imagejan
commented
7 years ago The problem is that SME_Stacking.jar defines class names that are already provided by the Apache commons-math3 included in Fiji. This leads to version skew and, as you experienced, can break existing plugins.
The solution (on the developer side) is to not override those classes, but either:
- properly depend on that third-party library using Maven (see https://github.com/biocompibens/SME/issues/2) as a dependency manager (and inheriting from
pom-scijavaas parent POM), and the ImageJ updater will take care that this dependency is uploaded to your update site (https://github.com/biocompibens/SME/issues/1) only if required; or - shadowing the required classes from commons-math by putting them in a package with different name, so you can use customized code without interfering with other plugins depending on commons-math.
From the user perspective, you can try to delete commons-math3-3.4.1.jar, but it will certainly break other plugins in your Fiji installation.
erexhepa
tlambert03
Error message when running plugin:
Padding Done ! There was a problem with the class org.apache.commons.math3.random.JDKRandomGenerator which can be found here: /Applications/Fiji.app/jars/commons-math3-3.4.1.jar /Applications/Fiji.app/plugins/SME_stacking.jar
WARNING: multiple locations found! java.lang.NoSuchMethodError: org.apache.commons.math3.random.JDKRandomGenerator.(I)V
at SME_PROJECTION_SRC.SME_ENS_KmeanControl.Kmeans(SME_ENS_Kmean_Control.java:351)
at SME_PROJECTION_SRC.SME_ENS_Kmean_Control.applyKmeans(SME_ENS_Kmean_Control.java:47)
at SME_PROJECTION_SRC.SME_Plugin_Get_Manifold.runKmeans(SME_Plugin_Get_Manifold.java:180)
at SME_PROJECTION_SRC.SME_Plugin_Simple_CONF.runKmeansStep(SME_Plugin_Simple_CONF.java:92)
at SME_PROJECTION_SRC.SME_Plugin_Simple_CONF.getManifold(SME_Plugin_Simple_CONF.java:78)
at SME_PROJECTION_SRC.SME_Plugin_Simple_CONF.runConfColour(SME_Plugin_Simple_CONF.java:329)
at SME_PROJECTION_SRC.SME_Plugin_Simple.run(SME_Plugin_Simple.java:249)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:748)
java.lang.NoSuchMethodException: Could not find method org.apache.commons.math3.random.JDKRandomGenerator.(I)V
There was a problem with the class org.apache.commons.math3.random.JDKRandomGenerator which can be found here:
/Applications/Fiji.app/jars/commons-math3-3.4.1.jar
/Applications/Fiji.app/plugins/SME_stacking.jar
WARNING: multiple locations found! java.lang.NoSuchMethodError: org.apache.commons.math3.random.JDKRandomGenerator.(I)V
at SME_PROJECTION_SRC.SME_ENS_KmeanControl.Kmeans(SME_ENS_Kmean_Control.java:351)
at SME_PROJECTION_SRC.SME_ENS_Kmean_Control.applyKmeans(SME_ENS_Kmean_Control.java:47)
at SME_PROJECTION_SRC.SME_Plugin_Get_Manifold.runKmeans(SME_Plugin_Get_Manifold.java:180)
at SME_PROJECTION_SRC.SME_Plugin_Simple_CONF.runKmeansStep(SME_Plugin_Simple_CONF.java:92)
at SME_PROJECTION_SRC.SME_Plugin_Simple_CONF.getManifold(SME_Plugin_Simple_CONF.java:78)
at SME_PROJECTION_SRC.SME_Plugin_Simple_CONF.runConfColour(SME_Plugin_Simple_CONF.java:329)
at SME_PROJECTION_SRC.SME_Plugin_Simple.run(SME_Plugin_Simple.java:249)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:748)