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Fix Rd \usage WARNING and NSE global variable NOTEs #9

Fix Rd \usage WARNING and NSE global variable NOTEs

Fix Rd \usage WARNING and NSE global variable NOTEs #9

Triggered via push March 14, 2026 15:26
Status Failure
Total duration 55m 57s
Artifacts 3

rworkflows.yml

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Matrix: rworkflows
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31 errors and 22 warnings
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AxiosError: Request failed with status code 403
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[Workflow Telemetry] AxiosError
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Process completed with exit code 1.
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windows-latest (auto)
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[Workflow Telemetry] AxiosError
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macOS-latest (auto)
AxiosError: Request failed with status code 403
macOS-latest (auto)
[Workflow Telemetry] AxiosError
macOS-latest (auto)
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macOS-latest (auto)
AxiosError: Request failed with status code 403
macOS-latest (auto)
[Workflow Telemetry] AxiosError
macOS-latest (auto)
[Workflow Telemetry] getStackedAreaGraph {"options":{"width":1000,"height":500,"xAxis":{"label":"Time"},"yAxis":{"label":"CPU Load (%)"},"timeTicks":{"unit":"auto"}},"areas":[{"label":"User Load","color":"#e41a1c99","points":[{"x":1773502031702,"y":26.94881349767754},{"x":1773502036697,"y":43.858477970627504},{"x":1773502041695,"y":40.25537634408602},{"x":1773502046695,"y":40},{"x":1773502051695,"y":37.86666666666667},{"x":1773502056694,"y":63.21070234113713},{"x":1773502061700,"y":49.667994687915005},{"x":1773502066695,"y":29.002009377093103},{"x":1773502071695,"y":23.342175066312997},{"x":1773502076696,"y":18.071476736345247},{"x":1773502081694,"y":31.036789297658864},{"x":1773502086696,"y":19.14609739826551},{"x":1773502091695,"y":30.440587449933243},{"x":1773502096697,"y":21.4},{"x":1773502101695,"y":19.98663101604278},{"x":1773502106694,"y":18.841544607190414},{"x":1773502111695,"y":23.678929765886288},{"x":1773502116696,"y":20.615796519410978},{"x":1773502121695,"y":17.423230974632844},{"x":1773502126695,"y":18.938885157824043},{"x":1773502131696,"y":16},{"x":1773502136695,"y":15.580926796507724},{"x":1773502141694,"y":9.866666666666667},{"x":1773502146695,"y":11.096256684491978},{"x":1773502151696,"y":13.529805760214334},{"x":1773502156695,"y":13.609072715143428},{"x":1773502161694,"y":15.627095908786048},{"x":1773502166696,"y":11.378848728246318},{"x":1773502171695,"y":25.13368983957219},{"x":1773502176696,"y":13.110367892976587},{"x":1773502181698,"y":20.466666666666665},{"x":1773502186696,"y":28.83845126835781},{"x":1773502191695,"y":28.210246174318033},{"x":1773502196695,"y":23.31329325317301},{"x":1773502201695,"y":29.506008010680908},{"x":1773502206695,"y":27.885256837891927},{"x":1773502211697,"y":30.4869913275517},{"x":1773502216696,"y":10.140093395597065},{"x":1773502221695,"y":19.692923898531376},{"x":1773502226696,"y":25.482368596141054},{"x":1773502231695,"y":14.601473543201607},{"x":1773502236697,"y":4.5668233713901945},{"x":1773502241697,"y":6.10738255033557},{"x":1773502246695,"y":7.656145063801209},{"x":1773502251696,"y":5.432595573440644},{"x":1773502256697,"y":7.997311827956989},{"x":1773502261694,"y":7.352941176470589},{"x":1773502266697,"y":7.8208556149732615},{"x":1773502271697,"y":4.963112005365526},{"x":1773502276696,"y":6.666666666666667},{"x":1773502281694,"y":5.443548387096774},{"x":1773502286695,"y":6.103286384976526},{"x":1773502291696,"y":6.103286384976526},{"x":1773502296696,"y":14.621059691482227},{"x":1773502301695,"y":6.3801208865010075},{"x":1773502306698,"y":7.032819825853985},{"x":1773502311695,"y":6.451612903225806},{"x":1773502316696,"y":15.838926174496645},{"x":1773502321696,"y":6.321452589105582},{"x":1773502326695,"y":7.794803464357095},{"x":1773502331696,"y":11.618535930154467},{"x":1773502336696,"y":11.729222520107237},{"x":1773502341698,"y":14.046822742474916},{"x":1773502346695,"y":14.333556597454788},{"x":1773502351696,"y":21.42377434519812},{"x":1773502356696,"y":16.98867421718854},{"x":1773502361697,"y":24.665775401069517},{"x":1773502366695,"y":32.46666666666667},{"x":1773502371695,"y":15.88156123822342},{"x":1773502376695,"y":11.63563829787234},{"x":1773502381694,"y":22.117962466487935},{"x":1773502386696,"y":25.56440903054449},{"x":1773502391701,"y":31.52610441767068},{"x":1773502396701,"y":13.615023474178404},{"x":1773502401695,"y":13.017356475300401},{"x":1773502406694,"y":28.093645484949832},{"x":1773502411701,"y":55.333333333333336},{"x":1773502416695,"y":57.76149233844103},{"x":1773502421696,"y":70.20708082832331},{"x":1773502426696,"y":73.86666666666667},{"x":1773502431695,"y":62.38348868175766},{"x":1773502436695,"y":43.87959866220736},{"x":1773502441697,"y":66.86626746506987},{"x":1773502446696,"y":67.35785953177258},{"x":1773502451696,"y":20.852764823451032},{"x":1773502456695,"y":28.60026917900404},{"x":1773502461701,"y":36.21837549933422},{"x":1773502466695,"y":57.53516409912927},{"x":1773502471696,"y":58.53333333333334},{"x":1773502476696,"y":66.02136181575435},{"x":1773502481693,"y":64.17611741160773},{"x":1773502486695,"y":60.55962691538974},{"x":177
macOS-latest (auto)
AxiosError: Request failed with status code 403
macOS-latest (auto)
[Workflow Telemetry] AxiosError
macOS-latest (auto)
Process completed with exit code 1.
macOS-latest (auto)
R CMD check found WARNINGs
ubuntu-latest (auto)
Error: connect ECONNREFUSED 127.0.0.1:7777
ubuntu-latest (auto)
[Workflow Telemetry] Error
ubuntu-latest (auto)
[Workflow Telemetry] Unable to report stat collector result
ubuntu-latest (auto)
Error: connect ECONNREFUSED 127.0.0.1:7777
ubuntu-latest (auto)
[Workflow Telemetry] Error
ubuntu-latest (auto)
[Workflow Telemetry] Unable to finish stat collector
windows-latest (auto)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache@v4, actions/checkout@v4, actions/upload-artifact@v4, catchpoint/workflow-telemetry-action@v2, r-lib/actions/setup-pandoc@v2, r-lib/actions/setup-r@v2. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
windows-latest (auto)
Unknown package 'echolocatoR' in Rd xrefs
windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh37'
windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh37'
windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh37'
windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh38'
windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh38'
windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh38'
windows-latest (auto)
file 'echoconda/configure' did not have execute permissions: corrected
windows-latest (auto)
dependencies 'BiocVersion', 'BiocStyle' are not available
macOS-latest (auto)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache@v4, actions/checkout@v4, actions/upload-artifact@v4, catchpoint/workflow-telemetry-action@v2, r-lib/actions/setup-pandoc@v2, r-lib/actions/setup-r@v2. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
macOS-latest (auto)
Unknown package ‘echolocatoR’ in Rd xrefs
macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh38’
macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh38’
macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh38’
macOS-latest (auto)
dependencies ‘BiocVersion’, ‘BiocStyle’ are not available
macOS-latest (auto)
fribidi 1.0.16 is already installed and up-to-date. To reinstall 1.0.16, run: brew reinstall fribidi
macOS-latest (auto)
harfbuzz 12.3.2 is already installed and up-to-date. To reinstall 12.3.2, run: brew reinstall harfbuzz
ubuntu-latest (auto)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache@v4, actions/checkout@v4, catchpoint/workflow-telemetry-action@v2, docker/build-push-action@v6, docker/login-action@v3, docker/setup-buildx-action@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Artifacts

Produced during runtime
Name Size Digest
RajLabMSSM~echoannot~05W3PO.dockerbuild
131 KB
sha256:ab233036f3b6968e09f37f719b5026f7fb4c851ede207e68ccdf13c4797e9fe8
Windows-biocversion-release-r-auto-results
6.79 MB
sha256:7748d8cb9b6bce6c0250ba21d8d52995ce8dafd95f993bb826b85c194ef388c8
macOS-biocversion-release-r-auto-results
7.42 MB
sha256:06fab9cc3f660f184b08ed17df84df461ff1fe125ba99c73bdcce8262de50604