My mod requires four dependencies, so I read the documentation for gradle and pulled a few lines from stackoverflow. Here is the relevant excerpt from my build file:

 

configurations{
    customCompile
}
dependencies {
    // http://mvnrepository.com/artifact/com.jcraft/jsch
    customCompile 'com.jcraft:jsch:0.1.53'


    // http://mvnrepository.com/artifact/org.eclipse.jgit/org.eclipse.jgit
    customCompile 'org.eclipse.jgit:org.eclipse.jgit:4.3.1.201605051710-r'


    // http://mvnrepository.com/artifact/org.slf4j/slf4j-api
    customCompile 'org.slf4j:slf4j-api:1.7.21'

    // http://mvnrepository.com/artifact/org.slf4j/slf4j-log4j12
    customCompile 'org.slf4j:slf4j-log4j12:1.7.21'

    // http://mvnrepository.com/artifact/log4j/log4j
    customCompile group: 'log4j', name: 'log4j', version: '1.2.17'
    compile configurations.customCompile


}
jar{
    from ( configurations.customCompile.collect { it.isDirectory() ? it : zipTree(it)}) { exclude 'META-INF/**' }
    manifest {
        attributes 'Main-Class': 'Test'
    }
}

 

My mod compiles with all of the classes for my dependencies bundled inside the jar, but when I actually use code that invokes the slf4j logger via jgit (from a server command while the game is running), I get the following error:

 

Exception in thread "Thread-13" [23:38:03] [Thread-13/INFO] [sTDERR]: [java.lang.ThreadGroup:uncaughtException:1052]: java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory
[23:38:03] [Thread-13/INFO] [sTDERR]: [java.lang.ThreadGroup:uncaughtException:1052]: 	at org.eclipse.jgit.util.FS.<clinit>(FS.java:160)
[23:38:03] [Thread-13/INFO] [sTDERR]: [java.lang.ThreadGroup:uncaughtException:1052]: 	at org.eclipse.jgit.api.Git.open(Git.java:99)
[23:38:03] [Thread-13/INFO] [sTDERR]: [java.lang.ThreadGroup:uncaughtException:1052]: 	at shoeboxam.gitstream.GitManager.pull(GitManager.java:123)
[23:38:03] [Thread-13/INFO] [sTDERR]: [java.lang.ThreadGroup:uncaughtException:1052]: 	at shoeboxam.gitstream.commands.CommandUpdateThread.remote_get(CommandUpdateThread.java:157)
[23:38:03] [Thread-13/INFO] [sTDERR]: [java.lang.ThreadGroup:uncaughtException:1052]: 	at shoeboxam.gitstream.commands.CommandUpdateThread.run(CommandUpdateThread.java:31)
[23:38:03] [Thread-13/INFO] [sTDERR]: [java.lang.ThreadGroup:uncaughtException:1061]: Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
[23:38:03] [Thread-13/INFO] [sTDERR]: [java.lang.ThreadGroup:uncaughtException:1061]: 	at net.minecraft.launchwrapper.LaunchClassLoader.findClass(LaunchClassLoader.java:101)
[23:38:03] [Thread-13/INFO] [sTDERR]: [java.lang.ThreadGroup:uncaughtException:1061]: 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
[23:38:03] [Thread-13/INFO] [sTDERR]: [java.lang.ThreadGroup:uncaughtException:1061]: 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
[23:38:03] [Thread-13/INFO] [sTDERR]: [java.lang.ThreadGroup:uncaughtException:1061]: 	... 5 more

 

The referenced file, org/slf4j/LoggerFactory.class, exists in my mod jar. Is slf4j failing to be included in the classpath? That's why I packed the jar. Please note, if I don't bundle the files via the customCompile, the Minecraft server errors on startup.

 

Any help is appreciated.

Also experiencing this issue.