diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-02-10 09:14:59 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-02-10 09:14:59 +0100 |
| commit | 2b06ba5be233f5b88a3a64f7de916ed476326067 (patch) | |
| tree | 721d08d9c9d1a6cd6285a904b9981466ad9de72e | |
| parent | d8f31d1323998f33d07535f55c81be380d93ca45 (diff) | |
GNUMakefile: Convince testthat to give dynamic output
This means that we still get the \r in the test logs so so the
postprocessing with sed works unmodified
| -rw-r--r-- | GNUmakefile | 9 | ||||
| -rw-r--r-- | test.log | 163 |
2 files changed, 11 insertions, 161 deletions
diff --git a/GNUmakefile b/GNUmakefile index 5f2b9bda..7052bc01 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -79,16 +79,15 @@ clean: $(RM) Rplots.pdf test: install - "$(RBIN)/Rscript" -e 'devtools::test()' 2>&1 | tee test.log - # The following does not have the desired effect with current testthat - sed -i -e "s/\r.*\r//" test.log + "$(RBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee test.log + sed -i -e "s/.*\r.*\r//" test.log devtest: install - "$(RDEVBIN)/Rscript" -e 'devtools::test()' 2>&1 | tee test_dev.log + "$(RDEVBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee test_dev.log sed -i -e "s/\r.*\r//" test_dev.log slowtests: install - NOT_CRAN=true "$(RBIN)/Rscript" -e 'library(mkin); testthat::test_dir("tests/testthat/slow")' 2>&1 | tee tests_slow.log + NOT_CRAN=true "$(RBIN)/Rscript" -e 'cli.dynamic = TRUE); library(mkin); testthat::test_dir("tests/testthat/slow")' 2>&1 | tee tests_slow.log sed -i -e "s/\r.*\r//" tests_slow.log testcheck: roxygen test check @@ -2,190 +2,41 @@ Loading required package: parallel ℹ Testing mkin ✔ | F W S OK | Context - -⠏ | 0 | AIC -⠏ | 0 | AIC calculation ✔ | 5 | AIC calculation - -⠏ | 0 | analytical -⠏ | 0 | Analytical solutions for coupled models -⠋ | 1 | Analytical solutions for coupled models -⠙ | 2 | Analytical solutions for coupled models -⠹ | 3 | Analytical solutions for coupled models -⠸ | 4 | Analytical solutions for coupled models -⠼ | 5 | Analytical solutions for coupled models -✔ | 5 | Analytical solutions for coupled models [3.4s] - -⠏ | 0 | aw -⠏ | 0 | Calculation of Akaike weights +✔ | 5 | Analytical solutions for coupled models [3.5s] ✔ | 5 | Calculation of Akaike weights - -⠏ | 0 | CAKE_export -⠏ | 0 | Export dataset for reading into CAKE ✔ | 2 | Export dataset for reading into CAKE - -⠏ | 0 | confidence -⠏ | 0 | Confidence intervals and p-values -⠼ | 5 | Confidence intervals and p-values -⠋ | 11 | Confidence intervals and p-values -⠙ | 12 | Confidence intervals and p-values ✔ | 12 | Confidence intervals and p-values [1.0s] - -⠏ | 0 | error_models -⠏ | 0 | Error model fitting -⠹ | 3 | Error model fitting -⠸ | 4 | Error model fitting -⠼ | 5 | Error model fitting -⠴ | 6 | Error model fitting -⠧ | 8 | Error model fitting -⠏ | 10 | Error model fitting -⠙ | 12 | Error model fitting -⠸ | 14 | Error model fitting -✔ | 14 | Error model fitting [4.9s] - -⠏ | 0 | f_time_norm -⠏ | 0 | Time step normalisation +✔ | 14 | Error model fitting [4.8s] ✔ | 5 | Time step normalisation - -⠏ | 0 | FOCUS_chi2_error_level -⠏ | 0 | Calculation of FOCUS chi2 error levels -⠙ | 2 | Calculation of FOCUS chi2 error levels -⠸ | 4 | Calculation of FOCUS chi2 error levels ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] - -⠏ | 0 | FOCUS_D_UBA_expertise -⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014) -⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) -⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) -⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] - -⠏ | 0 | from_max_mean -⠏ | 0 | Test fitting the decline of metabolites from their maximum -⠹ | 3 | Test fitting the decline of metabolites from their maximum -⠸ | 4 | Test fitting the decline of metabolites from their maximum -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] - -⠏ | 0 | logistic -⠏ | 0 | Fitting the logistic model -⠋ | 1 | Fitting the logistic model +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] ✔ | 1 | Fitting the logistic model [0.2s] - -⠏ | 0 | mixed -⠏ | 0 | Nonlinear mixed-effects models -⠙ | 2 | Nonlinear mixed-effects models -⠹ | 3 | Nonlinear mixed-effects models -⠸ | 4 | Nonlinear mixed-effects models -⠏ | 10 | Nonlinear mixed-effects models -⠙ | 12 | Nonlinear mixed-effects models -⠧ | 18 | Nonlinear mixed-effects models -⠙ | 22 | Nonlinear mixed-effects models -⠹ | 23 | Nonlinear mixed-effects models -✔ | 1 35 | Nonlinear mixed-effects models [26.6s] +✔ | 1 35 | Nonlinear mixed-effects models [26.8s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_mixed.R:161:3): saem results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve ──────────────────────────────────────────────────────────────────────────────── - -⠏ | 0 | mkinds -⠏ | 0 | Test dataset classes mkinds and mkindsg ✔ | 2 | Test dataset classes mkinds and mkindsg - -⠏ | 0 | mkinfit_errors -⠏ | 0 | Special cases of mkinfit calls -⠇ | 9 | Special cases of mkinfit calls -⠏ | 10 | Special cases of mkinfit calls ✔ | 10 | Special cases of mkinfit calls [0.4s] - -⠏ | 0 | mkinfit -⠏ | 0 | mkinfit features -⠋ | 1 | mkinfit features ✔ | 1 | mkinfit features [0.3s] - -⠏ | 0 | mkinmod -⠏ | 0 | mkinmod model generation and printing -⠧ | 8 | mkinmod model generation and printing ✔ | 8 | mkinmod model generation and printing [0.2s] - -⠏ | 0 | mkinpredict_SFO_SFO -⠏ | 0 | Model predictions with mkinpredict -⠋ | 1 | Model predictions with mkinpredict -✔ | 3 | Model predictions with mkinpredict [0.3s] - -⠏ | 0 | nafta -⠏ | 0 | Evaluations according to 2015 NAFTA guidance -⠙ | 2 | Evaluations according to 2015 NAFTA guidance -⠇ | 9 | Evaluations according to 2015 NAFTA guidance -⠏ | 10 | Evaluations according to 2015 NAFTA guidance +✔ | 3 | Model predictions with mkinpredict [0.4s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] - -⠏ | 0 | nlme -⠏ | 0 | Nonlinear mixed-effects models with nlme -⠋ | 1 | Nonlinear mixed-effects models with nlme -⠙ | 2 | Nonlinear mixed-effects models with nlme -⠼ | 5 | Nonlinear mixed-effects models with nlme -⠴ | 6 | Nonlinear mixed-effects models with nlme -⠧ | 8 | Nonlinear mixed-effects models with nlme -⠇ | 9 | Nonlinear mixed-effects models with nlme ✔ | 9 | Nonlinear mixed-effects models with nlme [8.3s] - -⠏ | 0 | nlmixr -⠏ | 0 | plot -⠏ | 0 | Plotting -⠋ | 1 | Plotting -⠇ | 9 | Plotting -⠹ | 13 | Plotting -⠼ | 15 | Plotting ✔ | 16 | Plotting [1.3s] - -⠏ | 0 | residuals -⠏ | 0 | Residuals extracted from mkinfit models ✔ | 4 | Residuals extracted from mkinfit models - -⠏ | 0 | schaefer07_complex_case -⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper -⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s] - -⠏ | 0 | SFORB -⠏ | 0 | Fitting the SFORB model -⠋ | 1 | Fitting the SFORB model -⠼ | 5 | Fitting the SFORB model ✔ | 7 | Fitting the SFORB model [3.9s] - -⠏ | 0 | summary_old_objects -⠏ | 0 | Summaries of old mkinfit objects ✔ | 1 | Summaries of old mkinfit objects - -⠏ | 0 | summary -⠏ | 0 | Summary -⠸ | 4 | Summary ✔ | 4 | Summary [0.1s] - -⠏ | 0 | synthetic_data_for_UBA_2014 -⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014) -⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014) -⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014) ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] - -⠏ | 0 | tests -⠏ | 0 | Hypothesis tests -⠼ | 5 | Hypothesis tests -⠴ | 6 | Hypothesis tests -⠧ | 8 | Hypothesis tests -⠇ | 9 | Hypothesis tests -✔ | 9 | Hypothesis tests [8.5s] - -⠏ | 0 | twa -⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs) -⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs) -⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs) -⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs) -⠸ | 4 | Calculation of maximum time weighted average concentrations (TWAs) +✔ | 9 | Hypothesis tests [8.6s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 69.0 s +Duration: 69.5 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting with saemix takes around 10 minutes when using deSolve (1) |