Last updated on 2025-11-30 12:49:55 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.2 | 12.74 | 192.70 | 205.44 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.2 | 8.88 | 138.67 | 147.55 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.2.2 | 31.00 | 178.77 | 209.77 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.2 | 25.00 | 304.09 | 329.09 | OK | |
| r-devel-windows-x86_64 | 0.2.2 | 17.00 | 185.00 | 202.00 | OK | |
| r-patched-linux-x86_64 | 0.2.2 | 10.34 | 181.19 | 191.53 | OK | |
| r-release-linux-x86_64 | 0.2.2 | 11.91 | 110.07 | 121.98 | ERROR | |
| r-release-macos-arm64 | 0.2.2 | OK | ||||
| r-release-macos-x86_64 | 0.2.2 | 14.00 | 136.00 | 150.00 | OK | |
| r-release-windows-x86_64 | 0.2.2 | 17.00 | 185.00 | 202.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.2 | OK | ||||
| r-oldrel-macos-x86_64 | 0.2.2 | 13.00 | 152.00 | 165.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.2 | 22.00 | 234.00 | 256.00 | OK |
Version: 0.2.2
Check: examples
Result: ERROR
Running examples in ‘nlmixr2rpt-Ex.R’ failed
The error most likely occurred in:
> ### Name: build_figures
> ### Title: Generates Figures for an 'nlmixr2' Report
> ### Aliases: build_figures
>
> ### ** Examples
>
> # We need an onbrand object to use below
> library(onbrand)
> obnd = read_template(
+ template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.docx"),
+ mapping = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))
>
> # We also need an nlmixr fit object
> fit = fetch_fit_example()
>
> # This reads in the report details as well
> rptdetails = yaml_read_fit(
+ obnd = obnd,
+ rptyaml = system.file(package="nlmixr2rpt", "examples", "report_fit_test.yaml"),
+ fit = fit)$rptdetails
>
> # Now we will build the figures
> bfres = build_figures(obnd = obnd,
+ fit = fit,
+ rptdetails = rptdetails)
Attaching package: ‘xpose’
The following object is masked from ‘package:stats’:
filter
Error in loadNamespace(x) : there is no package called ‘qs’
Calls: build_figures ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Accessing_Figures_and_Tables.Rmd’ using rmarkdown
Quitting from Accessing_Figures_and_Tables.Rmd:58-67 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'qs'
---
Backtrace:
▆
1. ├─nlmixr2rpt::build_figures(obnd = obnd, fit = fit, rptdetails = rptdetails)
2. │ ├─base::eval(parse(text = preamble_str))
3. │ │ └─base::eval(parse(text = preamble_str))
4. │ └─xpose.nlmixr2::xpose_data_nlmixr(fit)
5. │ ├─obj$dataMergeInner
6. │ └─nlmixr2est:::`$.nlmixr2FitData`(obj, "dataMergeInner")
7. │ ├─nlmixr2est::nmObjGetData(.lst)
8. │ └─nlmixr2est:::nmObjGetData.dataMergeInner(.lst)
9. │ └─nlmixr2est:::.dataMergeStub(.obj, preferFit = FALSE)
10. │ ├─obj$origData
11. │ └─nlmixr2est:::`$.nlmixr2FitData`(obj, "origData")
12. │ └─nlmixr2est:::`$.nlmixr2FitCore`(.env, arg, exact)
13. │ ├─nlmixr2est::nmObjGet(.lst)
14. │ └─nlmixr2est:::nmObjGet.default(.lst)
15. └─base::loadNamespace(x)
16. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
17. └─base (local) withOneRestart(expr, restarts[[1L]])
18. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Accessing_Figures_and_Tables.Rmd' failed with diagnostics:
there is no package called 'qs'
--- failed re-building ‘Accessing_Figures_and_Tables.Rmd’
--- re-building ‘Reporting_nlmixr_Fit_Results.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Reporting_nlmixr_Fit_Results.Rmd’
SUMMARY: processing the following file failed:
‘Accessing_Figures_and_Tables.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.2
Check: examples
Result: ERROR
Running examples in ‘nlmixr2rpt-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_figures
> ### Title: Generates Figures for an 'nlmixr2' Report
> ### Aliases: build_figures
>
> ### ** Examples
>
> # We need an onbrand object to use below
> library(onbrand)
> obnd = read_template(
+ template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.docx"),
+ mapping = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))
>
> # We also need an nlmixr fit object
> fit = fetch_fit_example()
>
> # This reads in the report details as well
> rptdetails = yaml_read_fit(
+ obnd = obnd,
+ rptyaml = system.file(package="nlmixr2rpt", "examples", "report_fit_test.yaml"),
+ fit = fit)$rptdetails
>
> # Now we will build the figures
> bfres = build_figures(obnd = obnd,
+ fit = fit,
+ rptdetails = rptdetails)
Attaching package: ‘xpose’
The following object is masked from ‘package:stats’:
filter
Error : package "qs" needed for this function to work
Warning: cannot deserialize object 'origData'; please ensure the 'qs2' or 'qs' package is installed
Warning in seq_len(nrow(.origData)) :
first element used of 'length.out' argument
Error in seq_len(nrow(.origData)) :
argument must be coercible to non-negative integer
Calls: build_figures ... nmObjGetData -> nmObjGetData.dataMergeInner -> .dataMergeStub
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/7s]
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(nlmixr2rpt)
>
> test_check("nlmixr2rpt")
Error : package "qs" needed for this function to work
Saving _problems/test-rptnlmixr-41.R
Error : package "qs" needed for this function to work
Saving _problems/test-rptnlmixr-119.R
Error : package "qs" needed for this function to work
Error : package "qs" needed for this function to work
Error : package "qs" needed for this function to work
Error : package "qs" needed for this function to work
Error : package "qs" needed for this function to work
Saving _problems/test-rptnlmixr-154.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 6 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-rptnlmixr.R:31:3'): build_figures ──────────────────────────────
Error in `seq_len(nrow(.origData))`: argument must be coercible to non-negative integer
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-rptnlmixr.R:31:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...)
4. │ └─base::withCallingHandlers(...)
5. └─nlmixr2rpt::build_figures(...)
6. ├─base::eval(parse(text = preamble_str))
7. │ └─base::eval(parse(text = preamble_str))
8. └─xpose.nlmixr2::xpose_data_nlmixr(fit)
9. ├─obj$dataMergeInner
10. └─nlmixr2est:::`$.nlmixr2FitData`(obj, "dataMergeInner")
11. ├─nlmixr2est::nmObjGetData(.lst)
12. └─nlmixr2est:::nmObjGetData.dataMergeInner(.lst)
13. └─nlmixr2est:::.dataMergeStub(.obj, preferFit = FALSE)
── Error ('test-rptnlmixr.R:98:3'): PowerPoint Workflow ────────────────────────
Error in `seq_len(nrow(.origData))`: argument must be coercible to non-negative integer
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-rptnlmixr.R:98:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressWarnings(...)
4. │ └─base::withCallingHandlers(...)
5. └─nlmixr2rpt::report_fit(...)
6. └─nlmixr2rpt::build_figures(...)
7. ├─base::eval(parse(text = preamble_str))
8. │ └─base::eval(parse(text = preamble_str))
9. └─xpose.nlmixr2::xpose_data_nlmixr(fit)
10. ├─obj$dataMergeInner
11. └─nlmixr2est:::`$.nlmixr2FitData`(obj, "dataMergeInner")
12. ├─nlmixr2est::nmObjGetData(.lst)
13. └─nlmixr2est:::nmObjGetData.dataMergeInner(.lst)
14. └─nlmixr2est:::.dataMergeStub(.obj, preferFit = FALSE)
── Error ('test-rptnlmixr.R:134:3'): Word Workflow ─────────────────────────────
Error in `seq_len(nrow(.origData))`: argument must be coercible to non-negative integer
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-rptnlmixr.R:134:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressWarnings(...)
4. │ └─base::withCallingHandlers(...)
5. └─nlmixr2rpt::report_fit(...)
6. └─nlmixr2rpt::build_figures(...)
7. ├─base::eval(parse(text = preamble_str))
8. │ └─base::eval(parse(text = preamble_str))
9. └─xpose.nlmixr2::xpose_data_nlmixr(fit)
10. ├─obj$dataMergeInner
11. └─nlmixr2est:::`$.nlmixr2FitData`(obj, "dataMergeInner")
12. ├─nlmixr2est::nmObjGetData(.lst)
13. └─nlmixr2est:::nmObjGetData.dataMergeInner(.lst)
14. └─nlmixr2est:::.dataMergeStub(.obj, preferFit = FALSE)
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 6 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Accessing_Figures_and_Tables.Rmd’ using rmarkdown
Quitting from Accessing_Figures_and_Tables.Rmd:58-67 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `seq_len()`:
! argument must be coercible to non-negative integer
---
Backtrace:
▆
1. └─nlmixr2rpt::build_figures(obnd = obnd, fit = fit, rptdetails = rptdetails)
2. ├─base::eval(parse(text = preamble_str))
3. │ └─base::eval(parse(text = preamble_str))
4. └─xpose.nlmixr2::xpose_data_nlmixr(fit)
5. ├─obj$dataMergeInner
6. └─nlmixr2est:::`$.nlmixr2FitData`(obj, "dataMergeInner")
7. ├─nlmixr2est::nmObjGetData(.lst)
8. └─nlmixr2est:::nmObjGetData.dataMergeInner(.lst)
9. └─nlmixr2est:::.dataMergeStub(.obj, preferFit = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Accessing_Figures_and_Tables.Rmd' failed with diagnostics:
argument must be coercible to non-negative integer
--- failed re-building ‘Accessing_Figures_and_Tables.Rmd’
--- re-building ‘Reporting_nlmixr_Fit_Results.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Reporting_nlmixr_Fit_Results.Rmd’
SUMMARY: processing the following file failed:
‘Accessing_Figures_and_Tables.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64