Adding a build section to the POM:
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>com.mycompany.app.App</Main-Class>
<Build-Number>123</Build-Number>
</manifestEntries>
</transformer>
</transformers>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
To the POM gives me a self contained runnable jar. Progress! I’m learning.
BUT as before when I run the jar, I get the Exception: No compatible service:
org.scijava.service.SciJavaService
=================================================================
[Michaels-Retina:~/temp/deleteme/my-app] michaelellis% java -jar
target/my-app-1.0-SNAPSHOT.jar
Hello World!
Exception: No compatible service: org.scijava.service.SciJavaService
=================================================================
Still vexed!
On 5 Dec 2014, at 17:17, Curtis Rueden <ctrue...@wisc.edu> wrote:
> Hi Michael,
>
> > mvn claims to build everything OK
>
> Yep, it did build successfully.
>
> > % java -cp target/my-app-1.0-SNAPSHOT.jar com.mycompany.app.App
> > Error: A JNI error has occurred, please check your installation and try
> > again
> > Exception in thread "main" java.lang.NoClassDefFoundError: io/scif/SCIFIO
>
> Maven is primarily a build tool. It puts the correct JARs on your classpath
> at compile time. In your case, that is scifio-0.17.1.jar and its dependencies.
>
> However, the way you are launching your program is not putting the required
> dependencies on the classpath. You put only my-app-1.0-SNAPSHOT.jar on the
> classpath, and its dependencies are missing. So of course Java cannot find
> the needed classes.
>
> The gist is: it is your responsibility to assemble the dependencies and
> ensure they are on the classpath somehow when you launch your application.
>
> There are several ways to accomplish this. Here is one generally useful way
> using Maven, which does not assume you are doing anything ImageJ-related:
>
> $ mvn dependency:copy-dependencies
> $ java -cp 'target/my-app-1.0-SNAPSHOT.jar:target/dependency/*'
> com.mycompany.app.App
>
> The "copy-dependencies" goal copies all the JAR files needed by your program
> into the target/dependency folder, for easy subsequent consumption.
>
> Alternately, the "ImageJ way" of dealing with deployment is to ship all
> needed dependencies in the "jars" folder of your ImageJ application. We
> created a Maven goal for this too, which you can use as follows:
>
> $ mvn -Dimagej.app.directory=/Applications/ImageJ.app
> -Ddelete.other.versions=true
>
> Which will copy your JAR and its dependencies into your ImageJ installation
> at /Applications/ImageJ.app. But note that in order for this goal to work,
> you must extend the pom-imagej parent (see
> https://github.com/imagej/minimal-ij1-plugin for an example).
>
> A third solution is to use the exec-maven-plugin to launch your application
> directly using Maven. E.g.:
> https://github.com/imagej/imagej/blob/imagej-2.0.0-rc-17/pom.xml#L255-L278
>
> Regards,
> Curtis
>
> On Fri, Dec 5, 2014 at 11:03 AM, Michael Ellis <michael.el...@dsuk.biz> wrote:
> Curtis,
>
> Thanks but it is still not working.
>
> I have cut out using NetBeans and am now just using the CLI and a text
> editor.
>
> POM as follows:
>
> ========================================================
> <project xmlns="http://maven.apache.org/POM/4.0.0";
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
> xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
> http://maven.apache.org/xsd/maven-4.0.0.xsd";>
> <modelVersion>4.0.0</modelVersion>
>
> <groupId>com.mycompany.app</groupId>
> <artifactId>my-app</artifactId>
> <version>1.0-SNAPSHOT</version>
> <packaging>jar</packaging>
>
> <name>my-app</name>
> <url>http://maven.apache.org</url>
>
> <properties>
> <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
> </properties>
>
> <repositories>
> <repository>
> <id>imagej.public</id>
> <url>http://maven.imagej.net/content/groups/public</url>
> </repository>
> </repositories>
>
> <dependencies>
> <dependency>
> <groupId>junit</groupId>
> <artifactId>junit</artifactId>
> <version>3.8.1</version>
> <scope>test</scope>
> </dependency>
>
> <dependency>
> <groupId>io.scif</groupId>
> <artifactId>scifio</artifactId>
> <version>0.17.1</version>
> </dependency>
>
> </dependencies>
> </project>
> ========================================================
>
> File hierarchy:
>
> .
