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      "date": "2026-07-07T06:08:03.000Z",
      "arch": "x86_64",
      "commit": "e1fc232267caadd3e517e61b86fb85a336d9ac23",
      "fileid": "https://r2.ropensci.org/cde0c2a67ae1282621b2dba419da5efd071d0d4e2af7d9b3b31e0c263b94d217",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28845067683"
    }
  ]
}