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Fix 16 test failures: add GOSHIFTER source files, fix clean_granges a… #14

Fix 16 test failures: add GOSHIFTER source files, fix clean_granges a…

Fix 16 test failures: add GOSHIFTER source files, fix clean_granges a… #14

Triggered via push March 15, 2026 05:17
Status Failure
Total duration 46m 50s
Artifacts 2

rworkflows.yml

on: push
Matrix: rworkflows
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[Workflow Telemetry] AxiosError
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":1773551878518,"y":0},{"x":1773551883528,"y":301},{"x":1773551888515,"y":0},{"x":1773551893514,"y":0},{"x":1773551898514,"y":69},{"x":1773551903514,"y":0},{"x":1773551908520,"y":0},{"x":1773551913514,"y":0},{"x":1773551918515,"y":0},{"x":1773551923514,"y":101},{"x":1773551928520,"y":0},{"x":1773551933514,"y":24},{"x":1773551938513,"y":0},{"x":1773551943515,"y":1},{"x":1773551948515,"y":2},{"x":1773551953519,"y":0},{"x":1773551958514,"y":478},{"x":1773551963518,"y":991},{"x":1773551968515,"y":915},{"x":1773551973515,"y":954},{"x":1773551978515,"y":212},{"x":1773551983523,"y":0},{"x":1773551988527,"y":0},{"x":1773551993515,"y":35},{"x":1773551998514,"y":303},{"x":1773552003513,"y":758},{"x":1773552008514,"y":817},{"x":1773552013514,"y":243},{"x":1773552018514,"y":0},{"x":1773552023514,"y":0},{"x":1773552028515,"y":0},{"x":1773552033514,"y":0},{"x":1773552038514,"y":0},{"x":1773552043516,"y":0},{"x":1773552048515,"y":0},{"x":1773552053514,"y":0},{"x":1773552058514,"y":0},{"x":1773552063514,"y":0},{"x":1773552068516,"y":0},{"x":1773552073514,"y":0},{"x":1773552078514,"y":0},{"x":1773552083515,"y":0},{"x":1773552088514,"y":0},{"x":1773552093514,"y":0},{"x":1773552098515,"y":0},{"x":1773552103515,"y":0},{"x":1773552108523,"y":0},{"x":1773552113515,"y":0},{"x":1773552118514,"y":0},{"x":1773552123514,"y":0},{"x":1773552128515,"y":0},{"x":1773552133512,"y":0},{"x":1773552138516,"y":0},{"x":1773552143512,"y":0},{"x":1773552148514,"y":0},{"x":1773552153515,"y":0},{"x":1773552158514,"y":0},{"x":1773552163514,"y":0},{"x":1773552168516,"y":0},{"x":1773552173514,"y":0},{"x":1773552178514,"y":0},{"x":1773552183514,"y":0},{"x":1773552188514,"y":0},{"x":1773552193514,"y":0},{"x":1773552198514,"y":0},{"x":1773552203514,"y":0},{"x":1773552208514,"y":0},{"x":1773552213514,"y":0},{"x":1773552218514,"y":0},{"x":1773552223517,"y":107},{"x":1773552228512,"y":0},{"x":1773552233515,"y":0},{"x":1773552238514,"y":0},{"x":1773552243515,"y":6},{"x":1773552248514,"y":0},{"x":1773552253514,"y":0},{"x":1773552258514,"y":0},{"x":1773552263514,"y":0},{"x":1773552268514,"y":0},{"x":1773552273514,"y":0},{"x":1773552278515,"y":0},{"x":1773552283512,"y":7},{"x":1773552288514,"y":4},{"x":1773552293515,"y":0},{"x":1773552298514,"y":0},{"x":1773552303517,"y":0},{"x":1773552308516,"y":0},{"x":1773552313515,"y":0},{"x":1773552318521,"y":0},{"x":1773552323514,"y":0},{"x":1773552328515,"y":0},{"x":1773552333523,"y":0},{"x":1773552338516,"y":0},{"x":1773552343514,"y":0},{"x":1773552348524,"y":0},{"x":1773552353514,"y":0},{"x":1773552358514,"y":0},{"x":1773552363513,"y":0},{"x":1773552368514,"y":0},{"x":1773552373519,"y":0},{"x":1773552378512,"y":0},{"x":1773552383514,"y":0},{"x":1773552388525,"y":0},{"x":1773552393514,"y":0},{"x":1773552398524,"y":0},{"x":1773552403522,"y":0},{"x":1773552408514,"y":0},{"x":1773552413514,"y":0},{"x":1773552418520,"y":0},{"x":1773552423514,"y":0},{"x":1773552428518,"y":0},{"x":1773552433517,"y":0},{"x":1773552438524,"y":0},{"x":1773552443514,"y":0},{"x":1773552448519,"y":0},{"x":1773552