Unable to initialize nextflow environment- Could not transfer artifact

[kenminsoo]

Bug report

Main issue:

Occurs after normal installation procedure.

CAPSULE EXCEPTION: Error resolving dependencies. while processing attribute Allow-Snapshots: false (for stack trace, run with -Dcapsule.log=verbose)
Unable to initialize nextflow environment

Expected behavior and actual behavior

Expected normal install on HPC cluster. I have previously installed nextflow. Perhaps something has changed with our system?

Steps to reproduce the problem

I load our Java 16.01 module, and attempt to run the standard nextflow install command.

Program output

CAPSULE EXCEPTION: Error resolving dependencies. while processing attribute Allow-Snapshots: false
java.lang.RuntimeException: Error resolving dependencies.
	at capsule.DependencyManager.resolve0(DependencyManager.java:382)
	at capsule.DependencyManager.resolveDependencies(DependencyManager.java:314)
	at MavenCapsule.resolve0(MavenCapsule.java:224)
	at Capsule.resolve(Capsule.java:3375)
	at Capsule.resolve(Capsule.java:3389)
	at Capsule.buildJavaProcess(Capsule.java:2228)
	at Capsule.buildProcess0(Capsule.java:1530)
	at Capsule.buildProcess(Capsule.java:1521)
	at Capsule.buildProcess(Capsule.java:1521)
	at Capsule.buildProcess(Capsule.java:1521)
	at Capsule.prelaunch0(Capsule.java:1494)
	at Capsule.prelaunch(Capsule.java:1487)
	at NextflowLoader.prelaunch(NextflowLoader.java:42)
	at Capsule.prepareForLaunch(Capsule.java:1339)
	at Capsule.launch(Capsule.java:1268)
	at Capsule.main0(Capsule.java:399)
	at Capsule.main(Capsule.java:379)
Caused by: capsule.org.eclipse.aether.resolution.DependencyResolutionException: Failed to collect dependencies at org.multiverse:multiverse-core:jar:0.7.0
	at org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies(DefaultRepositorySystem.java:387)
	at capsule.DependencyManager.resolve0(DependencyManager.java:377)
	... 16 more
Caused by: capsule.org.eclipse.aether.collection.DependencyCollectionException: Failed to collect dependencies at org.multiverse:multiverse-core:jar:0.7.0
	at org.eclipse.aether.internal.impl.DefaultDependencyCollector.collectDependencies(DefaultDependencyCollector.java:291)
	at org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies(DefaultRepositorySystem.java:341)
	... 17 more
Caused by: capsule.org.eclipse.aether.resolution.ArtifactDescriptorException: Failed to read artifact descriptor for org.multiverse:multiverse-core:jar:0.7.0
	at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.loadPom(DefaultArtifactDescriptorReader.java:282)
	at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.readArtifactDescriptor(DefaultArtifactDescriptorReader.java:198)
	at org.eclipse.aether.internal.impl.DefaultDependencyCollector.resolveCachedArtifactDescriptor(DefaultDependencyCollector.java:535)
	at org.eclipse.aether.internal.impl.DefaultDependencyCollector.getArtifactDescriptorResult(DefaultDependencyCollector.java:519)
	at org.eclipse.aether.internal.impl.DefaultDependencyCollector.processDependency(DefaultDependencyCollector.java:409)
	at org.eclipse.aether.internal.impl.DefaultDependencyCollector.processDependency(DefaultDependencyCollector.java:363)
	at org.eclipse.aether.internal.impl.DefaultDependencyCollector.process(DefaultDependencyCollector.java:351)
	at org.eclipse.aether.internal.impl.DefaultDependencyCollector.collectDependencies(DefaultDependencyCollector.java:254)
	... 18 more
Caused by: capsule.org.eclipse.aether.resolution.ArtifactResolutionException: Could not transfer artifact org.multiverse:multiverse-core:pom:0.7.0 from/to central (https://repo1.maven.org/maven2/): No locks available
	at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:444)
	at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:246)
	at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifact(DefaultArtifactResolver.java:223)
	at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.loadPom(DefaultArtifactDescriptorReader.java:267)
	... 25 more
Caused by: capsule.org.eclipse.aether.transfer.ArtifactTransferException: Could not transfer artifact org.multiverse:multiverse-core:pom:0.7.0 from/to central (https://repo1.maven.org/maven2/): No locks available
	at org.eclipse.aether.connector.basic.ArtifactTransportListener.transferFailed(ArtifactTransportListener.java:43)
	at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run(BasicRepositoryConnector.java:355)
	at org.eclipse.aether.util.concurrency.RunnableErrorForwarder$1.run(RunnableErrorForwarder.java:67)
	at org.eclipse.aether.connector.basic.BasicRepositoryConnector$DirectExecutor.execute(BasicRepositoryConnector.java:581)
	at org.eclipse.aether.connector.basic.BasicRepositoryConnector.get(BasicRepositoryConnector.java:249)
	at org.eclipse.aether.internal.impl.DefaultArtifactResolver.performDownloads(DefaultArtifactResolver.java:520)
	at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:421)
	... 28 more
Caused by: java.io.IOException: No locks available
	at sun.nio.ch.FileDispatcherImpl.lock0(Native Method)
	at sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96)
	at sun.nio.ch.FileChannelImpl.lock(FileChannelImpl.java:1262)
	at io.takari.filemanager.internal.DefaultFileManager$LockFile.open(DefaultFileManager.java:380)
	at io.takari.filemanager.internal.DefaultFileManager$LockFile.lock(DefaultFileManager.java:313)
	at io.takari.filemanager.internal.DefaultFileManager$IndirectFileLock.lock(DefaultFileManager.java:243)
	at io.takari.filemanager.internal.DefaultFileManager$IndirectFileLock.open(DefaultFileManager.java:199)
	at io.takari.filemanager.internal.DefaultFileManager$IndirectFileLock.lock(DefaultFileManager.java:147)
	at io.takari.filemanager.internal.DefaultFileManager.move(DefaultFileManager.java:642)
	at io.takari.aether.concurrency.LockingFileProcessor.move(LockingFileProcessor.java:58)
	at org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask(BasicRepositoryConnector.java:472)
	at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run(BasicRepositoryConnector.java:350)
	... 33 more
Unable to initialize nextflow environment

Environment

• Nextflow version: NA
• Java version: openjdk version "16.0.1" 2021-04-20
  OpenJDK Runtime Environment (build 16.0.1+9-24)
  OpenJDK 64-Bit Server VM (build 16.0.1+9-24, mixed mode, sharing)
• Operating system: linux
• Bash version: GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu)

Additional context

Does it have something to do with this repo?
https://repo1.maven.org/maven2/org/multiverse/multiverse-core/0.7.0/

What I've tried:

1. Changing networks (which I suppose wouldn't help since its an HPC ...)
2. Using older version of Java
3. Attempting to download the "nextflow-all" from the github repo. However, a similar error is given after giving it execution permission and then trying to run nextflow.
4. Deleting any old hidden versions (previous installations) of nextflow.

[pditommaso]

Perhaps something has changed with our system?

We don't manage your system!

[kenminsoo]

So it's probably an issue with the environment?

[bentsherman]

Hi @kenminsoo , yes I think so. I recommend you experiment with different Java versions or distributions if you can. You might be able to use SDKMAN to install Java to your home directory, see these docs for more info. I would speak to your sys admins as well if the problem persists.

[kenminsoo]

Alright, thank you! I'll try that and put a note if it ends up working.