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)$rptdetails > > # Now we will build the figures > bfres = build_figures(obnd = obnd, + fit = fit, + rptdetails = rptdetails) Attaching package: ‘xpose’ The following object is masked from ‘package:stats’: filter Error : package "qs" needed for this function to work Warning: cannot deserialize object 'origData'; please ensure the 'qs2' or 'qs' package is installed Warning in seq_len(nrow(.origData)) : first element used of 'length.out' argument Error in seq_len(nrow(.origData)) : argument must be coercible to non-negative integer Calls: build_figures ... nmObjGetData -> nmObjGetData.dataMergeInner -> .dataMergeStub Execution halted Package: nlmixr2rpt Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Accessing_Figures_and_Tables.Rmd’ using rmarkdown Quitting from Accessing_Figures_and_Tables.Rmd:58-67 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `seq_len()`: ! argument must be coercible to non-negative integer --- Backtrace: ▆ 1. └─nlmixr2rpt::build_figures(obnd = obnd, fit = fit, rptdetails = rptdetails) 2. ├─base::eval(parse(text = preamble_str)) 3. │ └─base::eval(parse(text = preamble_str)) 4. └─xpose.nlmixr2::xpose_data_nlmixr(fit) 5. ├─obj$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 Package: nlmixr2rpt Check: tests New result: ERROR Running ‘testthat.R’ [3s/3s] 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 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 5.0.2 ✔ 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") Error : package "qs" needed for this function to work Saving _problems/test-gof_plot-10.R xdg-open: file '/home/hornik/tmp/scratch/RtmpQVDa84/files/analysis/run1/par_table.html' does not exist Saving _problems/test-update_inits-9.R [ FAIL 2 | WARN 0 | SKIP 11 | PASS 23 ] ══ Skipped tests (11) ══════════════════════════════════════════════════════════ • 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' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-gof_plot.R:10:3'): gof_plot works as expected ────────────────── Error in `seq_len(nrow(.origData))`: argument must be coercible to non-negative integer Backtrace: ▆ 1. ├─base::suppressWarnings(gof_plot(res, ptype = "all", type = "xpose")) at test-gof_plot.R:10:3 2. │ └─base::withCallingHandlers(...) 3. └─shinyMixR::gof_plot(res, ptype = "all", type = "xpose") 4. └─xpose.nlmixr2::xpose_data_nlmixr2(dfrm) 5. ├─obj$dataMergeInner 6. └─nlmixr2est:::`$.nlmixr2FitData`(obj, "dataMergeInner") 7. ├─nlmixr2est::nmObjGetData(.lst) 8. └─nlmixr2est:::nmObjGetData.dataMergeInner(.lst) 9. └─nlmixr2est:::.dataMergeStub(.obj, preferFit = FALSE) ── Error ('test-update_inits.R:9:3'): update_inits works as expected ─────────── Error: package "qs" needed for this function to work Backtrace: ▆ 1. └─shinyMixR::update_inits(...) at test-update_inits.R:9:3 2. ├─ores$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 2 | WARN 0 | SKIP 11 | 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’ [150s/151s] 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") Error : package "qs" needed for this function to work Saving _problems/test-nlmixr2-11.R Error : package "qs" needed for this function to work Saving _problems/test-nlmixr2-14.R Error : package "qs" needed for this function to work Saving _problems/test-nlmixr2-18.R [ FAIL 3 | WARN 8 | SKIP 9 | PASS 799 ] ══ 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 `seq_len()`: ! argument must be coercible to non-negative integer ── 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 `seq_len()`: ! argument must be coercible to non-negative integer ── Error ('test-nlmixr2.R:15:3'): nlmixr2 is compatible ──────────────────────── Error in `backfill_nlmixr2_props(.)`: No `nlmixr2` fit object found. Caused by error in `seq_len()`: ! argument must be coercible to non-negative integer 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. ├─xpose.xtras::backfill_nlmixr2_props(.) 16. │ └─xpose.xtras:::assert_nlmixr2fit(xpdb) 17. │ ├─xpose.xtras:::xpa(...) 18. │ │ ├─rlang::try_fetch(...) 19. │ │ │ ├─base::tryCatch(...) 20. │ │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 21. │ │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 22. │ │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 23. │ │ │ └─base::withCallingHandlers(...) 24. │ │ └─rlang::exec(...) 25. │ └─xpose.xtras::test_nlmixr2_has_fit(xpdb) 26. │ └─xpose::check_xpdb(xpdb) 27. │ └─xpose::is.xpdb(xpdb) 28. ├─xpose.xtras:::mutate_files(...) 29. │ └─xpose::check_xpdb(xpdb) 30. │ └─xpose::is.xpdb(xpdb) 31. ├─xpose.xtras::set_prop(., file = mod_name) 32. │ └─xpose::get_summary(xpdb) 33. │ └─xpose::check_xpdb(xpdb, check = "summary") 34. │ └─xpose::is.xpdb(xpdb) 35. ├─xpose.xtras::as_xp_xtras(.) 36. │ └─xpose.xtras::as_xpdb_x(x) 37. │ └─base::structure(x, class = c("xp_xtras", "uneval")) 38. ├─xpose.xtras::attach_nlmixr2(., obj) 39. │ └─xpose::check_xpdb(xpdb) 40. │ └─xpose::is.xpdb(xpdb) 41. └─base::.handleSimpleError(...) 42. └─rlang (local) h(simpleError(msg, call)) 43. └─handlers[[1L]](cnd) 44. └─rlang::abort(...) [ FAIL 3 | WARN 8 | SKIP 9 | PASS 799 ] Error: ! Test failures. Execution halted