List of race-condition errors related to BiocFileCache

[HenrikBengtsson]

Background

During the Bioc Technical Advisor Board (TAB) call on 2025-01-02, I asked about race-condition errors related to BiocFileCache. Others reported that they see that at times to, and in order to attach the problem, we need to come up with some reproducible example.

Reproducible examples for race conditions is hard, but the first step towards that is to collect enough breadcrumbs to have something to work with. I'll use this issue to paste in various warnings and error messages that I observe when I run reverse package dependency checks in parallel. Hopefully, that'll eventually give us something to work with.

Examples of BiocFileCache race-condition errors

Package 'atena'

Warning: Corrupt Cache: index file
  cache: /c4/home/henrik/.cache/R/AnnotationHub
  multiple entries for filename: annotationhub.index.rds
  Attempting to clean cache and regenerate

Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': ℹ In argument: `rpath = unname(bfcrpath(x, rids = rids))`.
Caused by error in `bfcrpath()`:
! all(rids %in% bfcrid(x)) is not TRUE
Calls: annotaTEs ... .Call -> unname -> bfcrpath -> bfcrpath -> stopifnot

This was with BiocFileCache 2.14.0 on R 4.4.2 for Linux.