> ./.DS_Store
> ./pom.xml
> ./src
> ./src/main
> ./src/main/java
> ./src/main/java/com
> ./src/main/java/com/mycompany
> ./src/main/java/com/mycompany/app
> ./src/main/java/com/mycompany/app/App.java
> ./src/test
> ./src/test/java
> ./src/test/java/com
> ./src/test/java/com/mycompany
> ./src/test/java/com/mycompany/app
> ./src/test/java/com/mycompany/app/AppTest.java
> ========================================================
>
> App.java as follows:
>
> package com.mycompany.app;
>
> import io.scif.FormatException;
> import io.scif.ImageMetadata;
> import io.scif.Plane;
> import io.scif.Reader;
> import io.scif.SCIFIO;
>
> public class App
> {
> public static void main( String[] args )
> {
> try {
> System.out.println( "Hello World!" );
> SCIFIO scifio = new SCIFIO();
> String sampleImage
> =
> "8bit-signed&pixelType=int8&lengths=50,50,3,5,7&axes=X,Y,Z,Channel,Time.fake";
> final Reader reader =
> scifio.initializer().initializeReader(sampleImage);
> System.out.printf("reader=%s%n", reader );
> } catch (Exception e) {
> System.out.printf("Exception: %s%n", e.getMessage() );
> }
> }
> }
>
> ========================================================
>
> mvm -U install
>
> [Michaels-Retina:~/temp/deleteme/my-app] michaelellis% mvn -U install
> [INFO] Scanning for projects...
> [INFO]
>
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Building my-app 1.0-SNAPSHOT
> [INFO]
> ------------------------------------------------------------------------
> [INFO]
> [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ my-app
> ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] skip non existing resourceDirectory
> /Users/michaelellis/temp/deleteme/my-app/src/main/resources
> [INFO]
> [INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ my-app ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 1 source file to
> /Users/michaelellis/temp/deleteme/my-app/target/classes
> [INFO]
> [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @
> my-app ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] skip non existing resourceDirectory
> /Users/michaelellis/temp/deleteme/my-app/src/test/resources
> [INFO]
> [INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @
> my-app ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 1 source file to
> /Users/michaelellis/temp/deleteme/my-app/target/test-classes
> [INFO]
> [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ my-app ---
> [INFO] Surefire report directory:
> /Users/michaelellis/temp/deleteme/my-app/target/surefire-reports
>
> -------------------------------------------------------
> T E S T S
> -------------------------------------------------------
> Running com.mycompany.app.AppTest
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec
>
> Results :
>
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0
>
> [INFO]
> [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ my-app ---
> [INFO] Building jar:
> /Users/michaelellis/temp/deleteme/my-app/target/my-app-1.0-SNAPSHOT.jar
> [INFO]
> [INFO] --- maven-install-plugin:2.4:install (default-install) @ my-app ---
> [INFO] Installing
> /Users/michaelellis/temp/deleteme/my-app/target/my-app-1.0-SNAPSHOT.jar to
> /Users/michaelellis/.m2/repository/com/mycompany/app/my-app/1.0-SNAPSHOT/my-app-1.0-SNAPSHOT.jar
> [INFO] Installing /Users/michaelellis/temp/deleteme/my-app/pom.xml to
> /Users/michaelellis/.m2/repository/com/mycompany/app/my-app/1.0-SNAPSHOT/my-app-1.0-SNAPSHOT.pom
> [INFO]
> ------------------------------------------------------------------------
> [INFO] BUILD SUCCESS
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Total time: 1.962 s
> [INFO] Finished at: 2014-12-05T16:59:50+00:00
> [INFO] Final Memory: 18M/242M
> [INFO] ————————————————————————————————————
>
> ========================================================
>
> mvn claims to build everything OK there seems to be no inclusion of any scif
> libraries or class files.
