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It's current state is: startFailed #52

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nick-youngblut opened this issue Nov 11, 2024 · 10 comments
Open

It's current state is: startFailed #52

nick-youngblut opened this issue Nov 11, 2024 · 10 comments

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@nick-youngblut
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nick-youngblut commented Nov 11, 2024 •
edited
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None of the Nextflow extension features are working.

I'm getting the following Runtime Status:

Screenshot 2024-11-11 at 11 48 48 AM

Re-installing the extension does not help.

I'm using v1.0.0 of the extension on a MacOS Sonoma 14.7 (23H124)

java --version
openjdk 11.0.25 2024-10-15
OpenJDK Runtime Environment Homebrew (build 11.0.25+0)
OpenJDK 64-Bit Server VM Homebrew (build 11.0.25+0, mixed mode)
@ameintjes
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The minimum Java version is now "Java 17 (or later, up to 23)"

@nvnieuwk
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I also have this issue when trying to load the extension on a remote session:

Stacktrace 
2024-11-12 12:15:06.021 [info] Extension host with pid 2647756 started
2024-11-12 12:15:06.021 [error] Error: EEXIST: file already exists, open '/user/gent/448/vsc44804/.local/share/code-server/User/workspaceStorage/-6392ac68/vscode.lock'
2024-11-12 12:15:06.023 [info] Lock '/user/gent/448/vsc44804/.local/share/code-server/User/workspaceStorage/-6392ac68/vscode.lock': Could not acquire lock, checking if the file is stale.
2024-11-12 12:15:06.025 [info] Lock '/user/gent/448/vsc44804/.local/share/code-server/User/workspaceStorage/-6392ac68/vscode.lock': The lock does not look stale, elapsed: 714 ms, giving up.
2024-11-12 12:15:06.029 [error] Error: EEXIST: file already exists, open '/user/gent/448/vsc44804/.local/share/code-server/User/workspaceStorage/-6392ac68-1/vscode.lock'
2024-11-12 12:15:06.029 [info] Lock '/user/gent/448/vsc44804/.local/share/code-server/User/workspaceStorage/-6392ac68-1/vscode.lock': Could not acquire lock, checking if the file is stale.
2024-11-12 12:15:06.029 [info] Lock '/user/gent/448/vsc44804/.local/share/code-server/User/workspaceStorage/-6392ac68-1/vscode.lock': The lock does not look stale, elapsed: 356 ms, giving up.
2024-11-12 12:15:06.032 [info] Lock '/user/gent/448/vsc44804/.local/share/code-server/User/workspaceStorage/-6392ac68-2/vscode.lock': Lock acquired.
2024-11-12 12:15:06.391 [info] ExtensionService#_doActivateExtension vscode.emmet, startup: false, activationEvent: 'onLanguage'
2024-11-12 12:15:06.392 [info] ExtensionService#_doActivateExtension nextflow.nextflow, startup: false, activationEvent: 'onLanguage:nextflow-config'
2024-11-12 12:15:06.504 [info] ExtensionService#_doActivateExtension vscode.git-base, startup: true, activationEvent: '*', root cause: vscode.git
2024-11-12 12:15:06.543 [info] ExtensionService#_doActivateExtension vscode.git, startup: true, activationEvent: '*'
2024-11-12 12:15:06.543 [info] ExtensionService#_doActivateExtension vscode.github, startup: true, activationEvent: '*'
2024-11-12 12:15:06.782 [info] Eager extensions activated
2024-11-12 12:15:06.782 [info] ExtensionService#_doActivateExtension vscode.debug-auto-launch, startup: false, activationEvent: 'onStartupFinished'
2024-11-12 12:15:06.782 [info] ExtensionService#_doActivateExtension vscode.merge-conflict, startup: false, activationEvent: 'onStartupFinished'
2024-11-12 12:15:07.618 [info] ExtensionService#_doActivateExtension vscode.github-authentication, startup: false, activationEvent: 'onAuthenticationRequest:github'
2024-11-12 12:15:07.656 [error] Error: Pending response rejected since connection got disposed
	at Object.dispose (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:17797:27)
	at Object.dispose (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3880:35)
	at LanguageClient.handleConnectionClosed (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3471:34)
	at LanguageClient.handleConnectionClosed (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:12410:22)
	at closeHandler (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3458:18)
	at CallbackList.invoke (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:17935:39)
	at Emitter.fire (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:17997:36)
	at closeHandler (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:16944:26)
	at CallbackList.invoke (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:17935:39)
	at Emitter.fire (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:17997:36)
	at StreamMessageWriter.fireClose (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:18882:27)
	at Socket.<anonymous> (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:18914:42)
	at Socket.emit (node:events:519:28)
	at Pipe.<anonymous> (node:net:338:12)
2024-11-12 12:15:07.657 [error] Error: Client is not running and can't be stopped. It's current state is: starting
	at LanguageClient.shutdown (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3280:19)
	at LanguageClient.stop (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3251:21)
	at LanguageClient.stop (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:12380:22)
	at LanguageClient.doInitialize (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3233:27)
	at async LanguageClient.start (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3088:13)
2024-11-12 12:15:07.764 [error] Error: Client is not running and can't be stopped. It's current state is: startFailed
	at LanguageClient.shutdown (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3280:19)
	at LanguageClient.stop (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3251:21)
	at LanguageClient.stop (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:12380:22)
	at LanguageClient.doInitialize (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3233:27)
	at async LanguageClient.start (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3088:13)
2024-11-12 12:15:07.887 [error] Error: Client is not running and can't be stopped. It's current state is: startFailed
	at LanguageClient.shutdown (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3280:19)
	at LanguageClient.stop (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3251:21)
	at LanguageClient.stop (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:12380:22)
	at LanguageClient.doInitialize (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3233:27)
	at async LanguageClient.start (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3088:13)
2024-11-12 12:15:07.996 [error] Error: Client is not running and can't be stopped. It's current state is: startFailed
	at LanguageClient.shutdown (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3280:19)
	at LanguageClient.stop (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3251:21)
	at LanguageClient.stop (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:12380:22)
	at LanguageClient.doInitialize (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3233:27)
	at async LanguageClient.start (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3088:13)
2024-11-12 12:15:08.107 [error] Error: Client is not running and can't be stopped. It's current state is: startFailed
	at LanguageClient.shutdown (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3280:19)
	at LanguageClient.stop (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3251:21)
	at LanguageClient.stop (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:12380:22)
	at LanguageClient.doInitialize (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3233:27)
	at async LanguageClient.start (/kyukon/home/gent/448/vsc44804/.local/share/code-server/extensions/nextflow.nextflow-1.0.0-universal/extension.js:3088:13)
2024-11-12 12:15:08.926 [debug] ProxyResolver#loadSystemCertificates count 150
2024-11-12 12:15:08.927 [debug] ProxyResolver#loadSystemCertificates parse error Error: error:0480006C:PEM routines::no start line
	at new X509Certificate (node:internal/crypto/x509:119:21)
	at /kyukon/home/apps/RHEL8/cascadelake-ib/software/code-server/4.93.1/lib/vscode/node_modules/@vscode/proxy-agent/out/index.js:518:48
	at Array.filter (<anonymous>)
	at /kyukon/home/apps/RHEL8/cascadelake-ib/software/code-server/4.93.1/lib/vscode/node_modules/@vscode/proxy-agent/out/index.js:516:26
	at Generator.next (<anonymous>)
	at fulfilled (/kyukon/home/apps/RHEL8/cascadelake-ib/software/code-server/4.93.1/lib/vscode/node_modules/@vscode/proxy-agent/out/index.js:32:58)
2024-11-12 12:15:08.957 [debug] ProxyResolver#loadSystemCertificates count filtered 149
2024-11-12 12:15:08.958 [debug] ProxyResolver#resolveProxy unconfigured https://mobile.events.data.microsoft.com/OneCollector/1.0?cors=true&content-type=application/x-json-stream DIRECT 
2024-11-12 12:15:09.214 [debug] ProxyResolver#resolveProxy unconfigured https://mobile.events.data.microsoft.com/OneCollector/1.0?cors=true&content-type=application/x-json-stream DIRECT

@nick-youngblut
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nick-youngblut commented Nov 12, 2024 •
edited
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Thanks @ameintjes

A caveat of the extension is that it assumes Nextflow is installed in the user's base environment. Many users want to separate software into isolated environments. I've always installed Nextflow via conda, and so AFAIK the extension will not utilize java & nextflow installed in a conda env (I don't see anything in the settings).

More generally, it would help if the README and the blog post on the extension updates pointed out that Java v17 or higher are required, especially given that some users have Nextflow installed via conda, so the extension just "won't work" in that situation.

Lastly, it would be helpful if the error messages in the extension's Runtime Status window showed more helpful error messages (e.g., "Java v17-23 not found").

@nick-youngblut
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I've installed java and nextflow in my base (os-level) environment:

openjdk 23.0.1 2024-10-15
OpenJDK Runtime Environment Homebrew (build 23.0.1)
OpenJDK 64-Bit Server VM Homebrew (build 23.0.1, mixed mode, sharing)
nextflow -version 

      N E X T F L O W
      version 24.10.0 build 5928
      created 27-10-2024 18:36 UTC (11:36 PDT)
      cite doi:10.1038/nbt.3820
      http://nextflow.io

...and I'm still getting the same error:

Screenshot 2024-11-12 at 8 31 52 AM

Re-installing the extension and/or reloading the VS Code window does not help.

@bentsherman
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Try setting the "Nextflow > Java > Home" extension setting to an explicit Java path (should be the path containing the bin directory)

I'm beginning to suspect that Java installed via homebrew is not being auto-detected for some reason

@nvnieuwk
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That's what fixed the issue for us yesterday! Thank you!

@bentsherman
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@nvnieuwk are you using the homebrew install of Java?

@nvnieuwk
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Our issue was mainly that we were running it on a remote SSH connection with our HPC. The default Java version there is Java 8 which was too low.

I don't know in what way Java was installed on the HPC tho

@bentsherman
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I haven't investigated the SSH setup too much but I'm glad you got it working. My understanding is that you would install the Nextflow extension through your local VS Code editor but install it to "SSH Remote" instead of "Local", is that right?

@nvnieuwk
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I haven't investigated the SSH setup too much but I'm glad you got it working. My understanding is that you would install the Nextflow extension through your local VS Code editor but install it to "SSH Remote" instead of "Local", is that right?

Yes that's what we did. It was actually a browser code editor but that should work basically the same as a remote SSH

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@nick-youngblut @ameintjes @bentsherman @nvnieuwk