Package: ggPMX Check: tests New result: ERROR Running ‘testthat.R’ [448s/422s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ggPMX) > library(data.table) > setDTthreads(1) > test_check("ggPMX") Attaching package: 'dplyr' The following objects are masked from 'package:data.table': between, first, last The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union convergence of SAEM parameter estimates file does not exist. convergence of SAEM parameter estimates file does not exist. convergence of SAEM parameter estimates file does not exist. Error in loadNamespace(x) : there is no package called 'qs' Saving _problems/test-pmx-all-plots-134.R convergence of SAEM parameter estimates file does not exist. convergence of SAEM parameter estimates file does not exist. convergence of SAEM parameter estimates file does not exist. convergence of SAEM parameter estimates file does not exist. convergence of SAEM parameter estimates file does not exist. convergence of SAEM parameter estimates file does not exist. Error in loadNamespace(x) : there is no package called 'qs' Error in loadNamespace(x) : there is no package called 'qs' Saving _problems/test-pmx_nlmixr-28.R convergence of SAEM parameter estimates file does not exist. convergence of SAEM parameter estimates file does not exist. convergence of SAEM parameter estimates file does not exist. [ FAIL 3 | WARN 0 | SKIP 15 | PASS 988 ] ══ Skipped tests (15) ══════════════════════════════════════════════════════════ • On CRAN (12): 'test-nlmixr.R:3:5', 'test-nlmixr.R:43:5', 'test-nlmixr.R:117:5', 'test-nonmem_reader.R:115:13', 'test-pmx-report.R:68:7', 'test-pmx-report.R:79:7', 'test-pmx-report.R:98:7', 'test-pmx-report.R:117:7', 'test-pmx-report.R:157:7', 'test-pmx-report.R:174:7', 'test-utils.R:107:5', 'test-vdiff.R:6:5' • empty test (1): 'test-nonmem_reader.R:98:3' • file.exists(test_path("censoring1_project.zip")) is not TRUE (1): 'test-simBlq-npde.R:1:1' • skipping ChartsData export warning test (1): 'test-utils.R:89:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-pmx-all-plots.R:132:7'): pmx_plot_generic with nlmixr controller: params: ctr, pname result: identical inherits, names ── Error: there is no package called 'qs' Backtrace: ▆ 1. ├─nlmixr2est::nlmixr(...) at test-pmx-all-plots.R:132:7 2. └─nlmixr2est:::nlmixr2.function(...) 3. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-pmx-report.R:205:7'): (code run outside of `test_that()`) ────── Error: there is no package called 'qs' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-pmx-report.R:2:3 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. ├─nlmixr2est::nlmixr(...) at test-pmx-report.R:205:7 5. └─nlmixr2est:::nlmixr2.function(...) 6. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-pmx_nlmixr.R:26:3'): (code run outside of `test_that()`) ─────── Error: there is no package called 'qs' Backtrace: ▆ 1. ├─nlmixr2est::nlmixr(...) at test-pmx_nlmixr.R:26:3 2. └─nlmixr2est:::nlmixr2.function(...) 3. └─nlmixr2est:::nlmixr2Est0(.env) [ FAIL 3 | WARN 0 | SKIP 15 | PASS 988 ] Error: ! Test failures. Execution halted Package: nlmixr2 Check: tests New result: ERROR Running ‘testthat.R’ [10s/10s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(nlmixr2) ── Attaching packages ───────────────────────────────────────── nlmixr2 4.0.1 ── ✔ lotri 1.0.2 ✔ nlmixr2extra 3.0.2 ✔ nlmixr2data 2.0.9 ✔ nlmixr2plot 3.0.3 ✔ nlmixr2est 4.1.1 ✔ rxode2 5.0.0 ── Optional Packages Loaded/Ignored ─────────────────────────── nlmixr2 4.0.1 ── ✖ babelmixr2 ✖ nonmem2rx ✖ ggPMX ✖ posologyr ✖ monolix2rx ✖ shinyMixR ✖ nlmixr2lib ✖ xpose.nlmixr2 ✖ nlmixr2rpt ── Conflicts ───────────────────────────────────────────── nlmixr2conflicts() ── ✖ rxode2::boxCox() masks nlmixr2est::boxCox() ✖ rxode2::yeoJohnson() masks nlmixr2est::yeoJohnson() > > test_check("nlmixr2") Error in loadNamespace(x) : there is no package called 'qs' Saving _problems/test-basic-nlmixr2-50.R [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-basic-nlmixr2.R:47:3'): basic nlmixr tests ───────────────────── Error: there is no package called 'qs' Backtrace: ▆ 1. ├─base::suppressMessages(...) at test-basic-nlmixr2.R:47:3 2. │ └─base::withCallingHandlers(...) 3. ├─nlmixr2est::nlmixr(...) 4. └─nlmixr2est:::nlmixr2.function(...) 5. └─nlmixr2est:::nlmixr2Est0(.env) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ] Error: ! Test failures. Execution halted Package: nlmixr2plot Check: tests New result: ERROR Running ‘testthat.R’ [16s/16s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(nlmixr2plot) > > test_check("nlmixr2plot") Error in loadNamespace(x) : there is no package called 'qs' Saving _problems/test-nlmixr2PlotList-46.R Error in loadNamespace(x) : there is no package called 'qs' Saving _problems/test-plots-41.R [ FAIL 2 | WARN 0 | SKIP 2 | PASS 5 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test-plots-cens.R:2:3', 'test-plots-multiple-endpoints.R:2:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-nlmixr2PlotList.R:38:3'): test addition operator ─────────────── Error: there is no package called 'qs' Backtrace: ▆ 1. ├─base::suppressMessages(...) at test-nlmixr2PlotList.R:38:3 2. │ └─base::withCallingHandlers(...) 3. ├─nlmixr2est::nlmixr(...) 4. └─nlmixr2est:::nlmixr2.function(...) 5. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-plots.R:33:3'): test plots with vdiffr ───────────────────────── Error: there is no package called 'qs' Backtrace: ▆ 1. ├─base::suppressMessages(...) at test-plots.R:33:3 2. │ └─base::withCallingHandlers(...) 3. ├─nlmixr2est::nlmixr(...) 4. └─nlmixr2est:::nlmixr2.function(...) 5. └─nlmixr2est:::nlmixr2Est0(.env) [ FAIL 2 | WARN 0 | SKIP 2 | PASS 5 ] Error: ! Test failures. Execution halted Package: nlmixr2rpt Check: examples New 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)$rptdetails > > # Now we will build the figures > bfres = build_figures(obnd = obnd, + fit = fit, + rptdetails = rptdetails) Attaching package: ‘xpose’ The following object is masked from ‘package:stats’: filter Error in loadNamespace(x) : there is no package called ‘qs’ Calls: build_figures ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted Package: nlmixr2rpt Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Accessing_Figures_and_Tables.Rmd’ using rmarkdown Quitting from Accessing_Figures_and_Tables.Rmd:58-67 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `loadNamespace()`: ! there is no package called 'qs' --- Backtrace: ▆ 1. ├─nlmixr2rpt::build_figures(obnd = obnd, fit = fit, rptdetails = rptdetails) 2. │ ├─base::eval(parse(text = preamble_str)) 3. │ │ └─base::eval(parse(text = preamble_str)) 4. │ └─xpose.nlmixr2::xpose_data_nlmixr(fit) 5. │ ├─obj$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 Package: shinyMixR Check: tests New result: ERROR Running ‘testthat.R’ [5s/5s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # see https://github.com/rstudio/shinytest2/issues/351 > options(chromote.timeout = 120) > > library(testthat) > library(shinyMixR) Loading required package: shiny Loading required package: ggplot2 > library(nlmixr2) ── Attaching packages ───────────────────────────────────────── nlmixr2 4.0.1 ── ✔ lotri 1.0.2 ✔ nlmixr2plot 3.0.3 ✔ nlmixr2data 2.0.9 ✔ rxode2 5.0.0 ✔ nlmixr2est 4.1.1 ✔ xpose.nlmixr2 0.4.1 ✔ nlmixr2extra 3.0.2 ── Optional Packages Loaded/Ignored ─────────────────────────── nlmixr2 4.0.1 ── ✔ shinyMixR ✖ nlmixr2lib ✔ xpose.nlmixr2 ✖ nlmixr2rpt ✖ babelmixr2 ✖ nonmem2rx ✖ ggPMX ✖ posologyr ✖ monolix2rx ── Conflicts ───────────────────────────────────────────── nlmixr2conflicts() ── ✖ rxode2::boxCox() masks nlmixr2est::boxCox() ✖ rxode2::yeoJohnson() masks nlmixr2est::yeoJohnson() > > test_check("shinyMixR") xdg-open: file '/home/hornik/tmp/scratch/RtmpgwwsCN/files/analysis/run1/par_table.html' does not exist Saving _problems/test-update_inits-9.R [ FAIL 1 | WARN 0 | SKIP 12 | PASS 23 ] ══ Skipped tests (12) ══════════════════════════════════════════════════════════ • On CRAN (11): 'test-module_dataexplore.R:3:3', 'test-module_metadata.R:3:3', 'test-module_report.R:4:3', 'test-module_run.R:3:3', 'test-module_script.R:3:3', 'test-module_settings.R:3:3', 'test-run_nmx.R:3:3', 'test-run_shinymixr.R:3:3', 'test-shinymixr-01-model-run1.R:8:3', 'test-shinymixr-02-parameter-table.R:6:3', 'test-shinymixr-03-create-newmodel.R:6:3' • {qs} is not installed. (1): 'test-gof_plot.R:10:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-update_inits.R:9:3'): update_inits works as expected ─────────── Error: package "qs" needed for this function to work Backtrace: ▆ 1. └─shinyMixR::update_inits(...) at test-update_inits.R:9:3 2. ├─ores$ui 3. └─nlmixr2est:::`$.nlmixr2FitData`(ores, "ui") 4. └─nlmixr2est:::`$.nlmixr2FitCore`(.env, arg, exact) 5. ├─nlmixr2est::nmObjGet(.lst) 6. └─nlmixr2est:::nmObjGet.ui(.lst) 7. ├─nlmixr2est:::.cloneEnv(rxode2::rxUiDecompress(get("ui", .env))) 8. └─rxode2::rxUiDecompress(get("ui", .env)) 9. └─rxode2::rxReq("qs") [ FAIL 1 | WARN 0 | SKIP 12 | PASS 23 ] Deleting unused snapshots: 'shinymixr-02-parameter-table/run2-model-001.json', 'shinymixr-02-parameter-table/run2-model-001_.png', 'shinymixr-02-parameter-table/run2-model-002.json', 'shinymixr-02-parameter-table/run2-model-002_.png', 'shinymixr-03-create-newmodel/run3-model-001.json', 'shinymixr-03-create-newmodel/run3-model-001_.png', 'shinymixr-03-create-newmodel/run3-model-002.json', and 'shinymixr-03-create-newmodel/run3-model-002_.png' Error: ! Test failures. Execution halted Package: xpose.xtras Check: examples New result: ERROR Running examples in ‘xpose.xtras-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: backfill_nlmixr2_props > ### Title: Populate some properties from nlmixr2 fit > ### Aliases: backfill_nlmixr2_props > > ### ** Examples > > > xpdb_nlmixr2 %>% + set_prop(condn = "not implemented") %>% + get_prop("condn") [1] "not implemented" > > xpdb_nlmixr2 %>% + set_prop(condn = "not implemented") %>% + backfill_nlmixr2_props() %>% + get_prop("condn") Error: package "qs" needed for this function to work Execution halted Package: xpose.xtras Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [157s/157s] 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 is not currently attached. Attaching package: 'xpose.xtras' The following object is masked from 'package:stats': filter > > test_check("xpose.xtras") Saving _problems/test-nlmixr2-11.R Saving _problems/test-nlmixr2-14.R Saving _problems/test-nlmixr2-18.R Error in loadNamespace(x) : there is no package called 'qs' Saving _problems/test-nlmixr2-320.R [ FAIL 4 | WARN 2 | SKIP 9 | PASS 792 ] ══ Skipped tests (9) ═══════════════════════════════════════════════════════════ • On CRAN (7): 'test-covariates.R:123:3', 'test-xplot_boxplot.R:157:3', 'test-xplot_pairs.R:44:3', 'test-xset_features.R:170:3', 'test-xset_features.R:170:3', 'test-xset_features.R:170:3', 'test-xset_features.R:170:3' • requireNamespace("rxode2", quietly = TRUE) && "rxDerived" %in% getNamespaceExports("rxode2") is TRUE (2): 'test-diag_constants.R:123:3', 'test-diag_constants.R:129:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-nlmixr2.R:9:3'): nlmixr2 is compatible ─────────────────────── Expected `nlmixr2_as_xtra(fit_example)` not to throw any errors. Actually got a with message: No `nlmixr2` fit object found. Caused by error in `loadNamespace()`: ! there is no package called 'qs' ── Failure ('test-nlmixr2.R:12:3'): nlmixr2 is compatible ────────────────────── Expected `nlmixr2_as_xtra(fit_example, .skip_assoc = TRUE)` not to throw any errors. Actually got a with message: No `nlmixr2` fit object found. Caused by error in `loadNamespace()`: ! there is no package called 'qs' ── Error ('test-nlmixr2.R:15:3'): nlmixr2 is compatible ──────────────────────── Error in `backfill_nlmixr2_props(.)`: No `nlmixr2` fit object found. Caused by error in `loadNamespace()`: ! there is no package called 'qs' Backtrace: ▆ 1. ├─testthat::expect_failure(...) at test-nlmixr2.R:15:3 2. │ └─testthat:::capture_success_failure(expr) 3. │ └─base::withCallingHandlers(...) 4. ├─testthat::expect_identical(...) 5. │ └─testthat::quasi_label(enquo(object), label) 6. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 7. ├─xpose.xtras::nlmixr2_as_xtra(fit_example) 8. │ ├─... %>% backfill_nlmixr2_props() 9. │ └─xpose.nlmixr2::xpose_data_nlmixr2(obj = obj, ...) 10. │ ├─obj$dataMergeInner 11. │ └─nlmixr2est:::`$.nlmixr2FitData`(obj, "dataMergeInner") 12. │ ├─nlmixr2est::nmObjGetData(.lst) 13. │ └─nlmixr2est:::nmObjGetData.dataMergeInner(.lst) 14. │ └─nlmixr2est:::.dataMergeStub(.obj, preferFit = FALSE) 15. │ ├─obj$origData 16. │ └─nlmixr2est:::`$.nlmixr2FitData`(obj, "origData") 17. │ └─nlmixr2est:::`$.nlmixr2FitCore`(.env, arg, exact) 18. │ ├─nlmixr2est::nmObjGet(.lst) 19. │ └─nlmixr2est:::nmObjGet.default(.lst) 20. ├─xpose.xtras::backfill_nlmixr2_props(.) 21. │ └─xpose.xtras:::assert_nlmixr2fit(xpdb) 22. │ ├─xpose.xtras:::xpa(...) 23. │ │ ├─rlang::try_fetch(...) 24. │ │ │ ├─base::tryCatch(...) 25. │ │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 26. │ │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 27. │ │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 28. │ │ │ └─base::withCallingHandlers(...) 29. │ │ └─rlang::exec(...) 30. │ └─xpose.xtras::test_nlmixr2_has_fit(xpdb) 31. │ └─xpose::check_xpdb(xpdb) 32. │ └─xpose::is.xpdb(xpdb) 33. ├─xpose.xtras:::mutate_files(...) 34. │ └─xpose::check_xpdb(xpdb) 35. │ └─xpose::is.xpdb(xpdb) 36. ├─xpose.xtras::set_prop(., file = mod_name) 37. │ └─xpose::get_summary(xpdb) 38. │ └─xpose::check_xpdb(xpdb, check = "summary") 39. │ └─xpose::is.xpdb(xpdb) 40. ├─xpose.xtras::as_xp_xtras(.) 41. │ └─xpose.xtras::as_xpdb_x(x) 42. │ └─base::structure(x, class = c("xp_xtras", "uneval")) 43. ├─xpose.xtras::attach_nlmixr2(., obj) 44. │ └─xpose::check_xpdb(xpdb) 45. │ └─xpose::is.xpdb(xpdb) 46. ├─base::loadNamespace(x) 47. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 48. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 49. │ │ └─base (local) doWithOneRestart(return(expr), restart) 50. │ └─base::stop(cond) 51. └─rlang (local) ``(``) 52. └─handlers[[1L]](cnd) 53. └─rlang::abort(...) ── Error ('test-nlmixr2.R:319:5'): pure LL fits can be used ──────────────────── Error: there is no package called 'qs' Backtrace: ▆ 1. ├─base::suppressMessages(...) at test-nlmixr2.R:318:3 2. │ └─base::withCallingHandlers(...) 3. ├─nlmixr2est::nlmixr(...) at test-nlmixr2.R:319:5 4. └─nlmixr2est:::nlmixr2.function(...) 5. └─nlmixr2est:::nlmixr2Est0(.env) [ FAIL 4 | WARN 2 | SKIP 9 | PASS 792 ] Error: ! Test failures. Execution halted