mvn site fails because of some problem with DiffOperation

[matentzn]

When running mvn site, I get this error:

It must have been around for a while, but it would be good to solve it at some point if we want to test stuff locally.. @beckyjackson and I share the problem. @jamesaoverton does not. Notably, I am using Java 14, Becky Java 8 and James Java 8 as well.. Maybe some kind of missing deep dependency?

@balhoff not urgent, but if you could take a look after the holidays, that would be great!

[jamesaoverton]

I was able to reproduce this problem using Docker and the official Maven image: https://hub.docker.com/_/maven/

[jamesaoverton]

I was able to fix this by updating the maven-javadoc-plugin to the latest 3.2.0 and using excludePackageNames.

      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-javadoc-plugin</artifactId>
        <version>3.2.0</version>
        <configuration>
          <links>
            <link>https://commons.apache.org/proper/commons-cli/javadocs/api-1.2/</link>
            <link>http://owlcs.github.io/owlapi/apidocs_4/</link>
          </links>
          <excludePackageNames>org.geneontology.*</excludePackageNames>
        </configuration>
      </plugin>

I guess it would be better if it was fixed upstream. What do you think @balhoff?

[balhoff]

@jamesaoverton thanks for adding that! Right now I'm not sure what else to do. These packages do exist. 😕

[balhoff]

What version of Maven is everyone using? I'm using 3.5.2 on my machine, and I don't encounter this problem.

[beckyjackson]

I'm on 3.6.3 @balhoff

[jamesaoverton]

I'm using Apache Maven 3.6.3 (cecedd343002696d0abb50b32b541b8a6ba2883f) and I don't see the problem. But I was able to reproduce in Docker latest back in November.

[balhoff]

Maybe the varying factor is Java version? I don't have the problem with Java 8, but just tested Java 13 and I do see the problem. @matentzn is using this environment:

Apache Maven 3.6.3 (cecedd343002696d0abb50b32b541b8a6ba2883f)
Maven home: /usr/local/Cellar/maven/3.6.3_1/libexec
Java version: 14.0.1, vendor: N/A, runtime: /usr/local/Cellar/openjdk/14.0.1/libexec/openjdk.jdk/Contents/Home
Default locale: en_GB, platform encoding: UTF-8
OS name: "mac os x", version: "10.16", arch: "x86_64", family: "mac"

[jamesaoverton]

Yes, I think it's something to do with the Java version. But I'm hoping that the fix is as simple as updating all our Maven plugins #798.

[beckyjackson]

Here's my full environment too:

Apache Maven 3.6.3 (cecedd343002696d0abb50b32b541b8a6ba2883f)
Maven home: /usr/local/Cellar/maven/3.6.3_1/libexec
Java version: 13.0.2, vendor: N/A, runtime: /usr/local/Cellar/openjdk/13.0.2+8_2/libexec/openjdk.jdk/Contents/Home
Default locale: en_US, platform encoding: UTF-8
OS name: "mac os x", version: "10.14.6", arch: "x86_64", family: "mac"

[beckyjackson]

I'm now able to run mvn site after updating everything in #837. Maybe this was caused by some dependency issue.