Running ‘testthat.R’ [15m/17m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggPMX)
  > 
  > test_check("ggPMX")
  style: equal
    one of 8 possible partitions of this variable into 2 classes
   [0,6) [6,12] 
       6      3 
  
  
  |data_name |data_file |data_label |
  |:---------|:---------|:----------|
  
  
  |plot_name       |plot_type |
  |:---------------|:---------|
  |abs_iwres_ipred |SCATTER   |
  |abs_iwres_time  |SCATTER   |
  |iwres_ipred     |SCATTER   |
  |iwres_time      |SCATTER   |
  |iwres_dens      |PMX_DENS  |
  |iwres_qq        |PMX_QQ    |
  |npde_time       |SCATTER   |
  |npde_pred       |SCATTER   |
  |npde_qq         |PMX_QQ    |
  |dv_pred         |SCATTER   |
  |dv_ipred        |SCATTER   |
  |individual      |IND       |
  |eta_hist        |DIS       |
  |eta_box         |DIS       |
  |eta_matrix      |ETA_PAIRS |
  |eta_cats        |ETA_COV   |
  |eta_conts       |ETA_COV   |
  |eta_qq          |PMX_QQ    |
  |pmx_vpc         |VPC       |
  
  
  |data_name |data_file |data_label |
  |:---------|:---------|:----------|
  
  
  |plot_name       |plot_type |
  |:---------------|:---------|
  |abs_iwres_ipred |SCATTER   |
  |abs_iwres_time  |SCATTER   |
  |iwres_ipred     |SCATTER   |
  |iwres_time      |SCATTER   |
  |iwres_dens      |PMX_DENS  |
  |iwres_qq        |PMX_QQ    |
  |npde_time       |SCATTER   |
  |npde_pred       |SCATTER   |
  |npde_qq         |PMX_QQ    |
  |dv_pred         |SCATTER   |
  |dv_ipred        |SCATTER   |
  |individual      |IND       |
  |eta_hist        |DIS       |
  |eta_box         |DIS       |
  |eta_matrix      |ETA_PAIRS |
  |eta_cats        |ETA_COV   |
  |eta_conts       |ETA_COV   |
  |eta_qq          |PMX_QQ    |
  |pmx_vpc         |VPC       |
  character(0)
  
  
  |data_name |data_file |data_label |
  |:---------|:---------|:----------|
  
  
  |plot_name       |plot_type |
  |:---------------|:---------|
  |abs_iwres_ipred |SCATTER   |
  |abs_iwres_time  |SCATTER   |
  |iwres_ipred     |SCATTER   |
  |iwres_time      |SCATTER   |
  |iwres_dens      |PMX_DENS  |
  |iwres_qq        |PMX_QQ    |
  |npde_time       |SCATTER   |
  |npde_pred       |SCATTER   |
  |npde_qq         |PMX_QQ    |
  |dv_pred         |SCATTER   |
  |dv_ipred        |SCATTER   |
  |individual      |IND       |
  |eta_hist        |DIS       |
  |eta_box         |DIS       |
  |eta_matrix      |ETA_PAIRS |
  |eta_cats        |ETA_COV   |
  |eta_conts       |ETA_COV   |
  |eta_qq          |PMX_QQ    |
  |pmx_vpc         |VPC       |
  $is.title
  [1] TRUE
  
  $axis.title
  $axis.title$size
  [1] 12
  
  
  $axis.text
  $axis.text$size
  [1] 10
  
  
  $ranges
  NULL
  
  $is.smooth
  [1] TRUE
  
  $smooth
  $smooth$se
  [1] FALSE
  
  $smooth$linetype
  [1] 1
  
  $smooth$linewidth
  [1] 1.5
  
  $smooth$method
  [1] "loess"
  
  $smooth$colour
  [1] "red"
  
  
  $is.band
  [1] FALSE
  
  $band
  $band$yintercept
  [1] -1.96  1.96
  
  $band$linetype
  [1] 2
  
  $band$linewidth
  [1] 0.5
  
  
  $is.draft
  [1] TRUE
  
  $draft
  $draft$size
  [1] 5
  
  $draft$label
  [1] "DRAFT"
  
  $draft$colour
  [1] "grey50"
  
  $draft$x
  [1] Inf
  
  $draft$y
  [1] -Inf
  
  
  $discrete
  [1] FALSE
  
  $is.identity_line
  [1] FALSE
  
  $identity_line
  $identity_line$colour
  [1] "blue"
  
  $identity_line$intercept
  [1] 0
  
  
  $scale_x_log10
  [1] FALSE
  
  $scale_y_log10
  [1] FALSE
  
  $color.scales
  NULL
  
  $is.legend
  [1] FALSE
  
  $legend.position
  [1] "right"
  
  $labels
  $labels$title
  [1] "hello"
  
  
  $is.title
  [1] TRUE
  
  $axis.title
  $axis.title$size
  [1] 12
  
  
  $axis.text
  $axis.text$size
  [1] 10
  
  
  $ranges
  NULL
  
  $is.smooth
  [1] TRUE
  
  $smooth
  $smooth$se
  [1] FALSE
  
  $smooth$linetype
  [1] 1
  
  $smooth$linewidth
  [1] 1.5
  
  $smooth$method
  [1] "loess"
  
  $smooth$colour
  [1] "red"
  
  
  $is.band
  [1] FALSE
  
  $band
  $band$yintercept
  [1] -1.96  1.96
  
  $band$linetype
  [1] 2
  
  $band$linewidth
  [1] 0.5
  
  
  $is.draft
  [1] TRUE
  
  $draft
  $draft$size
  [1] 5
  
  $draft$label
  [1] "DRAFT"
  
  $draft$colour
  [1] "grey50"
  
  $draft$x
  [1] Inf
  
  $draft$y
  [1] -Inf
  
  
  $discrete
  [1] FALSE
  
  $is.identity_line
  [1] FALSE
  
  $identity_line
  $identity_line$colour
  [1] "blue"
  
  $identity_line$intercept
  [1] 0
  
  
  $scale_x_log10
  [1] FALSE
  
  $scale_y_log10
  [1] FALSE
  
  $color.scales
  NULL
  
  $is.legend
  [1] FALSE
  
  $legend.position
  [1] "right"
  
  $labels
  $labels$title
  [1] "hello"
  
  
  No data eta provided for plot eta_hist 
  No data eta provided for plot eta_box 
  No data eta provided for plot eta_matrix 
  No data eta provided for plot eta_cats 
  No data eta provided for plot eta_conts 
  No data eta provided for plot eta_qq 
  No data eta provided for plot eta_hist 
  No data eta provided for plot eta_box 
  No data eta provided for plot eta_matrix 
  No data eta provided for plot eta_cats 
  No data eta provided for plot eta_conts 
  No data eta provided for plot eta_qq 
  No data IND1 provided for plot individual 
        ID    TIME     PRED    IPRED  AMT   Y EVID WT0 AGE0 SEX STUD DV isobserv
     1:  1  0.2182  51.3092  53.6590 2000   0    1  87   73   1    1 NA accepted
     2:  1  0.5091 112.9294 118.0946    0 130    0  87   73   1    1 NA accepted
     3:  1  0.8000 167.4284 175.0867    0 130    0  87   73   1    1 NA accepted
     4:  1  1.0909 215.4506 225.3192    0 228    0  87   73   1    1 NA accepted
     5:  1  1.3818 257.5859 269.4167    0 228    0  87   73   1    1 NA accepted
    ---                                                                         
  4546: 50 25.2364  49.0518  84.7612    0 121    0  92   19   1    2 NA accepted
  4547: 50 25.5273  47.1749  82.1470    0 121    0  92   19   1    2 NA accepted
  4548: 50 25.8182  45.3679  79.6108    0 121    0  92   19   1    2 NA accepted
  4549: 50 26.1091  43.6283  77.1504    0 121    0  92   19   1    2 NA accepted
  4550: 50 26.4000  41.9537  74.7639    0 121    0  92   19   1    2 NA accepted
  
  pmx object:
  
  pmx object:
  
  
  |PARAM                |VALUE |
  |:--------------------|:-----|
  |working directory    |      |
  |Modelling input file |      |
  |dv                   |Y     |
  |dvid                 |DVID  |
  
  
  |data_name   |data_file       |data_label                                |
  |:-----------|:---------------|:-----------------------------------------|
  |predictions |predictions.txt |model predictions file                    |
  |estimates   |estimates.txt   |parameter estimates file                  |
  |eta         |indiv_eta.txt   |invidual estimates of random effects file |
  |finegrid    |finegrid.txt    |finegrid file                             |
  |input       |data_pk.csv     |modelling input                           |
  
  
  |plot_name       |plot_type |
  |:---------------|:---------|
  |abs_iwres_ipred |SCATTER   |
  |abs_iwres_time  |SCATTER   |
  |iwres_ipred     |SCATTER   |
  |iwres_time      |SCATTER   |
  |iwres_dens      |PMX_DENS  |
  |iwres_qq        |PMX_QQ    |
  |npde_time       |SCATTER   |
  |npde_pred       |SCATTER   |
  |npde_qq         |PMX_QQ    |
  |dv_pred         |SCATTER   |
  |dv_ipred        |SCATTER   |
  |individual      |IND       |
  |eta_hist        |DIS       |
  |eta_box         |DIS       |
  |eta_matrix      |ETA_PAIRS |
  |eta_cats        |ETA_COV   |
  |eta_conts       |ETA_COV   |
  |eta_qq          |PMX_QQ    |
  |pmx_vpc         |VPC       |
  
  pmx object:
  
  
  |PARAM                |VALUE |
  |:--------------------|:-----|
  |working directory    |      |
  |Modelling input file |      |
  |dv                   |Y     |
  |dvid                 |DVID  |
  
  
  |data_name   |data_file       |data_label                                |
  |:-----------|:---------------|:-----------------------------------------|
  |predictions |predictions.txt |model predictions file                    |
  |estimates   |estimates.txt   |parameter estimates file                  |
  |eta         |indiv_eta.txt   |invidual estimates of random effects file |
  |finegrid    |finegrid.txt    |finegrid file                             |
  |input       |data_pk.csv     |modelling input                           |
  
  
  |plot_name       |plot_type |
  |:---------------|:---------|
  |abs_iwres_ipred |SCATTER   |
  |abs_iwres_time  |SCATTER   |
  |iwres_ipred     |SCATTER   |
  |iwres_time      |SCATTER   |
  |iwres_dens      |PMX_DENS  |
  |iwres_qq        |PMX_QQ    |
  |npde_time       |SCATTER   |
  |npde_pred       |SCATTER   |
  |npde_qq         |PMX_QQ    |
  |dv_pred         |SCATTER   |
  |dv_ipred        |SCATTER   |
  |individual      |IND       |
  |eta_hist        |DIS       |
  |eta_box         |DIS       |
  |eta_matrix      |ETA_PAIRS |
  |eta_cats        |ETA_COV   |
  |eta_conts       |ETA_COV   |
  |eta_qq          |PMX_QQ    |
  |pmx_vpc         |VPC       |
  
  pmx object:
  
  
  |PARAM                |VALUE        |
  |:--------------------|:------------|
  |working directory    |theophylline |
  |Modelling input file |data_pk.csv  |
  |dv                   |Y            |
  |dvid                 |dvid         |
  |cats                 |SEX          |
  |conts                |WT0,AGE0     |
  |strats               |STUD         |
  
  
  |data_name   |data_file       |data_label                                |
  |:-----------|:---------------|:-----------------------------------------|
  |predictions |predictions.txt |model predictions file                    |
  |estimates   |estimates.txt   |parameter estimates file                  |
  |eta         |indiv_eta.txt   |invidual estimates of random effects file |
  |finegrid    |finegrid.txt    |finegrid file                             |
  |input       |data_pk.csv     |modelling input                           |
  
  
  |plot_name       |plot_type |
  |:---------------|:---------|
  |abs_iwres_ipred |SCATTER   |
  |abs_iwres_time  |SCATTER   |
  |iwres_ipred     |SCATTER   |
  |iwres_time      |SCATTER   |
  |iwres_dens      |PMX_DENS  |
  |iwres_qq        |PMX_QQ    |
  |npde_time       |SCATTER   |
  |npde_pred       |SCATTER   |
  |npde_qq         |PMX_QQ    |
  |dv_pred         |SCATTER   |
  |dv_ipred        |SCATTER   |
  |individual      |IND       |
  |eta_hist        |DIS       |
  |eta_box         |DIS       |
  |eta_matrix      |ETA_PAIRS |
  |eta_cats        |ETA_COV   |
  |eta_conts       |ETA_COV   |
  |eta_qq          |PMX_QQ    |
  |pmx_vpc         |VPC       |
  use  predictions1.txt  as  model predictions file .
  use  finegrid1.txt  as  finegrid file .
  use  predictions2.txt  as  model predictions file .
  use  finegrid2.txt  as  finegrid file .
  [ FAIL 1 | WARN 25 | SKIP 18 | PASS 1017 ]
  
  ══ Skipped tests (18) ══════════════════════════════════════════════════════════
  • On CRAN (16): 'test-nlmixr.R:3:5', 'test-nlmixr.R:42:5',
    'test-nlmixr.R:115:5', 'test-pmx-report.R:56:3', 'test-pmx-report.R:142:3',
    'test-pmx-report.R:151:3', 'test-pmx-report.R:161:3',
    'test-pmx-report.R:178:3', 'test-pmx-report.R:224:5',
    'test-pmx-report.R:258:3', 'test-pmx-report.R:292:3',
    'test-pmx-report.R:347:3', 'test-pmx-report.R:381:3',
    'test-pmx-report.R:397:3', 'test-pmx-report.R:450:3', 'test-utils.R:100:3'
  • TRUE is TRUE (1): 'test-vdiff.R:3:3'
  • empty test (1): 'test-nonmem_reader.R:77:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-reader.R:88:3'): read_mlx18_res: 11params: path is wrong, subfolder is not empty,
            file exists; result: identical structure ──
  read_mlx18_res(ipath, x$finegrid) is not an S3 object
  
  [ FAIL 1 | WARN 25 | SKIP 18 | PASS 1017 ]
  Deleting unused snapshots:
  • vdiff/fun-pmx-plot-abs-iwres-ipred.svg
  • vdiff/fun-pmx-plot-dv-ipred.svg
  • vdiff/fun-pmx-plot-dv-pred.svg
  • vdiff/fun-pmx-plot-eta-box.svg
  • vdiff/fun-pmx-plot-eta-cats.svg
  • vdiff/fun-pmx-plot-eta-conts.svg
  • vdiff/fun-pmx-plot-eta-hist.svg
  • vdiff/fun-pmx-plot-eta-matrix.svg
  • vdiff/fun-pmx-plot-eta-qq.svg
  • vdiff/fun-pmx-plot-individual.svg
  • vdiff/fun-pmx-plot-iwres-dens.svg
  • vdiff/fun-pmx-plot-iwres-ipred.svg
  • vdiff/fun-pmx-plot-iwres-qq.svg
  • vdiff/fun-pmx-plot-iwres-time.svg
  • vdiff/fun-pmx-plot-npde-pred.svg
  • vdiff/fun-pmx-plot-npde-qq.svg
  • vdiff/fun-pmx-plot-npde-time.svg
  • vdiff/fun-pmx-plot-vpc.svg
  Error: Test failures
  Execution halted