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jpackage creates 2 copies of JRE

I use jpackage (with JDK 14) for creating a standalone JavaFX application.
The output of jpackage looks strange, it consists of two the same copies of JRE and all files in app folder, except App.cfg file, can be deleted without any problem.
Does jpackage can do not generate unnecessary files?
What I have:
I have a simple project created from Maven archetype org.openjfx:javafx-archetype-simple:0.0.3.
And I just added maven-shade-plugin for creating jar with dependencies and a simple launching class for it (like NewMain class here).
I do:
mvn package
mvn javafx:jlink
jpackage --package-type app-image --dest targetApp --name App --runtime-image target/image --main-jar testApp-1.0-SNAPSHOT.jar --input target
As result I have two folders with JRE (absolutely the same ones):
targetApp\App\runtime
targetApp\App\app\image
And all files (and folders) (JRE (~53 MB), Jar (~9 MB), classes...) in targetApp\App\app can be safely deleted, except App.cfg file.
After deleting these files I run targetApp\App\App.exe and it works fine.
The deleting reduces the size of App from 118 to 56 MB.
An additional question: I use Windows and jpackage generates the result for Windows (a lot of dll files and exe), do I can create a standalone application in Windows for Mac and Linux?

You get this result because you already created an uber-jar which contains everything in addition to what you specified via --input target which, according to the documentation, has the following effect.
All files in the input directory will be packaged into the
application image.
Try whether it works to just remove the option --input target or don't create the uber-jar. Instead use the maven-dependency-plugin to copy all dependencies into a single folder, say target/libs, and then explicitly specify --input target/libs.
Your second question:
You cannot cross-create applications for other targets, if that is your question.

You might want to check out the JPackageScriptFX project on GitHub. It contains a sample multi-module maven project structure and build scripts for Mac and Windows that will build all available package types and executables for both platforms. You can find it here: https://github.com/dlemmermann/JPackageScriptFX

My solution without Oracle's jpackage: AdoptOpenJDK + jpackager + macOS => .pkg, .dmg
Download AdoptOpenJDK_13. Unzip and put into /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk
Download jpackager for (in my case osx) from https://mail.openjdk.java.net/pipermail/openjfx-dev/2018-September/022500.html. Unzip.
Copy jdk.packager.jar and jpackager to the /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bin (!!!)
In /yourworkspace/target should be the programA.jar file. (In my case it is a small program created with OpenJFX + openjdk13)
The /yourworkspace/jlink denotes on your JRE with bin,lib etc. you might have created via jlink. (In my case I have my custom JRE + JavaFX modules)
The /yourworkspace/icons contains .icns .
create jpackager.command file in your workspace with the content:
#! /bin/bash
ABSPATH=$(cd "$(dirname "$0")"; pwd -P)
launcher=`ls $ABSPATH/target/*.jar`
for eachfile in $launcher
do
if [ -f "$eachfile" ];then
echo Creating .pkg ...
echo "$eachfile"
basename="${eachfile##*/}"
/Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bin/jpackager \
create-installer \
--runtime-image $ABSPATH/jlink \
--name ProgramA \
--input $ABSPATH/target \
--main-jar $basename \
--version 1.0 \
--copyright "Nikita Gromov 2020" \
--name "ProgramA-macos" \
--mac-bundle-name "ProgramA" \
--output $ABSPATH/appimage \
--icon $ABSPATH/icons/20200220101822955_easyicon_net_32.icns
fi
done
Double click on jpackager.command which is located in /yourworkspace and wait until the jpackager has created ProgramA-macos-1.0.pkg and ProgramA-macos-1.0.dmg under /yourworkspace/appimage
My solution without Oracle's jpackage: AdoptOpenJDK + jpackager + Windows => .msi
Install WiX (!!!) Important step.
Download AdoptOpenJDK_11. Will be installed under C:\Program Files\AdoptOpenJDK\jdk-11.0.6.10-hotspot
Download jpackager (in this case win) from https://mail.openjdk.java.net/pipermail/openjfx-dev/2018-September/022500.html. Unzip.
Copy jdk.packager.jar and jpackager to the C:\Program Files\AdoptOpenJDK\jdk-11.0.6.10-hotspot\bin (!!!)
In /yourworkspace/target should be the programA.jar file. (In my case it is a small program created with OpenJFX + openjdk11)
The /yourworkspace/jlink denotes on your JRE with bin,lib etc. you might have created via jlink. (In my case I have my custom JRE + JavaFX modules)
The /yourworkspace/icons contains .icns .
create jpackager.bat file in your /yourworkspace folder with the content:
set openjdk=C:\Program Files\AdoptOpenJDK\jdk-11.0.6.10-hotspot\bin
set saveto=%cd%
cd %openjdk%
jpackager create-installer --runtime-image %saveto%/jlink --input %saveto%/target --main-jar ProgramA.jar --version 1.0 --copyright "Nikita Gromov" --name "ProgramA-win" --output %saveto%/appimage --icon %saveto%/icons/icon.ico --win-menu --win-shortcut --win-dir-chooser
Note The ProgramA.jar should be in /yourworkspace/target path (!!!)
Double click on jpackager.bat which is located in /yourworkspace and wait until the jpackager has created ProgramA-win-1.0.msi under /yourworkspace/appimage
Custom JRE + JavaFX mods on Windows
Create /yourworkspace/jlink.bat file. The content of it should be:
SET openjdk=C:\Program Files\AdoptOpenJDK\jdk-11.0.6.10-hotspot\bin
SET fx=C:\Programme\AdoptOpenJDK\javafx-jmods-11.0.2
set saveto=%cd%
cd %openjdk%
jlink --module-path %fx% --add-modules=javafx.base --add-modules=javafx.controls --add-modules=javafx.fxml --add-modules=javafx.graphics --add-modules=javafx.web --add-modules=javafx.media --add-modules=javafx.swing --bind-services --output "%saveto%\jlink"
This creates the /yourworkspace/jlink folder with a custom JRE+JavaFX libraries which you will link to jpackager.

