* using log directory ‘/srv/hornik/tmp/CRAN_pretest/whirl.Rcheck’
* using R Under development (unstable) (2025-07-07 r88391)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3)
    Debian flang-new version 19.1.7 (3)
* running under: Debian GNU/Linux 13 (trixie)
* using session charset: UTF-8
* checking for file ‘whirl/DESCRIPTION’ ... OK
* this is package ‘whirl’ version ‘0.3.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/6s] NOTE
Maintainer: ‘Aksel Thomsen <oath@novonordisk.com>’

Found the following (possibly) invalid URLs:
  URL: https://wiki.biocomputeobject.org (moved to https://wiki.biocomputeobject.org/Main_Page)
    From: man/write_biocompute.Rd
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* 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 ... NOTE
Non-standard files/directories found at top level:
  ‘dev.R’ ‘log_schema.json’
* 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 ... [283s/201s] ERROR
  Running ‘testthat.R’ [283s/201s]
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 2 | WARN 0 | SKIP 13 | PASS 131 ]
  
  ══ Skipped tests (13) ══════════════════════════════════════════════════════════
  • On CRAN (11): 'test-biocompute.R:14:3', 'test-custom_logging.R:55:3',
    'test-examples.R:26:3', '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-whirl_queue.R:9:3'
  • On Linux (1): 'test-strace.R:54:3'
  • TODO: Consistency for results and that all output formats are created
    correctly (1): 'test-output.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-strace.R:28:7'): strace works ────────────────────────────────
  any(grepl(x = test$write$file, pattern = "mtcars.rds")) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  Backtrace:
      ▆
   1. ├─withr::with_tempdir(...) at test-strace.R:14:3
   2. │ └─withr::with_dir(tmp, code)
   3. │   └─base::force(code)
   4. └─testthat::expect_true(any(grepl(x = test$write$file, pattern = "mtcars.rds"))) at test-strace.R:28:7
  ── Failure ('test-strace.R:35:7'): strace works ────────────────────────────────
  any(grepl(x = test$write$file, pattern = "mtcars.rds")) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  Backtrace:
      ▆
   1. ├─withr::with_tempdir(...) at test-strace.R:14:3
   2. │ └─withr::with_dir(tmp, code)
   3. │   └─base::force(code)
   4. └─testthat::expect_true(any(grepl(x = test$write$file, pattern = "mtcars.rds"))) at test-strace.R:35:7
  
  [ FAIL 2 | WARN 0 | SKIP 13 | PASS 131 ]
  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 ... [2s/2s] 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, 2 NOTEs