Run failed: pages build and deployment

[aemcdani]

I created a repository to use manubot in (https://github.com/UCSC-Treehouse/TUBI-2023). I'd like CI to run on github. I ran
bash <( curl --location https://github.com/manubot/rootstock/raw/main/setup.bash) locally. When I update the code in the repository (e.g. content/01.abstract.md), I get an error message: Run failed: pages build and deployment - main (3310304).

Run actions/jekyll-build-pages@v1 /usr/bin/docker run --name ghcrioactionsjekyllbuildpagesv108_d30a3e --label 5bedb4 --workdir /github/workspace --rm -e "INPUT_SOURCE" -e "INPUT_DESTINATION" -e "INPUT_FUTURE" -e "INPUT_BUILD_REVISION" -e "INPUT_VERBOSE" -e "INPUT_TOKEN" -e "HOME" -e "GITHUB_JOB" -e "GITHUB_REF" -e "GITHUB_SHA" -e "GITHUB_REPOSITORY" -e "GITHUB_REPOSITORY_OWNER" -e "GITHUB_REPOSITORY_OWNER_ID" -e "GITHUB_RUN_ID" -e "GITHUB_RUN_NUMBER" -e "GITHUB_RETENTION_DAYS" -e "GITHUB_RUN_ATTEMPT" -e "GITHUB_REPOSITORY_ID" -e "GITHUB_ACTOR_ID" -e "GITHUB_ACTOR" -e "GITHUB_TRIGGERING_ACTOR" -e "GITHUB_WORKFLOW" -e "GITHUB_HEAD_REF" -e "GITHUB_BASE_REF" -e "GITHUB_EVENT_NAME" -e "GITHUB_SERVER_URL" -e "GITHUB_API_URL" -e "GITHUB_GRAPHQL_URL" -e "GITHUB_REF_NAME" -e "GITHUB_REF_PROTECTED" -e "GITHUB_REF_TYPE" -e "GITHUB_WORKFLOW_REF" -e "GITHUB_WORKFLOW_SHA" -e "GITHUB_WORKSPACE" -e "GITHUB_ACTION" -e "GITHUB_EVENT_PATH" -e "GITHUB_ACTION_REPOSITORY" -e "GITHUB_ACTION_REF" -e "GITHUB_PATH" -e "GITHUB_ENV" -e "GITHUB_STEP_SUMMARY" -e "GITHUB_STATE" -e "GITHUB_OUTPUT" -e "RUNNER_OS" -e "RUNNER_ARCH" -e "RUNNER_NAME" -e "RUNNER_ENVIRONMENT" -e "RUNNER_TOOL_CACHE" -e "RUNNER_TEMP" -e "RUNNER_WORKSPACE" -e "ACTIONS_RUNTIME_URL" -e "ACTIONS_RUNTIME_TOKEN" -e "ACTIONS_CACHE_URL" -e "ACTIONS_ID_TOKEN_REQUEST_URL" -e "ACTIONS_ID_TOKEN_REQUEST_TOKEN" -e GITHUB_ACTIONS=true -e CI=true -v "/var/run/docker.sock":"/var/run/docker.sock" -v "/home/runner/work/_temp/_github_home":"/github/home" -v "/home/runner/work/_temp/_github_workflow":"/github/workflow" -v "/home/runner/work/_temp/_runner_file_commands":"/github/file_commands" -v "/home/runner/work/TUBI-2023/TUBI-2023":"/github/workspace" ghcr.io/actions/jekyll-build-pages:v1.0.8 Configuration file: none Logging at level: debug GitHub Pages: github-pages v228 GitHub Pages: jekyll v3.9.3 Theme: jekyll-theme-primer Theme source: /usr/local/bundle/gems/jekyll-theme-primer-0.6.0 Requiring: jekyll-github-metadata To use retry middleware with Faraday v2.0+, install faraday-retrygem /usr/local/bundle/gems/pathutil-0.16.2/lib/pathutil.rb:292:inin_path?': No such file or directory @ rb_check_realpath_internal - /github/workspace/webpage/images (Errno::ENOENT)
from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/entry_filter.rb:83:in symlink_outside_site_source?' from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/entry_filter.rb:74:in symlink?'
from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/entry_filter.rb:35:in block in filter' from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/entry_filter.rb:33:in reject'
from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/entry_filter.rb:33:in filter' from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/reader.rb:117:in filter_entries'
from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/reader.rb:42:in block in read_directories' from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/reader.rb:42:in chdir'
from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/reader.rb:42:in read_directories' from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/reader.rb:80:in block in retrieve_dirs'
from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/reader.rb:76:in each' from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/reader.rb:76:in retrieve_dirs'
from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/reader.rb:51:in read_directories' from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/reader.rb:16:in read'
from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/site.rb:164:in read' from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/site.rb:69:in process'
from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/command.rb:28:in process_site' from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/commands/build.rb:65:in build'
from /usr/local/bundle/gems/jekyll-3.9.3/lib/jekyll/commands/build.rb:36:in process' from /usr/local/bundle/gems/github-pages-228/bin/github-pages:70:in block (3 levels) in <top (required)>'
from /usr/local/bundle/gems/mercenary-0.3.6/lib/mercenary/command.rb:220:in block in execute' from /usr/local/bundle/gems/mercenary-0.3.6/lib/mercenary/command.rb:220:in each'
from /usr/local/bundle/gems/mercenary-0.3.6/lib/mercenary/command.rb:220:in execute' from /usr/local/bundle/gems/mercenary-0.3.6/lib/mercenary/program.rb:42:in go'
from /usr/local/bundle/gems/mercenary-0.3.6/lib/mercenary.rb:19:in program' from /usr/local/bundle/gems/github-pages-228/bin/github-pages:6:in <top (required)>'
from /usr/local/bundle/bin/github-pages:23:in load' from /usr/local/bundle/bin/github-pages:23:in

'
Requiring: jekyll-seo-tag
Requiring: jekyll-coffeescript
Requiring: jekyll-commonmark-ghpages
Requiring: jekyll-gist
Requiring: jekyll-github-metadata
Requiring: jekyll-paginate
Requiring: jekyll-relative-links
Requiring: jekyll-optional-front-matter
Requiring: jekyll-readme-index
Requiring: jekyll-default-layout
Requiring: jekyll-titles-from-headings
GitHub Metadata: Initializing...
Source: /github/workspace/.
Destination: /github/workspace/./_site
Incremental build: disabled. Enable with --incremental
Generating...
github-pages 228 | Error: No such file or directory @ rb_check_realpath_internal - /github/workspace/webpage/images`

[agitter]

I wasn't able to diagnose the details of that error message, but I believe I understand the problem by looking at the https://github.com/UCSC-Treehouse/TUBI-2023 repository. That repository has some of the Manubot rootstock files but not all of them. Specifically, I noticed it doesn't have the files that run the GitHub Actions workflow that run Manubot on the content and update the files on the output and gh-pages branches. That left the repository in an incomplete state where GitHub Pages is trying to deploy something but failing.

Did you make a few initial commits in that repository before running the Manubot setup script? The setup script will only work on a newly initialized empty repository. It needs to be able to copy the full rootstock commit history to the new repository (relevant to the recent discussion here #504).

If you did not customize too many files in your repository, the most reliable solution may be to create a new empty repository and run the setup script again before commiting anything to that repository. If that succeeds, you could copy any customized files from https://github.com/UCSC-Treehouse/TUBI-2023 into the new repository.