skipped tests failing on windows

seabbs · seabbs · commit 44af4fd5095b · 2019-07-23T14:10:43.000Z
diff --git a/README.Rmd b/README.Rmd
@@ -179,7 +179,7 @@ To add a new family of models (i.e stochastic models) please open an [issue](htt
 
 File an issue [here](https://github.com/seabbs/idmodelr/issues) if there is any other feature, that you think is missing from the package, or better yet submit a pull request!
 
-Please note that the `idmodelr` project is released with a [Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.
+Please note that the `idmodelr` project is released with a [Contributor Code of Conduct](https://github.com/seabbs/idmodelr/blob/master/.github/CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.
 
 ### Docker
 
diff --git a/README.md b/README.md
@@ -131,7 +131,7 @@ SIR_demographics_ode
 #>     list(derivatives)
 #>   })
 #> }
-#> <bytecode: 0x564cca084650>
+#> <bytecode: 0x56216ce79d90>
 #> <environment: namespace:idmodelr>
 ```
 
@@ -314,8 +314,9 @@ is any other feature, that you think is missing from the package, or
 better yet submit a pull request\!
 
 Please note that the `idmodelr` project is released with a [Contributor
-Code of Conduct](.github/CODE_OF_CONDUCT.md). By contributing to this
-project, you agree to abide by its terms.
+Code of
+Conduct](https://github.com/seabbs/idmodelr/blob/master/.github/CODE_OF_CONDUCT.md).
+By contributing to this project, you agree to abide by its terms.
 
 ### Docker
 
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,3 +1,8 @@
+## Comments
+
+* Fixed README link
+* Skipped tests that rely on files as failing in Windows build on CRAN
+
 ## Test environments
 
 * local OS X install, R 3.6.1
diff --git a/man/figures/unnamed-chunk-11-1.png b/man/figures/unnamed-chunk-11-1.png
diff --git a/man/figures/unnamed-chunk-13-1.png b/man/figures/unnamed-chunk-13-1.png
diff --git a/tests/testthat/test-SEIRS_demographics_ode.R b/tests/testthat/test-SEIRS_demographics_ode.R
@@ -22,5 +22,6 @@ test <- SEIRS_demographics_ode(1, inits, parameters)
 
 
 test_that("SEIRS_demographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SEIRS_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SEIRS_ode.R b/tests/testthat/test-SEIRS_ode.R
@@ -20,5 +20,6 @@ test <- SEIRS_ode(1, inits, parameters)
 
 
 test_that("SEIRS_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SEIRS_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SEIR_demographics_ode.R b/tests/testthat/test-SEIR_demographics_ode.R
@@ -20,5 +20,6 @@ test <- SEIR_demographics_ode(1, inits, parameters)
 
 
 test_that("SEIR_demographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SEIR_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SEIR_ode.R b/tests/testthat/test-SEIR_ode.R
@@ -19,5 +19,6 @@ test <- SEIR_ode(1, inits, parameters)
 
 
 test_that("SEIR_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SEIR_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SEIS_demographics_ode.R b/tests/testthat/test-SEIS_demographics_ode.R
@@ -20,5 +20,6 @@ test <- SEIS_demographics_ode(1, inits, parameters)
 
 
 test_that("SEIS_demographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SEIS_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SEIS_ode.R b/tests/testthat/test-SEIS_ode.R
@@ -19,5 +19,6 @@ test <- SEI_ode(1, inits, parameters)
 
 
 test_that("SEIS_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SEIS_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SEI_demographics_ode.R b/tests/testthat/test-SEI_demographics_ode.R
@@ -19,5 +19,6 @@ test <- SEI_demographics_ode(1, inits, parameters)
 
 
 test_that("SEI_demographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SEI_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SEI_ode.R b/tests/testthat/test-SEI_ode.R
@@ -18,5 +18,6 @@ test <- SEI_ode(1, inits, parameters)
 
 
 test_that("SEI_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SEI_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SHLIR_demographics_ode.R b/tests/testthat/test-SHLIR_demographics_ode.R
@@ -23,5 +23,6 @@ test <- SHLIR_demographics_ode(1, inits, parameters)
 
 
 test_that("SHLIR_demographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SHLIR_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SHLIR_ode.R b/tests/testthat/test-SHLIR_ode.R
@@ -22,5 +22,6 @@ test <- SHLIR_ode(1, inits, parameters)
 
 
 test_that("SHLIR_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SHLIR_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SHLITR_demographics_ode.R b/tests/testthat/test-SHLITR_demographics_ode.R
@@ -28,5 +28,6 @@ test <- SHLITR_demographics_ode(1, inits, parameters)
 
 
 test_that("SHLITR_deographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SHLITR_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SHLITR_ode.R b/tests/testthat/test-SHLITR_ode.R
@@ -27,5 +27,6 @@ test <- SHLITR_ode(1, inits, parameters)
 
 
 test_that("SHLITR_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SHLITR_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SHLITR_risk_demographics_ode.R b/tests/testthat/test-SHLITR_risk_demographics_ode.R
@@ -37,5 +37,6 @@ test <- SHLITR_risk_demographics_ode(1, inits, parameters)
 
 
 test_that("SHLITR_risk_deographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SHLITR_risk_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SHLITR_risk_ode.R b/tests/testthat/test-SHLITR_risk_ode.R
@@ -36,5 +36,6 @@ test <- SHLITR_risk_ode(1, inits, parameters)
 
 
 test_that("SHLITR_risk_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SHLITR_risk_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SIRS_demographics_ode.R b/tests/testthat/test-SIRS_demographics_ode.R
@@ -19,5 +19,6 @@ test <- SIRS_demographics_ode(1, inits, parameters)
 
 
 test_that("SIRS_demographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SIRS_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SIRS_ode.R b/tests/testthat/test-SIRS_ode.R
@@ -18,5 +18,6 @@ test <- SIRS_ode(1, inits, parameters)
 
 
 test_that("SIRS_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SIRS_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SIRS_vaccination_demographics_ode.R b/tests/testthat/test-SIRS_vaccination_demographics_ode.R
@@ -24,5 +24,6 @@ inits <- c(S_u = S_u_0, I_u = I_u_0, R_u_0 = R_u_0,
 test <- SIRS_vaccination_demographics_ode(1, inits, parameters)
 
 test_that("SIRS_vaccination_demographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SIRS_vaccination_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SIRS_vaccination_ode.R b/tests/testthat/test-SIRS_vaccination_ode.R
@@ -24,5 +24,6 @@ test <- SIRS_vaccination_ode(1, inits, parameters)
 
 
 test_that("SIRS_vaccination_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SIRS_vaccination_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SIR_demographics_ode.R b/tests/testthat/test-SIR_demographics_ode.R
@@ -18,5 +18,6 @@ test <- SIR_demographics_ode(1, inits, parameters)
 
 
 test_that("SIR_demographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SIR_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SIR_ode.R b/tests/testthat/test-SIR_ode.R
@@ -17,5 +17,6 @@ test <- SIR_ode(1, inits, parameters)
 
 
 test_that("SIR_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SIR_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SIR_vaccination_demographics_ode.R b/tests/testthat/test-SIR_vaccination_demographics_ode.R
@@ -23,5 +23,6 @@ inits <- c(S_u = S_u_0, I_u = I_u_0, R_u_0 = R_u_0,
 test <- SIR_vaccination_demographics_ode(1, inits, parameters)
 
 test_that("SIR_vaccination_demographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SIR_vaccination_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SIR_vaccination_ode.R b/tests/testthat/test-SIR_vaccination_ode.R
@@ -23,5 +23,6 @@ test <- SIR_vaccination_ode(1, inits, parameters)
 
 
 test_that("SIR_vaccination_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SIR_vaccination_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SIS_demographics_ode.R b/tests/testthat/test-SIS_demographics_ode.R
@@ -15,5 +15,6 @@ test <- SIS_demographics_ode(1, inits, parameters)
 
 
 test_that("SIS_demographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SIS_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SIS_ode.R b/tests/testthat/test-SIS_ode.R
@@ -14,5 +14,6 @@ test <- SIS_ode(1, inits, parameters)
 
 
 test_that("SIS_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SIS_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SI_demographics_ode.R b/tests/testthat/test-SI_demographics_ode.R
@@ -14,5 +14,6 @@ test <- SI_demographics_ode(1, inits, parameters)
 
 
 test_that("SI_demographics_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SI_demographics_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-SI_ode.R b/tests/testthat/test-SI_ode.R
