Class that is also contained in a dependency was modified, but has the same name and package.

[pstutz]

Hi Richard,

The class is:
https://github.com/rwl/ParallelColt/blob/master/src/main/java/edu/emory/mathcs/utils/ConcurrencyUtils.java
The dependency to jplasma adds a modified version of this class to the class path.
This leads to problems when attempting to package with sbt assembly. One way to solve it would be to remove the class and use the one from the dependency. Alternatively, if it really does something differently, it could get a new name/package to get rid of the ambiguity.

Thanks and kind regards,
Philip

[rwl]

The file in ParallelColt has some notable additions. Your suggestion of moving it to a new package might be the best solution.

[rwl]

Refactoring the package name causes the tests for the interface to JTransforms to fail. Some work will be required to update JTransforms to use the new package.

[thorstenwagner]

I've the same issue. Anything what I can do when I need the paracolt library AND the jtransforms library?

[beyondpie]

I have this issue on mvn, would you publish a new version on that?

[ctrueden]

@beyondpie @thorstenwagner @tischi @rwl
I looked through the 0.11.x tags of parallelcolt. Of those, only 0.11.4 is properly formed; the others declare a SNAPSHOT version in the pom.xml. Fortunately, 0.11.4 is the latest version. I rebuilt and deployed that version to https://maven.imagej.net/content/repositories/thirdparty, to make use from downstream projects easier.

I then did some testing on whether this problem of duplicate classes is really fixed. Unfortunately, as @tischi points out in #9, it is not. Here is a sample pom.xml for reproducing the issue:

<?xml version="1.0" encoding="UTF-8"?>
<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>test</groupId>
	<artifactId>test</artifactId>
	<version>0-SNAPSHOT</version>

	<repositories>
		<!-- NB: imagej.public hosts parallelcolt dependency. -->
		<repository>
			<id>imagej.public</id>
			<url>https://maven.imagej.net/content/groups/public</url>
		</repository>
	</repositories>

	<dependencies>
		<dependency>
			<groupId>net.sourceforge.parallelcolt</groupId>
			<artifactId>parallelcolt</artifactId>
			<version>0.11.4</version>
		</dependency>
	</dependencies>

	<build>
		<plugins>
			<plugin>
				<artifactId>maven-enforcer-plugin</artifactId>
				<version>1.4.1</version>
				<dependencies>
					<dependency>
						<groupId>org.codehaus.mojo</groupId>
						<artifactId>extra-enforcer-rules</artifactId>
						<version>1.0-beta-9</version>
					</dependency>
				</dependencies>
				<executions>
					<execution>
						<id>enforce-rules</id>
						<goals>
							<goal>enforce</goal>
						</goals>
					</execution>
				</executions>
				<configuration>
					<rules>
						<banDuplicateClasses>
							<message>No Duplicate Classes Allowed!</message>
							<findAllDuplicates>true</findAllDuplicates>
						</banDuplicateClasses>
					</rules>
				</configuration>
			</plugin>
		</plugins>
	</build>
</project>

And here is the result:

$ mvn compile
[INFO] Scanning for projects...
[INFO]
[INFO] -----------------------------< test:test >------------------------------
[INFO] Building test 0-SNAPSHOT
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-rules) @ test ---
[INFO] Adding ignore: module-info
[INFO] Adding ignore: META-INF/versions/*/module-info
[WARNING] Rule 0: org.apache.maven.plugins.enforcer.BanDuplicateClasses failed with message:
No Duplicate Classes Allowed!

  Found in:
    net.sourceforge.jplasma:jplasma:jar:1.2.0:compile
    net.sourceforge.parallelcolt:parallelcolt:jar:0.11.4:compile
  Duplicate classes:
    edu/emory/mathcs/utils/ConcurrencyUtils$CustomThreadFactory.class
    edu/emory/mathcs/utils/ConcurrencyUtils$CustomExceptionHandler.class
    edu/emory/mathcs/utils/ConcurrencyUtils.class

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------

The problem can be worked around by adding:

<ignoreClasses>edu.emory.mathcs.utils.ConcurrencyUtils*</ignoreClasses>

to the banDuplicateClasses configuration, although this is not ideal, since the classpath order at run time could then affect behavior. (Projects extending the pom-scijava parent can achieve this easily by adding a line to <properties> that reads <allowedDuplicateClasses>edu.emory.mathcs.utils.ConcurrencyUtils*</allowedDuplicateClasses>.)

The parallelcolt dependency tree also has other problems, which manifest when trying to combine it with other large projects. I attempted to combine it with Fiji and received the following (abbreviated) list of class conflicts:

No Duplicate Classes Allowed!
- For duplicate transitive dependencies, add dependency exclusions.
- For duplications between direct dependencies, resolve or add
  ignored classes to this rule's configuration.

  Found in:
    net.sourceforge.f2j:arpack_combined_all:jar:0.1:compile
    org.netlib:lapack:jar:0.8:runtime
  Duplicate classes:
    org/netlib/lapack/*

  Found in:
    org.netlib:f2jutil:jar:0.8:runtime
    net.sourceforge.f2j:arpack_combined_all:jar:0.1:compile
  Duplicate classes:
    org/j_paine/formatter/*
    org/netlib/util/*

  Found in:
    org.netlib:blas:jar:0.8:runtime
    net.sourceforge.f2j:arpack_combined_all:jar:0.1:compile
  Duplicate classes:
    org/netlib/blas/*

  Found in:
    net.sourceforge.jplasma:jplasma:jar:1.2.0:compile
    edu.emory.mathcs:jtransforms:jar:2.4:runtime
  Duplicate classes:
    edu.emory.mathcs.utils.ConcurrencyUtils*

  Found in:
    net.sourceforge.f2j:arpack_combined_all:jar:0.1:compile
    org.netlib:xerbla:jar:0.8:runtime
  Duplicate classes:
    org.netlib.err.Xerbla

  Found in:
    com.googlecode.netlib-java:netlib-java:jar:0.9.3:compile
    org.netlib:netlib-java:jar:0.9.3-renjin-patched-2:runtime
  Duplicate classes:
    org/netlib/*

The root problems are as follows:

1. Dependency on the unshaded uberjar arpack_combined_all, which bundles dependencies that may be used elsewhere in the dependency tree.
2. The jplasma clash discussed above.
3. A clash between the vanilla netlib-java version 0.9.3, and a patched version used by the Renjin project. (This is not a problem with parallelcolt, but rather with Renjin—they should have shaded that patched version to avoid issues like this.)

Without digging more deeply, I cannot recommend a specific course of action to address (1), although I do think it should be addressed somehow.