Package: corporaexplorer
Check: tests
New result: ERROR
    Running ‘testthat.R’ [3s/3s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(corporaexplorer)
    > 
    > test_check("corporaexplorer")
    [ FAIL 1 | WARN 0 | SKIP 2 | PASS 0 ]
    
    ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
    • On CRAN (2): 'test_explorer_app.R:8:3', 'test_extractor_app.R:8:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_prep_func.R:12:3'): prepare_data() works ─────────────────────
    `test_obj` not equal to corporaexplorer::test_data.
    Component "original_matrix": Component "data_dok": Attributes: < Component "index": Attributes: < Component "__i": Attributes: < Modes: list, NULL > > >
    Component "original_matrix": Component "data_dok": Attributes: < Component "index": Attributes: < Component "__i": Attributes: < Lengths: 6, 0 > > >
    Component "original_matrix": Component "data_dok": Attributes: < Component "index": Attributes: < Component "__i": Attributes: < names for target but not for current > > >
    Component "original_matrix": Component "data_dok": Attributes: < Component "index": Attributes: < Component "__i": Attributes: < current is not list-like > > >
    
    [ FAIL 1 | WARN 0 | SKIP 2 | PASS 0 ]
    Error: Test failures
    Execution halted

Package: do
Check: whether package can be installed
New result: ERROR
  Installation failed.

Package: lgrExtra
Check: tests
New result: ERROR
    Running ‘testthat.R’ [6s/6s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(lgrExtra)
    > 
    > test_check("lgrExtra")
    [ FAIL 6 | WARN 3 | SKIP 6 | PASS 56 ]
    
    ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
    Error in `[.data.table`(dd, , sel, with = FALSE) : 
      showProgress must be TRUE or FALSE
    Calls: <Anonymous> ... [ -> [.data.table -> stopf -> raise_condition -> signal
    • '/var/log/syslog' is not readable (1): 'test_AppenderSyslog.R:24:3'
    • Cannot establish connection (3): 'test_AppenderDbi.R:123:5',
      'test_AppenderDbi.R:123:5', 'test_AppenderDbi.R:123:5'
    • SQLite doesn't support schemas (2): 'test_AppenderDbi.R:219:7',
      'test_AppenderDbi.R:250:7'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_AppenderDt.R:20:3'): AppenderDt: appending multiple rows works ──
    Error in ``[.data.table`(private$.data, !is.na(private$.data$.id), )`: showProgress must be TRUE or FALSE
    Backtrace:
        ▆
     1. ├─testthat::expect_true(data.table::is.data.table(app$dt)) at test_AppenderDt.R:20:3
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─data.table::is.data.table(app$dt)
     5. └─lgrExtra (local) `<fn>`()
     6.   ├─private$.data[!is.na(private$.data$.id), ]
     7.   └─data.table:::`[.data.table`(...)
     8.     └─data.table:::stopf("%s must be TRUE or FALSE", "showProgress")
     9.       └─data.table:::raise_condition(...)
    ── Error ('test_AppenderDt.R:57:3'): AppenderDt: works with list columns ───────
    Error in ``[.data.table`(private$.data, !is.na(private$.data$.id), )`: showProgress must be TRUE or FALSE
    Backtrace:
         ▆
      1. ├─testthat::expect_true(is.null(app$data$list[[1]])) at test_AppenderDt.R:57:3
      2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
      3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
      4. ├─lgrExtra (local) `<fn>`()
      5. │ └─base::as.data.frame(self$dt)
      6. └─lgrExtra (local) `<fn>`()
      7.   ├─private$.data[!is.na(private$.data$.id), ]
      8.   └─data.table:::`[.data.table`(...)
      9.     └─data.table:::stopf("%s must be TRUE or FALSE", "showProgress")
     10.       └─data.table:::raise_condition(...)
    ── Error ('test_AppenderDt.R:114:3'): AppenderDt: .fields works ────────────────
    Error in ``[.data.table`(private$.data, !is.na(private$.data$.id), )`: showProgress must be TRUE or FALSE
    Backtrace:
         ▆
      1. ├─testthat::expect_true(is_empty(app$data$.fields[[1]])) at test_AppenderDt.R:114:3
      2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
      3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
      4. ├─lgrExtra:::is_empty(app$data$.fields[[1]])
      5. ├─lgrExtra (local) `<fn>`()
      6. │ └─base::as.data.frame(self$dt)
      7. └─lgrExtra (local) `<fn>`()
      8.   ├─private$.data[!is.na(private$.data$.id), ]
      9.   └─data.table:::`[.data.table`(...)
     10.     └─data.table:::stopf("%s must be TRUE or FALSE", "showProgress")
     11.       └─data.table:::raise_condition(...)
    ── Error ('test_AppenderDt.R:138:3'): AppenderDt: memory cycling works ─────────
    Error in ``[.data.table`(private$.data, !is.na(private$.data$.id), )`: showProgress must be TRUE or FALSE
    Backtrace:
         ▆
      1. ├─testthat::expect_equal(app1$data$.id, 3:12) at test_AppenderDt.R:138:3
      2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
      3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
      4. ├─lgrExtra (local) `<fn>`()
      5. │ └─base::as.data.frame(self$dt)
      6. └─lgrExtra (local) `<fn>`()
      7.   ├─private$.data[!is.na(private$.data$.id), ]
      8.   └─data.table:::`[.data.table`(...)
      9.     └─data.table:::stopf("%s must be TRUE or FALSE", "showProgress")
     10.       └─data.table:::raise_condition(...)
    ── Error ('test_AppenderDt.R:160:3'): AppenderDt: default format for show_log() looks like format.LogEvent() ──
    Error in ``[.data.table`(private$.data, !is.na(private$.data$.id), )`: showProgress must be TRUE or FALSE
    Backtrace:
        ▆
     1. ├─utils::capture.output(lg$appenders$memory$show(n = 1)) at test_AppenderDt.R:160:3
     2. │ └─base::withVisible(...elt(i))
     3. ├─lg$appenders$memory$show(n = 1)
     4. └─lgrExtra (local) `<fn>`()
     5.   ├─private$.data[!is.na(private$.data$.id), ]
     6.   └─data.table:::`[.data.table`(...)
     7.     └─data.table:::stopf("%s must be TRUE or FALSE", "showProgress")
     8.       └─data.table:::raise_condition(...)
    ── Error ('test_SerializerJson.R:48:3'): unpack_json_cols works ────────────────
    Error in ``[.data.table`(dd, , sel, with = FALSE)`: showProgress must be TRUE or FALSE
    Backtrace:
        ▆
     1. └─l$appenders$db$flush() at test_SerializerJson.R:48:3
     2.   ├─dd[, sel, with = FALSE]
     3.   └─data.table:::`[.data.table`(dd, , sel, with = FALSE)
     4.     └─data.table:::stopf("%s must be TRUE or FALSE", "showProgress")
     5.       └─data.table:::raise_condition(...)
    
    [ FAIL 6 | WARN 3 | SKIP 6 | PASS 56 ]
    Error: Test failures
    Execution halted

Package: msmtools
Check: examples
New result: ERROR
  Running examples in ‘msmtools-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: polish
  > ### Title: Remove observations with different states occurring at the same
  > ###   time
  > ### Aliases: polish
  > 
  > ### ** Examples
  > 
  > 
  > # loading data
  > data( hosp )
  > 
  > # augmenting longitudinal data
  > hosp_aug = augment( data = hosp, data_key = subj, n_events = adm_number,
  +                     pattern = label_3, t_start = dateIN, t_end = dateOUT,
  +                     t_cens = dateCENS )
  Warning in augment(data = hosp, data_key = subj, n_events = adm_number,  :
    no t_death has been passed. Assuming that dateCENS contains both censoring and death times
  -------------------------------------
  # # # # setting everything up # # # #
  -------------------------------------
  checking monotonicity of adm_number
  Ok, adm_number is monotonic
  ---
  checking label_3 and defining patterns
  Ok, detected 3 values
  ---
  augmenting data
  Ok, data have been augmented
  ---
  defining dimesions
  Ok, dimensions computed
  ---
  adding status flag
  status flag has been added successfully 
  ---
  adding numeric status flag
  numeric status has been added successfully 
  ---
  adding sequential status flag
  sequential status flag has been added successfully 
  ---
  adding variable augmented as new time variable
  variables "augmented" and "augmented_int" successfully added and repositioned
  ---
  ---------------------------
  augment() took: 0.025 sec. 
  ---------------------------
  > 
  > # cleaning any targeted occurrence
  > hosp_aug_clean = polish( data = hosp_aug, data_key = subj, pattern = label_3 )
  -------------------------------------
  # # # # setting everything up # # # #
  -------------------------------------
  checking label_3 and defining patterns
  Ok, detected 3 values
  ---
  Error in polish(data = hosp_aug, data_key = subj, pattern = label_3) : 
    argument "time" is missing, with no default
  Calls: polish -> duplicated -> duplicated.data.table -> eval
  Execution halted

Package: msmtools
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘msmtools.Rmd’ using rmarkdown_notangle
  
  Quitting from lines 300-318 [multistate_model] (msmtools.Rmd)
  Error: processing vignette 'msmtools.Rmd' failed with diagnostics:
  object 'augmented_int' not found
  --- failed re-building ‘msmtools.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘msmtools.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: phenofit
Check: tests
New result: ERROR
    Running ‘testthat.R’ [63s/63s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(phenofit)
    > 
    > test_check("phenofit")
    List of 5
     $ AG    : tibble [6 × 8] (S3: tbl_df/tbl/data.frame)
     $ Beck  : tibble [6 × 7] (S3: tbl_df/tbl/data.frame)
     $ Elmore: tibble [6 × 8] (S3: tbl_df/tbl/data.frame)
     $ Gu    : tibble [6 × 10] (S3: tbl_df/tbl/data.frame)
     $ Zhang : tibble [6 × 8] (S3: tbl_df/tbl/data.frame)
    NULL
    # A tibble: 6 × 8
      flag      t0    mn    mx     rsp    a3     rau    a5
      <chr>  <dbl> <dbl> <dbl>   <dbl> <dbl>   <dbl> <dbl>
    1 1999_1 -135. 0.201 0.636 0.00932  2.85 0.00852  2   
    2 2000_1  189. 0.238 0.635 0.0126   2.47 0.00801  3.21
    3 2001_1  569. 0.252 0.626 0.0108   2.96 0.00950  2.96
    4 2002_1  892. 0.253 0.614 0.0159   2    0.00724  3.08
    5 2003_1 1268. 0.236 0.577 0.0121   2.88 0.00723  2.88
    6 2004_1 1677. 0.202 0.576 0.00832  2.84 0.00990  3.48
         meth        R2       NSE         R         RMSE        pvalue n_sim
       <char>     <num>     <num>     <num>        <num>         <num> <num>
    1:     AG 0.9986908 0.9985845 0.9993452 9.940385e-03  4.489925e-65    46
    2:   Beck 1.0000000 1.0000000 1.0000000 1.389780e-09  0.000000e+00    46
    3: Elmore 1.0000000 1.0000000 1.0000000 4.161813e-10  0.000000e+00    46
    4:     Gu 1.0000000 1.0000000 1.0000000 4.891365e-11  0.000000e+00    46
    5:  Zhang 1.0000000 1.0000000 1.0000000 5.529073e-06 8.043461e-208    46
    $AG
     formula:	mn + (mx - mn) * exp(-((t0 - t) * rsp)^a3)
      formula:	mn + (mx - mn) * exp(-((t - t0) * rau)^a5)
    pars:
                 t0        mn        mx         rsp a3         rau a5
    nlminb 149.8926 0.1020656 0.7095242 0.009389263  6 0.009367765  6
    
