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      "fileid": "https://r2.ropensci.org/84444ca266a0659fe9480b6eafd8ea2572bcf6b4d7a97e5bd7e7c9c730f5d3cf",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007259448"
    }
  ]
}