>
>
> When I run it I get:
>
> [Michaels-Retina:~/temp/deleteme/my-app] michaelellis% java -cp
> target/my-app-1.0-SNAPSHOT.jar com.mycompany.app.App
> Error: A JNI error has occurred, please check your installation and try again
> Exception in thread "main" java.lang.NoClassDefFoundError: io/scif/SCIFIO
> at java.lang.Class.getDeclaredMethods0(Native Method)
> at java.lang.Class.privateGetDeclaredMethods(Class.java:2699)
> at java.lang.Class.privateGetMethodRecursive(Class.java:3046)
> at java.lang.Class.getMethod0(Class.java:3016)
> at java.lang.Class.getMethod(Class.java:1782)
> at
> sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
> at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
> Caused by: java.lang.ClassNotFoundException: io.scif.SCIFIO
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> ... 7 more
>
>
> ========================================================
>
> I’ve been banging my head against this for two days now.
>
> So any help appreciated
>
>
> On 5 Dec 2014, at 16:35, Curtis Rueden <ctrue...@wisc.edu> wrote:
>
>> Hi Michael,
>>
>> > The POM for io.scif:scifio:jar:0.17.1 is missing, no dependency
>> > information available
>>
>> Make sure you have the following <repositories> block in your POM:
>>
>> <repositories>
>> <repository>
>> <id>imagej.public</id>
>> <url>http://maven.imagej.net/content/groups/public</url>
>> </repository>
>> </repositories>
>>
>> Then rebuild with the "-U" flag. I don't know how to do this from NetBeans,
>> but you only need to do it once from the CLI -- then you can return to
>> NetBeans and it should work.
>>
>> Regards,
>> Curtis
>>
>> On Fri, Dec 5, 2014 at 6:07 AM, Michael Ellis <michael.el...@dsuk.biz> wrote:
>> I have followed the advice offered by Curtis regarding adding the io.scif:
>> scifio dependency to my POM
>>
>> The dependency part of my POM looks like this:
>>
>> <dependencies>
>> <dependency>
>> <groupId>net.imglib2</groupId>
>> <artifactId>imglib2</artifactId>
>> <version>2.2.1-SNAPSHOT</version>
>> <type>jar</type>
>> </dependency>
>> <dependency>
>> <groupId>io.scif</groupId>
>> <artifactId>scifio</artifactId>
>> <version>0.17.1</version>
>> <type>jar</type>
>> </dependency>
>> </dependencies>
>>
>> I am using NetBeans IDE, configured for use with maven project (I am slo
>> using Java 8 and JavaFX)
>>
>> However when I attempt to Build (or Build with Dependencies) within
>> NetBeans, I get the following error message:
>> ============================================================
>>
>> cd /Users/michaelellis/Documents/Development/MavenImgLib2FX;
>> JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_40.jdk/Contents/Home
>> "/Applications/NetBeans/NetBeans
>> 8.0.app/Contents/Resources/NetBeans/java/maven/bin/mvn" install
>> Scanning for projects...
>>
>> ------------------------------------------------------------------------
>> Building MavenImgLib2FX 1.0-SNAPSHOT
>> ------------------------------------------------------------------------
>> The POM for io.scif:scifio:jar:0.17.1 is missing, no dependency information
>> available
>> ------------------------------------------------------------------------
>> BUILD FAILURE
>> ------------------------------------------------------------------------
>> Total time: 0.341s
>> Finished at: Fri Dec 05 10:34:41 GMT 2014
>> Final Memory: 7M/245M
>> ------------------------------------------------------------------------
>> Failed to execute goal on project MavenImgLib2FX: Could not resolve
>> dependencies for project biz.dsuk:MavenImgLib2FX:jar:1.0-SNAPSHOT: Failure
>> to find io.scif:scifio:jar:0.17.1 in http://repo.maven.apache.org/maven2 was
>> cached in the local repository, resolution will not be reattempted until the
>> update interval of central has elapsed or updates are forced -> [Help 1]
>>
>> To see the full stack trace of the errors, re-run Maven with the -e switch.
