Support Automa 1 and GenomicFeatures 3 (#20) #93
Annotations
3 errors, 11 warnings, and 2 notices
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Documentation
Process completed with exit code 1.
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/Documenter.jl#L777
Failed to push:
exception =
failed process: Process(setenv(`/usr/bin/git fetch upstream`,["GOROOT_1_26_X64=/opt/hostedtoolcache/go/1.26.8/x64", "MEMORY_PRESSURE_WRITE=c29tZSAyMDAwMDAgMjAwMDAwMAA=", "POWERSHELL_DISTRIBUTION_CHANNEL=GitHub-Actions-Linux", "GITHUB_ARTIFACTS_LIST=/home/runner/work/_temp/_runner_file_commands/artifacts_list_d5e37147-198b-469b-b7dd-c2995bf80525", "AZURE_EXTENSION_DIR=/opt/az/azcliextensions", "GITHUB_TOKEN=***", "GITHUB_SHA=d3a42aeb787b9270f5dc5c9ea05e9455542d11c4", "OPENBLAS_MAIN_FREE=1", "GITHUB_WORKFLOW_REF=BioJulia/GFF3.jl/.github/workflows/Documentation.yml@refs/heads/develop", "SHELL=/bin/bash", "GITHUB_STATE=/home/runner/work/_temp/_runner_file_commands/save_state_d5e37147-198b-469b-b7dd-c2995bf80525", "GHCUP_INSTALL_BASE_PREFIX=/usr/local", "JAVA_HOME_8_X64=/usr/lib/jvm/temurin-8-jdk-amd64", "ImageOS=ubuntu24", "GITHUB_GRAPHQL_URL=https://api.github.com/graphql", "GITHUB_PATH=/home/runner/work/_temp/_runner_file_commands/add_path_d5e37147-198b-469b-b7dd-c2995bf80525", "RUNNER_WORKSPACE=/home/runner/work/GFF3.jl", "BOOTSTRAP_HASKELL_NONINTERACTIVE=1", "AGENT_TOOLSDIRECTORY=/opt/hostedtoolcache", "SELENIUM_JAR_PATH=/usr/share/java/selenium-server.jar", "GITHUB_RUN_ID=36977458172", "XDG_CONFIG_HOME=/home/runner/.config", "JAVA_HOME_25_X64=/usr/lib/jvm/temurin-25-jdk-amd64", "PIPX_BIN_DIR=/opt/pipx_bin", "GITHUB_ARTIFACTS=/home/runner/work/_temp/_runner_file_commands/artifacts_d5e37147-198b-469b-b7dd-c2995bf80525", "ANT_HOME=/usr/share/ant", "GITHUB_ACTION=__julia-actions_julia-docdeploy", "GITHUB_REF=refs/heads/develop", "RUNNER_OS=Linux", "PIPX_HOME=/opt/pipx", "ANDROID_SDK_ROOT=/usr/local/lib/android/sdk", "RUNNER_TOOL_CACHE=/opt/hostedtoolcache", "XDG_RUNTIME_DIR=/run/user/1001", "GITHUB_WORKFLOW=Documentation", "DEBIAN_FRONTEND=noninteractive", "GITHUB_REF_TYPE=branch", "INVOCATION_ID=af904bfc013f4bca9e3875f0615b842b", "ACTIONS_ORCHESTRATION_ID=58d93577-50cf-86d4-b057-962b6f348e7d.Documenter.__default", "JOURNAL_STREAM=9:12039", "CHROME_BIN=/usr/bin/google-chrome", "SYSTEMD_EXEC_PID=2085", "GITHUB_ACTION_PATH=/home/runner/work/_actions/julia-actions/julia-docdeploy/v1", "PSModulePath=/root/.local/share/powershell/Modules:/usr/local/share/powershell/Modules:/opt/microsoft/powershell/7/Modules:/usr/share/az_15.6.1", "GITHUB_EVENT_PATH=/home/runner/work/_temp/_github_workflow/event.json", "GITHUB_REF_NAME=develop", "GITHUB_JOB=Documenter", "JULIA_PKG_SERVER_REGISTRY_PREFERENCE=eager", "GITHUB_WORKFLOW_SHA=d3a42aeb787b9270f5dc5c9ea05e9455542d11c4", "JAVA_HOME_21_X64=/usr/lib/jvm/temurin-21-jdk-amd64", "USER=runner", "ANDROID_NDK=/usr/local/lib/android/sdk/ndk/27.3.13750724", "GIT_SSH_COMMAND=ssh -F /tmp/jl_cs2XhE", "GITHUB_ACTOR=CiaranOMara", "GITHUB_ACTOR_ID=24236593", "GRADLE_HOME=/usr/share/gradle-9.8.0", "SHLVL=1", "GITHUB_OUTPUT=/home/runner/work/_temp/_runner_file_commands/set_output_d5e37147-198b-469b-b7dd-c2995bf80525", "HCA_CLOUD_PROVIDER=azure", "MEMORY_PRESSURE_WATCH=/sys/fs/cgroup/system.slice/hosted-compute-agent.service/memory.pressure", "GITHUB_API_URL=https://api.github.com", "RUNNER_TEMP=/home/runner/work/_temp", "RUNNER_ENVIRONMENT=github-hosted", "GITHUB_EVENT_NAME=push", "ANDROID_HOME=/usr/local/lib/android/sdk", "GECKOWEBDRIVER=/usr/local/share/gecko_driver", "GITHUB_ACTIONS=true", "GITHUB_ACTION_REF=", "_=/usr/bin/julia", "ENABLE_RUNNER_TRACING=true", "LANG=C.UTF-8", "VCPKG_INSTALLATION_ROOT=/usr/local/share/vcpkg", "SWIFT_PATH=/usr/share/swift/usr/bin", "RUNNER_TRACKING_ID=github_1c755325-b836-4d7a-9949-60e773c9d67f", "JAVA_HOME=/usr/lib/jvm/temurin-17-jdk-amd64", "ACTIONS_RUNNER_ACTION_ARCHIVE_CACHE=/opt/actionarchivecache", "CONDA=/usr/share/miniconda", "GITHUB_STEP_SUMMARY=/home/runner/work/_temp/_runner_file_commands/step_summary_d5e37147-198b-469b-b7dd-c2995bf80525", "RUNNER_NAME=GitHub Actions 1000015521", "JAVA_HOME_11_X64=/usr/lib/jvm/temurin-11-jdk-amd64", "ACTIONS_RUNNER_RETURN_JOB_RESULT_FOR_HOSTED=1", "HOMEBREW_NO_AUTO_UPDATE=1", "GITHUB_RUN_NUMBER=93", "DOTNET_MULTILEVEL_LOOKUP=0", "GITHUB_REF_PROTECTED=false", "GITHUB_BASE_REF=", "JAVA_HOME_17_X
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/Documenter.jl#L652
Git failed to fetch git@github.com:BioJulia/GFF3.jl.git
This can be caused by a DOCUMENTER_KEY variable that is not correctly set up.
