bridgedb / bridgedb/BridgeDb

java.lang.RuntimeException on groovysh :grab

Open
#169 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
Java
Stars
37
Forks
22
PR merge metrics
No merged PRs in 30d

Description

When I tried to install bridgedb with groovysh `:grab`, I got the following error.

```
groovy:000> :grab 'org.bridgedb:org.bridgedb.bio:3.0.1'
ERROR java.lang.RuntimeException:
Error grabbing Grapes -- [unresolved dependency: commonj.sdo#commonj.sdo;2.1.1.v201112051852: not found]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at org.apache.groovy.groovysh.commands.GrabCommand.grab (GrabCommand.groovy:65)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at org.apache.groovy.groovysh.commands.GrabCommand.execute (GrabCommand.groovy:42)
at org.apache.groovy.groovysh.Command$execute.call (Unknown Source)
at org.apache.groovy.groovysh.Command$execute.call (Unknown Source)
at org.apache.groovy.groovysh.Shell.execute (Shell.groovy:103)
at org.apache.groovy.groovysh.Groovysh.super$2$execute (Groovysh.groovy)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at org.apache.groovy.groovysh.Groovysh.executeCommand (Groovysh.groovy:308)
at org.apache.groovy.groovysh.Groovysh.execute (Groovysh.groovy:171)
at org.apache.groovy.groovysh.Shell.leftShift (Shell.groovy:121)
at org.apache.groovy.groovysh.Shell$leftShift$0.call (Unknown Source)
at org.apache.groovy.groovysh.ShellRunner.work (ShellRunner.groovy:93)
at org.apache.groovy.groovysh.InteractiveShellRunner.super$2$work (InteractiveShellRunner.groovy)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at org.apache.groovy.groovysh.InteractiveShellRunner.work (InteractiveShellRunner.groovy:157)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at org.apache.groovy.groovysh.ShellRunner.run (ShellRunner.groovy:57)
at org.apache.groovy.groovysh.InteractiveShellRunner.super$2$run (InteractiveShellRunner.groovy)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at org.apache.groovy.groovysh.InteractiveShellRunner.run (InteractiveShellRunner.groovy:116)
at java_lang_Runnable$run.call (Unknown Source)
at org.apache.groovy.groovysh.Groovysh.run (Groovysh.groovy:653)
at org.apache.groovy.groovysh.Groovysh$run$0.callCurrent (Unknown Source)
at org.apache.groovy.groovysh.Groovysh.run (Groovysh.groovy:618)
at org.apache.groovy.groovysh.Groovysh$run.call (Unknown Source)
at org.apache.groovy.groovysh.Main.startGroovysh (Main.groovy:190)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at org.apache.groovy.groovysh.Main.main (Main.groovy:156)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
groovy:000>
```

The environment is
```
Groovy Shell (3.0.8, JVM: 11.0.12)
Type ':help' or ':h' for help.
-------------------------------------------------------------------------------
```

Contributor guide

No contributing guide indexed for this repository

Research direction

Reproduce the failure with Groovy Shell 3.0.8 on JVM 11 using :grab 'org.bridgedb:org.bridgedb.bio:3.0.1'. Start with the GrabCommand.groovy stack-trace entry point and investigate why commonj.sdo#commonj.sdo;2.1.1.v201112051852 is unresolved. Done means the dependency can be grabbed without the RuntimeException.

Written by the indexing model from the issue text.

Assessment

Tech stack
groovy, java
Domain
cli
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.