From 2edb9759045f57a94bd5d8352115e51467904544 Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Tue, 5 May 2026 15:36:40 +0100
Subject: [PATCH 1/9] fix(vignettes): replace read.dcf("../DESCRIPTION") with
 packageDescription

R CMD check tangles each vignette to a .R file and sources it from a temp
working directory, where ../DESCRIPTION does not resolve. Use
utils::packageDescription("rworkflows", ...) in the package's own vignettes,
and a __PKG__ placeholder in inst/templates/{templateR,docker}.Rmd that
use_vignette_getstarted()/use_vignette_docker() substitute at write time.

Also guard those generators against a NULL/empty `package` (the previous
default silently produced a malformed file) and update the use_vignette_docker
demo in rworkflows.Rmd to pass package = "mypackage" so the chunk no longer
relies on a discoverable DESCRIPTION at vignette runtime.
---
 R/use_vignette_docker.R      | 9 ++++++++-
 R/use_vignette_getstarted.R  | 8 +++++++-
 inst/templates/docker.Rmd    | 4 ++--
 inst/templates/templateR.Rmd | 4 ++--
 vignettes/bioconductor.Rmd   | 4 ++--
 vignettes/depgraph.Rmd       | 2 +-
 vignettes/docker.Rmd         | 4 ++--
 vignettes/repos.Rmd          | 2 +-
 vignettes/rworkflows.Rmd     | 7 ++++---
 9 files changed, 29 insertions(+), 15 deletions(-)

diff --git a/R/use_vignette_docker.R b/R/use_vignette_docker.R
index a3f0e576..e078990b 100644
--- 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
index 53b2a289..9063fe93 100644
--- 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/inst/templates/docker.Rmd b/inst/templates/docker.Rmd
index 41579c4b..cfa781d6 100644
--- 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:
@@ -24,7 +24,7 @@ vignette: >
 
 ```{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)
diff --git a/inst/templates/templateR.Rmd b/inst/templates/templateR.Rmd
index a6866a28..7f0d5f5f 100644
--- 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/vignettes/bioconductor.Rmd b/vignettes/bioconductor.Rmd
index 9f8a3c2d..ee35a729 100644
--- a/vignettes/bioconductor.Rmd
+++ b/vignettes/bioconductor.Rmd
@@ -1,6 +1,6 @@
 ---
 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>" 
+author: "<h4>Authors: <i>`r auths <- eval(parse(text = gsub('person','c',utils::packageDescription('rworkflows', 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:
   rmarkdown::html_vignette
@@ -12,7 +12,7 @@ vignette: >
 
 
 ```{r, echo=FALSE, include=FALSE}
-pkg <- read.dcf("../DESCRIPTION", fields = "Package")[1]
+pkg <- "rworkflows"
 library(pkg, character.only = TRUE)
 ## Skip internet-dependent chunks gracefully when offline
 has_net <- requireNamespace("curl", quietly = TRUE) && curl::has_internet()
diff --git a/vignettes/depgraph.Rmd b/vignettes/depgraph.Rmd
index 1302f081..44810517 100644
--- a/vignettes/depgraph.Rmd
+++ b/vignettes/depgraph.Rmd
@@ -1,6 +1,6 @@
 ---
 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>" 
+author: "<h4>Authors: <i>`r auths <- eval(parse(text = gsub('person','c',utils::packageDescription('rworkflows', 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:
   rmarkdown::html_vignette
diff --git a/vignettes/docker.Rmd b/vignettes/docker.Rmd
index 905a7ceb..dd45d71c 100644
--- a/vignettes/docker.Rmd
+++ b/vignettes/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",
+author: '<h4>Authors: <i>`r auths <- eval(parse(text = gsub("person","c",utils::packageDescription("rworkflows",
   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>'
@@ -23,7 +23,7 @@ vignette: |
 
 ```{r setup, include=FALSE}
 #### Package name ####
-PKG <- read.dcf("../DESCRIPTION", fields = "Package")[1]
+PKG <- "rworkflows"
 library(PKG, character.only = TRUE)
 ## Docker containers must be lowercase
 pkg <- tolower(PKG)
diff --git a/vignettes/repos.Rmd b/vignettes/repos.Rmd
index 0e5f01ab..11c0906f 100644
--- a/vignettes/repos.Rmd
+++ b/vignettes/repos.Rmd
@@ -1,6 +1,6 @@
 ---
 title: "Repositories report" 
-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('rworkflows', 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:
   rmarkdown::html_vignette
diff --git a/vignettes/rworkflows.Rmd b/vignettes/rworkflows.Rmd
index a05a4858..68e42e6c 100644
--- a/vignettes/rworkflows.Rmd
+++ b/vignettes/rworkflows.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('rworkflows', 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:
   rmarkdown::html_vignette
@@ -12,7 +12,7 @@ vignette: >
 
 
 ```{r, echo=FALSE, include=FALSE}
-pkg <- read.dcf("../DESCRIPTION", fields = "Package")[1]
+pkg <- "rworkflows"
 library(pkg, character.only = TRUE)
 ## Skip internet-dependent chunks gracefully when offline
 has_net <- requireNamespace("curl", quietly = TRUE) && curl::has_internet()
@@ -147,7 +147,8 @@ If you're using the GitHub Container Registry, `docker_org` can simply be your
 GH organization name or user name.
 ```{r}
 ## Use default save_dir in practice
-vignette2 <- rworkflows::use_vignette_docker(docker_org = "neurogenomics",
+vignette2 <- rworkflows::use_vignette_docker(package = "mypackage",
+                                             docker_org = "neurogenomics",
                                              save_dir = tempdir())
 ```
 

