Last updated on 2026-11-15 07:51:04 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.2 | 18.35 | 608.65 | 627.00 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.2 | 11.53 | 412.93 | 424.46 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.2 | 13.00 | 479.79 | 492.79 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.2 | 13.00 | 491.07 | 504.07 | ERROR | |
| r-devel-windows-x86_64 | 0.2.2 | 25.00 | 881.00 | 906.00 | OK | |
| r-patched-linux-x86_64 | 0.2.2 | 22.92 | 552.73 | 575.65 | OK | |
| r-release-linux-x86_64 | 0.2.2 | 17.03 | 553.37 | 570.40 | OK | |
| r-release-macos-arm64 | 0.2.2 | 5.00 | 145.00 | 150.00 | OK | |
| r-release-macos-x86_64 | 0.2.2 | 13.00 | 496.00 | 509.00 | OK | |
| r-release-windows-x86_64 | 0.2.2 | 22.00 | 729.00 | 751.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.2 | 4.00 | 162.00 | 166.00 | OK | |
| r-oldrel-macos-x86_64 | 0.2.2 | 13.00 | 549.00 | 562.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.2 | 31.00 | 1030.00 | 1061.00 | OK |
Version: 0.2.2
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [175s/175s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(xpose.xtras)
ℹ xpose isn't attached; its own functions (e.g. `dv_vs_ipred()`) won't be
available until you load it.
Load it before xpose.xtras (or load conflicted) so its `irep()` bugfix takes
effect too.
Attaching package: 'xpose.xtras'
The following object is masked from 'package:stats':
filter
>
> test_check("xpose.xtras")
Using data from $prob no.1
Filtering data by EVID == 0
Returning parameter estimates from $prob no.1, subprob no.1, method foce
Returning data from run001.cor, $prob no.1, subprob no.1, method foce
Returning data from run001.cor, $prob no.1, subprob no.1, method foce
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
i For nlmixr2 models, sometimes '@file' is a better `axis.text`, instead of '@run'.
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, DOSE, AMT, SS, II ... and 23 more variables
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Added `process_preset()`("2")
Added `process_preset()`("1")
Added `process_preset()`("2")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("describe")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("drop_eta5")
* "drop_eta5": `~.x %>% as_xpdb_x() %>% set_var_types(na = "ETA5")`
Added `process_preset()`("convert")
Added `process_preset()`("convert2")
Removed `process_preset()`("convert2")
Added `process_preset()`("convert")
Added `process_preset()`("describe")
Added `process_preset()`("describe")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
i About to update the process-preset block in '/home/hornik/tmp/scratch/Rtmplbivg2/file100529d5cd723':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x %>% as_xpdb_x(), name = "convert",
overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Added `process_preset()`("convert")
i About to update the process-preset block in '/home/hornik/tmp/scratch/Rtmplbivg2/file100529e1ec872':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x %>% as_xpdb_x(), name = "convert",
overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Process presets written to '/home/hornik/tmp/scratch/Rtmplbivg2/file100529e1ec872'
Removed `process_preset()`("convert")
Process presets written to '/home/hornik/tmp/scratch/Rtmplbivg2/file100529e1ec872'
Added `process_preset()`("convert")
Process presets written to '/home/hornik/tmp/scratch/Rtmplbivg2/file1005294d372cc6'
Added `process_preset()`("convert")
i About to update the process-preset block in '/home/hornik/tmp/scratch/Rtmplbivg2/file100529347730ba':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x %>% as_xpdb_x(), name = "convert",
overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Process presets written to '/home/hornik/tmp/scratch/Rtmplbivg2/file100529347730ba'
Added `process_preset()`("convert")
i About to update the process-preset block in '/home/hornik/tmp/scratch/Rtmplbivg2/file100529347730ba':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x, name = "convert", overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Process presets written to '/home/hornik/tmp/scratch/Rtmplbivg2/file100529347730ba'
Removed `process_preset()`("convert")
i About to update the process-preset block in '/home/hornik/tmp/scratch/Rtmplbivg2/file100529347730ba':
Process presets written to '/home/hornik/tmp/scratch/Rtmplbivg2/file100529347730ba'
.
Reading: run16tab [$prob no.1]
Looking for nonmem output files
Reading: run18.cor, run18.cov, run18.ext, run18.phi, run18.shk
Saving _problems/test-xplot_boxplot-168.R
Saving _problems/test-xplot_boxplot-171.R
Saving _problems/test-xplot_boxplot-11.R
Using data from $prob no.1
Using data from $prob no.1
........
........
.
.
.
.
..
..
..
.
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
# A tibble: 3 x 10
param covariate covtype level value is_ref effect ci_low ci_high ci_method
<chr> <chr> <chr> <chr> <chr> <lgl> <dbl> <dbl> <dbl> <chr>
1 TVCL CLCR cont low 40 FALSE 0.997 0.995 0.998 simulation
2 TVCL CLCR cont ref 64 TRUE 1 1 1 simulation
3 TVCL CLCR cont high 102 FALSE 1.00 1.00 1.00 simulation
# A tibble: 0 x 10
# i 10 variables: param <chr>, covariate <chr>, covtype <chr>, level <chr>,
# value <chr>, is_ref <lgl>, effect <dbl>, ci_low <dbl>, ci_high <dbl>,
# ci_method <chr>
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Filtering data by EVID == 0
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Filtering data by EVID == 0
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
! 1 of 3 plot(s) failed and was skipped: "stop"
Using data from $prob no.1
Filtering data by EVID == 0
.Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
i xpose isn't attached; its own functions (e.g. `dv_vs_ipred()`) won't be available until you load it.
i xpose isn't attached; its own functions (e.g. `dv_vs_ipred()`) won't be available until you load it.
Load it before xpose.xtras (or load conflicted) so its `irep()` bugfix takes effect too.
[ FAIL 3 | WARN 0 | SKIP 51 | PASS 1565 ]
══ Skipped tests (51) ══════════════════════════════════════════════════════════
• On CRAN (40): 'test-colinearity.R:82:3', 'test-colinearity.R:124:3',
'test-colinearity.R:241:3', 'test-covariates.R:123:3',
'test-diag_constants.R:227:3', 'test-diag_constants.R:241:3',
'test-fixes.R:627:3', 'test-modavg_xpdb.R:2:3', 'test-nlmixr2.R:60:3',
'test-nlmixr2.R:102:3', 'test-nlmixr2.R:135:3', 'test-nlmixr2.R:181:3',
'test-nlmixr2.R:447:3', 'test-nlmixr2.R:483:3', 'test-nlmixr2.R:505:3',
'test-nlmixr2.R:529:3', 'test-nlmixr2.R:548:3', 'test-nlmixr2.R:567:3',
'test-nlmixr2.R:586:3', 'test-nlmixr2.R:605:3', 'test-utils.R:402:5',
'test-utils.R:482:3', 'test-xplot_pairs.R:44:3', 'test-xplot_pairs.R:165:3',
'test-xplot_pairs.R:320:3', 'test-xplot_rocplot.R:36:3',
'test-xplot_rocplot.R:131:3', 'test-xset_features.R:192:3',
'test-xset_features.R:192:3', 'test-xset_features.R:192:3',
'test-xset_features.R:192:3', 'test-xset_plots.R:220:3',
'test-xset_plots.R:490:3', 'test-xset_plots.R:553:3',
'test-xset_shark.R:2:3', 'test-xset_waterfall.R:2:3', 'test-zzz.R:62:7',
'test-zzz.R:62:7', 'test-zzz.R:62:7', 'test-zzz.R:62:7'
• requireNamespace("rxode2", quietly = TRUE) && "rxDerived" %in%
getNamespaceExports("rxode2") is TRUE (2): 'test-diag_constants.R:188:3',
'test-diag_constants.R:194:3'
• {bbr} is not installed (8): 'test-bbr.R:2:3', 'test-bbr.R:14:3',
'test-bbr.R:25:3', 'test-bbr.R:35:3', 'test-bbr.R:45:3', 'test-bbr.R:53:3',
'test-bbr.R:60:3', 'test-bbr.R:70:3'
• {qs} is not installed (1): 'test-nlmixr2.R:624:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-xplot_boxplot.R:166:3'): xplot_boxplot ───────────────────────
Expected `... <- NULL` not to throw any errors.
