• using R version 4.5.1 (2025-06-13)
• using platform: x86_64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
• 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 ... [7s/10s] OK See the install log 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 ... [1s/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/7s] 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/10s] ERROR   Running ‘testthat.R’ [7s/10s] 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/15s] OK
• checking PDF version of manual ... [6s/13s] OK
• DONE Status: 1 ERROR
• using check arguments '--no-clean-on-error '