reducing tests on CRAN

tests/testthat/test-add_header_rows.R

@@ -140,6 +140,7 @@ test_that("test tidy_add_header_rows() checks", {
 })
 
 test_that("tidy_add_header_rows() works with nnet::multinom", {
+  skip_on_cran()
   mod <- nnet::multinom(grade ~ stage + marker + age + trt, data = gtsummary::trial, trace = FALSE)
   res <- mod %>%
     tidy_and_attach() %>%
@@ -201,6 +202,7 @@ test_that("test tidy_add_header_rows() bad single row request", {
 
 
 test_that("tidy_add_header_rows() and mixed model", {
+  skip_on_cran()
   skip_if_not_installed("lme4")
   mod <- lme4::lmer(
     age ~ stage + (stage | grade) + (1 | grade),

tests/testthat/test-add_n.R

@@ -171,12 +171,14 @@ test_that("tidy_add_n() works with lme4::glmer", {
 
 
 test_that("tidy_add_n() works with survival::coxph", {
+  skip_on_cran()
   df <- survival::lung %>% dplyr::mutate(sex = factor(sex))
   mod <- survival::coxph(survival::Surv(time, status) ~ ph.ecog + age + sex, data = df)
   expect_error(mod %>% tidy_and_attach() %>% tidy_add_n(), NA)
 })
 
 test_that("tidy_add_n() works with survival::survreg", {
+  skip_on_cran()
   mod <- survival::survreg(
     survival::Surv(futime, fustat) ~ factor(ecog.ps) + rx,
     survival::ovarian,
@@ -186,6 +188,7 @@ test_that("tidy_add_n() works with survival::survreg", {
 })
 
 test_that("tidy_add_n() works with nnet::multinom", {
+  skip_on_cran()
   mod <- nnet::multinom(grade ~ stage + marker + age, data = gtsummary::trial, trace = FALSE)
   expect_error(mod %>% tidy_and_attach() %>% tidy_add_n(), NA)
 

tests/testthat/test-add_reference_rows.R

@@ -215,6 +215,7 @@ test_that("tidy_add_reference_rows() use var_label if available", {
 })
 
 test_that("tidy_add_reference_rows() works with nnet::multinom", {
+  skip_on_cran()
   mod <- nnet::multinom(grade ~ stage + marker + age, data = gtsummary::trial, trace = FALSE)
   res <- mod %>%
     tidy_and_attach() %>%
@@ -247,9 +248,9 @@ test_that("tidy_add_reference_rows() works with lme4::glmer", {
 
 
 test_that("tidy_add_reference_rows() works with glmmTMB::glmmTMB", {
+  skip_on_cran()
   skip_if_not_installed("glmmTMB")
   skip_if_not_installed("broom.mixed")
-  skip_on_cran()
 
   mod <- glmmTMB::glmmTMB(count ~ mined + spp,
                           ziformula = ~ mined,

tests/testthat/test-add_term_labels.R

@@ -184,6 +184,7 @@ test_that("tidy_add_term_labels() works with poly or helmert contrasts", {
 
 
 test_that("tidy_add_term_labels() works with variables having non standard name", {
+  skip_on_cran()
   df <- gtsummary::trial %>% dplyr::rename(
     `grade of kids...` = grade,
     `?? treatment ++ response ...` = response
@@ -222,6 +223,7 @@ test_that("tidy_add_term_labels() works with variables having non standard name"
 
 
 test_that("tidy_add_term_labels() works with stats::poly()", {
+  skip_on_cran()
   df <- iris %>% labelled::set_variable_labels(Petal.Length = "Length of petal")
   mod <- lm(Sepal.Length ~ poly(Sepal.Width, 3) + poly(Petal.Length, 2), df)
   res <- mod %>%
@@ -257,12 +259,14 @@ test_that("tidy_add_term_labels() works with lme4::glmer", {
 
 
 test_that("tidy_add_term_labels() works with survival::coxph", {
+  skip_on_cran()
   df <- survival::lung %>% dplyr::mutate(sex = factor(sex))
   mod <- survival::coxph(survival::Surv(time, status) ~ ph.ecog + age + sex, data = df)
   expect_error(mod %>% tidy_and_attach() %>% tidy_add_term_labels(), NA)
 })
 
 test_that("tidy_add_term_labels() works with survival::survreg", {
+  skip_on_cran()
   mod <- survival::survreg(
     survival::Surv(futime, fustat) ~ ecog.ps + rx,
     survival::ovarian,
@@ -272,36 +276,42 @@ test_that("tidy_add_term_labels() works with survival::survreg", {
 })
 
 test_that("tidy_add_term_labels() works with nnet::multinom", {
+  skip_on_cran()
   mod <- nnet::multinom(grade ~ stage + marker + age, data = gtsummary::trial, trace = FALSE)
   expect_error(mod %>% tidy_and_attach() %>% tidy_add_term_labels(), NA)
 })
 
 test_that("tidy_add_term_labels() works with survey::svyglm", {
+  skip_on_cran()
   skip_if_not_installed("survey")
   df <- survey::svydesign(~1, weights = ~1, data = gtsummary::trial)
   mod <- survey::svyglm(response ~ age + grade * trt, df, family = quasibinomial)
   expect_error(mod %>% tidy_and_attach() %>% tidy_add_term_labels(), NA)
 })
 
 test_that("tidy_add_term_labels() works with ordinal::clm", {
+  skip_on_cran()
   mod <- ordinal::clm(rating ~ temp * contact, data = ordinal::wine)
   expect_error(mod %>% tidy_and_attach() %>% tidy_add_term_labels(), NA)
 })
 
 
 test_that("tidy_add_term_labels() works with ordinal::clmm", {
+  skip_on_cran()
   mod <- ordinal::clmm(rating ~ temp * contact + (1 | judge), data = ordinal::wine)
   expect_error(mod %>% tidy_and_attach() %>% tidy_add_term_labels(), NA)
 })
 
 
 test_that("tidy_add_term_labels() works with MASS::polr", {
+  skip_on_cran()
   mod <- MASS::polr(Sat ~ Infl + Type + Cont, weights = Freq, data = MASS::housing)
   expect_error(mod %>% tidy_and_attach() %>% tidy_add_term_labels(), NA)
 })
 
 
 test_that("tidy_add_term_labels() works with geepack::geeglm", {
+  skip_on_cran()
   skip_if(packageVersion("geepack") < 1.3)
 
   df <- geepack::dietox
@@ -315,6 +325,7 @@ test_that("tidy_add_term_labels() works with geepack::geeglm", {
 
 
 test_that("tidy_add_term_labels() works with gam::gam", {
+  skip_on_cran()
   skip_if_not_installed("gam")
   data(kyphosis, package = "gam")
   mod <- gam::gam(Kyphosis ~ gam::s(Age, 4) + Number, family = binomial, data = kyphosis)
@@ -329,6 +340,7 @@ test_that("tidy_add_term_labels() works with gam::gam", {
 
 
 test_that("tidy_add_term_labels() works with lavaan::lavaan", {
+  skip_on_cran()
   skip_if_not_installed("lavaan")
   df <- lavaan::HolzingerSwineford1939
   df$grade <- factor(df$grade, ordered = TRUE)

tests/testthat/test-model_get_n.R

@@ -180,6 +180,7 @@ test_that("model_get_n() works with different contrasts", {
 
 
 test_that("model_get_n() works with stats::poly()", {
+  skip_on_cran()
   mod <- lm(Sepal.Length ~ poly(Sepal.Width, 3) + poly(Petal.Length, 2), iris)
   expect_error(res <- mod %>% model_get_n(), NA)
   expect_equivalent(names(res), c("term", "n_obs"))
@@ -224,6 +225,7 @@ test_that("model_get_n() works with lme4::glmer", {
 
 
 test_that("model_get_n() works with survival::coxph", {
+  skip_on_cran()
   df <- survival::lung %>% dplyr::mutate(sex = factor(sex))
   mod <- survival::coxph(survival::Surv(time, status) ~ ph.ecog + age + sex, data = df)
   expect_error(res <- mod %>% model_get_n(), NA)
@@ -244,6 +246,7 @@ test_that("model_get_n() works with survival::coxph", {
 })
 
 test_that("model_get_n() works with survival::survreg", {
+  skip_on_cran()
   mod <- survival::survreg(
     survival::Surv(futime, fustat) ~ factor(ecog.ps) + rx,
     survival::ovarian,
@@ -254,6 +257,7 @@ test_that("model_get_n() works with survival::survreg", {
 })
 
 test_that("model_get_n() works with nnet::multinom", {
+  skip_on_cran()
   mod <- nnet::multinom(grade ~ stage + marker + age, data = gtsummary::trial, trace = FALSE)
   expect_error(res <- mod %>% model_get_n(), NA)
   expect_equivalent(names(res), c("y.level", "term", "n_obs", "n_event"))
@@ -277,6 +281,7 @@ test_that("model_get_n() works with nnet::multinom", {
 })
 
 test_that("model_get_n() works with survey::svyglm", {
+  skip_on_cran()
   skip_if_not_installed("survey")
   df <- survey::svydesign(~1, weights = ~1, data = gtsummary::trial)
   mod <- survey::svyglm(response ~ age + grade * trt, df, family = quasibinomial)
@@ -301,6 +306,7 @@ test_that("model_get_n() works with survey::svyglm", {
 })
 
 test_that("model_get_n() works with ordinal::clm", {
+  skip_on_cran()
   mod <- ordinal::clm(rating ~ temp * contact, data = ordinal::wine)
   expect_error(res <- mod %>% model_get_n(), NA)
   expect_equivalent(names(res), c("term", "n_obs"))
@@ -309,20 +315,23 @@ test_that("model_get_n() works with ordinal::clm", {
 
 
 test_that("model_get_n() works with ordinal::clmm", {
+  skip_on_cran()
   mod <- ordinal::clmm(rating ~ temp * contact + (1 | judge), data = ordinal::wine)
   expect_error(res <- mod %>% model_get_n(), NA)
   expect_equivalent(names(res), c("term", "n_obs"))
 })
 
 
 test_that("model_get_n() works with MASS::polr", {
+  skip_on_cran()
   mod <- MASS::polr(Sat ~ Infl + Type + Cont, weights = Freq, data = MASS::housing)
   expect_error(res <- mod %>% model_get_n(), NA)
   expect_equivalent(names(res), c("term", "n_obs"))
 })
 
 
 test_that("model_get_n() works with geepack::geeglm", {
+  skip_on_cran()
   skip_if(packageVersion("geepack") < 1.3)
 
   df <- geepack::dietox
@@ -343,6 +352,7 @@ test_that("model_get_n() works with geepack::geeglm", {
 
 
 test_that("model_get_n() works with gam::gam", {
+  skip_on_cran()
   skip_if_not_installed("gam")
   data(kyphosis, package = "gam")
   mod <- gam::gam(Kyphosis ~ gam::s(Age, 4) + Number, family = binomial, data = kyphosis)
@@ -352,6 +362,7 @@ test_that("model_get_n() works with gam::gam", {
 
 
 test_that("model_get_n() works with lavaan::lavaan", {
+  skip_on_cran()
   skip_if_not_installed("lavaan")
   df <- lavaan::HolzingerSwineford1939
   df$grade <- factor(df$grade, ordered = TRUE)

tests/testthat/test-tidy_plus_plus.R

@@ -52,6 +52,7 @@ test_that("tidy_plus_plus() works with no intercept models", {
 })
 
 test_that("tidy_plus_plus() and functionnal programming", {
+  skip_on_cran()
   # works with glm
   expect_error(
     res <- dplyr::tibble(grade = c("I", "II", "III")) %>%
@@ -122,6 +123,7 @@ test_that("tidy_plus_plus() with mice objects", {
 
 
 test_that("tidy_plus_plus() with tidyselect", {
+  skip_on_cran()
   # build regression model
   mod <- lm(age ~ trt + marker + grade, gtsummary::trial)
 
@@ -152,6 +154,7 @@ test_that("tidy_plus_plus() with tidyselect", {
 })
 
 test_that("tidy_plus_plus() works with stats::aov", {
+  skip_on_cran()
   mod <- aov(yield ~ block + N * P * K, npk)
   expect_error(
     res <- tidy_plus_plus(mod),
@@ -212,6 +215,7 @@ test_that("tidy_plus_plus() works with lme4::glmer.nb", {
 })
 
 test_that("tidy_plus_plus() works with survival::coxph", {
+  skip_on_cran()
   df <- survival::lung %>% dplyr::mutate(sex = factor(sex))
   mod <- survival::coxph(survival::Surv(time, status) ~ ph.ecog + age + sex, data = df)
   expect_error(
@@ -221,6 +225,7 @@ test_that("tidy_plus_plus() works with survival::coxph", {
 })
 
 test_that("tidy_plus_plus() works with survival::survreg", {
+  skip_on_cran()
   mod <- survival::survreg(
     survival::Surv(futime, fustat) ~ ecog.ps + rx,
     survival::ovarian,
@@ -289,8 +294,8 @@ test_that("tidy_plus_plus() works with nnet::multinom", {
 })
 
 test_that("tidy_plus_plus() works with survey::svyglm", {
-  skip_if_not_installed("survey")
   skip_on_cran()
+  skip_if_not_installed("survey")
   df <- survey::svydesign(~1, weights = ~1, data = gtsummary::trial)
   mod <- survey::svyglm(response ~ age + grade * trt, df, family = quasibinomial)
   expect_error(
@@ -300,8 +305,8 @@ test_that("tidy_plus_plus() works with survey::svyglm", {
 })
 
 test_that("tidy_plus_plus() works with survey::svycoxph", {
-  skip_if_not_installed("survey")
   skip_on_cran()
+  skip_if_not_installed("survey")
   dpbc <- survey::svydesign(id = ~ 1, prob = ~ 1, strata = ~ edema, data = survival::pbc)
   mod <- survey::svycoxph(
     Surv(time, status > 0) ~ log(bili) + protime + albumin,
@@ -314,8 +319,8 @@ test_that("tidy_plus_plus() works with survey::svycoxph", {
 })
 
 test_that("tidy_plus_plus() works with survey::svyolr", {
-  skip_if_not_installed("survey")
   skip_on_cran()
+  skip_if_not_installed("survey")
   data(api, package = "survey")
   fpc <- survey::svydesign(id = ~ dnum, weights = ~ pw, data = apiclus1, fpc = ~ fpc)
   fpc <- update(fpc, mealcat = cut(meals, c(0, 25, 50, 75, 100)))
@@ -347,6 +352,7 @@ test_that("tidy_plus_plus() works with ordinal::clmm", {
 
 
 test_that("tidy_plus_plus() works with MASS::polr", {
+  skip_on_cran()
   mod <- MASS::polr(Sat ~ Infl + Type + Cont, weights = Freq, data = MASS::housing)
   expect_error(
     res <- mod %>% tidy_plus_plus(),
@@ -454,6 +460,7 @@ test_that("tidy_plus_plus() works with tidycmprsk::crr", {
 
 
 test_that("tidy_plus_plus() works with stats::nls", {
+  skip_on_cran()
   mod <- stats::nls(
     Petal.Width ~ a * Petal.Length - (Sepal.Width + Sepal.Length) / b + a^2,
     data = iris,