Actually got a <expressionStackOverflowError> with message:
evaluation nested too deeply: infinite recursion / options(expressions=)?
── Failure ('test-xplot_boxplot.R:169:3'): xplot_boxplot ───────────────────────
Expected `old_b <- xplot_boxplot(xpdb_x, aes(MED1, ETA1), type = "b", quiet = TRUE)` not to throw any errors.
Actually got a <expressionStackOverflowError> with message:
evaluation nested too deeply: infinite recursion / options(expressions=)?
── Error ('test-xplot_boxplot.R:11:18'): xplot_boxplot ─────────────────────────
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'old_bo' not found
Backtrace:
▆
1. ├─testthat::expect_setequal(geoms_lists(old_bo), "GeomBoxplot") at test-xplot_boxplot.R:172:3
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─xpose.xtras (local) geoms_lists(old_bo)
5. └─purrr::map_chr(gg$layers, ~class(.x$geom)[1]) at test-xplot_boxplot.R:11:18
6. └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
7. └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
[ FAIL 3 | WARN 0 | SKIP 51 | PASS 1565 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.2
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [236s/238s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(xpose.xtras)
ℹ xpose isn't attached; its own functions (e.g. `dv_vs_ipred()`) won't be
available until you load it.
Load it before xpose.xtras (or load conflicted) so its `irep()` bugfix takes
effect too.
Attaching package: 'xpose.xtras'
The following object is masked from 'package:stats':
filter
>
> test_check("xpose.xtras")
Using data from $prob no.1
Filtering data by EVID == 0
Returning parameter estimates from $prob no.1, subprob no.1, method foce
Returning data from run001.cor, $prob no.1, subprob no.1, method foce
Returning data from run001.cor, $prob no.1, subprob no.1, method foce
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
i For nlmixr2 models, sometimes '@file' is a better `axis.text`, instead of '@run'.
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, DOSE, AMT, SS, II ... and 23 more variables
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Added `process_preset()`("2")
Added `process_preset()`("1")
Added `process_preset()`("2")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("describe")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("drop_eta5")
* "drop_eta5": `~.x %>% as_xpdb_x() %>% set_var_types(na = "ETA5")`
Added `process_preset()`("convert")
Added `process_preset()`("convert2")
Removed `process_preset()`("convert2")
Added `process_preset()`("convert")
Added `process_preset()`("describe")
Added `process_preset()`("describe")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
i About to update the process-preset block in '/tmp/Rtmpcavijj/working_dir/RtmpL1NwzT/file390ad14bc5eda6':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x %>% as_xpdb_x(), name = "convert",
overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Added `process_preset()`("convert")
i About to update the process-preset block in '/tmp/Rtmpcavijj/working_dir/RtmpL1NwzT/file390ad12b0cca5a':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x %>% as_xpdb_x(), name = "convert",
overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Process presets written to '/tmp/Rtmpcavijj/working_dir/RtmpL1NwzT/file390ad12b0cca5a'
Removed `process_preset()`("convert")
Process presets written to '/tmp/Rtmpcavijj/working_dir/RtmpL1NwzT/file390ad12b0cca5a'
Added `process_preset()`("convert")
Process presets written to '/tmp/Rtmpcavijj/working_dir/RtmpL1NwzT/file390ad1430dad13'
Added `process_preset()`("convert")
i About to update the process-preset block in '/tmp/Rtmpcavijj/working_dir/RtmpL1NwzT/file390ad15333058':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x %>% as_xpdb_x(), name = "convert",
overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Process presets written to '/tmp/Rtmpcavijj/working_dir/RtmpL1NwzT/file390ad15333058'
Added `process_preset()`("convert")
i About to update the process-preset block in '/tmp/Rtmpcavijj/working_dir/RtmpL1NwzT/file390ad15333058':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x, name = "convert", overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Process presets written to '/tmp/Rtmpcavijj/working_dir/RtmpL1NwzT/file390ad15333058'
Removed `process_preset()`("convert")
i About to update the process-preset block in '/tmp/Rtmpcavijj/working_dir/RtmpL1NwzT/file390ad15333058':
Process presets written to '/tmp/Rtmpcavijj/working_dir/RtmpL1NwzT/file390ad15333058'
.
Reading: run16tab [$prob no.1]
Looking for nonmem output files
Reading: run18.cor, run18.cov, run18.ext, run18.phi, run18.shk
Saving _problems/test-xplot_boxplot-168.R
Saving _problems/test-xplot_boxplot-171.R
Saving _problems/test-xplot_boxplot-11.R
Using data from $prob no.1
Using data from $prob no.1
...............
...............
.
..
.
.
..
..
..
.
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
# A tibble: 3 x 10
param covariate covtype level value is_ref effect ci_low ci_high ci_method
<chr> <chr> <chr> <chr> <chr> <lgl> <dbl> <dbl> <dbl> <chr>
1 TVCL CLCR cont low 40 FALSE 0.997 0.995 0.998 simulation
2 TVCL CLCR cont ref 64 TRUE 1 1 1 simulation
3 TVCL CLCR cont high 102 FALSE 1.00 1.00 1.00 simulation
# A tibble: 0 x 10
# i 10 variables: param <chr>, covariate <chr>, covtype <chr>, level <chr>,
# value <chr>, is_ref <lgl>, effect <dbl>, ci_low <dbl>, ci_high <dbl>,
# ci_method <chr>
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Filtering data by EVID == 0
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Filtering data by EVID == 0
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
! 1 of 3 plot(s) failed and was skipped: "stop"
Using data from $prob no.1
Filtering data by EVID == 0
.Using data from $prob no.1
Filtering data by EVID == 0
.Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
i xpose isn't attached; its own functions (e.g. `dv_vs_ipred()`) won't be available until you load it.
i xpose isn't attached; its own functions (e.g. `dv_vs_ipred()`) won't be available until you load it.
Load it before xpose.xtras (or load conflicted) so its `irep()` bugfix takes effect too.
[ FAIL 3 | WARN 0 | SKIP 51 | PASS 1565 ]
══ Skipped tests (51) ══════════════════════════════════════════════════════════
• On CRAN (40): 'test-colinearity.R:82:3', 'test-colinearity.R:124:3',
'test-colinearity.R:241:3', 'test-covariates.R:123:3',
'test-diag_constants.R:227:3', 'test-diag_constants.R:241:3',
'test-fixes.R:627:3', 'test-modavg_xpdb.R:2:3', 'test-nlmixr2.R:60:3',
'test-nlmixr2.R:102:3', 'test-nlmixr2.R:135:3', 'test-nlmixr2.R:181:3',
'test-nlmixr2.R:447:3', 'test-nlmixr2.R:483:3', 'test-nlmixr2.R:505:3',
'test-nlmixr2.R:529:3', 'test-nlmixr2.R:548:3', 'test-nlmixr2.R:567:3',
'test-nlmixr2.R:586:3', 'test-nlmixr2.R:605:3', 'test-utils.R:402:5',
'test-utils.R:482:3', 'test-xplot_pairs.R:44:3', 'test-xplot_pairs.R:165:3',
'test-xplot_pairs.R:320:3', 'test-xplot_rocplot.R:36:3',
'test-xplot_rocplot.R:131:3', 'test-xset_features.R:192:3',
'test-xset_features.R:192:3', 'test-xset_features.R:192:3',
'test-xset_features.R:192:3', 'test-xset_plots.R:220:3',
'test-xset_plots.R:490:3', 'test-xset_plots.R:553:3',
'test-xset_shark.R:2:3', 'test-xset_waterfall.R:2:3', 'test-zzz.R:62:7',
'test-zzz.R:62:7', 'test-zzz.R:62:7', 'test-zzz.R:62:7'
• requireNamespace("rxode2", quietly = TRUE) && "rxDerived" %in%
getNamespaceExports("rxode2") is TRUE (2): 'test-diag_constants.R:188:3',
'test-diag_constants.R:194:3'
• {bbr} is not installed (8): 'test-bbr.R:2:3', 'test-bbr.R:14:3',
'test-bbr.R:25:3', 'test-bbr.R:35:3', 'test-bbr.R:45:3', 'test-bbr.R:53:3',
'test-bbr.R:60:3', 'test-bbr.R:70:3'
• {qs} is not installed (1): 'test-nlmixr2.R:624:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-xplot_boxplot.R:166:3'): xplot_boxplot ───────────────────────
Expected `... <- NULL` not to throw any errors.
Actually got a <expressionStackOverflowError> with message:
evaluation nested too deeply: infinite recursion / options(expressions=)?
── Failure ('test-xplot_boxplot.R:169:3'): xplot_boxplot ───────────────────────
Expected `old_b <- xplot_boxplot(xpdb_x, aes(MED1, ETA1), type = "b", quiet = TRUE)` not to throw any errors.
Actually got a <expressionStackOverflowError> with message:
evaluation nested too deeply: infinite recursion / options(expressions=)?
── Error ('test-xplot_boxplot.R:11:18'): xplot_boxplot ─────────────────────────
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'old_bo' not found
Backtrace:
▆
1. ├─testthat::expect_setequal(geoms_lists(old_bo), "GeomBoxplot") at test-xplot_boxplot.R:172:3
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─xpose.xtras (local) geoms_lists(old_bo)
5. └─purrr::map_chr(gg$layers, ~class(.x$geom)[1]) at test-xplot_boxplot.R:11:18
6. └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
7. └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
[ FAIL 3 | WARN 0 | SKIP 51 | PASS 1565 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.2
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [235s/237s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(xpose.xtras)
ℹ xpose isn't attached; its own functions (e.g. `dv_vs_ipred()`) won't be
available until you load it.
Load it before xpose.xtras (or load conflicted) so its `irep()` bugfix takes
effect too.
Attaching package: 'xpose.xtras'
The following object is masked from 'package:stats':
filter
>
> test_check("xpose.xtras")
Using data from $prob no.1
Filtering data by EVID == 0
Returning parameter estimates from $prob no.1, subprob no.1, method foce
Returning data from run001.cor, $prob no.1, subprob no.1, method foce
Returning data from run001.cor, $prob no.1, subprob no.1, method foce
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
i For nlmixr2 models, sometimes '@file' is a better `axis.text`, instead of '@run'.
