[Bioc-devel] AnnotationHub corrupted cache on nebbiolo1

[Matteo Tiberti]

Hi,

I can confirm it did clean up – thanks for your help!

Cheers

Matteo Tiberti

Danish Cancer Institute
Strandboulevarden 49
DK-2100 Copenhagen
Telephone: +45 35 25 73 07
– a part of the Danish Cancer Society

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From: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Date: Monday, 11 March 2024 at 17.16
To: bioc-devel using r-project.org <bioc-devel using r-project.org>, Matteo Tiberti <tiberti using cancer.dk>
Subject: Re: AnnotationHub corrupted cache on nebbiolo1
I noticed that as well and just did the necessary steps to clean the cache. I expect this to clean up on the next build.




Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Matteo Tiberti via Bioc-devel <bioc-devel using r-project.org>
Sent: Monday, March 11, 2024 12:11 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] AnnotationHub corrupted cache on nebbiolo1

Dear BioC developers,

We are getting a strange test fail for our Moonlight2R package when tests are run on nebbiolo1 (Linux) only:

ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: Corrupt Cache: index file
    See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache
    cache: /home/biocbuild/.cache/R/AnnotationHub
    filename: annotationhub.index.rds
  Backtrace:
      ▆
   1. └─Moonlight2R::DMA(...) at test-DMA.R:14:1
   2.   └─Moonlight2R::LiftMAF(Infile = mut_only, Current_Build = "GRCh38")
   3.     └─AnnotationHub::AnnotationHub()
   4.       └─AnnotationHub::.Hub(...)
   5.         └─AnnotationHub:::.db_create_index(hub)

This doesn’t happen to us when testing locally, so we were wondering if there’s any problem on the builder or is it anything we can fix ourselves?

Many thanks

Matteo Tiberti

Danish Cancer Institute
Strandboulevarden 49
DK-2100 Copenhagen
Telephone: +45 35 25 73 07
– a part of the Danish Cancer Society

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