NoClassDefFoundError: java/util/HashMap$Entry

[sjackman]

./nextflow http://goo.gl/ngf8dL
N E X T F L O W  ~  version 0.8.1
ERROR: java.lang.NoClassDefFoundError: java/util/HashMap$Entry -- See the file '.nextflow.log' for more error details

[sjackman]

.nextflow.log gist

[pditommaso]

This looks something related to a not compatible Java version.

Could please paste the result of "java -version" command. Also, is the JAVA_HOME variable defined in your system? If so double check that it points to the same version of java on you PATH, or "unset" it and to launch it again.

[sjackman]

I installed java using Homebrew-cask brew cask install java. JAVA_HOME is not set.

~ ❯❯❯ java -version
java version "1.8.0_05"
Java(TM) SE Runtime Environment (build 1.8.0_05-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.5-b02, mixed mode)
~ ❯❯❯ echo $JAVA_HOME

[pditommaso]

I think homebrew install OpenJDK instead of Oracle JDK. I never tested with the first, it could be the problem. Unfortunatly I can't investigate it before next week. Anyway I will let you know as soon as possible. Thanks for reporting the issue.

[sjackman]

Homebrew-cask installs the Oracle JDK. No rush. I'm looking forward to trying out nextflow. It looks very interesting as a replacement for make.

[pditommaso]

I see, what does it return the command "/usr/libexec/java_home -V" ?

[pditommaso]

Anyway, it looks there's still some odd incompatibility with Java 8. If you want to start to play with it you may want to downgrade to Java 7

http://www.oracle.com/technetwork/java/javase/downloads/index.html?ssSourceSiteId=otnjp

[sjackman]

/usr/libexec/java_home -V
Matching Java Virtual Machines (3):
    1.8.0_05, x86_64:   "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home
    1.6.0_65-b14-462, x86_64:   "Java SE 6" /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
    1.6.0_65-b14-462, i386: "Java SE 6" /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home

/Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home

[pditommaso]

The problem was due to a (private) API change in Java 8 as described here
https://groups.google.com/d/msg/groovy-user/MeHXv6fz15o/mkrB4VjXGJsJ

I've just uploaded a fixed version (0.8.2) that solve the issue.

Happy hacking.

[sjackman]

Thanks, Paolo. It works.

[pditommaso]

Thanks to you for reporting the issue.