diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-11 10:43:56 +0100 | 
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-11 10:43:56 +0100 | 
| commit | 0cbabc98850e436b1e0703c659cf8a00b52d7503 (patch) | |
| tree | 9c7b25c2d27affd492a84cbf2f5ce4069a62864a | |
| parent | df4de0abf471c7013a38b0e6be173a072c4bb74b (diff) | |
Skip vdiffr tests on travis as they are not robust
As can be seen in the miniscule change seen on R-devel in the reference
plot updated with this commit
| -rw-r--r-- | man/summary.saem.mmkin.Rd | 3 | ||||
| -rw-r--r-- | test_dev.log | 18 | ||||
| -rw-r--r-- | tests/figs/deps.txt | 2 | ||||
| -rw-r--r-- | tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg | 2 | ||||
| -rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 | ||||
| -rw-r--r-- | tests/testthat/test_nafta.R | 2 | ||||
| -rw-r--r-- | tests/testthat/test_plot.R | 1 | 
7 files changed, 17 insertions, 13 deletions
| diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd index f3e3fde3..67cb3cbb 100644 --- a/man/summary.saem.mmkin.Rd +++ b/man/summary.saem.mmkin.Rd @@ -87,7 +87,8 @@ ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) {  \dontrun{  # Evaluate using mmkin and saem -f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, quiet = TRUE, error_model = "tc", cores = 5) +f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, +  quiet = TRUE, error_model = "tc", cores = 5)  f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)  summary(f_saem_dfop_sfo, data = TRUE)  } diff --git a/test_dev.log b/test_dev.log index b5f8fd8e..c57bb958 100644 --- a/test_dev.log +++ b/test_dev.log @@ -3,14 +3,14 @@ Testing mkin  ✔ |  OK F W S | Context  ✔ |   4       | AIC calculation  ✔ |   2       | Export dataset for reading into CAKE -✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8 s] +✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9 s]  ✔ |   4       | Calculation of FOCUS chi2 error levels [0.4 s] -✔ |   7       | Fitting the SFORB model [3.0 s] -✔ |   5       | Analytical solutions for coupled models [2.9 s] +✔ |   7       | Fitting the SFORB model [3.1 s] +✔ |   5       | Analytical solutions for coupled models [2.8 s]  ✔ |   5       | Calculation of Akaike weights  ✔ |  10       | Confidence intervals and p-values [0.9 s] -✔ |  14       | Error model fitting [3.4 s] -✔ |   4       | Test fitting the decline of metabolites from their maximum [0.2 s] +✔ |  14       | Error model fitting [3.8 s] +✔ |   4       | Test fitting the decline of metabolites from their maximum [0.3 s]  ✔ |   1       | Fitting the logistic model [0.2 s]  ✔ |   1       | Test dataset class mkinds used in gmkin  ✔ |   1       | mkinfit features [0.2 s] @@ -18,18 +18,18 @@ Testing mkin  ✔ |   8       | mkinmod model generation and printing [0.2 s]  ✔ |   3       | Model predictions with mkinpredict [0.3 s]  ✔ |  16       | Evaluations according to 2015 NAFTA guidance [1.3 s] -✔ |   9       | Nonlinear mixed-effects models [7.0 s] +✔ |   9       | Nonlinear mixed-effects models [7.3 s]  ✔ |  14       | Plotting [1.3 s]  ✔ |   4       | Residuals extracted from mkinfit models -✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.3 s] +✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]  ✔ |   4       | Summary  ✔ |   1       | Summaries of old mkinfit objects  ✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.0 s] -✔ |   9       | Hypothesis tests [7.1 s] +✔ |   9       | Hypothesis tests [7.4 s]  ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]  ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 35.6 s +Duration: 36.9 s  OK:       162  Failed:   0 diff --git a/tests/figs/deps.txt b/tests/figs/deps.txt index fa7c5968..8d7f66b6 100644 --- a/tests/figs/deps.txt +++ b/tests/figs/deps.txt @@ -1,3 +1,3 @@  - vdiffr-svg-engine: 1.0 -- vdiffr: 0.3.2 +- vdiffr: 0.3.3  - freetypeharfbuzz: 0.2.5 diff --git a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg index 8c234234..d8e3644b 100644 --- a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg +++ b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg @@ -222,7 +222,7 @@  <line x1='451.66' y1='486.94' x2='451.66' y2='479.30' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />  <line x1='447.84' y1='480.11' x2='455.47' y2='480.11' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />  <line x1='451.66' y1='483.93' x2='451.66' y2='476.29' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' /> -<line x1='437.55' y1='249.04' x2='445.19' y2='249.04' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' /> +<line x1='437.55' y1='249.05' x2='445.19' y2='249.05' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />  <line x1='441.37' y1='252.86' x2='441.37' y2='245.23' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />  <line x1='437.55' y1='423.26' x2='445.19' y2='423.26' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />  <line x1='441.37' y1='427.07' x2='441.37' y2='419.44' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' /> diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index a0e63657..7d562426 100644 --- a/tests/testthat/FOCUS_2006_D.csf +++ b/tests/testthat/FOCUS_2006_D.csf @@ -5,7 +5,7 @@ Description:  MeasurementUnits: % AR  TimeUnits: days  Comments: Created using mkin::CAKE_export -Date: 2020-11-08 +Date: 2020-11-11  Optimiser: IRLS  [Data] diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R index 62c88983..fcab4ffb 100644 --- a/tests/testthat/test_nafta.R +++ b/tests/testthat/test_nafta.R @@ -20,6 +20,7 @@ test_that("Test data from Appendix B are correctly evaluated", {    expect_known_output(print(res), "NAFTA_SOP_Appendix_B.txt") +  skip_on_travis()    plot_nafta <- function() plot(res)    if(requireNamespace("vdiffr", quietly = TRUE)) {      skip_if(getRversion() < "4.1.0") @@ -48,6 +49,7 @@ test_that("Test data from Appendix D are correctly evaluated", {    expect_known_output(print(res), "NAFTA_SOP_Appendix_D.txt") +  skip_on_travis()    plot_nafta <- function() plot(res)    if(requireNamespace("vdiffr", quietly = TRUE)) {      skip_if(getRversion() < "4.1.0") diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R index 40d5928f..587ec02e 100644 --- a/tests/testthat/test_plot.R +++ b/tests/testthat/test_plot.R @@ -2,6 +2,7 @@ context("Plotting")  test_that("Plotting mkinfit and mmkin objects is reproducible", {    skip_on_cran() +  skip_on_travis()    plot_default_FOCUS_C_SFO <- function() plot(fits[["SFO", "FOCUS_C"]])    plot_res_FOCUS_C_SFO <- function() plot(fits[["SFO", "FOCUS_C"]], show_residuals = TRUE)    plot_res_FOCUS_C_SFO_2 <- function() plot_res(fits[["SFO", "FOCUS_C"]]) | 
