Fix Rd \usage WARNING and NSE global variable NOTEs #9
Annotations
31 errors and 22 warnings
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windows-latest (auto)
[Workflow Telemetry] AxiosError
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windows-latest (auto)
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windows-latest (auto)
AxiosError: Request failed with status code 403
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[Workflow Telemetry] AxiosError
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windows-latest (auto)
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windows-latest (auto)
AxiosError: Request failed with status code 403
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windows-latest (auto)
[Workflow Telemetry] AxiosError
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windows-latest (auto)
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AxiosError: Request failed with status code 403
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[Workflow Telemetry] AxiosError
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windows-latest (auto)
Process completed with exit code 1.
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R CMD check found ERRORs
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windows-latest (auto)
error writing to connection
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macOS-latest (auto)
[Workflow Telemetry] getLineGraph {"options":{"width":1000,"height":500,"xAxis":{"label":"Time"},"yAxis":{"label":"Network I/O Read (MB)"},"timeTicks":{"unit":"auto"}},"lines":[{"label":"Read","color":"#be4d25","points":[{"x":1773502031702,"y":0},{"x":1773502036697,"y":308},{"x":1773502041695,"y":0},{"x":1773502046695,"y":0},{"x":1773502051695,"y":69},{"x":1773502056694,"y":0},{"x":1773502061700,"y":0},{"x":1773502066695,"y":0},{"x":1773502071695,"y":0},{"x":1773502076696,"y":102},{"x":1773502081694,"y":0},{"x":1773502086696,"y":23},{"x":1773502091695,"y":0},{"x":1773502096697,"y":3},{"x":1773502101695,"y":0},{"x":1773502106694,"y":0},{"x":1773502111695,"y":49},{"x":1773502116696,"y":555},{"x":1773502121695,"y":658},{"x":1773502126695,"y":662},{"x":1773502131696,"y":233},{"x":1773502136695,"y":0},{"x":1773502141694,"y":0},{"x":1773502146695,"y":0},{"x":1773502151696,"y":0},{"x":1773502156695,"y":0},{"x":1773502161694,"y":0},{"x":1773502166696,"y":0},{"x":1773502171695,"y":0},{"x":1773502176696,"y":0},{"x":1773502181698,"y":0},{"x":1773502186696,"y":0},{"x":1773502191695,"y":0},{"x":1773502196695,"y":0},{"x":1773502201695,"y":0},{"x":1773502206695,"y":0},{"x":1773502211697,"y":0},{"x":1773502216696,"y":0},{"x":1773502221695,"y":0},{"x":1773502226696,"y":0},{"x":1773502231695,"y":0},{"x":1773502236697,"y":0},{"x":1773502241697,"y":0},{"x":1773502246695,"y":0},{"x":1773502251696,"y":0},{"x":1773502256697,"y":0},{"x":1773502261694,"y":0},{"x":1773502266697,"y":0},{"x":1773502271697,"y":0},{"x":1773502276696,"y":0},{"x":1773502281694,"y":0},{"x":1773502286695,"y":0},{"x":1773502291696,"y":0},{"x":1773502296696,"y":0},{"x":1773502301695,"y":0},{"x":1773502306698,"y":0},{"x":1773502311695,"y":0},{"x":1773502316696,"y":0},{"x":1773502321696,"y":0},{"x":1773502326695,"y":0},{"x":1773502331696,"y":0},{"x":1773502336696,"y":44},{"x":1773502341698,"y":63},{"x":1773502346695,"y":0},{"x":1773502351696,"y":0},{"x":1773502356696,"y":0},{"x":1773502361697,"y":0},{"x":1773502366695,"y":84},{"x":1773502371695,"y":0},{"x":1773502376695,"y":1},{"x":1773502381694,"y":136},{"x":1773502386696,"y":0},{"x":1773502391701,"y":0},{"x":1773502396701,"y":0},{"x":1773502401695,"y":3},{"x":1773502406694,"y":0},{"x":1773502411701,"y":0},{"x":1773502416695,"y":0},{"x":1773502421696,"y":0},{"x":1773502426696,"y":0},{"x":1773502431695,"y":0},{"x":1773502436695,"y":0},{"x":1773502441697,"y":0},{"x":1773502446696,"y":219},{"x":1773502451696,"y":32},{"x":1773502456695,"y":0},{"x":1773502461701,"y":391},{"x":1773502466695,"y":519},{"x":1773502471696,"y":526},{"x":1773502476696,"y":565},{"x":1773502481693,"y":547},{"x":1773502486695,"y":508},{"x":1773502491695,"y":191},{"x":1773502496693,"y":0},{"x":1773502501695,"y":0},{"x":1773502506702,"y":0},{"x":1773502511697,"y":0},{"x":1773502516697,"y":0},{"x":1773502521695,"y":0},{"x":1773502526695,"y":0},{"x":1773502531698,"y":0},{"x":1773502536696,"y":0},{"x":1773502541696,"y":0},{"x":1773502546695,"y":0},{"x":1773502551694,"y":0},{"x":1773502556696,"y":0},{"x":1773502561696,"y":0},{"x":1773502566698,"y":0},{"x":1773502571694,"y":0},{"x":1773502576695,"y":0},{"x":1773502581696,"y":0},{"x":1773502586703,"y":0},{"x":1773502591695,"y":0},{"x":1773502596695,"y":0},{"x":1773502601695,"y":4},{"x":1773502606695,"y":2},{"x":1773502611694,"y":0},{"x":1773502616696,"y":0},{"x":1773502621696,"y":0},{"x":1773502626698,"y":0},{"x":1773502631699,"y":0},{"x":1773502636697,"y":0},{"x":1773502641694,"y":12},{"x":1773502646695,"y":0},{"x":1773502651699,"y":0},{"x":1773502656698,"y":0},{"x":1773502661696,"y":0},{"x":1773502666699,"y":0},{"x":1773502671695,"y":0},{"x":1773502676696,"y":0},{"x":1773502681696,"y":0},{"x":1773502686695,"y":0},{"x":1773502691697,"y":0},{"x":1773502696696,"y":0},{"x":1773502701695,"y":0},{"x":1773502706700,"y":0},{"x":1773502711699,"y":0},{"x":1773502716698,"y":0},{"x":1773502721696,"y":0},{"x":1773502726696,"y":0},{"x":1773502731700,"y":0},{"x":1773502736696,"y":0},{"x":1773502741696,"y":0},{"x":1773502746697,"y":0},{"x":1773502751699,"y":0},{"x":1773502756698,"y":0},{"x":1773502761705,"y":0},{"x":1773502766
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macOS-latest (auto)
AxiosError: Request failed with status code 403
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macOS-latest (auto)
[Workflow Telemetry] AxiosError
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macOS-latest (auto)
[Workflow Telemetry] getStackedAreaGraph {"options":{"width":1000,"height":500,"xAxis":{"label":"Time"},"yAxis":{"label":"Memory Usage (MB)"},"timeTicks":{"unit":"auto"}},"areas":[{"label":"Used","color":"#377eb899","points":[{"x":1773502031702,"y":2929.046875},{"x":1773502036697,"y":2924.4375},{"x":1773502041695,"y":2816.203125},{"x":1773502046695,"y":2875.875},{"x":1773502051695,"y":2796.96875},{"x":1773502056694,"y":2896.796875},{"x":1773502061700,"y":2793.734375},{"x":1773502066695,"y":2858.1875},{"x":1773502071695,"y":2815.609375},{"x":1773502076696,"y":2535.5},{"x":1773502081694,"y":2731.28125},{"x":1773502086696,"y":2848.828125},{"x":1773502091695,"y":2851.578125},{"x":1773502096697,"y":1409.765625},{"x":1773502101695,"y":1547.875},{"x":1773502106694,"y":1788.46875},{"x":1773502111695,"y":1915.859375},{"x":1773502116696,"y":1903.375},{"x":1773502121695,"y":1893.296875},{"x":1773502126695,"y":1892.03125},{"x":1773502131696,"y":2041.703125},{"x":1773502136695,"y":2099.484375},{"x":1773502141694,"y":2357.625},{"x":1773502146695,"y":2358.265625},{"x":1773502151696,"y":2303.390625},{"x":1773502156695,"y":2308.984375},{"x":1773502161694,"y":2288.09375},{"x":1773502166696,"y":1603.515625},{"x":1773502171695,"y":1711.078125},{"x":1773502176696,"y":1683.78125},{"x":1773502181698,"y":1770.296875},{"x":1773502186696,"y":1794.875},{"x":1773502191695,"y":1681.140625},{"x":1773502196695,"y":1729.875},{"x":1773502201695,"y":1863.703125},{"x":1773502206695,"y":1721.953125},{"x":1773502211697,"y":1864.53125},{"x":1773502216696,"y":1748.578125},{"x":1773502221695,"y":1843.921875},{"x":1773502226696,"y":1798.96875},{"x":1773502231695,"y":1806.234375},{"x":1773502236697,"y":1837.203125},{"x":1773502241697,"y":1826.140625},{"x":1773502246695,"y":1824.640625},{"x":1773502251696,"y":1823.34375},{"x":1773502256697,"y":1858.015625},{"x":1773502261694,"y":1893.375},{"x":1773502266697,"y":1902.28125},{"x":1773502271697,"y":1902.390625},{"x":1773502276696,"y":1902.703125},{"x":1773502281694,"y":1901.6875},{"x":1773502286695,"y":1903.609375},{"x":1773502291696,"y":1719.8125},{"x":1773502296696,"y":1802.78125},{"x":1773502301695,"y":1808.75},{"x":1773502306698,"y":1800.09375},{"x":1773502311695,"y":1800.796875},{"x":1773502316696,"y":1811.625},{"x":1773502321696,"y":1810.765625},{"x":1773502326695,"y":1822.53125},{"x":1773502331696,"y":1770.5625},{"x":1773502336696,"y":1505.21875},{"x":1773502341698,"y":1597.28125},{"x":1773502346695,"y":1714.65625},{"x":1773502351696,"y":1822.03125},{"x":1773502356696,"y":1891.015625},{"x":1773502361697,"y":1824.984375},{"x":1773502366695,"y":2079.359375},{"x":1773502371695,"y":2235.984375},{"x":1773502376695,"y":2258.75},{"x":1773502381694,"y":2256.6875},{"x":1773502386696,"y":2352.03125},{"x":1773502391701,"y":2463.09375},{"x":1773502396701,"y":2260.28125},{"x":1773502401695,"y":2331.59375},{"x":1773502406694,"y":2324.34375},{"x":1773502411701,"y":2769.578125},{"x":1773502416695,"y":2263.609375},{"x":1773502421696,"y":2577.984375},{"x":1773502426696,"y":2506.484375},{"x":1773502431695,"y":2255.3125},{"x":1773502436695,"y":2261.265625},{"x":1773502441697,"y":2360.375},{"x":1773502446696,"y":2440.734375},{"x":1773502451696,"y":2374.625},{"x":1773502456695,"y":2356.265625},{"x":1773502461701,"y":2311.21875},{"x":1773502466695,"y":2344.296875},{"x":1773502471696,"y":2462.359375},{"x":1773502476696,"y":2527.953125},{"x":1773502481693,"y":2539.3125},{"x":1773502486695,"y":2509.140625},{"x":1773502491695,"y":2776.796875},{"x":1773502496693,"y":2764.453125},{"x":1773502501695,"y":2708.171875},{"x":1773502506702,"y":2501.21875},{"x":1773502511697,"y":2715.40625},{"x":1773502516697,"y":2177.28125},{"x":1773502521695,"y":2221.828125},{"x":1773502526695,"y":1395.46875},{"x":1773502531698,"y":1444.609375},{"x":1773502536696,"y":1467.5625},{"x":1773502541696,"y":1558.3125},{"x":1773502546695,"y":1573.5625},{"x":1773502551694,"y":2665.625},{"x":1773502556696,"y":2479.09375},{"x":1773502561696,"y":2393.109375},{"x":1773502566698,"y":1291.984375},{"x":1773502571694,"y":1620.875},{"x":1773502576695,"y":1872.953125},{"x":1773
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macOS-latest (auto)
