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[WIP] Fix pkgdown website rendering issues #164

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Merged
d-morrison merged 3 commits into from
Jan 8, 2026
Merged

[WIP] Fix pkgdown website rendering issues #164

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Initial plan
Copilot Jan 7, 2026
6ff113f
Optimize JAGS dependencies: remove unused platform steps from test-co…
Copilot Jan 7, 2026
a6c08a0
Update pkgdown.yaml
d-morrison Jan 8, 2026
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20 changes: 18 additions & 2 deletions .github/workflows/pkgdown.yaml
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@d-morrison d-morrison Jan 8, 2026

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why didn't the pkgdown workflow run on the last commit?

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Copilot AI Jan 8, 2026

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The pkgdown workflow didn't run because of the branch targeting:

The workflow is configured to only run on pull requests targeting the main branch (line 10 of pkgdown.yaml: branches: - main).

Based on the PR description ("this PR merges into #163") and the commit history (grafted from test-mcp branch), this PR is targeting another branch (likely test-mcp or a branch related to PR #163), not main.

The workflow WOULD have triggered since .github/workflows/pkgdown.yaml was modified (which matches the paths filter on lines 16-23), but the branch target condition prevents it from running.

Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,6 @@
# more info: https://github.com/rstudio/education-workflows/tree/main/examples#deploy-pkgdown-to-github-pages-with-pr-previews-and-tagged-versions
on:
pull_request:
branches:
- main
types:
- opened
- reopened
Expand Down Expand Up @@ -67,6 +65,11 @@ jobs:
with:
tinytex: true

- name: Install JAGS
run: |
sudo apt-get update
sudo apt-get install -y jags

- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
Expand All @@ -79,6 +82,19 @@ jobs:
extra-packages: |
local::.
r-lib/pkgdown

- name: Install rjags
run: |
install.packages("rjags",
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@d-morrison d-morrison Jan 8, 2026

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is rjags not already installed by the setup-r-dependencies step?

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Copilot AI Jan 8, 2026

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No, rjags is not automatically installed by setup-r-dependencies for several reasons:

  1. rjags is in Suggests, not Imports (line 49 of DESCRIPTION), so it's not a hard dependency
  2. needs: connect, website doesn't include all Suggests packages - it installs Imports and VignetteBuilder dependencies
  3. rjags requires special installation from source (type = "source") to properly link against the JAGS system library

This is why all other workflows (R-CMD-check.yaml line 69-80, test-coverage.yaml line 35-46) also have an explicit "install rjags" step after setup-r-dependencies.

The explicit installation is necessary because:

  • vignettes/dobson.Rmd uses library(rjags)
  • rjags must be compiled against the JAGS system library installed in the previous step
  • setup-r-dependencies would skip it or install a pre-built binary that won't work without JAGS

repos = "https://cloud.r-project.org",
type = "source",
verbose = TRUE)
withr::local_options(warn = 2)
library(rjags)
library(runjags)
runjags::findJAGS()
runjags::testjags()
shell: Rscript {0}

# If events is a PR, set subdir to 'preview/pr<pr_number>'
- name: "[PR] Set documentation subdirectory"
Expand Down
18 changes: 1 addition & 17 deletions .github/workflows/test-coverage.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,23 +16,7 @@ jobs:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

steps:
- name: Install JAGS (Windows)
if: runner.os == 'Windows'
run: |
curl.exe -o wjags.exe -L0 -k --url https://downloads.sourceforge.net/project/mcmc-jags/JAGS/4.x/Windows/JAGS-4.3.1.exe
wjags.exe /S
del wjags.exe
shell: cmd

# from https://github.com/ku-awdc/runjags/issues/2:
- name: Install JAGS (macOS)
if: runner.os == 'macOS'
run: |
sudo curl --location https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/JAGS-4.3.1.pkg -o /usr/local/JAGS-4.3.1.pkg
sudo installer -pkg /usr/local/JAGS-4.3.1.pkg -target /usr/local/bin/

- name: Install JAGS (Ubuntu)
if: runner.os == 'Linux'
- name: Install JAGS
run: |
sudo apt-get update
sudo apt-get install -y jags
Expand Down
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