Cannot build DMG from .JAR with javapackager

I've tried building a DMG file from my jar by running the following command:
/Library/Java/JavaVirtualMachines/jdk1.8.0_152.jdk/Contents/Home/bin/javapackager -deploy -native dmg -srcdir bin -srcfiles MyTest.jar -srcfiles p -appclass com.example.Test -name MyTest -outdir deploy -outfile MyTest -v
But it keeps giving the following error message:
Bundler DMG Installer skipped because of a configuration problem: Main application jar is missing.
Advice to fix: Make sure to use fx:jar task to create main application jar.
The funny thing is that if I copy the same folder into another Mac and run the same command, it will build DMG successfully. Therefore I believe it is something related to my config or system environment.
Do you have any idea what is going on and how to fix it?

I found that the order of the option -srcfiles is very important. The last -srcfiles should be the JAR file. In my case, I put -srcfiles p after -srcfiles MyTest.jar, that's why it did not work. Strangely it happened only to some Macs and some JDK, not all of them have this issue.

javapackager was deprecated from java11, and I had the same issue on my local setup even with java8. There is a new tool called jpackage, here is a simple example:
jpackage -t dmg -n AppName --main-class main.core -i . --main-jar AppName.jar --icon ~/Downloads/path-toicons8-log-96.icns

Make file for multi-directory project

I am trying to do a makefile for a java project that pretty much compiles the whole project and place the compiled files in a bin directory. This is my file architectures :
This is my makefile at the root directory :
BIN=./bin/
SOURCE=./src/
all:
cd src; make
clean:
rm -f $(BIN)*.class
and this is my makefile in the src directory :
BIN=../bin/
sourcefiles = \
MessageMondial.class \
Bonjour.class
classfiles = $(sourcefiles:.java=.class)
all: $(classfiles)
$(BIN)%.class: /src/%.java
javac -d $(BIN) -classpath . $<
if I go in the src directory and run the make all command everything gets compiled and is putted in the bin directory like it should.
However when I run the make all command from the root directory of the project I get this error :
How can I run the make all command from the root directory of the project?

This
sourcefiles = \
MessageMondial.class \
Bonjour.class
should be
sourcefiles = \
MessageMondial.java \
Bonjour.java
but I would also recommend you use maven, ant, gradle or sbt instead of make. Make was not a tool designed for building Java projects.

Convert Java application to Mac OS X app

Is there a way to convert a Java application into a Mac OS X executable app?
I use NetBeans to develop in Java, and I'd like to "pack" the "dist" folder into an app (just for convenience)

Use the Apple Java Extensions and its Guide
The Apple Java Extensions contains a very complete development guide with information on the deployment of Java applications on Mac OS X and the production of application bundles. It also introduces other aspects of the Apple Java Extensions, like the support for integration with the standard Mac OS X UI.
Other references:
JarBundler.
Make a Mac OS X App Bundle
Creating a osx app bundle in Java registered to a protocol url

There is a library that let's you package your Java app
Packr: https://github.com/libgdx/packr
Packages your JAR, assets and a JVM for distribution on Windows (ZIP), Linux (ZIP) and Mac OS X (.app), adding a native executable file to make it appear like the app is a native app.
It can even minimize the JRE for you.

jar2app
Packr is a great tool, but at the time I found that I wanted something "easier to use", so jar2app was born. I know this is an old question but perhaps other people might find this program easier to use than other alternatives. If they don't, there's a direct reference in the FAQ to other alternatives (such as Packr).

You can use javapackager tool to build the application and wrap it in into an installer, the following commands show how to convert a jar file into a bundle file:
commands
mkdir -p package/macosx
cp Test.icns package/macosx
jdk=$(/usr/libexec/java_home)
$jdk/bin/javapackager -deploy -native dmg \
-srcfiles Test.jar -appclass package.Test -name Test \
-outdir deploy -outfile Test -v
cp deploy/bundles/Test-1.0.dmg installer.dmg
ls -l
open installer.dmg
To change the application icon and more info MacJava.

As of JDK14 there is also 📦 jpackage (JEP-392), currently promoted from incubation phase to a production-ready feature.
Example usage that worked with an swt app (assumes all the required jar files reside in the files folder; you can also provide a custom resource folder with --resource-dir):
jpackage --type dmg \
-i files \
-n Bigly \
--main-class com.biglybt.ui.Main \
--main-jar BiglyBT.jar \
--java-options -XstartOnFirstThread \
--mac-package-name BiglyBt \
--icon app.icns \
--verbose
For the full option list use:
jpackage --help
WARNING: It's probably debatable whether it's a bug or not, and maybe it will be addressed in a future release, but in the current version, if you specify the input folder as -i ., and do not provide a custom destination with --dest then jpackage will bundle everything in the current folder... including the bundle it just created, i.e. it goes recursive on itself when . is both the input folder and the output :D .

Since some of the links in the accepted answer are no longer available or suitable in 2020, 8 years from the question was asked, I would like to share my findings that I confirmed working today.
There is a tool, javapackager, shipped with java, can package java application on Windows, Linux, macOS for you.
Here is the official manual: https://docs.oracle.com/javase/8/docs/technotes/tools/unix/javapackager.html
(Also there are other helpful tools here: https://docs.oracle.com/javase/8/docs/technotes/tools/ )
For packaging a mac application, I used this command:
javapackager \
-deploy \
-native image \
-srcdir ./csv-encrypt-tool-mac \
-srcfiles csv-encrypt-tool.jar \
-srcfiles dict \
-srcfiles config \
-srcfiles log \
-outdir ./dist \
-outfile csv-encrypt-tool \
-appclass some.package.CsvEncToolApp \
-name "csv-encrypt-tool" \
-title "csv-encrypt-tool" \
-nosign \
-v \
-BjvmOptions=-Xmx4096m \
-BmainJar=csv-encrypt-tool.jar \
-Bicon=icon.icns
And this is the explanation:
-deploy \ # Assembles the application package for redistribution with sys JRE
-native image \ # Build a .app file. If you want a .dmg, use -native dmg
-srcdir ./csv-encrypt-tool-mac \ # directory where my jar and resource files in
-srcfiles csv-encrypt-tool.jar \ # my executable jar, path relative to -srcdir
-srcfiles dict \ # one of my resource directories, path relative to -srcdir
-srcfiles config \ # another one of my resource directories, path relative to -srcdir
-srcfiles log \ # again, one of my resource directories, path relative to -srcdir
-outdir ./dist \ # where I want the package to be put
-outfile csv-encrypt-tool \ # the output file name without extension, the final file (or bundle which is a directory actually) will be csv-encrypt-tool.app
-appclass some.package.CsvEncToolApp \ # the class with main method, which is the entry point of the whole app
-name "csv-encrypt-tool" \ # the name (not very sure what this is for)
-title "csv-encrypt-tool" \ # the title (not sure what it is either)
-nosign \ # not sign the app since this is just an internal tool, if you want to publish it, signing is necessary
-v \ # verbose
-BjvmOptions=-Xmx4096m \ # I need 4GB max heap size
-BmainJar=csv-encrypt-tool.jar \ # the jar file with main class
-Bicon=icon.icns # the icon
After the command is executed, there will be some files and directories created in dist, where I want the package be, and one of the directories is bundles. The application is put in there.
Since I just built an internal tool, there is no need to sign and packaged without other production ready options. You can refer to the official manual for help.
Hope this help others who do not know how to package an application on macOS in 2020, just like me.

So none of these options worked for me (maybe because I am running OS X 10.15, maybe because most of these projects are years old, who knows). Installing Catalina made the existing app I had built around the Java app no longer work.
Ultimately, this post helped: Just use Automator to run a script that runs the java command to launch the jar. I wanted to make an app to launch Colossus, a Java version of the old Avalon Hill board game Titan. I wrote a shell script that looks like:java -Xmx256m -jar /my/path/to/the/game/Colossus.jar net.sf.colossus.appmain.Start and then created an automator application whose only action was "Run Shell Script" that launches that script. Works like a charm, no installing Ant, no command line apps requiring you to download java vms, and best of all it uses an Apple tool so will work with newer versions of OS X.

You can try this app , it bundles your jar file into Mac app
Edit: it's easy to use , select the Jar file and an Icon. Here you can see the screen shoot.
https://github.com/aprsn/Mac-App-Creator

Comparing two .jar files

How do I compare two .jar files?
Both of them have compiled .class files.
I want the difference in terms of method changes, etc.

JAPICC, sample usage:
japi-compliance-checker OLD.jar NEW.jar
Sample reports for log4j: http://abi-laboratory.pro/java/tracker/timeline/log4j/
PkgDiff, sample usage:
pkgdiff OLD.jar NEW.jar
See sample report for args4j.
Clirr, sample usage:
java -jar clirr-core-0.6-uber.jar -o OLD.jar -n NEW.jar

If you select two files in IntellijIdea and press Ctrl + Dthen it will show you the diff. I use Ultimate and don't know if it will work with Community edition.

Rename .jar to .zip
Extract
Decompile class files with jad
Recursive diff

Extract each jar to it's own directory using the jar command with parameters xvf. i.e. jar xvf myjar.jar for each jar.
Then, use the UNIX command diff to compare the two directories. This will show the differences in the directories. You can use diff -r dir1 dir2 two recurse and show the differences in text files in each directory(.xml, .properties, etc).
This will also show if binary class files differ. To actually compare the class files you will have to decompile them as noted by others.

Create a folder and create another 2 folders inside it like old and new. add relevant jar files to the folders. then open the first folder using IntelliJ. after that click whatever 2 files do you want to compare and right-click and click compare archives.

I use to ZipDiff lib (have both Java and ant API).

Here is my script to do the process described by sje397:
#!/bin/sh
# Needed if running on Windows
FIND="/usr/bin/find"
DIFF="diff -r"
# Extract the jar (war or ear)
JAR_FILE1=$1
JAR_FILE2=$2
JAR_DIR=${PWD} # to assign to a variable
TEMP_DIR=$(mktemp -d)
echo "Extracting jars in $TEMP_DIR"
EXT_DIR1="${TEMP_DIR}/${JAR_FILE1%.*}"
EXT_DIR2="${TEMP_DIR}/${JAR_FILE2%.*}"
mkdir ${EXT_DIR1}
cd ${EXT_DIR1}
jar xf ${JAR_DIR}/${JAR_FILE1}
jad -d . -o -t2 -safe -space -b -ff -s java -r **/*.class
cd ..
mkdir ${EXT_DIR2}
cd ${EXT_DIR2}
jar xf ${JAR_DIR}/${JAR_FILE2}
jad -d . -o -t2 -safe -space -b -ff -s java -r **/*.class
cd ..
# remove class files so the diff is clean
${FIND} ${TEMP_DIR} -name '*.class' | xargs rm
# diff recursively
${DIFF} ${EXT_DIR1} ${EXT_DIR2}
I can run it on Windows using GIT for Windows. Just open a command prompt. Run bash and then execute the script from there.

Use Java Decompiler to turn the jar file into source code file, and then use WinMerge to perform comparison.
You should consult the copyright holder of the source code, to see whether it is OK to do so.

In Linux/CygWin a handy script I use at times is:
#Extract the jar (war or ear)
cd dir1
jar xvf jar-file1
for i in `ls *.class`
do
javap $i > ${i}.txt #list the functions/variables etc
done
cd dir2
jar xvf jar-file2
for i in `ls *.class`
do
javap $i > ${i}.txt #list the functions/variables etc
done
diff -r dir1 dir2 #diff recursively

If you are using IntelliJ IDEA or Android Studio, add your jar files to a project under the libs folder.
Then select the both jar files, right click then select "Compare Archives"

use java decompiler and decompile all the .class files and save all files as project structure .
then use meld diff viewer and compare as folders ..

Here's an aparently free tool http://www.extradata.com/products/jarc/

Please try http://www.osjava.org/jardiff/ - tool is old and the dependency list is large. From the docs, it looks like worth trying.

This application may be what you need, works great and display a simple GUI showing differences. Try Jarcomp