* using log directory ‘/srv/hornik/tmp/CRAN_pretest/mkin.Rcheck’
* using R Under development (unstable) (2025-02-12 r87715)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.6 (1+b1)
    Debian flang-new version 19.1.6 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘mkin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mkin’ version ‘1.2.9’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/15s] 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 ‘mkin’ can be installed ... [7s/7s] 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 ... [12s/12s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] 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/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [42s/72s] ERROR
  Running ‘testthat.R’ [42s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mkin)
  > 
  > test_check("mkin")
  [ FAIL 1 | WARN 0 | SKIP 31 | PASS 123 ]
  
  ══ Skipped tests (31) ══════════════════════════════════════════════════════════
  • On CRAN (30): '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_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 ════════════════════════════════════════════════════════════════
  ── Error ('test_saemix_parent.R:168:3'): illparms finds a single random effect that is ill-defined ──
  Error in `.check_ncores(cores)`: 32 simultaneous processes spawned
  Backtrace:
      ▆
   1. └─mkin::mmkin("SFO", ds_sfo, error_model = "tc", quiet = TRUE) at test_saemix_parent.R:168:3
   2.   ├─base::system.time(...)
   3.   └─parallel::mclapply(...)
   4.     └─parallel:::.check_ncores(cores)
  
  [ FAIL 1 | WARN 0 | SKIP 31 | 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-errmod-with-focus-c-tc.svg
  • plot/plot-errmod-with-focus-d-obs-eigen.svg
  • plot/plot-res-for-focus-c.svg
  • 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 ... [20s/21s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR