- using R Under development (unstable) (2023-06-03 r84490)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 15.0.6
GNU Fortran (Debian 12.2.0-14) 12.2.0
- running under: Debian GNU/Linux 12 (bookworm)
- using session charset: UTF-8
- checking for file ‘ggPMX/DESCRIPTION’ ... OK
- this is package ‘ggPMX’ version ‘1.2.9’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... NOTE
Package suggested but not available for checking: ‘lixoftConnectors’
- 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 ‘ggPMX’ can be installed ... OK
- 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 ... [2s/3s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the package can be unloaded cleanly ... [2s/2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/4s] OK
- checking loading without being on the library search path ... [2s/3s] OK
- checking startup messages can be suppressed ... [2s/3s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [36s/46s] 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 ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [7s/8s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [14m/12m] ERROR
Running ‘testthat.R’ [14m/12m]
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 31 | SKIP 17 | PASS 1019 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (15)
• TRUE is TRUE (1)
• empty test (1)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-pmx-report.R:64:3'): pmx_draft: params result: create file ──
file.exists(draft) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 31 | SKIP 17 | PASS 1019 ]
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
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking re-building of vignette outputs ... [140s/147s] OK
- checking PDF version of manual ... [11s/16s] OK
- checking HTML version of manual ... [6s/11s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE