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

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edmundmiller opened this issue Sep 18, 2024 · 11 comments · May be fixed by #6286
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Caused by: java.nio.channels.OverlappingFileLockException #6664

edmundmiller opened this issue Sep 18, 2024 · 11 comments · May be fixed by #6286
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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

@ewels
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ewels commented Nov 8, 2024

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

@edmundmiller edmundmiller linked a pull request Nov 14, 2024 that will close this issue
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Use new nf-test features nf-core/modules
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@ewels @maxulysse @apeltzer @edmundmiller @SPPearce