* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/mkin.Rcheck’
* using R Under development (unstable) (2026-10-28 r90786)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
    GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-10-30 04:10:08 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘mkin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mkin’ version ‘1.2.10’
* 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 ‘mkin’ can be installed ... [12s/14s] 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [20s/22s] OK
* checking Rd files ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/22s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [77s/160s]
 [77s/160s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mkin)
  > 
  > test_check("mkin")
  Saving _problems/test_nlme-52.R
  Saving _problems/test_nlme-63.R
  Saving _problems/test_nlme-68.R
  [ FAIL 3 | WARN 1 | SKIP 32 | PASS 123 ]
  
  ══ Skipped tests (32) ══════════════════════════════════════════════════════════
  • On CRAN (31): 'test_FOCUS_D_UBA_expertise.R:32:3',
    'test_FOCUS_chi2_error_level.R:23:3', 'test_FOCUS_chi2_error_level.R:33:3',
    'test_analytical.R:4:3', 'test_analytical.R:51:3', 'test_aw.R:4:3',
    'test_deSolve.R:4:3', 'test_dmta.R:5:3', 'test_dmta.R:82:3',
    'test_error_models.R:4:3', 'test_error_models.R:10:3',
    'test_error_models.R:16:3', 'test_error_models.R:55:3', 'test_mhmkin.R:5:3',
    'test_mixed.R:18:3', 'test_mixed.R:26:3', 'test_mixed.R:52:3',
    'test_mixed.R:91:3', 'test_mixed.R:118:3', 'test_mkinds.R:12:3',
    'test_multistart.R:4:3', 'test_nafta.R:7:3', 'test_nafta.R:29:3',
    'test_nlme.R:98:3', 'test_plot.R:4:3', 'test_saemix_parent.R:5:3',
    'test_schaefer07_complex_case.R:5:3',
    'test_synthetic_data_for_UBA_2014.R:5:3',
    'test_synthetic_data_for_UBA_2014.R:24:3', 'test_tests.R:38:3',
    'test_twa.R:4:3'
  • This still takes almost 2.5 minutes although we do not solve ODEs (1):
    'test_saemix_parent.R:143:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_nlme.R:52:3'): nlme_function works correctly ─────────────────
  Expected `m_nlme_raw$coefficients` to equal `m_nlme_mkin$coefficients`.
  Differences:
  Component "fixed": Mean relative difference: 2.576135e-08
  Component "random": Component "ds": Mean relative difference: 5.732652e-06
  ── Failure ('test_nlme.R:63:3'): nlme_function works correctly ─────────────────
  Expected `m_nlme_raw_2$coefficients` to equal `m_nlme_mmkin$coefficients`.
  Differences:
  Component "random": Component "ds": Mean relative difference: 2.873268e-07
  ── Failure ('test_nlme.R:67:3'): nlme_function works correctly ─────────────────
  Expected `anova_nlme["m_nlme_mkin", "AIC"]` to equal `anova_nlme["m_nlme_raw", "AIC"]`.
  Differences:
  1/1 mismatches
  [1] 291 - 291 == 2.34e-05
  
  [ FAIL 3 | WARN 1 | SKIP 32 | PASS 123 ]
  Deleting unused snapshots: 'multistart/llhist-for-dfop-sfo-fit.svg',
  'multistart/llhist-for-sfo-fit.svg',
  'multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg',
  'multistart/parplot-for-dfop-sfo-fit.svg',
  'multistart/parplot-for-sfo-fit.svg', 'nafta/nafta-sop-appendix-b.svg',
  'nafta/plot-nafta-analysis.svg', 'plot/mixed-model-fit-for-mmkin-object.svg',
  'plot/mixed-model-fit-for-nlme-object.svg',
  'plot/mixed-model-fit-for-saem-object-with-saemix-transformations.svg',
  'plot/mkinerrplot-for-focus-c-sfo.svg',
  'plot/mkinfit-plot-for-focus-c-with-defaults.svg',
  'plot/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg',
  'plot/mkinfit-plot-for-focus-c-with-sep-true.svg',
  'plot/mkinparplot-for-focus-c-sfo.svg', 'plot/mmkin-plot-for-focus-c.svg',
  'plot/mmkin-plot-for-sfo-focus-c-and-d.svg', 'plot/plot-err-for-focus-d.svg',
  …, 'plot/plot-res-for-focus-c.svg', and 'plot/plot-res-for-focus-d.svg'
  Error:
  ! Test failures.
  Execution halted
  Error while shutting down parallel: unable to terminate some child processes
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [35s/44s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/localhost/ripley/R/packages/tests-MKL/mkin.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:41.35, 209.72 + 17.87