[Bioc-devel] AnnotationHub corrupted cache on nebbiolo1

[Kern, Lori]

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:
      �g
   1. �|�wMoonlight2R::DMA(...) at test-DMA.R:14:1
   2.   �|�wMoonlight2R::LiftMAF(Infile = mut_only, Current_Build = "GRCh38")
   3.     �|�wAnnotationHub::AnnotationHub()
   4.       �|�wAnnotationHub::.Hub(...)
   5.         �|�wAnnotationHub:::.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
�V a part of the Danish Cancer Society

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