Package check result: OK Changes to worse in reverse depends: Package: babelmixr2 Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [92s/92s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(babelmixr2) > > test_check("babelmixr2") Error in loadNamespace(x) : there is no package called 'qs2' Error in loadNamespace(x) : there is no package called 'qs2' Error in loadNamespace(x) : there is no package called 'qs2' Error in loadNamespace(x) : there is no package called 'qs2' Error in loadNamespace(x) : there is no package called 'qs2' Error in loadNamespace(x) : there is no package called 'qs2' Error in loadNamespace(x) : there is no package called 'qs2' i mu2 item: Rx_pow_di(WT, 2) i writing monolix files i done i run Monolix manually and rerun nlmixr() i mu2 item: Rx_pow_di(WT, 2) i leaving alone monolix files because 'monolixTest-monolix.txt' is present > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > finding duplicate expressions in EBE model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in EBE model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > compiling EBE model... using C compiler: ‘gcc-15 (Debian 15.2.0-7) 15.2.0’ v done > Calculating residuals/tables v done Error in loadNamespace(x) : there is no package called 'qs2' Error : nonmem minimization not successful Error in loadNamespace(x) : there is no package called 'qs2' Error in loadNamespace(x) : there is no package called 'qs2' Error in loadNamespace(x) : there is no package called 'qs2' > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i writing nonmem files i done i only exported NONMEM control stream/data > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i writing nonmem files i done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i mu2 item: Rx_pow_di(WT, 2) > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i writing nonmem files i done i only exported NONMEM control stream/data i mu2 item: Rx_pow_di(WT, 2) > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i only exported NONMEM control stream/data Error in bblDatToPknca(model = env$ui, data = rawData, rxControl = rxControl) : no dosing rows (EVID = 1 or 4) detected Error : no rows in event table or input data Error in nlmixr2Est(env, ...) : Could not detect DV assignment for unit conversion [ FAIL 11 | WARN 4 | SKIP 10 | PASS 259 ] ══ Skipped tests (10) ══════════════════════════════════════════════════════════ • On CRAN (9): 'test-as-nlmixr2.R:8:3', 'test-as-nlmixr2.R:66:3', 'test-bioavil-works.R:2:3', 'test-convert.R:2:3', 'test-convert.R:35:3', 'test-convert.R:215:3', 'test-convert.R:229:3', 'test-fmeMcmc.R:4:3', 'test-psuedoOptim.R:3:3' • empty test (1): ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-monolix-read.R:62:7'): test monolix reading for 2019, 2020, and 2021 ── Error: there is no package called 'qs2' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-monolix-read.R:60:5 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. └─babelmixr2 (local) .nlmixr(...) at test-monolix-read.R:62:7 5. ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24 6. │ └─base::withCallingHandlers(...) 7. ├─base::suppressMessages(nlmixr2est::nlmixr(...)) 8. │ └─base::withCallingHandlers(...) 9. ├─nlmixr2est::nlmixr(...) 10. └─nlmixr2est:::nlmixr2.function(...) 11. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-monolix-read.R:151:5'): test more nlmixr2/monolix features ───── Error: there is no package called 'qs2' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-monolix-read.R:149:3 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. └─babelmixr2 (local) .nlmixr(...) at test-monolix-read.R:151:5 5. ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24 6. │ └─base::withCallingHandlers(...) 7. ├─base::suppressMessages(nlmixr2est::nlmixr(...)) 8. │ └─base::withCallingHandlers(...) 9. ├─nlmixr2est::nlmixr(...) 10. └─nlmixr2est:::nlmixr2.function(...) 11. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-monolix-read.R:187:5'): test Monolix pheno ───────────────────── Error: there is no package called 'qs2' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-monolix-read.R:183:3 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. └─babelmixr2 (local) .nlmixr(pheno, nlmixr2data::pheno_sd, "monolix", control = monolixControl(modelName = "pheno")) at test-monolix-read.R:187:5 5. ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24 6. │ └─base::withCallingHandlers(...) 7. ├─base::suppressMessages(nlmixr2est::nlmixr(...)) 8. │ └─base::withCallingHandlers(...) 9. ├─nlmixr2est::nlmixr(...) 10. └─nlmixr2est:::nlmixr2.function(...) 11. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-monolix-read.R:322:5'): pbpk mavoglurant ─────────────────────── Error: there is no package called 'qs2' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-monolix-read.R:320:3 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. └─babelmixr2 (local) .nlmixr(pbpk, nlmixr2data::mavoglurant, "monolix", control = monolixControl(modelName = "pbpk")) at test-monolix-read.R:322:5 5. ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24 6. │ └─base::withCallingHandlers(...) 7. ├─base::suppressMessages(nlmixr2est::nlmixr(...)) 8. │ └─base::withCallingHandlers(...) 9. ├─nlmixr2est::nlmixr(...) 10. └─nlmixr2est:::nlmixr2.function(...) 11. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-monolix-read.R:386:5'): nimo test ────────────────────────────── Error: there is no package called 'qs2' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-monolix-read.R:384:3 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. ├─base::suppressWarnings(.nlmixr2(nimo, tmp, "monolix", control = monolixControl(modelName = "nimo"))) at test-monolix-read.R:386:5 5. │ └─base::withCallingHandlers(...) 6. └─babelmixr2 (local) .nlmixr2(nimo, tmp, "monolix", control = monolixControl(modelName = "nimo")) 7. ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24 8. │ └─base::withCallingHandlers(...) 9. ├─base::suppressMessages(nlmixr2est::nlmixr(...)) 10. │ └─base::withCallingHandlers(...) 11. ├─nlmixr2est::nlmixr(...) 12. └─nlmixr2est:::nlmixr2.function(...) 13. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-monolix-read.R:458:5'): Monolix wbc ──────────────────────────── Error: there is no package called 'qs2' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-monolix-read.R:455:3 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. ├─base::suppressWarnings(...) at test-monolix-read.R:458:5 5. │ └─base::withCallingHandlers(...) 6. └─babelmixr2 (local) .nlmixr2(wbc, nlmixr2data::wbcSim, "monolix", control = monolixControl(modelName = "wbc")) 7. ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24 8. │ └─base::withCallingHandlers(...) 9. ├─base::suppressMessages(nlmixr2est::nlmixr(...)) 10. │ └─base::withCallingHandlers(...) 11. ├─nlmixr2est::nlmixr(...) 12. └─nlmixr2est:::nlmixr2.function(...) 13. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-monolix-read.R:493:5'): Monolix wbc test 2 ───────────────────── Error: there is no package called 'qs2' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-monolix-read.R:490:3 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. ├─wbc %>% ini(prop.err = 15) %>% ... at test-monolix-read.R:493:5 5. └─babelmixr2 (local) .nlmixr2(., nlmixr2data::wbcSim, "monolix", control = monolixControl(modelName = "x")) 6. ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-monolix-read.R:1:24 7. │ └─base::withCallingHandlers(...) 8. ├─base::suppressMessages(nlmixr2est::nlmixr(...)) 9. │ └─base::withCallingHandlers(...) 10. ├─nlmixr2est::nlmixr(...) 11. └─nlmixr2est:::nlmixr2.rxUi(...) 12. └─nlmixr2est:::nlmixr2Est0(.env) ── Failure ('test-nonmem-pred.R:26:5'): nonmem $pred model ───────────────────── Expected `nlmixr2est::nlmixr(ipredWang2007, dat, "nonmem")` not to throw any errors. Actually got a with message: there is no package called 'qs2' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-nonmem-pred.R:24:3 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. ├─testthat::expect_error(...) at test-nonmem-pred.R:26:5 5. │ └─testthat:::expect_condition_matching_(...) 6. │ └─testthat:::quasi_capture(...) 7. │ ├─testthat (local) .capture(...) 8. │ │ └─base::withCallingHandlers(...) 9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 10. ├─nlmixr2est::nlmixr(ipredWang2007, dat, "nonmem") 11. └─nlmixr2est:::nlmixr2.function(ipredWang2007, dat, "nonmem") 12. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-nonmem-read.R:72:5'): warfarin NONMEM reading ────────────────── Error: there is no package called 'qs2' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-nonmem-read.R:62:3 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. └─babelmixr2 (local) .nlmixr(...) at test-nonmem-read.R:72:5 5. ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-nonmem-read.R:1:24 6. │ └─base::withCallingHandlers(...) 7. ├─base::suppressMessages(nlmixr2est::nlmixr(...)) 8. │ └─base::withCallingHandlers(...) 9. ├─nlmixr2est::nlmixr(...) 10. └─nlmixr2est:::nlmixr2.function(...) 11. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-nonmem-read.R:134:5'): pheno NONMEM reading ──────────────────── Error: there is no package called 'qs2' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-nonmem-read.R:132:3 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. └─babelmixr2 (local) .nlmixr(pheno, nlmixr2data::pheno_sd, "nonmem", control = nonmemControl(modelName = "pheno")) at test-nonmem-read.R:134:5 5. ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-nonmem-read.R:1:24 6. │ └─base::withCallingHandlers(...) 7. ├─base::suppressMessages(nlmixr2est::nlmixr(...)) 8. │ └─base::withCallingHandlers(...) 9. ├─nlmixr2est::nlmixr(...) 10. └─nlmixr2est:::nlmixr2.function(...) 11. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-nonmem-read.R:208:5'): wbc NONMEM reading ────────────────────── Error: there is no package called 'qs2' Backtrace: ▆ 1. ├─withr::with_tempdir(...) at test-nonmem-read.R:201:3 2. │ └─withr::with_dir(tmp, code) 3. │ └─base::force(code) 4. └─babelmixr2 (local) .nlmixr2(...) at test-nonmem-read.R:208:5 5. ├─base::suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...))) at test-nonmem-read.R:1:24 6. │ └─base::withCallingHandlers(...) 7. ├─base::suppressMessages(nlmixr2est::nlmixr(...)) 8. │ └─base::withCallingHandlers(...) 9. ├─nlmixr2est::nlmixr(...) 10. └─nlmixr2est:::nlmixr2.function(...) 11. └─nlmixr2est:::nlmixr2Est0(.env) [ FAIL 11 | WARN 4 | SKIP 10 | PASS 259 ] Error: ! Test failures. Execution halted Package: ggPMX Check: tests New result: ERROR Running ‘testthat.R’ [466s/443s] 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 'qs2' 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 'qs2' Error in loadNamespace(x) : there is no package called 'qs2' 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 'qs2' 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 'qs2' 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 'qs2' 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’ [9s/9s] 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 5.0.0 ✔ rxode2 4.1.1 ── 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 'qs2' 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 'qs2' 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’ [13s/13s] 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 'qs2' Saving _problems/test-nlmixr2PlotList-46.R Error in loadNamespace(x) : there is no package called 'qs2' 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 'qs2' 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 'qs2' 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 ‘qs2’ 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 'qs2' --- 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 'qs2' --- 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: xpose.xtras Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [147s/147s] 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 'qs2' 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 'qs2' ── 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 'qs2' ── 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 'qs2' 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 'qs2' 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