skip some tests on CRAN

HDash · Dec 29, 2023 · 185409b · 185409b
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diff --git a/.Rhistory b/.Rhistory
diff --git a/NEWS.md b/NEWS.md
@@ -2,12 +2,16 @@
 
 ## New features
 
-- Change command "\nodocker" to "[nodocker]" for consistency with other commands. 
+* Change command "\nodocker" to "[nodocker]" for consistency with other commands. 
 
 ## Bug fixes
 
-- *action.yml* 
+* *action.yml* 
   - `repository: ${{ github.repository }}` --> `repository: ${{ env.packageName }}`
+* CRAN: 
+  - Add convenient `testthat` functions `skip_on_cran()` and `skip_if_offline`.
+* Reduce package size by making vignettes `rmarkdown::html_vignette`
+  instead of `BiocStyle::html_document`.
 
 # rworkflows 1.0.0
 

diff --git a/tests/testthat/test-bioc_r_versions.R b/tests/testthat/test-bioc_r_versions.R
@@ -1,4 +1,7 @@
 test_that("bioc_r_versions works", {
+  ## Don't run on CRAN servers due to ongoing internet connectivity issues
+  testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   ver1 <- bioc_r_versions(bioc_version="devel")
   testthat::expect_true(ver1$bioc>="3.17")

diff --git a/tests/testthat/test-check_cont.R b/tests/testthat/test-check_cont.R
@@ -1,4 +1,7 @@
 test_that("check_cont works", {
+  ## Don't run on CRAN servers due to ongoing internet connectivity issues
+  testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   testthat::expect_no_warning(
     check_cont(cont = "bioconductor/bioconductor_docker:devel")

diff --git a/tests/testthat/test-check_r_version.R b/tests/testthat/test-check_r_version.R
@@ -1,4 +1,7 @@
 test_that("check_r_version works", {
+  ## Don't run on CRAN servers due to ongoing internet connectivity issues
+  testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   testthat::expect_equal(
     check_r_version(r = "4.1"),

diff --git a/tests/testthat/test-construct_conda_yml.R b/tests/testthat/test-construct_conda_yml.R
@@ -46,6 +46,10 @@ test_that("construct_conda_yml works", {
                                  save_path = save_path)
     testthat::expect_true(file.exists(path2))
 
+    ## Don't run on CRAN servers due to ongoing internet connectivity issues
+    testthat::skip_on_cran()
+    testthat::skip_if_offline()
+
     # conda <- conda_path()
     out <- reticulate::conda_create(environment = path2, 
                                     envname = envname)

diff --git a/tests/testthat/test-construct_cont.R b/tests/testthat/test-construct_cont.R
@@ -18,6 +18,10 @@ test_that("construct_cont works", {
   testthat::expect_null(cont3[[2]])
   testthat::expect_null(cont3[[3]])
 
+  ## Don't run on CRAN servers due to ongoing internet connectivity issues
+  testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   cont4 <- construct_cont(default_tag = "release",
                           default_registry = "ghcr.io",
                           run_check_cont = TRUE) 

diff --git a/tests/testthat/test-construct_runners.R b/tests/testthat/test-construct_runners.R
@@ -1,4 +1,7 @@
 test_that("construct_runners works", {
+  ## Don't run on CRAN servers due to ongoing internet connectivity issues
+  testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   #### Set up tests ####  
   run_tests <- function(runners){

diff --git a/tests/testthat/test-get_yaml.R b/tests/testthat/test-get_yaml.R
@@ -1,4 +1,5 @@
 test_that("get_yaml works", {
+  testthat::skip_if_offline()
 
   testthat::expect_type(
     rworkflows:::get_yaml(template = "rworkflows"),

diff --git a/tests/testthat/test-gha_python_versions.R b/tests/testthat/test-gha_python_versions.R
@@ -1,4 +1,7 @@
 test_that("gha_python_versions works", {
+  ## Don't run on CRAN servers due to ongoing internet connectivity issues
+  testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   testthat::expect_equal(gha_python_versions(python_version = "3.11"),"3.11")
   testthat::expect_equal(gha_python_versions(python_version = "3.x"),"3.x")

diff --git a/tests/testthat/test-url_exists.R b/tests/testthat/test-url_exists.R
@@ -1,4 +1,7 @@
 test_that("url_exists works", {
+  ## Don't run on CRAN servers due to ongoing internet connectivity issues
+  testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   testthat::expect_true(
     rworkflows:::url_exists("https://github.com/neurogenomics/rworkflows")

diff --git a/tests/testthat/test-use_badges.R b/tests/testthat/test-use_badges.R
@@ -1,5 +1,6 @@
 test_that("use_badges works", {
-
+  testthat::skip_if_offline()
+
   run_tests <- function(badges){
     testthat::expect_length(badges,1)
     testthat::expect_type(badges,"character")

diff --git a/tests/testthat/test-use_workflow.R b/tests/testthat/test-use_workflow.R
@@ -1,4 +1,5 @@
 test_that("use_workflow works", {
+  testthat::skip_if_offline()
 
   path <- use_workflow(save_dir = file.path(tempdir(),".github","workflows"))
   testthat::expect_true(file.exists(path))

diff --git a/vignettes/bioconductor.Rmd b/vignettes/bioconductor.Rmd
@@ -3,7 +3,7 @@ title: "Bioconductor"
 author: "<h4>Authors: <i>`r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`</i></h4>" 
 date: "<h4>Vignette updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
 output:
-  BiocStyle::html_document
+  rmarkdown::html_vignette
 vignette: >
     %\VignetteIndexEntry{Bioconductor} 
     %\usepackage[utf8]{inputenc}

diff --git a/vignettes/depgraph.Rmd b/vignettes/depgraph.Rmd
@@ -3,7 +3,7 @@ title: "Dependency graph"
 author: "<h4>Authors: <i>`r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`</i></h4>" 
 date: "<h4>Vignette updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
 output:
-  BiocStyle::html_document
+  rmarkdown::html_vignette
 vignette: >
     %\VignetteIndexEntry{depgraph} 
     %\usepackage[utf8]{inputenc}
@@ -51,13 +51,13 @@ saveRDS(res, here::here("reports","dep_graph_res.rds"))
 
 ## Count stars/clones/views
 
-``` r
+```r
 knitr::kable(res$report)
 ```
 
 # Show
 
-![rworkflow depgraph](https://github.com/neurogenomics/rworkflows/raw/master/reports/rworkflows_depgraph.png)
+## [rworkflow depgraph](https://github.com/neurogenomics/rworkflows/raw/master/reports/rworkflows_depgraph.png)
 
 Hover over each node to show additional metadata.
 

diff --git a/vignettes/docker.Rmd b/vignettes/docker.Rmd
@@ -5,7 +5,7 @@ author: '<h4>Authors: <i>`r auths <- eval(parse(text = gsub("person","c",read.dc
   collapse = ", ")`</i></h4>'
 date: '<h4>Vignette updated: <i>`r format( Sys.Date(), "%b-%d-%Y")`</i></h4>'
 output:
-  BiocStyle::html_document:
+  rmarkdown::html_vignette:
     md_extensions: -autolink_bare_uris
 params:
   cont:

diff --git a/vignettes/repos.Rmd b/vignettes/repos.Rmd
@@ -26,7 +26,7 @@ r_repos_res <- echogithub::r_repos(
   width = 9)
 ```
 
-[!Upset plot](https://github.com/neurogenomics/rworkflows/raw/master/reports/r_repos_upset.pdf)
+## [Upset plot](https://github.com/neurogenomics/rworkflows/raw/master/reports/r_repos_upset.pdf)
 
 ## Save results 
 

diff --git a/vignettes/rworkflows.Rmd b/vignettes/rworkflows.Rmd
@@ -3,7 +3,7 @@ title: "Get Started"
 author: "<h4>Authors: <i>`r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`</i></h4>"
 date: "<h4>Vignette updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
 output:
-  BiocStyle::html_document
+  rmarkdown::html_vignette
 vignette: >
     %\VignetteIndexEntry{rworkflows} 
     %\usepackage[utf8]{inputenc}