bpipe via Conda throws java.lang.NoClassDefFoundError

[marvel64]

Hi,

On macOS (?) there seems to be an issue with bpipe installed using conda:

This works using the Hello World example from the tutorials and the binary from the repository:

bpipe-0.9.11/bin/bpipe run helloworld.pipe

Also works in a new conda environment:

conda create new -n bpipe
conda activate bpipe
bpipe-0.9.11/bin/bpipe run helloworld.pipe

This does not work:

conda install bpipe

...
## Package Plan ##

  environment location: /Users/Kemal/miniconda3/envs/parpipe

  added / updated specs:
    - bpipe


The following NEW packages will be INSTALLED:

  bpipe              bioconda/noarch::bpipe-0.9.11-hdfd78af_0
  coreutils          conda-forge/osx-64::coreutils-9.2-hb7f2c08_0
  openjdk            conda-forge/osx-64::openjdk-17.0.3-hbc0c0cd_6
...

bpipe run helloworld.pipe *or*
bpipe-0.9.11/bin/bpipe run helloworld.pipe

Both give the following error:

java.lang.NoClassDefFoundError: Could not initialize class org.codehaus.groovy.vmplugin.v7.Java7
	at org.codehaus.groovy.vmplugin.VMPluginFactory.<clinit>(VMPluginFactory.java:43)
	at org.codehaus.groovy.reflection.GroovyClassValueFactory.<clinit>(GroovyClassValueFactory.java:35)
	at org.codehaus.groovy.reflection.ClassInfo.<clinit>(ClassInfo.java:107)
	at org.codehaus.groovy.reflection.ReflectionCache.getCachedClass(ReflectionCache.java:95)
	at org.codehaus.groovy.reflection.ReflectionCache.<clinit>(ReflectionCache.java:39)
	at org.codehaus.groovy.runtime.metaclass.MetaClassRegistryImpl.registerMethods(MetaClassRegistryImpl.java:209)
	at org.codehaus.groovy.runtime.metaclass.MetaClassRegistryImpl.<init>(MetaClassRegistryImpl.java:107)
	at org.codehaus.groovy.runtime.metaclass.MetaClassRegistryImpl.<init>(MetaClassRegistryImpl.java:85)
	at groovy.lang.GroovySystem.<clinit>(GroovySystem.java:36)
	at org.codehaus.groovy.runtime.InvokerHelper.<clinit>(InvokerHelper.java:86)
	at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.createMap(ScriptBytecodeAdapter.java:635)
	at bpipe.Tail.<clinit>(Tail.groovy:48)
	at bpipe.Tail9.main(Tail9.java:31)
Exception in thread "main" java.lang.NoClassDefFoundError: Could not initialize class org.codehaus.groovy.reflection.ReflectionCache
	at org.codehaus.groovy.runtime.dgmimpl.NumberNumberMetaMethod.<clinit>(NumberNumberMetaMethod.java:33)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
	at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)
	at java.base/jdk.internal.reflect.ReflectionFactory.newInstance(ReflectionFactory.java:347)
	at java.base/java.lang.Class.newInstance(Class.java:645)
	at org.codehaus.groovy.runtime.metaclass.MetaClassRegistryImpl.createMetaMethodFromClass(MetaClassRegistryImpl.java:257)
	at org.codehaus.groovy.runtime.metaclass.MetaClassRegistryImpl.<init>(MetaClassRegistryImpl.java:110)
	at org.codehaus.groovy.runtime.metaclass.MetaClassRegistryImpl.<init>(MetaClassRegistryImpl.java:85)
	at groovy.lang.GroovySystem.<clinit>(GroovySystem.java:36)
	at org.codehaus.groovy.runtime.InvokerHelper.<clinit>(InvokerHelper.java:86)
	at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.createMap(ScriptBytecodeAdapter.java:635)
	at bpipe.Tail.<clinit>(Tail.groovy:48)
	at bpipe.Tail9.main(Tail9.java:31)

Tried to see if it works uninstalling openjdk, but that also uninstalled all dependencies as well.

conda uninstall openjdk

Collecting package metadata (repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 22.11.1
  latest version: 23.1.0

Please update conda by running

    $ conda update -n base -c conda-forge conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.1.0



## Package Plan ##

  environment location: /Users/Kemal/miniconda3/envs/parpipe

  removed specs:
    - openjdk


The following packages will be REMOVED:

  bpipe-0.9.11-hdfd78af_0
  coreutils-9.2-hb7f2c08_0
  openjdk-17.0.3-hbc0c0cd_6


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Works.

bpipe-0.9.11/bin/bpipe run helloworld.pipe

This is on macOS 12.6.3
Zsh
conda 22.11.1