* using log directory ‘/srv/hornik/tmp/CRAN_pretest/whirl.Rcheck’ * using R Under development (unstable) (2025-08-24 r88696) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3+b1) Debian flang-new version 19.1.7 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘whirl/DESCRIPTION’ ... OK * this is package ‘whirl’ version ‘0.3.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/5s] OK * 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 ... [5s/5s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... 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 ... [7s/7s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 ... [332s/244s] ERROR Running ‘testthat.R’ [332s/244s] 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") Error in `rs_call(self, private, func, args, package)`: ! R session busy --- Backtrace: 1. testthat::test_check("whirl") 2. testthat::test_dir("testthat", package = package, reporter = reporter, ... 3. testthat:::test_files(test_dir = path, test_paths = test_paths, test_package = pack... 4. testthat:::test_files_serial(test_dir = test_dir, test_package = test_package, ... 5. testthat::with_reporter(reporters$multi, lapply(test_paths, test_one_file, ... 6. base::tryCatch(code, testthat_abort_reporter = function(cnd) { ... 7. base::tryCatchList(expr, classes, parentenv, handlers) 8. base::tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. base::doTryCatch(return(expr), name, parentenv, handler) 10. base::lapply(test_paths, test_one_file, env = env, desc = desc, error_call = e... 11. local FUN(X[[i]], ...) 12. testthat::source_file(path, env = env(env), desc = desc, error_call = error_call) 13. testthat:::test_code(test = NULL, code = exprs, env = env, reporter = get_reporter(... 14. base::tryCatch(withCallingHandlers({ ... 15. base::tryCatchList(expr, classes, parentenv, handlers) 16. base::tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), ... 17. base::doTryCatch(return(expr), name, parentenv, handler) 18. base::tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 19. base::tryCatchOne(expr, names, parentenv, handlers[[1L]]) 20. base::doTryCatch(return(expr), name, parentenv, handler) 21. base::withCallingHandlers({ ... 22. base::eval(code, test_env) 23. base::eval(code, test_env) 24. testthat::test_that("interactive whirl R session components not tested in run", ... at test-whirl_r_session.R:1:1 25. testthat:::test_code(desc, code, env = parent.frame(), reporter = reporter) 26. base::tryCatch(withCallingHandlers({ ... 27. base::tryCatchList(expr, classes, parentenv, handlers) 28. base::tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), ... 29. base::doTryCatch(return(expr), name, parentenv, handler) 30. base::tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 31. base::tryCatchOne(expr, names, parentenv, handlers[[1L]]) 32. base::doTryCatch(return(expr), name, parentenv, handler) 33. base::withCallingHandlers({ ... 34. base::eval(code, test_env) 35. base::eval(code, test_env) 36. base::gc() at test-whirl_r_session.R:32:3 37. base::(function (e) ... 38. .subset2(e, ".__enclos_env__")$private$finalize() 39. whirl:::wrs_finalize(self, private, super) 40. super$run(func = setwd, args = list(dir = getwd())) 41. callr:::rs_run(self, private, func, args, package) 42. callr:::rs_run_with_output(self, private, func, args, package) 43. self$call(func, args, package) 44. callr:::rs_call(self, private, func, args, package) 45. callr:::throw(new_error("R session busy")) [ FAIL 1 | WARN 0 | SKIP 15 | PASS 147 ] ══ Skipped tests (15) ══════════════════════════════════════════════════════════ • On CRAN (14): 'test-biocompute.R:16:3', 'test-custom_logging.R:55:3', 'test-examples.R:26:3', 'test-python.R:2:3', 'test-python.R:44:3', 'test-run.R:33:3', 'test-run.R:76:3', 'test-run.R:87:3', 'test-run.R:95:3', 'test-run.R:112:3', 'test-run.R:134:3', 'test-run.R:151:3', 'test-strace.R:42:3', 'test-whirl_queue.R:9:3' • On Linux (1): 'test-strace.R:82:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-util_queue_summary.R:14:3'): Summary tibble is created successfully ── Error in `wrs_check_status(self, private, super)`: Could not run '/srv/hornik/tmp/CRAN_pretest/whirl.Rcheck/tests/testthat/scripts/py_success.py' i Error from `quarto::quarto_render()`: processing file: log.qmd Error in utils::read.table(text = x) : no lines available in input Calls: .main ... -> read_python -> parse_pip_list -> Quitting from log.qmd:82-122 [Status] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `utils::read.table()`: ! no lines available in input --- Backtrace: x 1. +-global .main() 2. | \-execute(...) 3. | \-rmarkdown::render(...) 4. | \-knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 5. | \-knitr:::process_file(text, output) 6. | +-xfun:::handle_error(...) 7. | +-base::withCallingHandlers(...) 8. | \-knitr:::process_group(group) 9. | \-knitr:::call_block(x) 10. | \-knitr:::block_exec(params) 11. | \-knitr:::eng_r(options) 12. | +-knitr:::in_input_dir(...) 13. | | \-knitr:::in_dir(input_dir(), expr) 14. | \-knitr (local) evaluate(...) 15. | \-evaluate::evaluate(...) 16. | +-base::withRestarts(...) 17. | | \-base (local) withRestartList(expr, restarts) 18. | | +-base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 19. | | | \-base (local) doWithOneRestart(return(expr), restart) 20. | | \-base (local) withRestartList(expr, restarts[-nr]) 21. | | \-base (local) withOneRestart(expr, restarts[[1L]]) 22. | | \-base (local) doWithOneRestart(return(expr), restart) 23. | +-evaluate:::with_handlers(...) 24. | | +-base::eval(call) 25. | | | \-base::eval(call) 26. | | \-base::withCallingHandlers(...) 27. | +-base::withVisible(eval(expr, envir)) 28. | \-base::eval(expr, envir) 29. | \-base::eval(expr, envir) 30. \-whirl:::read_info(...) 31. \-whirl:::read_python(...) 32. \-whirl:::parse_pip_list(readRDS(pip_list)) 33. \-utils::read.table(text = x) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted Backtrace: ▆ 1. └─q$run(test_script(c("success.R", "py_success.py"))) at test-util_queue_summary.R:14:3 2. └─whirl:::wq_run(scripts, tag, self, private) 3. └─self$push(scripts = scripts, tag = tag)$wait() 4. └─whirl:::wq_wait(self, private, timeout) 5. └─self$poll(50) 6. └─whirl:::wq_poll(self, private, timeout) 7. └─private$.workers$session[[i]]$check_status() 8. └─whirl:::wrs_check_status(self, private, super) 9. └─cli::cli_abort(...) 10. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 15 | PASS 147 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR