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rcsb / symmetry

:ferris_wheel: Detect, analyze, and visualize protein symmetry
GNU Lesser General Public License v2.1
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mvn package does not work. [ERROR] Failed to execute goal on project symmetry-core: #111

Closed matskohe closed 2 years ago

matskohe commented 2 years ago

mvn package does not work.

(base) 11:24 matskohe@mbp symmetry % mvn package -e
[INFO] Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] RCSB Symmetry                                                      [pom]
[INFO] RCSB Symmetry Core                                                 [jar]
[INFO] RCSB Symmetry Tools                                                [jar]
[INFO] 
[INFO] ------------------------< org.biojava:symmetry >------------------------
[INFO] Building RCSB Symmetry 2.2.0-SNAPSHOT                              [1/3]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] ---------------------< org.biojava:symmetry-core >----------------------
[INFO] Building RCSB Symmetry Core 2.2.0-SNAPSHOT                         [2/3]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT is missing, no dependency information available
[WARNING] The POM for org.biojava:biojava-structure-gui:jar:6.0.0-SNAPCHAT is missing, no dependency information available
[WARNING] The POM for org.biojava:biojava-ws:jar:6.0.0-SNAPCHAT is missing, no dependency information available
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] RCSB Symmetry 2.2.0-SNAPSHOT ....................... SUCCESS [  0.003 s]
[INFO] RCSB Symmetry Core ................................. FAILURE [  0.099 s]
[INFO] RCSB Symmetry Tools 2.2.0-SNAPSHOT ................. SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.326 s
[INFO] Finished at: 2022-01-04T11:24:13+09:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project symmetry-core: Could not resolve dependencies for project org.biojava:symmetry-core:jar:2.2.0-SNAPSHOT: The following artifacts could not be resolved: org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT, org.biojava:biojava-structure-gui:jar:6.0.0-SNAPCHAT, org.biojava:biojava-ws:jar:6.0.0-SNAPCHAT: Failure to find org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT in http://www.biojava.org/download/maven/ was cached in the local repository, resolution will not be reattempted until the update interval of biojava-maven-repo has elapsed or updates are forced -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal on project symmetry-core: Could not resolve dependencies for project org.biojava:symmetry-core:jar:2.2.0-SNAPSHOT: The following artifacts could not be resolved: org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT, org.biojava:biojava-structure-gui:jar:6.0.0-SNAPCHAT, org.biojava:biojava-ws:jar:6.0.0-SNAPCHAT: Failure to find org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT in http://www.biojava.org/download/maven/ was cached in the local repository, resolution will not be reattempted until the update interval of biojava-maven-repo has elapsed or updates are forced
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies (LifecycleDependencyResolver.java:269)
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies (LifecycleDependencyResolver.java:147)
    at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved (MojoExecutor.java:246)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:200)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:154)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:146)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:954)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
    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 java.lang.reflect.Method.invoke (Method.java:566)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:289)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:229)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:415)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:356)
Caused by: org.apache.maven.project.DependencyResolutionException: Could not resolve dependencies for project org.biojava:symmetry-core:jar:2.2.0-SNAPSHOT: The following artifacts could not be resolved: org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT, org.biojava:biojava-structure-gui:jar:6.0.0-SNAPCHAT, org.biojava:biojava-ws:jar:6.0.0-SNAPCHAT: Failure to find org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT in http://www.biojava.org/download/maven/ was cached in the local repository, resolution will not be reattempted until the update interval of biojava-maven-repo has elapsed or updates are forced
    at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve (DefaultProjectDependenciesResolver.java:209)
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies (LifecycleDependencyResolver.java:243)
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies (LifecycleDependencyResolver.java:147)
    at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved (MojoExecutor.java:246)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:200)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:154)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:146)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:954)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
    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 java.lang.reflect.Method.invoke (Method.java:566)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:289)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:229)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:415)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:356)
Caused by: org.eclipse.aether.resolution.DependencyResolutionException: The following artifacts could not be resolved: org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT, org.biojava:biojava-structure-gui:jar:6.0.0-SNAPCHAT, org.biojava:biojava-ws:jar:6.0.0-SNAPCHAT: Failure to find org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT in http://www.biojava.org/download/maven/ was cached in the local repository, resolution will not be reattempted until the update interval of biojava-maven-repo has elapsed or updates are forced
    at org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies (DefaultRepositorySystem.java:355)
    at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve (DefaultProjectDependenciesResolver.java:202)
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies (LifecycleDependencyResolver.java:243)
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies (LifecycleDependencyResolver.java:147)
    at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved (MojoExecutor.java:246)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:200)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:154)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:146)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:954)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
    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 java.lang.reflect.Method.invoke (Method.java:566)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:289)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:229)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:415)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:356)
Caused by: org.eclipse.aether.resolution.ArtifactResolutionException: The following artifacts could not be resolved: org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT, org.biojava:biojava-structure-gui:jar:6.0.0-SNAPCHAT, org.biojava:biojava-ws:jar:6.0.0-SNAPCHAT: Failure to find org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT in http://www.biojava.org/download/maven/ was cached in the local repository, resolution will not be reattempted until the update interval of biojava-maven-repo has elapsed or updates are forced
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve (DefaultArtifactResolver.java:422)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts (DefaultArtifactResolver.java:224)
    at org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies (DefaultRepositorySystem.java:338)
    at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve (DefaultProjectDependenciesResolver.java:202)
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies (LifecycleDependencyResolver.java:243)
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies (LifecycleDependencyResolver.java:147)
    at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved (MojoExecutor.java:246)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:200)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:154)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:146)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:954)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
    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 java.lang.reflect.Method.invoke (Method.java:566)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:289)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:229)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:415)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:356)
Caused by: org.eclipse.aether.transfer.ArtifactNotFoundException: Failure to find org.biojava:biojava-structure:jar:6.0.0-SNAPCHAT in http://www.biojava.org/download/maven/ was cached in the local repository, resolution will not be reattempted until the update interval of biojava-maven-repo has elapsed or updates are forced
    at org.eclipse.aether.internal.impl.DefaultUpdateCheckManager.newException (DefaultUpdateCheckManager.java:233)
    at org.eclipse.aether.internal.impl.DefaultUpdateCheckManager.checkArtifact (DefaultUpdateCheckManager.java:208)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.gatherDownloads (DefaultArtifactResolver.java:563)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.performDownloads (DefaultArtifactResolver.java:481)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve (DefaultArtifactResolver.java:399)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts (DefaultArtifactResolver.java:224)
    at org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies (DefaultRepositorySystem.java:338)
    at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve (DefaultProjectDependenciesResolver.java:202)
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies (LifecycleDependencyResolver.java:243)
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies (LifecycleDependencyResolver.java:147)
    at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved (MojoExecutor.java:246)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:200)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:154)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:146)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:954)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
    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 java.lang.reflect.Method.invoke (Method.java:566)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:289)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:229)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:415)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:356)
[ERROR] 
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :symmetry-core

environment

macOS Big Sur 11.6 Apache Maven 3.5.4 (1edded0938998edf8bf061f1ceb3cfdeccf443fe; 2018-06-18T03:33:14+09:00) Maven home: /usr/local/Cellar/maven@3.5/3.5.4_1/libexec Java version: 11.0.12, vendor: Oracle Corporation, runtime: /Library/Java/JavaVirtualMachines/jdk-11.0.12.jdk/Contents/Home Default locale: ja_JP, platform encoding: UTF-8 OS name: "mac os x", version: "11.5", arch: "x86_64", family: "mac"

matskohe commented 2 years ago

I am not sure this is the right way, but the following change resolved the error.

changed file: symmetry/pom.xml row 33

before

<biojava.version>6.0.0-SNAPSHOT</biojava.version>

after

<biojava.version>6.0.0</biojava.version>
sbliven commented 2 years ago

Yes, you found the correct fix (although biojava:6.0.3 is the latest). CE-Symm was using some bug fixes from the master branch of biojava, so it temporarily depended on the 6.0.0-SNAPSHOT build (requiring biojava to be installed manually). This is bad practice, and I should have updated it as soon as 6.0.0 came out.

This was fixed in #112 and I will make a new CE-Symm release now.

matskohe commented 2 years ago

Thanks for your quick reply and fix ;)