- 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 '