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, DOSE, AMT, SS, II ... and 23 more variables
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Added `process_preset()`("2")
Added `process_preset()`("1")
Added `process_preset()`("2")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("describe")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("drop_eta5")
* "drop_eta5": `~.x %>% as_xpdb_x() %>% set_var_types(na = "ETA5")`
Added `process_preset()`("convert")
Added `process_preset()`("convert2")
Removed `process_preset()`("convert2")
Added `process_preset()`("convert")
Added `process_preset()`("describe")
Added `process_preset()`("describe")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
Added `process_preset()`("convert")
i About to update the process-preset block in '/tmp/Rtmpx1Ksht/working_dir/RtmpQSM8X6/file386e8d206441a8':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x %>% as_xpdb_x(), name = "convert",
overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Added `process_preset()`("convert")
i About to update the process-preset block in '/tmp/Rtmpx1Ksht/working_dir/RtmpQSM8X6/file386e8d32ca124':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x %>% as_xpdb_x(), name = "convert",
overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Process presets written to '/tmp/Rtmpx1Ksht/working_dir/RtmpQSM8X6/file386e8d32ca124'
Removed `process_preset()`("convert")
Process presets written to '/tmp/Rtmpx1Ksht/working_dir/RtmpQSM8X6/file386e8d32ca124'
Added `process_preset()`("convert")
Process presets written to '/tmp/Rtmpx1Ksht/working_dir/RtmpQSM8X6/file386e8d6b17b318'
Added `process_preset()`("convert")
i About to update the process-preset block in '/tmp/Rtmpx1Ksht/working_dir/RtmpQSM8X6/file386e8d38a1e7bd':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x %>% as_xpdb_x(), name = "convert",
overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Process presets written to '/tmp/Rtmpx1Ksht/working_dir/RtmpQSM8X6/file386e8d38a1e7bd'
Added `process_preset()`("convert")
i About to update the process-preset block in '/tmp/Rtmpx1Ksht/working_dir/RtmpQSM8X6/file386e8d38a1e7bd':
# >>> xpose.xtras process presets (auto-generated by
add_process_preset()/persist=TRUE; do not edit by hand) >>>
xpose.xtras::add_process_preset(~.x, name = "convert", overwrite = TRUE)
# <<< xpose.xtras process presets <<<
Process presets written to '/tmp/Rtmpx1Ksht/working_dir/RtmpQSM8X6/file386e8d38a1e7bd'
Removed `process_preset()`("convert")
i About to update the process-preset block in '/tmp/Rtmpx1Ksht/working_dir/RtmpQSM8X6/file386e8d38a1e7bd':
Process presets written to '/tmp/Rtmpx1Ksht/working_dir/RtmpQSM8X6/file386e8d38a1e7bd'
.
Reading: run16tab [$prob no.1]
Looking for nonmem output files
Reading: run18.cor, run18.cov, run18.ext, run18.phi, run18.shk
Saving _problems/test-xplot_boxplot-168.R
Saving _problems/test-xplot_boxplot-171.R
Saving _problems/test-xplot_boxplot-11.R
Using data from $prob no.1
Using data from $prob no.1
...............
...............
.
..
.
.
..
..
..
.
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
# A tibble: 3 x 10
param covariate covtype level value is_ref effect ci_low ci_high ci_method
<chr> <chr> <chr> <chr> <chr> <lgl> <dbl> <dbl> <dbl> <chr>
1 TVCL CLCR cont low 40 FALSE 0.997 0.995 0.998 simulation
2 TVCL CLCR cont ref 64 TRUE 1 1 1 simulation
3 TVCL CLCR cont high 102 FALSE 1.00 1.00 1.00 simulation
# A tibble: 0 x 10
# i 10 variables: param <chr>, covariate <chr>, covtype <chr>, level <chr>,
# value <chr>, is_ref <lgl>, effect <dbl>, ci_low <dbl>, ci_high <dbl>,
# ci_method <chr>
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Filtering data by EVID == 0
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Removing duplicated rows based on: ID
Using data from $prob no.1
Filtering data by EVID == 0
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
! 1 of 3 plot(s) failed and was skipped: "stop"
Using data from $prob no.1
Filtering data by EVID == 0
.Using data from $prob no.1
Filtering data by EVID == 0
.Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Removing duplicated rows based on: ID
Tidying data by ID, SEX, MED1, MED2, DOSE ... and 23 more variables
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
Using data from $prob no.1
Filtering data by EVID == 0
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
i xpose isn't attached; its own functions (e.g. `dv_vs_ipred()`) won't be available until you load it.
i xpose isn't attached; its own functions (e.g. `dv_vs_ipred()`) won't be available until you load it.
Load it before xpose.xtras (or load conflicted) so its `irep()` bugfix takes effect too.
[ FAIL 3 | WARN 0 | SKIP 51 | PASS 1565 ]
══ Skipped tests (51) ══════════════════════════════════════════════════════════
• On CRAN (40): 'test-colinearity.R:82:3', 'test-colinearity.R:124:3',
'test-colinearity.R:241:3', 'test-covariates.R:123:3',
'test-diag_constants.R:227:3', 'test-diag_constants.R:241:3',
'test-fixes.R:627:3', 'test-modavg_xpdb.R:2:3', 'test-nlmixr2.R:60:3',
'test-nlmixr2.R:102:3', 'test-nlmixr2.R:135:3', 'test-nlmixr2.R:181:3',
'test-nlmixr2.R:447:3', 'test-nlmixr2.R:483:3', 'test-nlmixr2.R:505:3',
'test-nlmixr2.R:529:3', 'test-nlmixr2.R:548:3', 'test-nlmixr2.R:567:3',
'test-nlmixr2.R:586:3', 'test-nlmixr2.R:605:3', 'test-utils.R:402:5',
'test-utils.R:482:3', 'test-xplot_pairs.R:44:3', 'test-xplot_pairs.R:165:3',
'test-xplot_pairs.R:320:3', 'test-xplot_rocplot.R:36:3',
'test-xplot_rocplot.R:131:3', 'test-xset_features.R:192:3',
'test-xset_features.R:192:3', 'test-xset_features.R:192:3',
'test-xset_features.R:192:3', 'test-xset_plots.R:220:3',
'test-xset_plots.R:490:3', 'test-xset_plots.R:553:3',
'test-xset_shark.R:2:3', 'test-xset_waterfall.R:2:3', 'test-zzz.R:62:7',
'test-zzz.R:62:7', 'test-zzz.R:62:7', 'test-zzz.R:62:7'
• requireNamespace("rxode2", quietly = TRUE) && "rxDerived" %in%
getNamespaceExports("rxode2") is TRUE (2): 'test-diag_constants.R:188:3',
'test-diag_constants.R:194:3'
• {bbr} is not installed (8): 'test-bbr.R:2:3', 'test-bbr.R:14:3',
'test-bbr.R:25:3', 'test-bbr.R:35:3', 'test-bbr.R:45:3', 'test-bbr.R:53:3',
'test-bbr.R:60:3', 'test-bbr.R:70:3'
• {qs} is not installed (1): 'test-nlmixr2.R:624:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-xplot_boxplot.R:166:3'): xplot_boxplot ───────────────────────
Expected `... <- NULL` not to throw any errors.
Actually got a <expressionStackOverflowError> with message:
evaluation nested too deeply: infinite recursion / options(expressions=)?
── Failure ('test-xplot_boxplot.R:169:3'): xplot_boxplot ───────────────────────
Expected `old_b <- xplot_boxplot(xpdb_x, aes(MED1, ETA1), type = "b", quiet = TRUE)` not to throw any errors.
Actually got a <expressionStackOverflowError> with message:
evaluation nested too deeply: infinite recursion / options(expressions=)?
── Error ('test-xplot_boxplot.R:11:18'): xplot_boxplot ─────────────────────────
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'old_bo' not found
Backtrace:
▆
1. ├─testthat::expect_setequal(geoms_lists(old_bo), "GeomBoxplot") at test-xplot_boxplot.R:172:3
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─xpose.xtras (local) geoms_lists(old_bo)
5. └─purrr::map_chr(gg$layers, ~class(.x$geom)[1]) at test-xplot_boxplot.R:11:18
6. └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
7. └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
[ FAIL 3 | WARN 0 | SKIP 51 | PASS 1565 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc