Running ‘spelling.R’
  Running ‘testthat.R’ [261s/272s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(babelmixr2)
  > 
  > test_check("babelmixr2")
  Error in loadNamespace(x) : there is no package called 'qs'
  Error in loadNamespace(x) : there is no package called 'qs'
  Error in loadNamespace(x) : there is no package called 'qs'
  Error in loadNamespace(x) : there is no package called 'qs'
  Error in loadNamespace(x) : there is no package called 'qs'
  Error in loadNamespace(x) : there is no package called 'qs'
  Error in loadNamespace(x) : there is no package called 'qs'
  i mu2 item: Rx_pow_di(WT, 2)
  i writing monolix files
  i done
  i run Monolix manually and rerun nlmixr()
  i mu2 item: Rx_pow_di(WT, 2)
  i leaving alone monolix files because 'monolixTest-monolix.txt' is present
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v 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
  Error in loadNamespace(x) : there is no package called 'qs'
  Error : nonmem minimization not successful
  Error in loadNamespace(x) : there is no package called 'qs'
  Error in loadNamespace(x) : there is no package called 'qs'
  Error in loadNamespace(x) : there is no package called 'qs'
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  i writing nonmem files
  i done
  i only exported NONMEM control stream/data
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  i writing nonmem files
  i done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  i mu2 item: Rx_pow_di(WT, 2)
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  i writing nonmem files
  i done
  i only exported NONMEM control stream/data
  i mu2 item: Rx_pow_di(WT, 2)
  > loading into symengine environment...
  > pruning branches (`if`/`else`) of full model...
  v done
  i only exported NONMEM control stream/data
  Error in bblDatToPknca(model = env$ui, data = rawData, rxControl = rxControl) : 
    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 11 | WARN 4 | SKIP 10 | PASS 259 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (9): 'test-as-nlmixr2.R:8:3', 'test-as-nlmixr2.R:66:3',
    'test-bioavil-works.R:2:3', 'test-convert.R:2:3', 'test-convert.R:35:3',
    'test-convert.R:215:3', 'test-convert.R:229:3', 'test-fmeMcmc.R:4:3',
    'test-psuedoOptim.R:3:3'
  • empty test (1):
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-monolix-read.R:62:7'): test monolix reading for 2019, 2020, and 2021 ──
  Error: there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─withr::with_tempdir(...) at test-monolix-read.R:60:5
    2. │ └─withr::with_dir(tmp, code)
    3. │   └─base::force(code)
    4. └─babelmixr2 (local) .nlmixr(...) at test-monolix-read.R:62:7
    5.   ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24
    6.   │ └─base::withCallingHandlers(...)
    7.   ├─base::suppressMessages(nlmixr2est::nlmixr(...))
    8.   │ └─base::withCallingHandlers(...)
    9.   ├─nlmixr2est::nlmixr(...)
   10.   └─nlmixr2est:::nlmixr2.function(...)
   11.     └─nlmixr2est:::nlmixr2Est0(.env)
  ── Error ('test-monolix-read.R:151:5'): test more nlmixr2/monolix features ─────
  Error: there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─withr::with_tempdir(...) at test-monolix-read.R:149:3
    2. │ └─withr::with_dir(tmp, code)
    3. │   └─base::force(code)
    4. └─babelmixr2 (local) .nlmixr(...) at test-monolix-read.R:151:5
    5.   ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24
    6.   │ └─base::withCallingHandlers(...)
    7.   ├─base::suppressMessages(nlmixr2est::nlmixr(...))
    8.   │ └─base::withCallingHandlers(...)
    9.   ├─nlmixr2est::nlmixr(...)
   10.   └─nlmixr2est:::nlmixr2.function(...)
   11.     └─nlmixr2est:::nlmixr2Est0(.env)
  ── Error ('test-monolix-read.R:187:5'): test Monolix pheno ─────────────────────
  Error: there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─withr::with_tempdir(...) at test-monolix-read.R:183:3
    2. │ └─withr::with_dir(tmp, code)
    3. │   └─base::force(code)
    4. └─babelmixr2 (local) .nlmixr(pheno, nlmixr2data::pheno_sd, "monolix", control = monolixControl(modelName = "pheno")) at test-monolix-read.R:187:5
    5.   ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24
    6.   │ └─base::withCallingHandlers(...)
