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24.10.x causes StackOverflowError #265

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drernie opened this issue Nov 19, 2024 · 5 comments · May be fixed by #268
Open

24.10.x causes StackOverflowError #265

drernie opened this issue Nov 19, 2024 · 5 comments · May be fixed by #268
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drernie commented Nov 19, 2024 

./nextflow run nf-core/fetchngs -plugins nf-quilt  -profile test,docker --input ../nf-quilt/wf/ids.csv --outdir s3://quilt-ernest-staging/nf-quilt/fetchngs

cat ../nf-quilt/wf/ids.csv
SRR9984183

Nov-18 17:17:06.585 [main] INFO org.pf4j.AbstractPluginManager - Plugin '[email protected]' resolved
ERROR nextflow.quilt.jep.QuiltPackage - toJson.error
groovy.lang.MissingMethodException: No signature of method: java.lang.Integer.multiply() is applicable for argument types: (ConfigObject) values: [[:]]
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drernie commented Nov 19, 2024

That error is benign (caught). The real crasher seems to be java.lang.StackOverflowError in writeNextflowMetadata[workflow]

Nov-18 18:06:25.242 [main] DEBUG nextflow.quilt.QuiltProduct - writeNextflowMetadata[workflow]: nf-quilt/workflow.json
Nov-18 18:06:25.242 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "runName" [28]
Nov-18 18:06:25.242 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "scriptId" [46]
Nov-18 18:06:25.242 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "scriptFile" [50]
Nov-18 18:06:25.242 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "scriptName" [21]
Nov-18 18:06:25.242 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "repository" [18]
Nov-18 18:06:25.242 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "commitId" [18]
Nov-18 18:06:25.242 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "revision" [18]
Nov-18 18:06:25.242 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "start" [46]
Nov-18 18:06:25.243 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "complete" [46]
Nov-18 18:06:25.243 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "duration" [17]
Nov-18 18:06:25.244 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "container" [17]
Nov-18 18:06:25.244 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "commandLine" [201]
Nov-18 18:06:25.244 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "nextflow" [256]
Nov-18 18:06:25.244 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "success" [18]
Nov-18 18:06:25.244 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "projectDir" [42]
Nov-18 18:06:25.244 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "projectName" [21]
Nov-18 18:06:25.244 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "launchDir" [42]
Nov-18 18:06:25.244 [main] DEBUG nextflow.quilt.jep.QuiltPackage - QuiltPackage.toJson: "outputDir" [50]
Nov-18 18:06:25.259 [main] DEBUG nextflow.Session - Session aborted -- Cause: java.lang.StackOverflowError
Nov-18 18:06:25.271 [main] DEBUG nextflow.Session - 
Thread[pool-2-thread-8,5,main]

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drernie commented Nov 19, 2024 •
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Ah! When I update from 24.09.2-edge to 24.10.0.5928 I can reproduce the error:

ERROR ~ Unexpected error [StackOverflowError]

Before, I could not. I wonder if 24.10.1 fixes it...
version 24.10.1 build 5930
Update: No, it does not.

@drernie drernie changed the title JSON ERROR ~ Unknown method invocation multiply on Integer type 24.10.x causes StackOverflowError Nov 19, 2024
@drernie drernie self-assigned this Nov 26, 2024
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drernie commented Nov 27, 2024

NXF_VER=24.10.1 ../nextflow/nextflow run nf-core/fetchngs -plugins nf-quilt -profile test,docker --input wf/ids.csv --outdir s3://quilt-ernest-staging/nf-quilt/fetchngs

@drernie drernie linked a pull request Nov 27, 2024 that will close this issue
fix #265: 24.10.x causes stackoverflowerror #268
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@drernie drernie linked a pull request Nov 27, 2024 that will close this issue
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drernie commented Nov 27, 2024

Interestingly, 24.09 uses "workDir" instead of 'outputDir'
workflow.json

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drernie commented Dec 6, 2024

Error still occurs on 24.10.1

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fix #265: 24.10.x causes stackoverflowerror quiltdata/nf-quilt
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