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-rw-r--r--check.log3
-rw-r--r--test.log39
-rw-r--r--tests/testthat/test_nafta.R2
-rw-r--r--tests/testthat/test_plots_summary_twa.R1
4 files changed, 29 insertions, 16 deletions
diff --git a/check.log b/check.log
index cc24b711..8064f9a6 100644
--- a/check.log
+++ b/check.log
@@ -1,5 +1,5 @@
* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.0.0 (2020-04-24)
+* using R Under development (unstable) (2020-05-10 r78402)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-tests --as-cran’
@@ -35,7 +35,6 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
-* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
diff --git a/test.log b/test.log
index 7822efdb..74e869da 100644
--- a/test.log
+++ b/test.log
@@ -2,35 +2,46 @@ Loading mkin
Testing mkin
✔ | OK F W S | Context
✔ | 2 | Export dataset for reading into CAKE
-✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.2 s]
+✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.1 s]
✔ | 4 | Calculation of FOCUS chi2 error levels [0.4 s]
-✔ | 7 | Fitting the SFORB model [3.5 s]
+✔ | 7 | Fitting the SFORB model [3.2 s]
✔ | 1 | Analytical solutions for coupled models [0.2 s]
✔ | 5 | Calculation of Akaike weights
-✔ | 10 | Confidence intervals and p-values [1.0 s]
-✔ | 14 | Error model fitting [3.8 s]
+✔ | 10 | Confidence intervals and p-values [0.9 s]
+✔ | 14 | Error model fitting [3.7 s]
✔ | 6 | Test fitting the decline of metabolites from their maximum [0.2 s]
✔ | 1 | Fitting the logistic model [0.2 s]
✔ | 1 | Test dataset class mkinds used in gmkin
✔ | 12 | Special cases of mkinfit calls [0.6 s]
✔ | 8 | mkinmod model generation and printing [0.2 s]
✔ | 3 | Model predictions with mkinpredict [0.3 s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.4 s]
-✔ | 9 | Nonlinear mixed-effects models [7.5 s]
-✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
+✔ | 14 2 | Evaluations according to 2015 NAFTA guidance [0.9 s]
+────────────────────────────────────────────────────────────────────────────────
+test_nafta.R:25: skip: Test data from Appendix B are correctly evaluated
+Reason: getRversion() > 4 is TRUE
+
+test_nafta.R:50: skip: Test data from Appendix D are correctly evaluated
+Reason: getRversion() > 4 is TRUE
+────────────────────────────────────────────────────────────────────────────────
+✔ | 9 | Nonlinear mixed-effects models [7.0 s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
✔ | 3 | Summary
-✔ | 14 | Plotting [1.7 s]
+✔ | 0 1 | Plotting [0.9 s]
+────────────────────────────────────────────────────────────────────────────────
+test_plots_summary_twa.R:98: skip: Plotting mkinfit and mmkin objects is reproducible
+Reason: getRversion() > 4 is TRUE
+────────────────────────────────────────────────────────────────────────────────
✔ | 4 | AIC calculation
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.3 s]
✔ | 1 | Summaries of old mkinfit objects
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
-✔ | 9 | Hypothesis tests [6.5 s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s]
+✔ | 9 | Hypothesis tests [7.2 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 35.1 s
+Duration: 32.9 s
-OK: 157
+OK: 141
Failed: 0
Warnings: 0
-Skipped: 0
+Skipped: 3
diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R
index a0acd152..2cc25f82 100644
--- a/tests/testthat/test_nafta.R
+++ b/tests/testthat/test_nafta.R
@@ -22,6 +22,7 @@ test_that("Test data from Appendix B are correctly evaluated", {
plot_nafta <- function() plot(res)
if(requireNamespace("vdiffr", quietly = TRUE)) {
+ skip_if(getRversion() > 4.0)
vdiffr::expect_doppelganger("NAFTA SOP Appendix B", plot_nafta)
}
})
@@ -46,6 +47,7 @@ test_that("Test data from Appendix D are correctly evaluated", {
plot_nafta <- function() plot(res)
if(requireNamespace("vdiffr", quietly = TRUE)) {
+ skip_if(getRversion() > 4.0)
vdiffr::expect_doppelganger("Plot NAFTA analysis", plot_nafta)
}
})
diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R
index bc3d29a8..aedc9da3 100644
--- a/tests/testthat/test_plots_summary_twa.R
+++ b/tests/testthat/test_plots_summary_twa.R
@@ -95,6 +95,7 @@ test_that("Plotting mkinfit and mmkin objects is reproducible", {
plot_errmod_fit_obs_1 <- function() plot_err(fit_obs_1, sep_obs = FALSE)
plot_errmod_fit_tc_1 <- function() plot_err(fit_tc_1, sep_obs = FALSE)
+ skip_if(getRversion() > 4.0)
vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with defaults", plot_default_FOCUS_C_SFO)
vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with residuals like in gmkin", plot_res_FOCUS_C_SFO)
vdiffr::expect_doppelganger("plot_res for FOCUS C", plot_res_FOCUS_C_SFO_2)

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