Make sure that the environment variable is properly set up as a Base64-encoded string
of the SSH private key. You may need to re-generate the keys with DocumenterTools.
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Documentation
Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@v2. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/Utilities/Utilities.jl#L34
linkcheck 'https://opencollective.com/biojulia/sponsor/1/website' status: 404.
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/DocChecks.jl#L248
linkcheck 'https://opencollective.com/biojulia/sponsor/0/website' status: 301, redirects to 'https://opencollective.com/biojulia?utm_source=opencollective&utm_medium=github&utm_campaign=biojulia#support'
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/Utilities/Utilities.jl#L34
`curl -sI --proto =http,https,ftp,ftps --user-agent 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36' -H 'accept-encoding: gzip, deflate, br' 'https://opencollective.com/biojulia#backer' --max-time 10 -o /dev/null --write-out '%{http_code} %{url_effective} %{redirect_url}'` failed:
exception =
failed process: Process(`curl -sI --proto =http,https,ftp,ftps --user-agent 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36' -H 'accept-encoding: gzip, deflate, br' 'https://opencollective.com/biojulia#backer' --max-time 10 -o /dev/null --write-out '%{http_code} %{url_effective} %{redirect_url}'`, ProcessExited(28)) [28]
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/Utilities/Utilities.jl#L34
`curl -sI --proto =http,https,ftp,ftps --user-agent 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36' -H 'accept-encoding: gzip, deflate, br' https://opencollective.com/biojulia --max-time 10 -o /dev/null --write-out '%{http_code} %{url_effective} %{redirect_url}'` failed:
exception =
failed process: Process(`curl -sI --proto =http,https,ftp,ftps --user-agent 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36' -H 'accept-encoding: gzip, deflate, br' https://opencollective.com/biojulia --max-time 10 -o /dev/null --write-out '%{http_code} %{url_effective} %{redirect_url}'`, ProcessExited(28)) [28]
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/DocChecks.jl#L248
linkcheck 'https://codecov.io/gh/BioJulia/GFF3.jl' status: 301, redirects to 'https://app.codecov.io/gh/BioJulia/GFF3.jl'
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/Utilities/Utilities.jl#L34
`curl -sI --proto =http,https,ftp,ftps --user-agent 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36' -H 'accept-encoding: gzip, deflate, br' https://github.com/BioJulia/GFF3.jl/tree/develop --max-time 10 -o /dev/null --write-out '%{http_code} %{url_effective} %{redirect_url}'` failed:
exception =
failed process: Process(`curl -sI --proto =http,https,ftp,ftps --user-agent 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36' -H 'accept-encoding: gzip, deflate, br' https://github.com/BioJulia/GFF3.jl/tree/develop --max-time 10 -o /dev/null --write-out '%{http_code} %{url_effective} %{redirect_url}'`, ProcessExited(28)) [28]
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/DocChecks.jl#L248
linkcheck 'http://semver.org' status: 301, redirects to 'https://semver.org/'
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/DocChecks.jl#L248
linkcheck 'https://biojulia.github.io/GFF3.jl/dev/' status: 301, redirects to 'https://biojulia.dev/GFF3.jl/dev/'
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/DocChecks.jl#L248
linkcheck 'https://biojulia.github.io/GFF3.jl/stable' status: 301, redirects to 'https://biojulia.dev/GFF3.jl/stable'
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Documentation:
../../../.julia/packages/Documenter/bYYzK/src/Utilities/Utilities.jl#L34
`curl -sI --proto =http,https,ftp,ftps --user-agent 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36' -H 'accept-encoding: gzip, deflate, br' https://github.com/BioJulia/GFF3.jl/blob/master/LICENSE --max-time 10 -o /dev/null --write-out '%{http_code} %{url_effective} %{redirect_url}'` failed:
exception =
failed process: Process(`curl -sI --proto =http,https,ftp,ftps --user-agent 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36' -H 'accept-encoding: gzip, deflate, br' https://github.com/BioJulia/GFF3.jl/blob/master/LICENSE --max-time 10 -o /dev/null --write-out '%{http_code} %{url_effective} %{redirect_url}'`, ProcessExited(28)) [28]
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[julia-buildpkg] Caching of the julia depot was not detected
Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache To ignore, set input `ignore-no-cache: true`
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Documentation
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
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