* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/whirl.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.3.1
* using session charset: UTF-8
* checking for file ‘whirl/DESCRIPTION’ ... OK
* this is package ‘whirl’ version ‘0.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘whirl’ can be installed ... [8s/13s] OK
See 'https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/whirl-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [1s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/6s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [7s/8s] ERROR
  Running ‘testthat.R’ [7s/8s]
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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11s/14s] OK
* checking PDF version of manual ... [6s/7s] OK
* DONE
Status: 1 ERROR
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 1:40