AxiosError: Request failed with status code 403
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macOS-latest (auto)
[Workflow Telemetry] AxiosError
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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
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macOS-latest (auto)
AxiosError: Request failed with status code 403
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macOS-latest (auto)
[Workflow Telemetry] AxiosError
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macOS-latest (auto)
Process completed with exit code 1.
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macOS-latest (auto)
R CMD check found WARNINGs
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ubuntu-latest (auto)
Error: connect ECONNREFUSED 127.0.0.1:7777
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ubuntu-latest (auto)
[Workflow Telemetry] Error
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ubuntu-latest (auto)
[Workflow Telemetry] Unable to report stat collector result
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ubuntu-latest (auto)
Error: connect ECONNREFUSED 127.0.0.1:7777
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ubuntu-latest (auto)
[Workflow Telemetry] Error
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ubuntu-latest (auto)
[Workflow Telemetry] Unable to finish stat collector
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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/
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windows-latest (auto)
Unknown package 'echolocatoR' in Rd xrefs
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windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh37'
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windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh37'
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windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh37'
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windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh38'
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windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh38'
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windows-latest (auto)
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh38'
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windows-latest (auto)
file 'echoconda/configure' did not have execute permissions: corrected
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windows-latest (auto)
dependencies 'BiocVersion', 'BiocStyle' are not available
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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/
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macOS-latest (auto)
Unknown package ‘echolocatoR’ in Rd xrefs
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macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
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macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
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macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
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macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh38’
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macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh38’
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macOS-latest (auto)
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh38’
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macOS-latest (auto)
dependencies ‘BiocVersion’, ‘BiocStyle’ are not available
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macOS-latest (auto)
fribidi 1.0.16 is already installed and up-to-date.
To reinstall 1.0.16, run:
brew reinstall fribidi
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macOS-latest (auto)
harfbuzz 12.3.2 is already installed and up-to-date.
To reinstall 12.3.2, run:
brew reinstall harfbuzz
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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/
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Artifacts
Produced during runtime
| Name | Size | Digest | |
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RajLabMSSM~echoannot~05W3PO.dockerbuild
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131 KB |
sha256:ab233036f3b6968e09f37f719b5026f7fb4c851ede207e68ccdf13c4797e9fe8
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Windows-biocversion-release-r-auto-results
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6.79 MB |
sha256:7748d8cb9b6bce6c0250ba21d8d52995ce8dafd95f993bb826b85c194ef388c8
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macOS-biocversion-release-r-auto-results
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7.42 MB |
sha256:06fab9cc3f660f184b08ed17df84df461ff1fe125ba99c73bdcce8262de50604
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