>> Re-run Maven using the -X switch to enable full debug logging.
>>
>> For more information about the errors and possible solutions, please read
>> the following articles:
>> [Help 1]
>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>
>> ============================================================
>>
>> If I open a terminal window and cd into the project directory and:
>>
>> mvn clean package
>>
>> It succeeds.
>>
>> However, when I then attempt to run the project with:
>>
>> java -cp MavenImgLib2FX-1.0-SNAPSHOT.jar biz.dsuk.mavenimglib2fx.MainApp
>>
>> The application starts to execute but throws “No compatible service:
>> io.scif.SCIFIOService” exception.
>> ============================================================
>>
>> img1=CellImg [20x30]
>> BufferedImage=BufferedImage@3137c585: type = 10 ColorModel: #pixelBits = 8
>> numComponents = 1 color space = java.awt.color.ICC_ColorSpace@134d9d5f
>> transparency = 1 has alpha = false isAlphaPre = false ByteInterleavedRaster:
>> width = 707 height = 699 #numDataElements 1 dataOff[0] = 0
>> Loading image...
>> Exception in Application start method
>> java.lang.reflect.InvocationTargetException
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:497)
>> at
>> com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:363)
>> at
>> com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:303)
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:497)
>> at sun.launcher.LauncherHelper$FXHelper.main(LauncherHelper.java:767)
>> Caused by: java.lang.RuntimeException: Exception in Application start method
>> at
>> com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:875)
>> at
>> com.sun.javafx.application.LauncherImpl.lambda$launchApplication$150(LauncherImpl.java:157)
>> at
>> com.sun.javafx.application.LauncherImpl$$Lambda$50/553264065.run(Unknown
>> Source)
>> at java.lang.Thread.run(Thread.java:745)
>> Caused by: java.lang.IllegalArgumentException: No compatible service:
>> io.scif.SCIFIOService
>> at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:243)
>> at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
>> at
>> org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:170)
>> at org.scijava.Context.<init>(Context.java:244)
>> at org.scijava.Context.<init>(Context.java:203)
>> at org.scijava.Context.<init>(Context.java:142)
>> at org.scijava.Context.<init>(Context.java:128)
>> at io.scif.SCIFIO.<init>(SCIFIO.java:81)
>> at biz.dsuk.mavenimglib2fx.MainApp.start(MainApp.java:38)
>> at
>> com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$156(LauncherImpl.java:821)
>> at
>> com.sun.javafx.application.LauncherImpl$$Lambda$53/681110827.run(Unknown
>> Source)
>> at
>> com.sun.javafx.application.PlatformImpl.lambda$runAndWait$169(PlatformImpl.java:326)
>> at
>> com.sun.javafx.application.PlatformImpl$$Lambda$47/693632176.run(Unknown
>> Source)
>> at
>> com.sun.javafx.application.PlatformImpl.lambda$null$167(PlatformImpl.java:295)
>> at
>> com.sun.javafx.application.PlatformImpl$$Lambda$49/1260282780.run(Unknown
>> Source)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at
>> com.sun.javafx.application.PlatformImpl.lambda$runLater$168(PlatformImpl.java:294)
>> at
>> com.sun.javafx.application.PlatformImpl$$Lambda$48/1364335809.run(Unknown
>> Source)
>> at
>> com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95)
>> Exception running application biz.dsuk.mavenimglib2fx.MainApp
>> ============================================================
>>
>> If I remove the calls to the SCIO code and build and run from the command
>> line, all works well.
>>
>> The SCIO source code that I am using is lifted/amended from one of the
>> tutorials and is as follows:
>>
>> ============================================================
>> imagePath =
>> "8bit-signed&pixelType=int8&lengths=50,50,3,5,7&axes=X,Y,Z,Channel,Time.fake";
>> System.out.println("Loading image... '" + imagePath + "'");
>> SCIFIO scifio = new SCIFIO();
>> final Reader reader =
>> scifio.initializer().initializeReader(imagePath);
>> ============================================================
>>
>> This source code works file in the SCIFIO tutorial.
>>
>> Any help gratefully appreciated!!!!!
>>
>> — Michael Ellis
>>
>>
>>
>>
>> On 3 Dec 2014, at 19:31, Curtis Rueden <ctrue...@wisc.edu> wrote:
>>
>>> Hi Michael,
>>>
>>> > How do I establish what Maven projects I need to include?
>>>
>>> One way to check is using the dependency-maven-plugin like so:
>>>
>>> mvn dependency:analyze
>>>
>>> This will tell you:
>>>
>>> A) Dependencies you declared but do not actually use; and
>>> B) Dependencies you did not declare directly, but actually need.
>>>
>>> Note that this will only work if your project compiles successfully. In
>>> other words, it is easier to start with "too many" dependencies and pare
>>> down, rather than trying to "build up" from zero.
>>>
>>> So in your case, you can start with the ImgLib2 Examples dependencies
>>> block, run dependency:analyze, and adjust the POM according to its
>>> recommendations.
>>>
>>> > When I go to my NetBeans project dependence, select Add dependency,
>>> > then type SCIF to the query text box, I get a huge list of
>>> > possibilities.
>>>
>>> The dependency you probably want is io.scif:scifio (i.e.: a groupId of
>>> io.scif, and an artifactId of scifio). Presumably at the latest version.
>>> You can search for that here:
>>>
>>> http://maven.imagej.net/index.html#nexus-search;gav~io.scif~scifio~~~
>>>
>>> So your dependency block in this case would be:
>>>
>>> <dependency>
>>> <groupId>io.scif</groupId>
>>> <artifactId>scifio</artifactId>
>>> <version>0.17.1</version>
>>> </dependency>
>>>
>>> Note that that block of XML is available for copy-pasting from the link
>>> above.
>>>
>>> > I am completely new to maven
>>>
>>> For more information, see:
>>> http://imagej.net/Maven
>>>
>>> Regards,
>>> Curtis
>>>
>>> On Tue, Dec 2, 2014 at 6:05 PM, Michael Ellis <michael.el...@dsuk.biz>
>>> wrote:
>>> I am investigating the using ImgLib2 for a project.
>>>
>>> I am using NetBeans and have managed to create a NetBeans Mavern project
>>> and have added a dependency for ImgLib2 Core Library and that seems to be
>>> working OK.
>>>
>>> I now want to add the least possible requirements for the purpose of
>>> opening some image files.
>>>
>>> How do I establish what Maven projects I need to include?
>>>
>>> I have cloned the ImgLib2 Examples project and got that working but that
>>> seems to include all manner of things that I suspect I do not need.
>>>
>>> When I go to my NetBeans project dependence, select Add dependency, then
>>> type SCIF to the query text box, I get a huge list of possibilities.
>>>
>>> I am completely new to maven and so do not know what I am doing with it!
>>>
>>> — Michael Ellis
>>> Digital Scientific UK Ltd.
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> ImageJ-devel mailing list
>>> ImageJ-devel@imagej.net
>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>
>>>
>>
>>
>> _______________________________________________
>> ImageJ-devel mailing list
>> ImageJ-devel@imagej.net
>> http://imagej.net/mailman/listinfo/imagej-devel
>>
>>
>
>
> _______________________________________________
> ImageJ-devel mailing list
> ImageJ-devel@imagej.net
> http://imagej.net/mailman/listinfo/imagej-devel
>
>
_______________________________________________
ImageJ-devel mailing list
ImageJ-devel@imagej.net
http://imagej.net/mailman/listinfo/imagej-devel
