Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(whirl)
  > 
  > test_check("whirl")
  
  [ FAIL 1 | WARN 1 | SKIP 17 | PASS 105 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • On CRAN (10): 'test-custom_logging.R:55:3', 'test-run.R:27:3',
    'test-run.R:70:3', 'test-run.R:81:3', 'test-run.R:89:3', 'test-run.R:106:3',
    'test-run.R:130:3', 'test-run.R:147:3', 'test-strace.R:11:3',
    'test-whirl_queue.R:9:3'
  • Quarto is not available (7): 'test-examples.R:2:3',
    'test-internal_run.R:2:3', 'test-mdformats.R:2:3', 'test-run.R:13:3',
    'test-run.R:61:3', 'test-util_queue_summary.R:8:3',
    'test-whirl_r_session.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-biocompute.R:3:3'): Biocompute object created correctly ────────
  Error in `gzfile(file, "rb")`: cannot open the connection
  Backtrace:
       ▆
    1. └─whirl::run(input = input_yml, out_formats = NULL, summary_file = NULL) at test-biocompute.R:3:3
    2.   └─whirl:::internal_run(...)
    3.     └─queue$run(scripts = files, tag = name)
    4.       └─whirl:::wq_run(scripts, tag, self)
    5.         └─self$push(scripts = scripts, tag = tag)$wait()
    6.           └─whirl:::wq_wait(self, private, timeout)
    7.             └─self$poll(50)
    8.               └─whirl:::wq_poll(self, private, timeout)
    9.                 └─whirl:::wq_next_step(self, private, i)
   10.                   └─session$log_finish()
   11.                     └─whirl:::wrs_log_finish(self, private, super)
   12.                       └─base::readRDS(file.path(private$wd, "result.rds"))
   13.                         └─base::gzfile(file, "rb")
  
  [ FAIL 1 | WARN 1 | SKIP 17 | PASS 105 ]
  Error: Test failures
  Execution halted