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-boun...@r-project.org> on behalf of Matteo Tiberti
via Bioc-devel <bioc-devel@r-project.org>
Sent: Monday, March 11, 2024 12:11 PM
To: bioc-devel@r-project.org <bioc-devel@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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