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Caused by: java.nio.channels.OverlappingFileLockException #6664

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edmundmiller opened this issue Sep 18, 2024 · 13 comments · Fixed by #6286 or #7019
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Caused by: java.nio.channels.OverlappingFileLockException #6664

edmundmiller opened this issue Sep 18, 2024 · 13 comments · Fixed by #6286 or #7019
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@edmundmiller
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edmundmiller commented Sep 18, 2024 •
edited by ewels
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When tests are run in CI or locally using conda the tests fail with:

  Caused by:
    java.nio.channels.OverlappingFileLockException

Caused by: #6600

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@edmundmiller edmundmiller added the bug Something isn't working label Sep 18, 2024
@edmundmiller edmundmiller pinned this issue Sep 18, 2024
@edmundmiller
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Options I see

@edmundmiller
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Alright confirmed that https://github.com/nf-core/modules/actions/runs/10926649144 doesn't seem to fail from an initial test standpoint, AND it's forward progress so it has my vote.

@maxulysse
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Sounds perfect to me

@edmundmiller edmundmiller linked a pull request Sep 18, 2024 that will close this issue
Use new nf-test features #6286
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@SPPearce
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Yep, lets give it a go, we wanted to move to that anyway.

@atrigila atrigila mentioned this issue Sep 20, 2024
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@apeltzer
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Any news on this fella? ;-) #6662 sits there and waiting :-P

@SPPearce
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Yep, I think we give this a go and revert if everything breaks.

@maxulysse
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#6685

@maxulysse maxulysse mentioned this issue Oct 16, 2024
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#6798

@sateeshperi sateeshperi mentioned this issue Oct 22, 2024
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@famosab famosab mentioned this issue Nov 1, 2024
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@edmundmiller
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Why did this not break when we wrote everything in the conda line before environment ymls?

@ewels ewels mentioned this issue Nov 8, 2024
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ewels commented Nov 8, 2024

Now hoping that we can fix this in Nextflow: nextflow-io/nextflow#5485

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ewels commented Nov 8, 2024

Fixed in nextflow-io/nextflow#5489 - any additional testing by folks very welcome!

@edmundmiller edmundmiller mentioned this issue Nov 14, 2024
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https://nfcore.slack.com/archives/CE6P95170/p1731943264640149

Nextflow v24.10.1 just released!

Basically this issue had been there when Nextflow tried to make concurrent conda / mamba environments for some time, but only (a) when using an environment.yml file that (b) had no name attribute. As such, it was rarely / if ever seen. Until we recently removed all name attributes from all nf-core #modules 🙄
Updating Nextflow to this patch release should solve this issue if you had hit it.
@ewels

Closing this but leaving it pinned in case anyones runs into this error

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I would have kept it open until we push up the minimal NXF version with a tools release

edmundmiller added a commit to nf-core/setup-nextflow that referenced this issue Nov 18, 2024
@edmundmiller
ci: Test 24.10.1
6f500db 
Because of nf-core/modules#6664 it's a little
critical
edmundmiller added a commit that referenced this issue Nov 18, 2024
@edmundmiller
ci(#6664): Bump all Nextflow versions to 24.10.1
6664af5
edmundmiller added a commit that referenced this issue Nov 18, 2024
@edmundmiller
ci(#6664): Bump all Nextflow versions to 24.10.1
af43264
@edmundmiller edmundmiller mentioned this issue Nov 18, 2024
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edmundmiller added a commit that referenced this issue Nov 19, 2024
@edmundmiller
Bump Nextflow Versions (#7019)
c0ef8c3 
* ci(renovate): Add custom VERSION updates in GitHub actions

https://docs.renovatebot.com/presets-customManagers/#custommanagersgithubactionsversions

* ci(#6664): Bump all Nextflow versions to 24.10.1

* ci: Add renovate comments to version in actions
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Use new nf-test features nf-core/modules
Bump Nextflow Versions nf-core/modules
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@ewels @maxulysse @apeltzer @edmundmiller @SPPearce