neurogenomics · HDash · May 6, 2026 · May 5, 2026 · May 5, 2026 · May 5, 2026
diff --git a/.github/workflows/rworkflows_static.yml b/.github/workflows/rworkflows_static.yml
@@ -90,7 +90,7 @@ jobs:
         echo "NOT_CRAN=${{ !env.as_cran }}" >> $GITHUB_ENV
       shell: bash {0}
     - name: ⏬ Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v6
     - name: "\U0001F40D Setup Miniconda"
       if: env.miniforge_variant != 'false'
       uses: conda-incubator/setup-miniconda@v4

diff --git a/NEWS.md b/NEWS.md
@@ -21,7 +21,8 @@
 resources:
     - Add `testthat::skip_if_offline()` to all tests whose call stacks may
       reach the internet (`test-check_bioc_version.R`, `test-fill_description.R`,
-      `test-get_authors.R`, `test-get_hex.R`, `test-infer_deps.R`).
+      `test-get_authors.R`, `test-get_hex.R`, `test-infer_biocviews.R`,
+      `test-infer_deps.R`).
     - Move the existing offline guard up in `test-construct_cont.R` so that
       the `versions_explicit = TRUE` branch (which calls `bioc_r_versions()`)
       is also skipped when offline.
@@ -35,6 +36,17 @@
       degrade gracefully when offline.
 * Add `curl` to `Suggests` to support the new offline guards in examples
 and vignettes.
+* Vignettes: replace `read.dcf("../DESCRIPTION", ...)` with
+  `utils::packageDescription("rworkflows", ...)` so the setup chunks no
+  longer fail under `R CMD check`'s `tools::checkVignettes()`, which
+  tangles each vignette to a `.R` file and sources it from a temp working
+  directory where `../DESCRIPTION` does not resolve. The same change is
+  applied to `inst/templates/{templateR,docker}.Rmd` via a `__PKG__`
+  placeholder that `use_vignette_getstarted()` / `use_vignette_docker()`
+  substitute at write time.
+* `use_vignette_getstarted()` / `use_vignette_docker()`: raise a clear
+  error when `package` is `NULL` or empty (previously they silently
+  produced a malformed file).
 
 ## Miscellaneous
 
@@ -43,9 +55,28 @@
   the action runtime to Node.js 24, which is supported by GitHub-hosted
   runners but requires self-hosted runners on a recent `actions/runner`
   release.
+* Bump `actions/checkout` from `@v4` to `@v6` (the bundled example
+  workflow goes from `@v3`). v5 moved the runtime to Node.js 24 (requires
+  runner >= v2.327.1, satisfied by all GitHub-hosted runners) and v6
+  persists git auth credentials to a separate `.gitauth` file instead of
+  `.git/config`; neither change affects this action.
 * Forward the `ncpus` input to `grimbough/bioc-actions/setup-bioc@v1` (as
   its `Ncpus` input) so non-Linux R installs use the configured parallel
   job count instead of the action's default of 3.
+* Tests: replace `is_gha()` gates that were guarding internet access
+  with host-specific `skip_if_offline(host=...)` calls
+  (`bioconductor.org`, `github.com`, `raw.githubusercontent.com`,
+  `ghcr.io`) so individual tests skip when their actual remote is
+  unreachable. This includes the `get_description` Bioc-repo block,
+  which previously gated on `is_gha() | is_rstudio()` to dodge CRAN
+  flakiness (#65); it now skips on `bioconductor.org` instead. Each
+  `skip_if_offline()` is then wrapped in `if (!is_gha())` so GitHub
+  Actions exercises the network path regardless of the offline probe;
+  developer machines and CRAN's check farm continue to skip when the
+  named host is unreachable. `is_gha()` is also retained for the
+  `construct_conda_yml` env-creation block, where the test is
+  genuinely GHA-only (creates and leaves a conda env behind, so should
+  not run on developer machines).
 
 # rworkflows 1.0.11
 
@@ -93,7 +124,7 @@

 ## New features

 * New arg for number of cores to use for R package installation (`ncpus`).
 * Add `CODECOV_TOKEN` and `ncpus` to `rworkflows.yml` template.
 * Update to `actions/cache@v4` as v3 is marked for deprecation.
 ## Documentation
@@ -169,7 +200,7 @@
 * Synchronise `rworkflows` package versioning with `rworkflows` action 
 Release versioning.
 * `use_vignette_docker`/`use_vignette_getstarted`
  - Autofill `package` arg if not provided.

 ## Bug fixes

@@ -187,7 +218,7 @@

 * Add step to enable conda envs: #78
  - Add subfunction: `gha_python_versions()` within `construct_runners`
  - Add new *action.yml* args:
    - `miniforge_variant`
    - `miniforge_version`
    - `activate_environment`

diff --git a/R/use_vignette_docker.R b/R/use_vignette_docker.R
@@ -65,6 +65,12 @@ use_vignette_docker <- function(package = names(get_description()),
                                 verbose=TRUE){
   # devoptera::args2vars(use_vignette_docker, reassign = TRUE)
 
+  force(package)
+  if (length(package) != 1L || is.na(package) || !nzchar(package)) {
+    stop("`package` must be a non-empty string. ",
+         "Could not be inferred from a local DESCRIPTION; ",
+         "pass `package` explicitly.")
+  }
   #### Check if file exists already ####
   if(file.exists(path) &
      isFALSE(force_new)){
@@ -82,8 +88,9 @@ use_vignette_docker <- function(package = names(get_description()),
                                  package = "rworkflows")
     #### Edit the yaml header ###
     l <- readLines(template_path)
+    l <- gsub("__PKG__", package, l, fixed = TRUE)
     yml_lines <- seq(grep("---",l)[1],
-                     rev(grep("---",l))[1] ) 
+                     rev(grep("---",l))[1] )
     yml <- yaml::read_yaml(text = l[yml_lines])
     #### Set params ####
     ## cont

diff --git a/R/use_vignette_getstarted.R b/R/use_vignette_getstarted.R
@@ -26,6 +26,11 @@ use_vignette_getstarted <- function(package = names(get_description()),
   # devoptera::args2vars(use_vignette_getstarted, reassign = TRUE)
 
   force(package)
+  if (length(package) != 1L || is.na(package) || !nzchar(package)) {
+    stop("`package` must be a non-empty string. ",
+         "Could not be inferred from a local DESCRIPTION; ",
+         "pass `package` explicitly.")
+  }
   #### Check if file exists already ####
   if(file.exists(path) &
      isFALSE(force_new)){
@@ -38,8 +43,9 @@ use_vignette_getstarted <- function(package = names(get_description()),
                                  package = "rworkflows")
     #### Edit the yaml header ###
     l <- readLines(template_path)
+    l <- gsub("__PKG__", package, l, fixed = TRUE)
     yml_lines <- seq(grep("---",l)[1],
-                     rev(grep("---",l))[1] ) 
+                     rev(grep("---",l))[1] )
     yml <- yaml::read_yaml(text = l[yml_lines]) 
     ## vignette title
     yml$title <- title 

diff --git a/action.yml b/action.yml
@@ -219,7 +219,7 @@ runs:
 
     ## Checkout before Miniconda so that environment_file can reference repo files
     - name: ⏬ Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v6
 
     - name: 🐍 Setup Miniconda
       if: inputs.miniforge_variant != 'false'

diff --git a/inst/example/check_rworkflows-merged.yml b/inst/example/check_rworkflows-merged.yml
@@ -26,7 +26,7 @@ jobs:
         run: |
             curl -fsSL https://deb.nodesource.com/setup_18.x | sudo -E bash -
             sudo apt-get install -y nodejs
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
       - uses: ./rworkflows-merged
         with:  
           run_bioccheck: true