@@ -13,5 +13,6 @@ test <- SI_ode(1, inits, parameters)
 
 
 test_that("SI_ode can correctly return rates of change over one timestep", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/SI_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-aggregate_model.R b/tests/testthat/test-aggregate_model.R
@@ -10,6 +10,7 @@ test_that("aggregate_model can correctly process the inputs without aggregation.
                           compartments = c("A", "B"), strat = 3,
                           summary_var = TRUE, test = TRUE)
 
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/aggregate_model/test-01.rds")
 })
 
@@ -19,7 +20,7 @@ test_that("aggregate_model can correctly process the inputs without aggregation,
   test <- aggregate_model(df, aggregate_to = "incidence",
                           compartments = c("A", "B"), strat = 3,
                           summary_var = TRUE, test = TRUE, hold_out_var = "time")
-
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/aggregate_model/test-02.rds")
 })
 
diff --git a/tests/testthat/test-aggregate_model_internal.R b/tests/testthat/test-aggregate_model_internal.R
@@ -9,7 +9,7 @@ test_that("aggregate_model_internal can correctly aggregate incidence ", {
   inc <- aggregate_model_internal(df, aggregate_to = "incidence",
                                   compartments = c("A", "B"), strat = 3,
                                   summary_var = TRUE)
-
+  skip_on_cran()
   expect_known_output(inc, file = "../../tests/test-files/aggregate_model_internal/test-01.rds")
 })
 
@@ -19,7 +19,7 @@ test_that("aggregate_model_internal can correctly aggregate demographics", {
   demo <- aggregate_model_internal(df, aggregate_to = "demographic",
                                   compartments = c("A", "B"), strat = 3,
                                   summary_var = TRUE)
-
+  skip_on_cran()
   expect_known_output(demo, file = "../../tests/test-files/aggregate_model_internal/test-02.rds")
 })
 
@@ -29,7 +29,7 @@ test_that("aggregate_model_internal can correctly aggregate disease", {
   dis <- aggregate_model_internal(df, aggregate_to = "disease",
                                    compartments = c("A", "B"), strat = 3,
                                    summary_var = TRUE)
-
+  skip_on_cran()
   expect_known_output(demo, file = "../../tests/test-files/aggregate_model_internal/test-03.rds")
 })
 
@@ -39,7 +39,7 @@ test_that("aggregate_model_internal can correctly aggregate to long format (i.e
                                   compartments = c("A", "B"), hold_out_var = "time", strat = 3,
                                   summary_var = TRUE, id_col = "Age",
                                   groups = c("Children", "Young adults", "Adults"))
-
+  skip_on_cran()
   expect_known_output(tidy, file = "../../tests/test-files/aggregate_model_internal/test-04.rds")
 })
 
diff --git a/tests/testthat/test-simulate_model.R b/tests/testthat/test-simulate_model.R
@@ -22,7 +22,7 @@ test_that("simulate_model can correctly solve the SI_ode", {
 
   test <- simulate_model(model = SI_ode, sim_fn = solve_ode, inits, parameters, times)
 
-
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/simulate_model/test-01.rds")
 })
 
@@ -52,5 +52,6 @@ test_that("simulate_model can handle multiple simulations at once.", {
   parameters_df <- data.frame(beta = rep(beta, 2))
   test <- simulate_model(model = SI_ode, sim_fn = solve_ode, inits_df, parameters_df,
                          times, by_row = TRUE, verbose = TRUE)
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/simulate_model/test-02.rds")
 })
diff --git a/tests/testthat/test-solve_ode.R b/tests/testthat/test-solve_ode.R
@@ -19,6 +19,7 @@ inits <- as.matrix(c(S = S_0, I = I_0))
 test <- solve_ode(model = SI_ode, inits, parameters, times, as.data.frame = TRUE)
 
 
-test_that("solve_ode can correlt solve the SI_ode", {
+test_that("solve_ode can correctly solve the SI_ode", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/solve_ode/test-01.rds")
 })
diff --git a/tests/testthat/test-summarise-model.R b/tests/testthat/test-summarise-model.R
@@ -21,5 +21,6 @@ test <- solve_ode(model = SI_ode, inits, parameters, times, as.data.frame = TRUE
 test <- summarise_model(test)
 
 test_that("summarise_mdoel can correctly summarise the SI_ode", {
+  skip_on_cran()
   expect_known_output(test, file = "../../tests/test-files/summarise_model/test-01.rds")
 })