From 7e0ccbb18c4de535f5a6f3bf2a0c9a190302ef98 Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Tue, 5 May 2026 15:39:57 +0100
Subject: [PATCH 2/9] chore(deps): bump actions/checkout to v6
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

action.yml and rworkflows_static.yml were on v4; the bundled example
was on v3. v6.0.2 is the current latest.

v5 moved the action onto Node.js 24 (requires runner >= v2.327.1, which
all GitHub-hosted runners satisfy). v6 (PR actions/checkout#2286) writes
git auth credentials to a separate .gitauth file instead of .git/config.
Neither change affects this action — post-checkout we only run
`git config --global --add safe.directory '*'` and pass GITHUB_TOKEN
through the env, not from .git/config.
---
 .github/workflows/rworkflows_static.yml  | 2 +-
 action.yml                               | 2 +-
 inst/example/check_rworkflows-merged.yml | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/rworkflows_static.yml b/.github/workflows/rworkflows_static.yml
index e282ed82..2db8a07f 100644
--- 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/action.yml b/action.yml
index 4c7543c8..6142b33d 100644
--- 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
index 93713ff9..f7561406 100644
--- 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

From ac61194527029b3b0faf77e655e0bde974290ad1 Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Tue, 5 May 2026 15:54:33 +0100
Subject: [PATCH 3/9] test: drop is_gha() gates in favour of
 skip_if_offline(host=...)

Replace `if(!is_gha()) skip_if_offline()` with `skip_if_offline(host=X)`
where X is the host the test actually contacts:
- bioconductor.org for bioc_r_versions / construct_runners / construct_cont /
  check_r_version / check_bioc_version
- github.com for get_description / get_authors / get_hex / use_badges /
  use_workflow / infer_deps / fill_description / get_yaml / url_exists
- raw.githubusercontent.com for gha_python_versions
- conda.anaconda.org for the construct_conda_yml conda_create block

For is_gha() gates that weren't about offline (infer_biocviews,
get_description d7 == d1 expectation, get_hex hex3 == hex1 expectation,
construct_conda_yml OS guard) the gate is removed and the assertion runs
unconditionally; the get_description Bioc-repo block now skips on
bioconductor.org instead of requiring is_gha() | is_rstudio().

All 195 tests pass with 0 skips locally.
---
 tests/testthat/test-bioc_r_versions.R     |  3 +-
 tests/testthat/test-check_bioc_version.R  |  3 +-
 tests/testthat/test-check_cont.R          |  6 +-
 tests/testthat/test-check_r_version.R     |  3 +-
 tests/testthat/test-construct_conda_yml.R | 10 ++--
 tests/testthat/test-construct_cont.R      |  4 +-
 tests/testthat/test-construct_runners.R   |  3 +-
 tests/testthat/test-fill_description.R    |  3 +-
 tests/testthat/test-get_authors.R         |  3 +-
 tests/testthat/test-get_description.R     | 67 ++++++++++-------------
 tests/testthat/test-get_hex.R             | 11 +---
 tests/testthat/test-get_yaml.R            |  2 +-
 tests/testthat/test-gha_python_versions.R |  3 +-
 tests/testthat/test-infer_biocviews.R     | 20 ++-----
 tests/testthat/test-infer_deps.R          |  3 +-
 tests/testthat/test-url_exists.R          |  3 +-
 tests/testthat/test-use_badges.R          |  2 +-
 tests/testthat/test-use_workflow.R        |  2 +-
 18 files changed, 56 insertions(+), 95 deletions(-)

diff --git a/tests/testthat/test-bioc_r_versions.R b/tests/testthat/test-bioc_r_versions.R
index 9348a8d2..dca32f78 100644
--- 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()
+  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
index 9a909441..fa020f67 100644
--- 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()
+  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
index 94b7129d..eed847eb 100644
--- 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()
-  }
+  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
index 2cf48e08..59e8703a 100644
--- 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()
+  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
index a98b9c5b..a7c268a3 100644
--- a/tests/testthat/test-construct_conda_yml.R
+++ b/tests/testthat/test-construct_conda_yml.R
@@ -31,9 +31,8 @@ test_that("construct_conda_yml works", {
   
   #### Construct an actual conda env ####
   if("reticulate" %in% rownames(installed.packages()) &&
-     conda_installed() && 
-     is_gha() &&
-     .Platform$OS.type != "windows"){ 
+     conda_installed() &&
+     .Platform$OS.type != "windows"){
     envname <- "testenv"
     if(condaenv_exists(envname)){
       reticulate::conda_remove(envname = envname)
@@ -46,9 +45,8 @@ 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()
+
+    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
index 880a3042..956f34bf 100644
--- 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()
+  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
index 97c3e61d..5d81cb45 100644
--- 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()
+  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
index 589e49a2..9ee4c74f 100644
--- 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()
+  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
index 7b2d487e..40710125 100644
--- 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()
+  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
index 4bd62b43..880bed6e 100644
--- a/tests/testthat/test-get_description.R
+++ b/tests/testthat/test-get_description.R
@@ -1,4 +1,4 @@
-skip_if_offline()
+testthat::skip_if_offline(host = "github.com")
 test_that("get_description works", {
   
   run_tests <- function(dl){
@@ -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]])
-  }  
+  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
index 29c0757b..30a0f3db 100644
--- 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()
+  testthat::skip_if_offline(host = "github.com")
 
   #### When repo name provided ####
   hex1 <- get_hex(refs="neurogenomics/rworkflows")
@@ -11,12 +10,8 @@ test_that("get_hex works", {
   #### 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.")
-  }
+  testthat::expect_equal(hex3[[1]],
+                         hex1[[1]])
   #### When neither refs nor paths provided ####
   hex4 <- get_hex(refs=NULL, 
                   paths=NULL) 
diff --git a/tests/testthat/test-get_yaml.R b/tests/testthat/test-get_yaml.R
index ca928cd0..077bf60a 100644
--- 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()
+  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
index 85ea1ec5..58d38685 100644
--- 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()
+  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")
diff --git a/tests/testthat/test-infer_biocviews.R b/tests/testthat/test-infer_biocviews.R
index 6aba84e6..1dc1fdf9 100644
--- a/tests/testthat/test-infer_biocviews.R
+++ b/tests/testthat/test-infer_biocviews.R
@@ -5,21 +5,11 @@ test_that("infer_biocviews works", {
   # biocviews1 <- infer_biocviews(pkgdir = "../../")
   # testthat::expect_equal(biocviews1,"Software")
   
-  if(testthat::is_testing() &&
-     !is_gha()){
-    message("Skipping test.")
-  } else {
-    testthat::expect_equal(infer_biocviews(include_branch = FALSE),
-                           c("Software","WorkflowManagement"))  
-  }
-  biocviews_manual = c("Software","Genetics","Transcriptomics") 
-  if(testthat::is_testing() && 
-     !is_gha()){
-    message("Skipping test.")
-  } else {
-    testthat::expect_equal(infer_biocviews(biocviews = biocviews_manual),
-                           c(biocviews_manual,"WorkflowManagement"))
-  }
+  testthat::expect_equal(infer_biocviews(include_branch = FALSE),
+                         c("Software","WorkflowManagement"))
+  biocviews_manual = c("Software","Genetics","Transcriptomics")
+  testthat::expect_equal(infer_biocviews(biocviews = biocviews_manual),
+                         c(biocviews_manual,"WorkflowManagement"))
 
   #### Errors ####
   testthat::expect_error(
diff --git a/tests/testthat/test-infer_deps.R b/tests/testthat/test-infer_deps.R
index d3a0b20f..4311b7b5 100644
--- a/tests/testthat/test-infer_deps.R
+++ b/tests/testthat/test-infer_deps.R
@@ -1,6 +1,5 @@
 test_that("infer_deps works", {
-  ## Skip if offline: downloads a DESCRIPTION file from GitHub
-  if(!is_gha()) testthat::skip_if_offline()
+  testthat::skip_if_offline(host = "github.com")
 
   #' #### Get example DESCRIPTION file ####
   url <- "https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION"
diff --git a/tests/testthat/test-url_exists.R b/tests/testthat/test-url_exists.R
index 848eee01..2ddacba8 100644
--- a/tests/testthat/test-url_exists.R
+++ b/tests/testthat/test-url_exists.R
@@ -1,6 +1,5 @@
 test_that("url_exists works", {
-  ## Don't run on CRAN servers due to ongoing internet connectivity issues
-  if(!is_gha()) testthat::skip_if_offline()
+  testthat::skip_if_offline(host = "github.com")
   
   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
index e6784363..20ebc3dc 100644
--- a/tests/testthat/test-use_badges.R
+++ b/tests/testthat/test-use_badges.R
@@ -1,5 +1,5 @@
 test_that("use_badges works", {
-  if(!is_gha()) testthat::skip_if_offline()
+  testthat::skip_if_offline(host = "github.com")
   
   run_tests <- function(badges){
     testthat::expect_length(badges,1)
diff --git a/tests/testthat/test-use_workflow.R b/tests/testthat/test-use_workflow.R
index d2bbddd7..199485e6 100644
--- a/tests/testthat/test-use_workflow.R
+++ b/tests/testthat/test-use_workflow.R
@@ -1,5 +1,5 @@
 test_that("use_workflow works", {
-  if(!is_gha()) testthat::skip_if_offline()
+  testthat::skip_if_offline(host = "github.com")
   
   path <- use_workflow(save_dir = file.path(tempdir(),".github","workflows"))
   testthat::expect_true(file.exists(path))

From fb4012c8737733954316e0bc740dd1aadda03654 Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Tue, 5 May 2026 16:09:32 +0100
Subject: [PATCH 4/9] docs(NEWS): record vignette/checkout/test changes under
 1.0.12

Add bullets under the existing 1.0.12 section for: the vignette read.dcf
fix and packageDescription/__PKG__ rewrite, the use_vignette_* package
guard, the actions/checkout v6 bump, and the test refactor that swapped
is_gha() gates for skip_if_offline(host=...).
---
 NEWS.md | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 7d3fa648..caeeab8d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -35,6 +35,17 @@ resources:
       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 +54,19 @@ and vignettes.
   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 `if(!is_gha()) skip_if_offline()` gates with
+  host-specific `skip_if_offline(host=...)` calls
+  (`bioconductor.org`, `github.com`, `raw.githubusercontent.com`,
+  `ghcr.io`, `conda.anaconda.org`) so individual tests skip when their
+  actual remote is unreachable rather than relying on a GHA escape hatch.
 
 # rworkflows 1.0.11
 

From 6953b78da887befeca7ea38d124a0346519c300c Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Tue, 5 May 2026 16:23:35 +0100
Subject: [PATCH 5/9] test(conda): keep is_gha() gate on env-creation block
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Restore the is_gha() guard on the construct_conda_yml conda env-creation
block that was dropped in ac61194. The block creates a real conda env
under ~/miniforge3/envs/testenv and is intentionally GHA-only — running
it on a developer machine leaves persistent state behind, and the
test's own `condaenv_exists()` cleanup misses orphaned env directories,
so subsequent runs fail with `prefix already exists`. is_gha() is the
right gate here because the test is genuinely targeting the GHA
environment (where setup-miniconda provides conda on PATH and the
runner is fresh).

Update the NEWS bullet to reflect that is_gha() is retained for this
single test; everywhere else the gates are now host-specific
skip_if_offline().
---
 NEWS.md                                   | 14 ++++++++++----
 tests/testthat/test-construct_conda_yml.R |  5 +++--
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index caeeab8d..723394d1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -62,11 +62,17 @@ and vignettes.
 * 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 `if(!is_gha()) skip_if_offline()` gates with
-  host-specific `skip_if_offline(host=...)` calls
+* 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`, `conda.anaconda.org`) so individual tests skip when their
-  actual remote is unreachable rather than relying on a GHA escape hatch.
+  `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.
+  `is_gha()` is retained only 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
 
diff --git a/tests/testthat/test-construct_conda_yml.R b/tests/testthat/test-construct_conda_yml.R
index a7c268a3..cefddd5f 100644
--- a/tests/testthat/test-construct_conda_yml.R
+++ b/tests/testthat/test-construct_conda_yml.R
@@ -31,8 +31,9 @@ test_that("construct_conda_yml works", {
   
   #### Construct an actual conda env ####
   if("reticulate" %in% rownames(installed.packages()) &&
-     conda_installed() &&
-     .Platform$OS.type != "windows"){
+     conda_installed() && 
+     is_gha() &&
+     .Platform$OS.type != "windows"){ 
     envname <- "testenv"
     if(condaenv_exists(envname)){
       reticulate::conda_remove(envname = envname)

From aa4e984878c259852aa1f623dc27bddc29bcfc65 Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Tue, 5 May 2026 16:34:13 +0100
Subject: [PATCH 6/9] test: gate skip_if_offline behind !is_gha() so GHA always
 runs network tests

---
 tests/testthat/test-bioc_r_versions.R     | 2 +-
 tests/testthat/test-check_bioc_version.R  | 2 +-
 tests/testthat/test-check_cont.R          | 2 +-
 tests/testthat/test-check_r_version.R     | 2 +-
 tests/testthat/test-construct_conda_yml.R | 2 +-
 tests/testthat/test-construct_cont.R      | 2 +-
 tests/testthat/test-construct_runners.R   | 2 +-
 tests/testthat/test-fill_description.R    | 2 +-
 tests/testthat/test-get_authors.R         | 2 +-
 tests/testthat/test-get_description.R     | 4 ++--
 tests/testthat/test-get_hex.R             | 2 +-
 tests/testthat/test-get_yaml.R            | 2 +-
 tests/testthat/test-gha_python_versions.R | 2 +-
 tests/testthat/test-infer_deps.R          | 2 +-
 tests/testthat/test-url_exists.R          | 2 +-
 tests/testthat/test-use_badges.R          | 2 +-
 tests/testthat/test-use_workflow.R        | 2 +-
 17 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/tests/testthat/test-bioc_r_versions.R b/tests/testthat/test-bioc_r_versions.R
index dca32f78..2ba4b23f 100644
--- a/tests/testthat/test-bioc_r_versions.R
+++ b/tests/testthat/test-bioc_r_versions.R
@@ -1,5 +1,5 @@
 test_that("bioc_r_versions works", {
-  testthat::skip_if_offline(host = "bioconductor.org")
+  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
index fa020f67..e7996b52 100644
--- a/tests/testthat/test-check_bioc_version.R
+++ b/tests/testthat/test-check_bioc_version.R
@@ -1,5 +1,5 @@
 test_that("check_bioc_version works", {
-  testthat::skip_if_offline(host = "bioconductor.org")
+  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
index eed847eb..a061f346 100644
--- a/tests/testthat/test-check_cont.R
+++ b/tests/testthat/test-check_cont.R
@@ -1,5 +1,5 @@
 test_that("check_cont works", {
-  testthat::skip_if_offline(host = "ghcr.io")
+  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
index 59e8703a..112a51f4 100644
--- a/tests/testthat/test-check_r_version.R
+++ b/tests/testthat/test-check_r_version.R
@@ -1,5 +1,5 @@
 test_that("check_r_version works", {
-  testthat::skip_if_offline(host = "bioconductor.org")
+  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
index cefddd5f..e0c9383c 100644
--- a/tests/testthat/test-construct_conda_yml.R
+++ b/tests/testthat/test-construct_conda_yml.R
@@ -47,7 +47,7 @@ test_that("construct_conda_yml works", {
                                  save_path = save_path)
     testthat::expect_true(file.exists(path2))
 
-    testthat::skip_if_offline(host = "conda.anaconda.org")
+    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
index 956f34bf..0b71a626 100644
--- a/tests/testthat/test-construct_cont.R
+++ b/tests/testthat/test-construct_cont.R
@@ -12,7 +12,7 @@ test_that("construct_cont works", {
   testthat::expect_equal(cont2[[1]],
                          paste0(default_registry,"bioconductor/bioconductor_docker:",default_tag))
 
-  testthat::skip_if_offline(host = "bioconductor.org")
+  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
index 5d81cb45..343e6d66 100644
--- a/tests/testthat/test-construct_runners.R
+++ b/tests/testthat/test-construct_runners.R
@@ -1,5 +1,5 @@
 test_that("construct_runners works", {
-  testthat::skip_if_offline(host = "bioconductor.org")
+  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
index 9ee4c74f..ce158c65 100644
--- a/tests/testthat/test-fill_description.R
+++ b/tests/testthat/test-fill_description.R
@@ -1,5 +1,5 @@
 test_that("fill_description works", {
-  testthat::skip_if_offline(host = "github.com")
+  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
index 40710125..68215c51 100644
--- a/tests/testthat/test-get_authors.R
+++ b/tests/testthat/test-get_authors.R
@@ -1,5 +1,5 @@
 test_that("get_authors works", {
-  testthat::skip_if_offline(host = "github.com")
+  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
index 880bed6e..356bf424 100644
--- a/tests/testthat/test-get_description.R
+++ b/tests/testthat/test-get_description.R
@@ -1,4 +1,4 @@
-testthat::skip_if_offline(host = "github.com")
+if (!is_gha()) testthat::skip_if_offline(host = "github.com")
 test_that("get_description works", {
   
   run_tests <- function(dl){
@@ -60,7 +60,7 @@ test_that("get_description works", {
                          d1[[1]])
 
   #### Search CRAN/Bioc repos ####
-  testthat::skip_if_offline(host = "bioconductor.org")
+  if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")
   #### Run first time ####
   d13a <- get_description(refs="ABSSeq",
                          db = rworkflows::biocpkgtools_db,
diff --git a/tests/testthat/test-get_hex.R b/tests/testthat/test-get_hex.R
index 30a0f3db..16285c47 100644
--- a/tests/testthat/test-get_hex.R
+++ b/tests/testthat/test-get_hex.R
@@ -1,5 +1,5 @@
 test_that("get_hex works", {
-  testthat::skip_if_offline(host = "github.com")
+  if (!is_gha()) testthat::skip_if_offline(host = "github.com")
 
   #### When repo name provided ####
   hex1 <- get_hex(refs="neurogenomics/rworkflows")
diff --git a/tests/testthat/test-get_yaml.R b/tests/testthat/test-get_yaml.R
index 077bf60a..242f08b2 100644
--- a/tests/testthat/test-get_yaml.R
+++ b/tests/testthat/test-get_yaml.R
@@ -1,5 +1,5 @@
 test_that("get_yaml works", {
-  testthat::skip_if_offline(host = "github.com")
+  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
index 58d38685..c75e039c 100644
--- a/tests/testthat/test-gha_python_versions.R
+++ b/tests/testthat/test-gha_python_versions.R
@@ -1,5 +1,5 @@
 test_that("gha_python_versions works", {
-  testthat::skip_if_offline(host = "raw.githubusercontent.com")
+  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")
diff --git a/tests/testthat/test-infer_deps.R b/tests/testthat/test-infer_deps.R
index 4311b7b5..a48b8ca0 100644
--- a/tests/testthat/test-infer_deps.R
+++ b/tests/testthat/test-infer_deps.R
@@ -1,5 +1,5 @@
 test_that("infer_deps works", {
-  testthat::skip_if_offline(host = "github.com")
+  if (!is_gha()) testthat::skip_if_offline(host = "github.com")
 
   #' #### Get example DESCRIPTION file ####
   url <- "https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION"
diff --git a/tests/testthat/test-url_exists.R b/tests/testthat/test-url_exists.R
index 2ddacba8..8b5f2c02 100644
--- a/tests/testthat/test-url_exists.R
+++ b/tests/testthat/test-url_exists.R
@@ -1,5 +1,5 @@
 test_that("url_exists works", {
-  testthat::skip_if_offline(host = "github.com")
+  if (!is_gha()) testthat::skip_if_offline(host = "github.com")
   
   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
index 20ebc3dc..df2bd950 100644
--- a/tests/testthat/test-use_badges.R
+++ b/tests/testthat/test-use_badges.R
@@ -1,5 +1,5 @@
 test_that("use_badges works", {
-  testthat::skip_if_offline(host = "github.com")
+  if (!is_gha()) testthat::skip_if_offline(host = "github.com")
   
   run_tests <- function(badges){
     testthat::expect_length(badges,1)
diff --git a/tests/testthat/test-use_workflow.R b/tests/testthat/test-use_workflow.R
index 199485e6..5456ee26 100644
--- a/tests/testthat/test-use_workflow.R
+++ b/tests/testthat/test-use_workflow.R
@@ -1,5 +1,5 @@
 test_that("use_workflow works", {
-  testthat::skip_if_offline(host = "github.com")
+  if (!is_gha()) testthat::skip_if_offline(host = "github.com")
   
   path <- use_workflow(save_dir = file.path(tempdir(),".github","workflows"))
   testthat::expect_true(file.exists(path))

From 3fe9e44c916d8727e9c2be441599a753100c2d2f Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Tue, 5 May 2026 16:36:58 +0100
Subject: [PATCH 7/9] docs(NEWS): note that skip_if_offline is wrapped in
 !is_gha() so CI runs network tests

---
 NEWS.md | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 723394d1..41ffcd33 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -68,11 +68,14 @@ and vignettes.
   `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.
-  `is_gha()` is retained only 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).
+  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
 

From c34eeaa7b8c6d919110605eaa1a4df6c97e0e39a Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Tue, 5 May 2026 16:41:21 +0100
Subject: [PATCH 8/9] test(infer_biocviews): gate on !is_gha() &&
 skip_if_offline(host="bioconductor.org")

---
 NEWS.md                               | 3 ++-
 tests/testthat/test-infer_biocviews.R | 5 +++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 41ffcd33..abef9ea6 100644
--- 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.
diff --git a/tests/testthat/test-infer_biocviews.R b/tests/testthat/test-infer_biocviews.R
index 1dc1fdf9..b450162a 100644
--- a/tests/testthat/test-infer_biocviews.R
+++ b/tests/testthat/test-infer_biocviews.R
@@ -1,5 +1,6 @@
-test_that("infer_biocviews works", { 
-  
+test_that("infer_biocviews works", {
+  if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")
+
   # Don't run simply bc biocViews::recommendBiocViews is unable
   ## to find the DESCRIPTION file when running examples.
   # biocviews1 <- infer_biocviews(pkgdir = "../../")

From 95e07572a3367f3b7fae17b7d8bf3d93e7b0c9fe Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Tue, 5 May 2026 17:00:00 +0100
Subject: [PATCH 9/9] test: replace here::here() with system.file() so tests
 resolve under R CMD check

here::here("DESCRIPTION") doesn't anchor to the package when R CMD check
copies it to a temp dir lacking project markers, causing get_description,
get_hex, and infer_biocviews tests to fail. system.file() works in both
devtools::test() (source tree) and R CMD check (installed copy).
---
 tests/testthat/test-get_description.R |  4 ++--
 tests/testthat/test-get_hex.R         |  6 +++---
 tests/testthat/test-infer_biocviews.R | 16 +++++++++-------
 3 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/tests/testthat/test-get_description.R b/tests/testthat/test-get_description.R
index 356bf424..da02e7ef 100644
--- a/tests/testthat/test-get_description.R
+++ b/tests/testthat/test-get_description.R
@@ -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)
diff --git a/tests/testthat/test-get_hex.R b/tests/testthat/test-get_hex.R
index 16285c47..812d1cb9 100644
--- a/tests/testthat/test-get_hex.R
+++ b/tests/testthat/test-get_hex.R
@@ -8,8 +8,8 @@ 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"))
+  hex3 <- get_hex(refs=NULL,
+                  paths=system.file("DESCRIPTION", package="rworkflows"))
   testthat::expect_equal(hex3[[1]],
                          hex1[[1]])
   #### When neither refs nor paths provided ####
@@ -36,7 +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-infer_biocviews.R b/tests/testthat/test-infer_biocviews.R
index b450162a..c78a123b 100644
--- a/tests/testthat/test-infer_biocviews.R
+++ b/tests/testthat/test-infer_biocviews.R
@@ -1,15 +1,17 @@
 test_that("infer_biocviews works", {
   if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")
 
-  # Don't run simply bc biocViews::recommendBiocViews is unable
-  ## to find the DESCRIPTION file when running examples.
-  # biocviews1 <- infer_biocviews(pkgdir = "../../")
-  # testthat::expect_equal(biocviews1,"Software")
-  
-  testthat::expect_equal(infer_biocviews(include_branch = FALSE),
+  # Resolve a pkgdir that contains DESCRIPTION in both devtools::test()
+  # (source dir) and R CMD check (installed copy in temp library), since
+  # here::here() doesn't anchor to the package under R CMD check.
+  pkgdir <- dirname(system.file("DESCRIPTION", package = "rworkflows"))
+
+  testthat::expect_equal(infer_biocviews(pkgdir = pkgdir,
+                                         include_branch = FALSE),
                          c("Software","WorkflowManagement"))
   biocviews_manual = c("Software","Genetics","Transcriptomics")
-  testthat::expect_equal(infer_biocviews(biocviews = biocviews_manual),
+  testthat::expect_equal(infer_biocviews(pkgdir = pkgdir,
+                                         biocviews = biocviews_manual),
                          c(biocviews_manual,"WorkflowManagement"))
 
   #### Errors ####