    7.   ├─base::suppressMessages(nlmixr2est::nlmixr(...))
    8.   │ └─base::withCallingHandlers(...)
    9.   ├─nlmixr2est::nlmixr(...)
   10.   └─nlmixr2est:::nlmixr2.function(...)
   11.     └─nlmixr2est:::nlmixr2Est0(.env)
  ── Error ('test-monolix-read.R:322:5'): pbpk mavoglurant ───────────────────────
  Error: there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─withr::with_tempdir(...) at test-monolix-read.R:320:3
    2. │ └─withr::with_dir(tmp, code)
    3. │   └─base::force(code)
    4. └─babelmixr2 (local) .nlmixr(pbpk, nlmixr2data::mavoglurant, "monolix", control = monolixControl(modelName = "pbpk")) at test-monolix-read.R:322:5
    5.   ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24
    6.   │ └─base::withCallingHandlers(...)
    7.   ├─base::suppressMessages(nlmixr2est::nlmixr(...))
    8.   │ └─base::withCallingHandlers(...)
    9.   ├─nlmixr2est::nlmixr(...)
   10.   └─nlmixr2est:::nlmixr2.function(...)
   11.     └─nlmixr2est:::nlmixr2Est0(.env)
  ── Error ('test-monolix-read.R:386:5'): nimo test ──────────────────────────────
  Error: there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─withr::with_tempdir(...) at test-monolix-read.R:384:3
    2. │ └─withr::with_dir(tmp, code)
    3. │   └─base::force(code)
    4. ├─base::suppressWarnings(.nlmixr2(nimo, tmp, "monolix", control = monolixControl(modelName = "nimo"))) at test-monolix-read.R:386:5
    5. │ └─base::withCallingHandlers(...)
    6. └─babelmixr2 (local) .nlmixr2(nimo, tmp, "monolix", control = monolixControl(modelName = "nimo"))
    7.   ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24
    8.   │ └─base::withCallingHandlers(...)
    9.   ├─base::suppressMessages(nlmixr2est::nlmixr(...))
   10.   │ └─base::withCallingHandlers(...)
   11.   ├─nlmixr2est::nlmixr(...)
   12.   └─nlmixr2est:::nlmixr2.function(...)
   13.     └─nlmixr2est:::nlmixr2Est0(.env)
  ── Error ('test-monolix-read.R:458:5'): Monolix wbc ────────────────────────────
  Error: there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─withr::with_tempdir(...) at test-monolix-read.R:455:3
    2. │ └─withr::with_dir(tmp, code)
    3. │   └─base::force(code)
    4. ├─base::suppressWarnings(...) at test-monolix-read.R:458:5
    5. │ └─base::withCallingHandlers(...)
    6. └─babelmixr2 (local) .nlmixr2(wbc, nlmixr2data::wbcSim, "monolix", control = monolixControl(modelName = "wbc"))
    7.   ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24
    8.   │ └─base::withCallingHandlers(...)
    9.   ├─base::suppressMessages(nlmixr2est::nlmixr(...))
   10.   │ └─base::withCallingHandlers(...)
   11.   ├─nlmixr2est::nlmixr(...)
   12.   └─nlmixr2est:::nlmixr2.function(...)
   13.     └─nlmixr2est:::nlmixr2Est0(.env)
  ── Error ('test-monolix-read.R:493:5'): Monolix wbc test 2 ─────────────────────
  Error: there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─withr::with_tempdir(...) at test-monolix-read.R:490:3
    2. │ └─withr::with_dir(tmp, code)
    3. │   └─base::force(code)
    4. ├─wbc %>% ini(prop.err = 15) %>% ... at test-monolix-read.R:493:5
    5. └─babelmixr2 (local) .nlmixr2(., nlmixr2data::wbcSim, "monolix", control = monolixControl(modelName = "x"))
    6.   ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24
    7.   │ └─base::withCallingHandlers(...)
    8.   ├─base::suppressMessages(nlmixr2est::nlmixr(...))
    9.   │ └─base::withCallingHandlers(...)
   10.   ├─nlmixr2est::nlmixr(...)
   11.   └─nlmixr2est:::nlmixr2.rxUi(...)
   12.     └─nlmixr2est:::nlmixr2Est0(.env)
  ── Failure ('test-nonmem-pred.R:26:5'): nonmem $pred model ─────────────────────
  Expected `nlmixr2est::nlmixr(ipredWang2007, dat, "nonmem")` not to throw any errors.
  Actually got a <simpleError> with message:
    there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─withr::with_tempdir(...) at test-nonmem-pred.R:24:3
    2. │ └─withr::with_dir(tmp, code)
    3. │   └─base::force(code)
    4. ├─testthat::expect_error(...) at test-nonmem-pred.R:26:5
    5. │ └─testthat:::expect_condition_matching_(...)
    6. │   └─testthat:::quasi_capture(...)
    7. │     ├─testthat (local) .capture(...)
    8. │     │ └─base::withCallingHandlers(...)
    9. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   10. ├─nlmixr2est::nlmixr(ipredWang2007, dat, "nonmem")
   11. └─nlmixr2est:::nlmixr2.function(ipredWang2007, dat, "nonmem")
   12.   └─nlmixr2est:::nlmixr2Est0(.env)
  ── Error ('test-nonmem-read.R:72:5'): warfarin NONMEM reading ──────────────────
  Error: there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─withr::with_tempdir(...) at test-nonmem-read.R:62:3
    2. │ └─withr::with_dir(tmp, code)
    3. │   └─base::force(code)
    4. └─babelmixr2 (local) .nlmixr(...) at test-nonmem-read.R:72:5
    5.   ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-nonmem-read.R:1:24
    6.   │ └─base::withCallingHandlers(...)
    7.   ├─base::suppressMessages(nlmixr2est::nlmixr(...))
    8.   │ └─base::withCallingHandlers(...)
    9.   ├─nlmixr2est::nlmixr(...)
   10.   └─nlmixr2est:::nlmixr2.function(...)
   11.     └─nlmixr2est:::nlmixr2Est0(.env)
  ── Error ('test-nonmem-read.R:134:5'): pheno NONMEM reading ────────────────────
  Error: there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─withr::with_tempdir(...) at test-nonmem-read.R:132:3
    2. │ └─withr::with_dir(tmp, code)
    3. │   └─base::force(code)
    4. └─babelmixr2 (local) .nlmixr(pheno, nlmixr2data::pheno_sd, "nonmem", control = nonmemControl(modelName = "pheno")) at test-nonmem-read.R:134:5
    5.   ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-nonmem-read.R:1:24
    6.   │ └─base::withCallingHandlers(...)
    7.   ├─base::suppressMessages(nlmixr2est::nlmixr(...))
    8.   │ └─base::withCallingHandlers(...)
    9.   ├─nlmixr2est::nlmixr(...)
   10.   └─nlmixr2est:::nlmixr2.function(...)
   11.     └─nlmixr2est:::nlmixr2Est0(.env)
  ── Error ('test-nonmem-read.R:208:5'): wbc NONMEM reading ──────────────────────
  Error: there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─withr::with_tempdir(...) at test-nonmem-read.R:201:3
    2. │ └─withr::with_dir(tmp, code)
    3. │   └─base::force(code)
    4. └─babelmixr2 (local) .nlmixr2(...) at test-nonmem-read.R:208:5
    5.   ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-nonmem-read.R:1:24
    6.   │ └─base::withCallingHandlers(...)
    7.   ├─base::suppressMessages(nlmixr2est::nlmixr(...))
    8.   │ └─base::withCallingHandlers(...)
    9.   ├─nlmixr2est::nlmixr(...)
   10.   └─nlmixr2est:::nlmixr2.function(...)
   11.     └─nlmixr2est:::nlmixr2Est0(.env)
  
  [ FAIL 11 | WARN 4 | SKIP 10 | PASS 259 ]
  Error:
  ! Test failures.
  Execution halted