* using log directory ‘/srv/hornik/tmp/CRAN/mmrm.Rcheck’
* using R Under development (unstable) (2023-09-18 r85166)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (13)
    GNU Fortran (Debian 13.2.0-3) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘mmrm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mmrm’ version ‘0.3.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/7s] NOTE
Maintainer: ‘Daniel Sabanes Bove <daniel.sabanes_bove@roche.com>’

Possibly misspelled words in DESCRIPTION:
  al (30:55)
  et (30:52)

Size of tarball: 5220184 bytes
* 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 ‘mmrm’ can be installed ... [214s/214s] OK
* used C++ compiler: ‘Debian clang version 16.0.6 (15)’
* checking C++ specification ... NOTE
  Specified C++14: please drop specification unless essential
* 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 R 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 whether startup messages can be suppressed ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : 
  invalid non-character version specification 'x' (type: logical)
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] OK
* checking Rd files ... [2s/2s] 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 ... NOTE
Documented arguments not in \usage in documentation object 'h_mmrm_tmb_fit':
  ‘data’ ‘weights’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [19s/19s] ERROR
  Running ‘testthat.R’ [19s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > pkg_name <- "mmrm"
  > library(pkg_name, character.only = TRUE)
  > testthat::test_check(pkg_name)
  Error in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : 
    invalid non-character version specification 'x' (type: logical)
  In addition: Warning message:
  In checkMatrixPackageVersion() : Package version inconsistency detected.
  TMB was built with Matrix version 1.6.1
  Current Matrix version is 1.6.1.1
  Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
  [ FAIL 8 | WARN 0 | SKIP 42 | PASS 1815 ]
  
  ══ Skipped tests (42) ══════════════════════════════════════════════════════════
  • On CRAN (42): 'test-between-within.R:29:3', 'test-empirical.R:6:3',
    'test-empirical.R:12:3', 'test-empirical.R:18:3', 'test-fit.R:214:3',
    'test-fit.R:274:3', 'test-fit.R:370:3', 'test-kenwardroger.R:4:3',
    'test-kenwardroger.R:9:3', 'test-kenwardroger.R:14:3',
    'test-kenwardroger.R:19:3', 'test-kenwardroger.R:24:3',
    'test-kenwardroger.R:29:3', 'test-kenwardroger.R:34:3',
    'test-kenwardroger.R:39:3', 'test-kenwardroger.R:44:3',
    'test-kenwardroger.R:49:3', 'test-kenwardroger.R:54:3',
    'test-kenwardroger.R:59:3', 'test-kenwardroger.R:64:3',
    'test-kenwardroger.R:69:3', 'test-kenwardroger.R:74:3',
    'test-kenwardroger.R:79:3', 'test-kenwardroger.R:84:3',
    'test-kenwardroger.R:89:3', 'test-kenwardroger.R:98:3',
    'test-kenwardroger.R:107:3', 'test-kenwardroger.R:348:3',
    'test-kenwardroger.R:356:3', 'test-kenwardroger.R:367:3',
    'test-kenwardroger.R:377:3', 'test-kenwardroger.R:389:3',
    'test-mmrm-methods.R:66:3', 'test-mmrm-methods.R:79:3',
    'test-mmrm-methods.R:85:3', 'test-mmrm-methods.R:91:3',
    'test-mmrm-methods.R:97:3', 'test-mmrm-methods.R:104:3',
    'test-testing.R:69:3', 'test-testing.R:84:3', 'test-tmb-methods.R:711:3',
    'test-tmb-methods.R:718:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fit.R:248:3'): h_summarize_all_fits works when some list elements are try-error objects ──
  `result` (`actual`) not equal to `expected` (`expected`).
  
  `actual$warnings[[3]]` is a character vector ('Model convergence problem: NEW_X.')
  `expected$warnings[[3]]` is NULL
  
    `actual$log_liks`: -1693.22493558 NA -2155.28688402
  `expected$log_liks`: -1693.22493559 NA -1693.22493812
  
