A word of warning: our previous Debian expert left the community a few years ago. He is one of the best programmers I have ever known, but the Debian packaging of Fiji was still too much for him, time-wise (and maybe bureaucracy/legal-wise).
Hi all, I'm getting a
java.lang.UnsatisfiedLinkError: Can't load library: <project path>//libgluegen-rt.so exception when trying to call Java 3D stuff from my code (new CustomTriangleMesh()). I guess I need JOGL to solve this. How do I add it via Maven? I tried adding a runtime dependency to net.java.jogl, but that didn't help.
@hinerm In test classes
StructureModelIndexTest and VolumeFractionTest
Okay, I managed to solve my own problem. The correct dependencies are:
<!-- JOGL dependencies -->
<dependency>
<groupId>org.jogamp.gluegen</groupId>
<artifactId>gluegen-rt-main</artifactId>
<version>2.3.2</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.jogamp.jogl</groupId>
<artifactId>jogl-all-main</artifactId>
<version>2.3.2</version>
<scope>runtime</scope>
</dependency>
Sorry that it is has been long enough now, where I can't remember why I did things that way. But there was a good reason.
Oh. Because your platform might be different.
running with option
-e gives the following trace:org.apache.maven.lifecycle.LifecycleExecutionException: Error configuring: org.apache.maven.plugins:maven-enforcer-plugin. Reason: Unable to parse the created DOM for plugin configuration
at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:723)
...
Any ideas what this could be about? At first I thought that I could solve this by stating the enforcer version in my POM, but that didn't solve it. I get the same error with 1.4.1 than 1.3.1
Here's the main POM for the project: https://github.com/bonej-org/BoneJ2/blob/mavenization/Legacy/pom.xml
wait, let me just fix that...
[INFO] Restricted to JDK 1.6 yet org.scijava:j3dcore:jar:1.6.0-scijava-2:compile contains org/scijava/java3d/DecalGroupRetained.class targeted to JDK 1.7
[INFO] Restricted to JDK 1.6 yet org.scijava:j3dutils:jar:1.6.0-scijava-2:compile contains org/scijava/java3d/internal/FloatBufferWrapper.class targeted to JDK 1.7
[WARNING] Rule 5: org.apache.maven.plugins.enforcer.EnforceBytecodeVersion failed with message:
Found Banned Dependency: org.scijava:j3dcore:jar:1.6.0-scijava-2
Found Banned Dependency: org.scijava:j3dutils:jar:1.6.0-scijava-2
The following patch makes the whole build succeed on my system:
diff --git a/Legacy/bonej/pom.xml b/Legacy/bonej/pom.xml
index 2cde652..372ecdd 100644
--- a/Legacy/bonej/pom.xml
+++ b/Legacy/bonej/pom.xml
@@ -88,6 +88,10 @@
</repository>
</repositories>
+ <properties>
+ <scijava.jvm.version>1.7</scijava.jvm.version>
+ </properties>
+
<dependencies>
<!-- BoneJ dependencies -->
<dependency>
It will definitely be built at Java 7 level then, which means Java 6 will throw an exception if you try to use it.
@rimadoma BTW:
$ mvn -v
Apache Maven 3.3.9 (bb52d8502b132ec0a5a3f4c09453c07478323dc5; 2015-11-10T10:41:47-06:00)
Maven home: /usr/local/Cellar/maven/3.3.9/libexec
Java version: 1.8.0_73, vendor: Oracle Corporation
Java home: /Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "mac os x", version: "10.11.4", arch: "x86_64", family: "mac"
You could try a different Maven core version to see if that makes a difference with your local enforcer error.
@ctrueden Ah, well I guess it's again related to the problems with legacy code, Java3d, Java 8, that forum thread (http://forum.imagej.net/t/java3d-issue-bonej-with-latest-fiji-version-problem-solved/1151/29). I made a post there earlier today, so let's take that jvm version discussion there, shall we?
@ctrueden Sure, I'll try a different core version, and report back later
@ctrueden Interestingly the newest maven from apt-get was 3.0.5, so I had to add a repo (https://launchpad.net/~andrei-pozolotin/+archive/ubuntu/maven3) to apt-get to install 3.3.9
@ctrueden Also when I googled for the exception I was getting I ran into this old conversation: https://groups.google.com/forum/#!topic/fiji-devel/k_6X3DY_cPY
If 3.0.5 really does not work, we should update the minimum requirement in pom-scijava accordingly.
@ctrueden ImageJ doesn’t currently run on 32-bit Windows 10 due to the 3/4 of available memory approximation for maximum heap space. This evaluates to 1.5G (=3/4*2G) on two different systems, which leads to the JVM telling me
Could not reserve enough space for 1572864KB object heap.. Can anyone confirm that issue? Also fails for 32-bit ImageJ/Fiji on a 64-bit Windows 10..
I have Win systems where 32-bit Java cannot start with as little as 1.1g. And others where it will start fine with 1.4g.