Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [198s/337s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(babelmixr2)
  Loading required package: nlmixr2
  Loading required package: nlmixr2data
  > 
  > test_check("babelmixr2")
  i parameter labels from comments will be replaced by 'label()'
  i writing monolix files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  using C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
  
  v done
  rxode2 2.1.0 using 3 threads (see ?getRxThreads)
    no cache: create with `rxCreateCache()`
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 27560
  i monolix parameter history integrated into fit object
  i writing monolix files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  using C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
  
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 27560
  i monolix parameter history needs expoted charts, please export charts
  i writing monolix files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 27560
  i monolix parameter history needs expoted charts, please export charts
  i writing monolix files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 27560
  i monolix parameter history needs expoted charts, please export charts
  i parameter labels from comments will be replaced by 'label()'
  i writing monolix files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  using C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
  
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 33192
  i monolix parameter history needs expoted charts, please export charts
  i writing monolix files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  using C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
  
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 202448
  i monolix parameter history needs expoted charts, please export charts
  i writing monolix files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  using C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
  
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 26856
  i monolix parameter history needs expoted charts, please export charts
  i writing monolix files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  using C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
  
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 12992
  i monolix parameter history needs expoted charts, please export charts
  i load saved nlmixr2 object
  i monolix parameter history integrated into fit object
  i load saved nlmixr2 object
  i writing monolix files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 12992
  i monolix parameter history integrated into fit object
  i change initial estimate of `prop.err` to `15`
  i writing monolix files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 12992
  i monolix parameter history integrated into fit object
  i change initial estimate of `prop.err` to `7`
  i writing monolix files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 12992
  i monolix parameter history integrated into fit object
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  using C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
  
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 1336
  > compress parHist in nlmixr2 object, save 1344
  
  
   WARNINGS AND ERRORS (IF ANY) FOR PROBLEM    1
  
   (WARNING  2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.
  
  
  0MINIMIZATION TERMINATED
   DUE TO ROUNDING ERRORS (ERROR=134)
   NO. OF FUNCTION EVALUATIONS USED:     1088
   NO. OF SIG. DIGITS UNREPORTABLE
  0PARAMETER ESTIMATE IS NEAR ITS BOUNDARY
  
  nonmem model: 'pk.turnover.emax3-nonmem/pk.turnover.emax3.nmctl'
  > terminated with rounding errors, can force nlmixr2/rxode2 to read with nonmemControl(readRounding=TRUE)
  Error : nonmem minimization not successful
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 27560
  > compress parHist in nlmixr2 object, save 4928
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > calculate jacobian
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > calculate sensitivities
  [====|====|====|====|====|====|====|====|====|====] 0:00:01 
  
  > calculate d(f)/d(eta)
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > finding duplicate expressions in inner model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in inner model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling inner model...
  using C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
  
  v done
  > finding duplicate expressions in FD model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in FD model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  using C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
  
  v done
  > compiling events FD model...
  using C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
  
  v done
  calculating covariance matrix
  [====|====|====|====|====|====|====|====|====|====] 0:00:13 
  > compress origData in nlmixr2 object, save 27560
  Updated original fit object f
  ! remove between subject variability `eta.ka`
  ! remove between subject variability `eta.emax`
  Error in dimnames(.omega) <- list(.n, .n) : 
    length of 'dimnames' [1] not equal to array extent
  i parameter labels from comments will be replaced by 'label()'
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====
  ==|====|====|====|====|====|====] 0:00:00 
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 33192
  > compress parHist in nlmixr2 object, save 2256
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > finding duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > optimizing duplicate expressions in EBE model...
  [====|====|====|====|====|====|====|====|====|====] 0:00:00 
  
  > compiling EBE model...
  v done
  > Calculating residuals/tables
  v done
  > compress origData in nlmixr2 object, save 12992
  > compress parHist in nlmixr2 object, save 2664
  ! remove between subject variability `eta.MTT`
  Error in dimnames(.omega) <- list(.n, .n) : 
    length of 'dimnames' [1] not equal to array extent
  i writing nonmem files
  i done
  Error in bblDatToPknca(model = env$ui, data = rawData) : 
    no dosing rows (EVID = 1 or 4) detected
  Error : no rows in event table or input data
  Error in nlmixr2Est(env, ...) : 
    Could not detect DV assignment for unit conversion
  [ FAIL 2 | WARN 3 | SKIP 1 | PASS 314 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-as-nlmixr2.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-nonmem-read.R:93:5'): warfarin NONMEM reading ──────────────────
  Error: length of 'dimnames' [1] not equal to array extent
  Backtrace:
      ▆
   1. ├─withr::with_tempdir(...) at test-nonmem-read.R:60:3
   2. │ └─withr::with_dir(tmp, code)
   3. │   └─base::force(code)
   4. ├─... %>% ... at test-nonmem-read.R:93:5
   5. ├─nlmixr2est::nlmixr(...)
   6. └─nlmixr2est:::nlmixr2.rxUi(...)
   7.   └─nlmixr2est:::nlmixr2Est0(.env)
  ── Error ('test-nonmem-read.R:212:5'): wbc NONMEM reading ──────────────────────
  Error: length of 'dimnames' [1] not equal to array extent
  Backtrace:
      ▆
   1. ├─withr::with_tempdir(...) at test-nonmem-read.R:199:3
   2. │ └─withr::with_dir(tmp, code)
   3. │   └─base::force(code)
   4. ├─... %>% ... at test-nonmem-read.R:212:5
   5. └─nlmixr2::nlmixr2(., nlmixr2data::wbcSim, "nonmem", control = nonmemControl(modelName = "wbc2"))
   6.   ├─nlmixr2est::nlmixr2(...)
   7.   └─nlmixr2est:::nlmixr2.rxUi(...)
   8.     └─nlmixr2est:::nlmixr2Est0(.env)
  
  [ FAIL 2 | WARN 3 | SKIP 1 | PASS 314 ]
  Error: Test failures
  Execution halted