  `actual$converged`:   TRUE FALSE FALSE
  `expected$converged`: TRUE FALSE TRUE 
  ── Error ('test-interop-parsnip.R:6:3'): parsnip works with a formula for the `covariance` specification outside of `fit()` ──
  Error in `parsnip::set_engine(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"), 
      covariance = ~us(AVISIT | USUBJID))`: Engine 'mmrm' is not supported for `linear_reg()`. See `show_engines('linear_reg')`.
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test-interop-parsnip.R:6:2
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─parsnip::fit(...)
   10. ├─parsnip::set_engine(...)
   11. └─parsnip:::set_engine.model_spec(...)
   12.   └─parsnip:::check_spec_mode_engine_val(...)
   13.     └─rlang::abort(...)
  ── Error ('test-interop-parsnip.R:21:3'): parsnip works with a `as.cov_struct` for the `covariance` specification outside of `fit()` ──
  Error in `parsnip::set_engine(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"), 
      covariance = as.cov_struct(~us(AVISIT | USUBJID)))`: Engine 'mmrm' is not supported for `linear_reg()`. See `show_engines('linear_reg')`.
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test-interop-parsnip.R:21:2
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─parsnip::fit(...)
   10. ├─parsnip::set_engine(...)
   11. └─parsnip:::set_engine.model_spec(...)
   12.   └─parsnip:::check_spec_mode_engine_val(...)
   13.     └─rlang::abort(...)
  ── Error ('test-interop-parsnip.R:36:3'): parsnip works with the covariance structure in the formula in `fit()` ──
  Error in `parsnip::set_engine(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))`: Engine 'mmrm' is not supported for `linear_reg()`. See `show_engines('linear_reg')`.
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test-interop-parsnip.R:36:2
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─parsnip::fit(...)
   10. ├─parsnip::set_engine(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))
   11. └─parsnip:::set_engine.model_spec(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))
   12.   └─parsnip:::check_spec_mode_engine_val(...)
   13.     └─rlang::abort(...)
  ── Error ('test-interop-parsnip.R:49:3'): parsnip works with predict ───────────
  Error in `parsnip::set_engine(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))`: Engine 'mmrm' is not supported for `linear_reg()`. See `show_engines('linear_reg')`.
  Backtrace:
      ▆
   1. ├─parsnip::fit(...) at test-interop-parsnip.R:49:2
   2. ├─parsnip::set_engine(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))
   3. └─parsnip:::set_engine.model_spec(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))
   4.   └─parsnip:::check_spec_mode_engine_val(...)
   5.     └─rlang::abort(...)
  ── Error ('test-interop-parsnip.R:60:3'): parsnip allows to pass additional arguments to predict with type `raw` via `opts` ──
  Error in `parsnip::set_engine(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))`: Engine 'mmrm' is not supported for `linear_reg()`. See `show_engines('linear_reg')`.
  Backtrace:
      ▆
   1. ├─parsnip::fit(...) at test-interop-parsnip.R:60:2
   2. ├─parsnip::set_engine(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))
   3. └─parsnip:::set_engine.model_spec(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))
   4.   └─parsnip:::check_spec_mode_engine_val(...)
   5.     └─rlang::abort(...)
  ── Error ('test-interop-parsnip.R:83:3'): parsnip works with augment and using `new_data` ──
  Error in `parsnip::set_engine(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))`: Engine 'mmrm' is not supported for `linear_reg()`. See `show_engines('linear_reg')`.
  Backtrace:
      ▆
   1. ├─parsnip::fit(...) at test-interop-parsnip.R:83:2
   2. ├─parsnip::set_engine(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))
   3. └─parsnip:::set_engine.model_spec(parsnip::linear_reg(), "mmrm", control = mmrm_control(method = "Satterthwaite"))
   4.   └─parsnip:::check_spec_mode_engine_val(...)
   5.     └─rlang::abort(...)
  ── Error ('test-interop.R:6:3'): check_package_version warns when version is not compatible ──
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: logical)
  Backtrace:
      ▆
   1. ├─testthat::expect_true(check_package_version("fakePackage")) at test-interop.R:6:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─mmrm:::check_package_version("fakePackage")
   5.   └─base::lapply(ver, numeric_version, strict = FALSE)
   6.     └─base (local) FUN(X[[i]], ...)
   7.       └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  
  [ FAIL 8 | WARN 0 | SKIP 42 | PASS 1815 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [18s/18s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘algorithm.Rmd’ using rmarkdown
--- finished re-building ‘algorithm.Rmd’

--- re-building ‘between_within.Rmd’ using rmarkdown
--- finished re-building ‘between_within.Rmd’

--- re-building ‘coef_vcov.Rmd’ using rmarkdown
--- finished re-building ‘coef_vcov.Rmd’

--- re-building ‘covariance.Rmd’ using rmarkdown
--- finished re-building ‘covariance.Rmd’

--- re-building ‘empirical_wls.Rmd’ using rmarkdown
--- finished re-building ‘empirical_wls.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 21-25 [unnamed-chunk-23] (./subsections/_intro-tidymodels.Rmd)

Quitting from lines 68-77 [unnamed-chunk-7] (./subsections/_intro-tidymodels.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Engine 'mmrm' is not supported for `linear_reg()`. See `show_engines('linear_reg')`.
--- failed re-building ‘introduction.Rmd’

--- re-building ‘kenward.Rmd’ using rmarkdown
--- finished re-building ‘kenward.Rmd’

--- re-building ‘methodological_introduction.Rmd’ using rmarkdown
--- finished re-building ‘methodological_introduction.Rmd’

--- re-building ‘mmrm_review_methods.Rmd’ using rmarkdown
--- finished re-building ‘mmrm_review_methods.Rmd’

--- re-building ‘package_structure.Rmd’ using rmarkdown
--- finished re-building ‘package_structure.Rmd’

--- re-building ‘predict.Rmd’ using rmarkdown
--- finished re-building ‘predict.Rmd’

--- re-building ‘satterthwaite.Rmd’ using rmarkdown
--- finished re-building ‘satterthwaite.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted

* 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: 2 ERRORs, 4 NOTEs