diff --git a/inst/templates/docker.Rmd b/inst/templates/docker.Rmd
@@ -1,6 +1,6 @@
 ---
 title: "Docker/Singularity Containers" 
-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>" 
+author: "<h4>Authors: <i>`r auths <- eval(parse(text = gsub('person','c',utils::packageDescription('__PKG__', 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:
@@ -24,16 +24,16 @@
 
 ```{r setup, include=FALSE}
 #### Package name ####
-PKG <- read.dcf("../DESCRIPTION", fields = "Package")[1]
+PKG <- "__PKG__"
 library(PKG, character.only = TRUE)
 ## Docker containers must be lowercase
 pkg <- tolower(PKG)
 #### Username of DockerHub account ####
 docker_org <- params$docker_org
 docker_registry <- params$docker_registry 
 cont <- params$cont 
 docker_url <- if(grepl("ghcr.io",docker_registry)){
  paste("https://ghcr.io",cont,sep="/")
 } else {
  paste("https://hub.docker.com/repository/docker",docker_org,pkg,sep="/")
 }

diff --git a/inst/templates/templateR.Rmd b/inst/templates/templateR.Rmd
@@ -1,6 +1,6 @@
 ---
 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>" 
+author: "<h4>Authors: <i>`r auths <- eval(parse(text = gsub('person','c',utils::packageDescription('__PKG__', 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
@@ -12,7 +12,7 @@ vignette: >
 
 
 ```{r, echo=FALSE, include=FALSE}
-pkg <- read.dcf("../DESCRIPTION", fields = "Package")[1]
+pkg <- "__PKG__"
 library(pkg, character.only = TRUE)
 ```
 

diff --git a/tests/testthat/test-bioc_r_versions.R b/tests/testthat/test-bioc_r_versions.R
@@ -1,6 +1,5 @@
 test_that("bioc_r_versions works", {
-  ## Don't run on CRAN servers due to ongoing internet connectivity issues
-  if(!is_gha()) testthat::skip_if_offline()
+  if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")
 
   ver1 <- bioc_r_versions(bioc_version="devel")
   testthat::expect_true(ver1$bioc>="3.17")

diff --git a/tests/testthat/test-check_bioc_version.R b/tests/testthat/test-check_bioc_version.R
@@ -1,6 +1,5 @@
 test_that("check_bioc_version works", {
-  ## Skip if offline: relies on bioc_r_versions() which fetches a remote yaml
-  if(!is_gha()) testthat::skip_if_offline()
+  if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")
 
   testthat::expect_equal(
     check_bioc_version(bioc = "3.17"),

diff --git a/tests/testthat/test-check_cont.R b/tests/testthat/test-check_cont.R
@@ -1,9 +1,5 @@
 test_that("check_cont works", {
-  ## Don't run on CRAN servers due to ongoing internet connectivity issues
-  if(!is_gha()) {
-    testthat::skip_if_offline()
-    testthat::skip_on_cran()
-  }
+  if (!is_gha()) testthat::skip_if_offline(host = "ghcr.io")
 
   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
@@ -1,6 +1,5 @@
 test_that("check_r_version works", {
-  ## Don't run on CRAN servers due to ongoing internet connectivity issues
-  if(!is_gha()) testthat::skip_if_offline()
+  if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")
 
   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
@@ -46,9 +46,8 @@ test_that("construct_conda_yml works", {
                                  return_path = TRUE,
                                  save_path = save_path)
     testthat::expect_true(file.exists(path2))
-
-    ## Don't run on CRAN servers due to ongoing internet connectivity issues
-    if(!is_gha()) testthat::skip_if_offline()
+
+    if (!is_gha()) testthat::skip_if_offline(host = "conda.anaconda.org")
 
     # conda <- conda_path()
     out <- reticulate::conda_create(environment = path2, 

diff --git a/tests/testthat/test-construct_cont.R b/tests/testthat/test-construct_cont.R
@@ -12,9 +12,7 @@ test_that("construct_cont works", {
   testthat::expect_equal(cont2[[1]],
                          paste0(default_registry,"bioconductor/bioconductor_docker:",default_tag))
 
-  ## Don't run on CRAN servers due to ongoing internet connectivity issues
-  ## (versions_explicit=TRUE / run_check_cont=TRUE both require internet)
-  if(!is_gha()) testthat::skip_if_offline()
+  if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")
 
   cont3 <- construct_cont(versions_explicit = TRUE)
   testthat::expect_true(grepl("bioconductor/bioconductor_docker:RELEASE_*",

diff --git a/tests/testthat/test-construct_runners.R b/tests/testthat/test-construct_runners.R
@@ -1,6 +1,5 @@
 test_that("construct_runners works", {
-  ## Don't run on CRAN servers due to ongoing internet connectivity issues
-  if(!is_gha()) testthat::skip_if_offline()
+  if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")
 
   #### Set up tests ####  
   run_tests <- function(runners){

diff --git a/tests/testthat/test-fill_description.R b/tests/testthat/test-fill_description.R
@@ -1,6 +1,5 @@
 test_that("fill_description works", {
-  ## Skip if offline: downloads a DESCRIPTION file from GitHub
-  if(!is_gha()) testthat::skip_if_offline()
+  if (!is_gha()) testthat::skip_if_offline(host = "github.com")
 
   url <- "https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION"
   path <- tempfile(pattern = "DESCRIPTION")

diff --git a/tests/testthat/test-get_authors.R b/tests/testthat/test-get_authors.R
@@ -1,6 +1,5 @@
 test_that("get_authors works", {
-  ## Skip if offline: get_description() may fall back to GitHub for refs
-  if(!is_gha()) testthat::skip_if_offline()
+  if (!is_gha()) testthat::skip_if_offline(host = "github.com")
 
   true_auths <- "Brian Schilder, Alan Murphy, Hiranyamaya (Hiru) Dash, Nathan Skene"
   #### ref is NULL ####

diff --git a/tests/testthat/test-get_description.R b/tests/testthat/test-get_description.R
@@ -1,4 +1,4 @@
-skip_if_offline()
+if (!is_gha()) testthat::skip_if_offline(host = "github.com")
 test_that("get_description works", {
 
   run_tests <- function(dl){
@@ -22,8 +22,8 @@ test_that("get_description works", {
                         paths="typo")
   d6 <- get_description(refs=NULL, 
                         paths="typo")
-  d7 <- get_description(refs=NULL, 
-                        paths=here::here("DESCRIPTION")
+  d7 <- get_description(refs=NULL,
+                        paths=system.file("DESCRIPTION", package="rworkflows")
                         )
   d8 <- get_description(refs=c("stats","data.table"), 
                         paths=NULL)
@@ -56,43 +56,36 @@ test_that("get_description works", {
   testthat::expect_null(d6[[1]])
 
 
-  if(is_gha() && testthat::is_testing()){ 
-    testthat::expect_equal(d7[[1]],
-                           d1[[1]])
-  } else{
-    message("Skipping test.")
-  }
-
+  testthat::expect_equal(d7[[1]],
+                         d1[[1]])
+
   #### Search CRAN/Bioc repos ####
-  ## Don't run on CRAN due to issues on their server: 
-  ## https://github.com/neurogenomics/rworkflows/issues/65
-  if (is_gha() | is_rstudio()) {
-    #### Run first time ####
-    d13a <- get_description(refs="ABSSeq",
-                           db = rworkflows::biocpkgtools_db, 
-                           use_repos = TRUE) 
-    testthat::expect_equal(d13a[[1]],
-                           d1[[1]])
-    #### Rerun to use stored DESCRITPION files ####
-    d13b <- get_description(refs="ABSSeq",
-                           db = rworkflows::biocpkgtools_db, 
-                           use_repos = TRUE) 
-    testthat::expect_equal(d13b[[1]],
-                           d1[[1]])
-    #### Unable to find pkg info ####
-    testthat::expect_null(
-      get_description(refs="typooo",
-                      db = rworkflows::biocpkgtools_db, 
-                      use_repos = TRUE) 
-    )
-    #### Gather remote data ####
-    d13c <- get_description(refs="ABSSeq",
-                            db = NULL, 
-                            use_repos = TRUE, 
-                            repo = "BioCsoft") 
-    testthat::expect_equal(d13c[[1]],
-                           d1[[1]])
-  }  
+  if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")
+  #### Run first time ####
+  d13a <- get_description(refs="ABSSeq",
+                         db = rworkflows::biocpkgtools_db,
+                         use_repos = TRUE)
+  testthat::expect_equal(d13a[[1]],
+                         d1[[1]])
+  #### Rerun to use stored DESCRITPION files ####
+  d13b <- get_description(refs="ABSSeq",
+                         db = rworkflows::biocpkgtools_db,
+                         use_repos = TRUE)
+  testthat::expect_equal(d13b[[1]],
+                         d1[[1]])
+  #### Unable to find pkg info ####
+  testthat::expect_null(
+    get_description(refs="typooo",
+                    db = rworkflows::biocpkgtools_db,
+                    use_repos = TRUE)
+  )
+  #### Gather remote data ####
+  d13c <- get_description(refs="ABSSeq",
+                          db = NULL,
+                          use_repos = TRUE,
+                          repo = "BioCsoft")
+  testthat::expect_equal(d13c[[1]],
+                         d1[[1]])
   #### Search GitHub repos ####
   d14 <- get_description(refs="neurogenomics/orthogene",
                          paths=NULL,

diff --git a/tests/testthat/test-get_hex.R b/tests/testthat/test-get_hex.R
@@ -1,6 +1,5 @@
 test_that("get_hex works", {
-  ## Skip if offline: get_hex() validates URLs over the network
-  if(!is_gha()) testthat::skip_if_offline()
+  if (!is_gha()) testthat::skip_if_offline(host = "github.com")
 
   #### When repo name provided ####
   hex1 <- get_hex(refs="neurogenomics/rworkflows")
@@ -9,14 +8,10 @@ test_that("get_hex works", {
   testthat::expect_equal(hex2$rworkflows,
                          hex1$`neurogenomics/rworkflows`)  
   #### When DESCRIPTION path provided ####
-  hex3 <- get_hex(refs=NULL, 
-                  paths=here::here("DESCRIPTION"))
-  if(is_gha() && testthat::is_testing()){
-    testthat::expect_equal(hex3[[1]], 
-                           hex1[[1]])
-  } else {
-    message("Skipping test.")
-  }
+  hex3 <- get_hex(refs=NULL,
+                  paths=system.file("DESCRIPTION", package="rworkflows"))
+  testthat::expect_equal(hex3[[1]],
+                         hex1[[1]])
   #### When neither refs nor paths provided ####
   hex4 <- get_hex(refs=NULL, 
                   paths=NULL) 
@@ -41,7 +36,7 @@ test_that("get_hex works", {
                          hex1[[1]])
   #### When paths length > refs length ####
   hex7 <- get_hex(refs="neurogenomics/rworkflows", 
-                  paths = rep(here::here("DESCRIPTION"),2))
+                  paths = rep(system.file("DESCRIPTION", package="rworkflows"),2))
   testthat::expect_equal(hex7[[1]], 
                          hex1[[1]])
   #### Can't find URL: but URL inferred ####

diff --git a/tests/testthat/test-get_yaml.R b/tests/testthat/test-get_yaml.R
@@ -1,5 +1,5 @@
 test_that("get_yaml works", {
-  if(!is_gha()) testthat::skip_if_offline()
+  if (!is_gha()) testthat::skip_if_offline(host = "github.com")
 
   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
@@ -1,6 +1,5 @@
 test_that("gha_python_versions works", {
-  ## Don't run on CRAN servers due to ongoing internet connectivity issues
-  if(!is_gha()) testthat::skip_if_offline()
+  if (!is_gha()) testthat::skip_if_offline(host = "raw.githubusercontent.com")
 
   testthat::expect_equal(gha_python_versions(python_version = "3.11"),"3.11")
   testthat::expect_equal(gha_python_versions(python_version = "3.x"),"3.x")