has been converted to a Java double.
As mentioned, a Java IDE will probably take care of the messy compilation arguments and the packaging.
As of Clojure 1.6.0, there is a new preferred way to load and invoke Clojure functions. This method is now preferred to calling RT directly (and supersedes many of the other answers here). The javadoc is here - the main entry point is clojure.java.api.Clojure.
To lookup and call a Clojure function:
IFn plus = Clojure.var("clojure.core", "+");
plus.invoke(1, 2);
Functions in clojure.core are automatically loaded. Other namespaces can be loaded via require:
IFn require = Clojure.var("clojure.core", "require");
require.invoke(Clojure.read("clojure.set"));
IFns can be passed to higher order functions, e.g. the example below passes plus to read:
IFn map = Clojure.var("clojure.core", "map");
IFn inc = Clojure.var("clojure.core", "inc");
map.invoke(inc, Clojure.read("[1 2 3]"));
Most IFns in Clojure refer to functions. A few, however, refer to non-function data values. To access these, use deref instead of fn:
IFn printLength = Clojure.var("clojure.core", "*print-length*");
IFn deref = Clojure.var("clojure.core", "deref");
deref.invoke(printLength);
Sometimes (if using some other part of the Clojure runtime), you may need to ensure that the Clojure runtime is properly initialized - calling a method on the Clojure class is sufficient for this purpose. If you do not need to call a method on Clojure, then simply causing the class to load is sufficient (in the past there has been a similar recommendation to load the RT class; this is now preferred):
Class.forName("clojure.java.api.Clojure")
EDIT This answer was written in 2010, and worked at that time. See Alex Miller's answer for more modern solution.
What kind of code are calling from Java? If you have class generated with gen-class, then simply call it. If you want to call function from script, then look to following example.
If you want to evaluate code from string, inside Java, then you can use following code:
import clojure.lang.RT;
import clojure.lang.Var;
import clojure.lang.Compiler;
import java.io.StringReader;
public class Foo {
public static void main(String[] args) throws Exception {
// Load the Clojure script -- as a side effect this initializes the runtime.
String str = "(ns user) (defn foo [a b] (str a \" \" b))";
//RT.loadResourceScript("foo.clj");
Compiler.load(new StringReader(str));
// Get a reference to the foo function.
Var foo = RT.var("user", "foo");
// Call it!
Object result = foo.invoke("Hi", "there");
System.out.println(result);
}
}
EDIT: I wrote this answer almost three years ago. In Clojure 1.6 there is a proper API exactly for the purpose of calling Clojure from Java. Please Alex Miller's answer for up to date information.
Original answer from 2011:
As I see it, the simplest way (if you don't generate a class with AOT compilation) is to use clojure.lang.RT to access functions in clojure. With it you can mimic what you would have done in Clojure (no need to compile things in special ways):
;; Example usage of the "bar-fn" function from the "foo.ns" namespace from Clojure
(require 'foo.ns)
(foo.ns/bar-fn 1 2 3)
And in Java:
// Example usage of the "bar-fn" function from the "foo.ns" namespace from Java
import clojure.lang.RT;
import clojure.lang.Symbol;
...
RT.var("clojure.core", "require").invoke(Symbol.intern("foo.ns"));
RT.var("foo.ns", "bar-fn").invoke(1, 2, 3);
It is a bit more verbose in Java, but I hope it's clear that the pieces of code are equivalent.
This should work as long as Clojure and the source files (or compiled files) of your Clojure code is on the classpath.
I agree with clartaq's answer, but I felt that beginners could also use:
step-by-step information on how to actually get this running
information that's current for Clojure 1.3 and recent versions of leiningen.
a Clojure jar that also includes a main function, so it can be run standalone or linked as a library.
So I covered all that in this blog post.
The Clojure code looks like this:
(ns ThingOne.core
(:gen-class
:methods [#^{:static true} [foo [int] void]]))
(defn -foo [i] (println "Hello from Clojure. My input was " i))
(defn -main [] (println "Hello from Clojure -main." ))
The leiningen 1.7.1 project setup looks like this:
(defproject ThingOne "1.0.0-SNAPSHOT"
:description "Hello, Clojure"
:dependencies [[org.clojure/clojure "1.3.0"]]
:aot [ThingOne.core]
:main ThingOne.core)
The Java code looks like this:
import ThingOne.*;
class HelloJava {
public static void main(String[] args) {
System.out.println("Hello from Java!");
core.foo (12345);
}
}
Or you can also get all the code from this project on github.
This works with Clojure 1.5.0:
public class CljTest {
public static Object evalClj(String a) {
return clojure.lang.Compiler.load(new java.io.StringReader(a));
}
public static void main(String[] args) {
new clojure.lang.RT(); // needed since 1.5.0
System.out.println(evalClj("(+ 1 2)"));
}
}
If the use case is to include a JAR built with Clojure in a Java application, I have found having a separate namespace for the interface between the two worlds to be beneficial:
(ns example-app.interop
(:require [example-app.core :as core])
;; This example covers two-way communication: the Clojure library
;; relies on the wrapping Java app for some functionality (through
;; an interface that the Clojure library provides and the Java app
;; implements) and the Java app calls the Clojure library to perform
;; work. The latter case is covered by a class provided by the Clojure lib.
;;
;; This namespace should be AOT compiled.
;; The interface that the java app can implement
(gen-interface
:name com.example.WeatherForecast
:methods [[getTemperature [] Double]])
;; The class that the java app instantiates
(gen-class
:name com.example.HighTemperatureMailer
:state state
:init init
;; Dependency injection - take an instance of the previously defined
;; interface as a constructor argument
:constructors {[com.example.WeatherForecast] []}
:methods [[sendMails [] void]])
(defn -init [weather-forecast]
[[] {:weather-forecast weather-forecast}])
;; The actual work is done in the core namespace
(defn -sendMails
[this]
(core/send-mails (.state this)))
The core namespace can use the injected instance to accomplish its tasks:
(ns example-app.core)
(defn send-mails
[{:keys [weather-forecast]}]
(let [temp (.getTemperature weather-forecast)] ...))
For testing purposes, the interface can be stubbed:
(example-app.core/send-mails
(reify com.example.WeatherForecast (getTemperature [this] ...)))
Other technique that works also with other languages on top of JVM is to declare an interface for functions you want to call and then use 'proxy' function to create instance that implemennts them.
You can also use AOT compilation to create class files representing your clojure code. Read the documentation about compilation, gen-class and friends in the Clojure API docs for the details about how to do this, but in essence you will create a class that calls clojure functions for each method invocation.
Another alternative is to use the new defprotocol and deftype functionality, which will also require AOT compilation but provide better performance. I don't know the details of how to do this yet, but a question on the mailing list would probably do the trick.