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.65502e-16); attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.19427e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.65502e-16); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.33432e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.03034e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.33432e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.08395e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.36432e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 6.97437e-18); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.11109e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 6.04329e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.94249e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.84957e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 8.58712e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.09346e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.82199e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38705e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 5.88785e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 7.40149e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 6.20634e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.11109e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 4.38854e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.00786e-16); attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.46031e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 5.02097e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.25524e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-curvefit.R:18:5'): curvefit works ────────────────────────────
    all.equal(p1, p2, tolerance = 1e-06) is not TRUE
    
    `actual` is a character vector ('Component "Elmore": Component "mn": Mean relative difference: 1.990404e-06')
    `expected` is a logical vector (TRUE)
    
    [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ]
    Error: Test failures
    Execution halted

Package: polle
Check: tests
New result: ERROR
    Running ‘test-all.R’ [93s/84s]
  Running the tests in ‘tests/test-all.R’ failed.
  Complete output:
    > suppressPackageStartupMessages(library("testthat"))
    > test_check("polle")
    Loading required package: polle
    Loading required package: SuperLearner
    Loading required package: nnls
    Loading required package: gam
    Loading required package: splines
    Loading required package: foreach
    Loaded gam 1.22-4
    
    Super Learner
    Version: 2.0-29
    Package created on 2024-02-06
    
    [ FAIL 5 | WARN 0 | SKIP 0 | PASS 452 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-policy_data.R:260:3'): policy_data melts wide data correctly in a two stage case. ──
    pd$stage_data not equal to `target_stage_data`.
    Attributes: < Component "index": Attributes: < Component "__event": Attributes: < target is NULL, current is list > > >
    ── Failure ('test-policy_data.R:303:3'): policy_data melts wide data correctly in a two stage case. ──
    pd$stage_data not equal to `target_stage_data`.
    Attributes: < Component "index": Attributes: < Component "__event": Attributes: < target is NULL, current is list > > >
    ── Failure ('test-policy_data.R:359:3'): policy_data melts wide data correctly in a single stage case. ──
    pd$stage_data not equal to `target_stage_data`.
    Attributes: < Component "index": Attributes: < Component "__event": Attributes: < target is NULL, current is list > > >
    ── Failure ('test-policy_data.R:381:3'): policy_data melts wide data correctly in a single stage case. ──
    ...$stage_data not equal to `target_stage_data`.
    Attributes: < Component "index": Attributes: < Component "__event": Attributes: < target is NULL, current is list > > >
    ── Failure ('test-policy_data.R:387:3'): policy_data melts wide data correctly in a single stage case. ──
    ...$stage_data not equal to `target_stage_data`.
    Attributes: < Component "index": Attributes: < Component "__event": Attributes: < target is NULL, current is list > > >
    
    [ FAIL 5 | WARN 0 | SKIP 0 | PASS 452 ]
    Error: Test failures
    Execution halted

Package: TrialEmulation
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Getting-Started.Rmd’ using rmarkdown
  
  Quitting from lines 136-137 [unnamed-chunk-2] (Getting-Started.Rmd)
  Error: processing vignette 'Getting-Started.Rmd' failed with diagnostics:
  argument 3 matches multiple formal arguments
  --- failed re-building ‘Getting-Started.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Getting-Started.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: TrialEmulation
Check: tests
New result: ERROR
    Running ‘testthat.R’ [111s/100s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(TrialEmulation)
    > 
    > data.table::setDTthreads(2)
    > test_check("TrialEmulation")
    Starting data manipulation
    Starting data extension
    Summary of extended data:
    Number of observations: 1939053
    ------------------------------------------------------------
    
    Starting data manipulation
    P(treatment = 1 | previous treatment = 0) for denominator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept) -3.84325    0.04785  -80.31   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 4329.7  on 21263  degrees of freedom
    Residual deviance: 4329.7  on 21263  degrees of freedom
    AIC: 4331.7
    
    Number of Fisher Scoring iterations: 6
    
    P(treatment = 1 | previous treatment = 0) for numerator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept) -3.84325    0.04785  -80.31   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 4329.7  on 21263  degrees of freedom
    Residual deviance: 4329.7  on 21263  degrees of freedom
    AIC: 4331.7
    
    Number of Fisher Scoring iterations: 6
    
    P(treatment = 1 | previous treatment = 1) for denominator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept)  4.37616    0.06815   64.21   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 2346.7  on 17555  degrees of freedom
    Residual deviance: 2346.7  on 17555  degrees of freedom
    AIC: 2348.7
    
    Number of Fisher Scoring iterations: 7
    
    P(treatment = 1 | previous treatment = 1) for numerator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept)  4.37616    0.06815   64.21   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 2346.7  on 17555  degrees of freedom
    Residual deviance: 2346.7  on 17555  degrees of freedom
    AIC: 2348.7
    
    Number of Fisher Scoring iterations: 7
    
    Starting data extension
    Summary of extended data:
    Number of observations: 963883
    ------------------------------------------------------------
    
    Starting data manipulation
    P(treatment = 1 | previous treatment = 0) for denominator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept) -3.32517    0.03599   -92.4   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 6948.7  on 23042  degrees of freedom
    Residual deviance: 6948.7  on 23042  degrees of freedom
    AIC: 6950.7
    
    Number of Fisher Scoring iterations: 6
    
    P(treatment = 1 | previous treatment = 0) for numerator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept) -3.32517    0.03599   -92.4   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 6948.7  on 23042  degrees of freedom
    Residual deviance: 6948.7  on 23042  degrees of freedom
    AIC: 6950.7
    
    Number of Fisher Scoring iterations: 6
    
    P(treatment = 1 | previous treatment = 1) for denominator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept)   3.9124     0.0453   86.37   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 4892.8  on 25356  degrees of freedom
    Residual deviance: 4892.8  on 25356  degrees of freedom
    AIC: 4894.8
    
    Number of Fisher Scoring iterations: 6
    
    P(treatment = 1 | previous treatment = 1) for numerator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept)   3.9124     0.0453   86.37   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 4892.8  on 25356  degrees of freedom
    Residual deviance: 4892.8  on 25356  degrees of freedom
    AIC: 4894.8
    
    Number of Fisher Scoring iterations: 6
    
    Starting data extension
    Summary of extended data:
    Number of observations: 1939053
    ------------------------------------------------------------
    
    [ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
    
    ══ Skipped tests (24) ══════════════════════════════════════════════════════════
    • On CRAN (24): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
      'test-data_utils.R:131:3', 'test-generics.R:66:3', 'test-generics.R:95:3',
      'test-modelling.R:99:3', 'test-modelling.R:154:3', 'test-modelling.R:175:3',
      'test-modelling.R:205:3', 'test-modelling.R:229:3', 'test-modelling.R:266:3',
      'test-modelling.R:290:3', 'test-modelling.R:314:3', 'test-modelling.R:357:3',
      'test-predict.R:26:3', 'test-predict.R:51:3', 'test-predict.R:108:3',
      'test-sampling.R:5:3', 'test-sampling.R:15:3', 'test-sampling.R:34:3',
      'test-sampling.R:54:3', 'test-sampling.R:86:3', 'test-sampling.R:103:3',
      'test-sampling.R:180:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-generics.R:25:3'): summary for data_preparation separate=TRUE ──
    Error in `print.data.table(data.table(data = object$data), topn = 3, n = 5, 
        col.names = "none", ...)`: argument 3 matches multiple formal arguments
    Backtrace:
        ▆
     1. └─testthat::expect_snapshot(...) at test-generics.R:25:3
     2.   └─rlang::cnd_signal(state$error)
    
    [ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
    Error: Test failures
    Execution halted