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Caused by: java.nio.channels.OverlappingFileLockException

Open edmundmiller opened this issue 1 year ago • 8 comments

When tests are run in CI or locally using conda the tests fail with:

  Caused by:
    java.nio.channels.OverlappingFileLockException

Caused by: https://github.com/nf-core/modules/pull/6600

Previous issues

  • https://github.com/nf-core/modules/pull/5802#issuecomment-2333658568
  • https://nextflow.slack.com/archives/C0477AS31T5/p1718212230419419

edmundmiller avatar Sep 18 '24 16:09 edmundmiller

Options I see

  • Switch CI to micromamba
  • Nextflow work around for the conda bug
  • #6286 might work for some reason?

edmundmiller avatar Sep 18 '24 16:09 edmundmiller

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.

edmundmiller avatar Sep 18 '24 17:09 edmundmiller

Sounds perfect to me

maxulysse avatar Sep 18 '24 17:09 maxulysse

Yep, lets give it a go, we wanted to move to that anyway.

SPPearce avatar Sep 18 '24 22:09 SPPearce

Any news on this fella? ;-) #6662 sits there and waiting :-P

apeltzer avatar Sep 23 '24 10:09 apeltzer

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

SPPearce avatar Sep 23 '24 18:09 SPPearce

https://github.com/nf-core/modules/pull/6685

maxulysse avatar Sep 24 '24 09:09 maxulysse

https://github.com/nf-core/modules/pull/6798

maxulysse avatar Oct 18 '24 15:10 maxulysse

Why did this not break when we wrote everything in the conda line before environment ymls?

edmundmiller avatar Nov 07 '24 17:11 edmundmiller

Now hoping that we can fix this in Nextflow: https://github.com/nextflow-io/nextflow/issues/5485

ewels avatar Nov 08 '24 12:11 ewels

Fixed in https://github.com/nextflow-io/nextflow/pull/5489 - any additional testing by folks very welcome!

ewels avatar Nov 08 '24 16:11 ewels

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

edmundmiller avatar Nov 18 '24 16:11 edmundmiller

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

maxulysse avatar Nov 18 '24 16:11 maxulysse