453514,"y":0},{"x":1773552458518,"y":0},{"x":1773552463514,"y":0},{"x":1773552468525,"y":0},{"x":1773552473525,"y":0},{"x":1773552478514,"y":0},{"x":1773552483515,"y":0},{"x":1773552488515,"y":83},{"x":1773552493515,"y":101},{"x":1773552498515,"y":103},{"x":1773552503524,"y":76},{"x":1773552508514,"y":133},{"x":1773552513524,"y":103},{"x":1773552518514,"y":85},{"x":1773552523517,"y":44},{"x":1773552528515,"y":13},{"x":1773552533524,"y":0},{"x":1773552538515,"y":0},{"x":1773552543527,"y":0},{"x":1773552548516,"y":9},{"x":1773552553516,"y":150},{"x":1773552558516,"y":152},{"x":1773552563520,"y":134},{"x":1773552568516,"y":158},{"x":1773552573518,"y":74},{"x":1773552578514,"y":108},{"x":1773552583513,"y":115},{"x":1773552588515,"y":120},{"x":1773552593513,"y":145},{"x":1773552598515,"y":114},{"x":1773552603516,"y":62},{"x":1773552608514,
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":"Memory Usage (MB)"},"timeTicks":{"unit":"auto"}},"areas":[{"label":"Used","color":"#377eb899","points":[{"x":1773551878518,"y":2857.984375},{"x":1773551883528,"y":2891.890625},{"x":1773551888515,"y":2869.1875},{"x":1773551893514,"y":2863.984375},{"x":1773551898514,"y":2860.921875},{"x":1773551903514,"y":2773.484375},{"x":1773551908520,"y":2768.296875},{"x":1773551913514,"y":2771.140625},{"x":1773551918515,"y":2862.15625},{"x":1773551923514,"y":2490.1875},{"x":1773551928520,"y":2832.375},{"x":1773551933514,"y":2807.484375},{"x":1773551938513,"y":2881.453125},{"x":1773551943515,"y":1632.234375},{"x":1773551948515,"y":1909.296875},{"x":1773551953519,"y":1808.828125},{"x":1773551958514,"y":2073.59375},{"x":1773551963518,"y":2075.046875},{"x":1773551968515,"y":2108.546875},{"x":1773551973515,"y":2141.546875},{"x":1773551978515,"y":2133.265625},{"x":1773551983523,"y":2787.078125},{"x":1773551988527,"y":1508.671875},{"x":1773551993515,"y":1766.765625},{"x":1773551998514,"y":1802.421875},{"x":1773552003513,"y":1790.34375},{"x":1773552008514,"y":1808.875},{"x":1773552013514,"y":1848.453125},{"x":1773552018514,"y":1842.453125},{"x":1773552023514,"y":1837.875},{"x":1773552028515,"y":1824.046875},{"x":1773552033514,"y":1842.828125},{"x":1773552038514,"y":1816.640625},{"x":1773552043516,"y":1796.984375},{"x":1773552048515,"y":1631.9375},{"x":1773552053514,"y":1724.09375},{"x":1773552058514,"y":1691.5},{"x":1773552063514,"y":1636.21875},{"x":1773552068516,"y":1701.15625},{"x":1773552073514,"y":1728.8125},{"x":1773552078514,"y":1728.34375},{"x":1773552083515,"y":1754.9375},{"x":1773552088514,"y":1748},{"x":1773552093514,"y":1812.015625},{"x":1773552098515,"y":1799.46875},{"x":1773552103515,"y":1807.171875},{"x":1773552108523,"y":1802.296875},{"x":1773552113515,"y":1865.828125},{"x":1773552118514,"y":1899.390625},{"x":1773552123514,"y":1923.6875},{"x":1773552128515,"y":1905.375},{"x":1773552133512,"y":1950.078125},{"x":1773552138516,"y":1964.8125},{"x":1773552143512,"y":1976.984375},{"x":1773552148514,"y":2023.59375},{"x":1773552153515,"y":2002.15625},{"x":1773552158514,"y":2026.109375},{"x":1773552163514,"y":2037.203125},{"x":1773552168516,"y":2035.515625},{"x":1773552173514,"y":2046.890625},{"x":1773552178514,"y":2053.046875},{"x":1773552183514,"y":1788.5625},{"x":1773552188514,"y":1827.109375},{"x":1773552193514,"y":1833.4375},{"x":1773552198514,"y":1842.578125},{"x":1773552203514,"y":1835.90625},{"x":1773552208514,"y":1840.53125},{"x":1773552213514,"y":1858.046875},{"x":1773552218514,"y":1536.015625},{"x":1773552223517,"y":1760.671875},{"x":1773552228512,"y":1870.203125},{"x":1773552233515,"y":1999.46875},{"x":1773552238514,"y":2045.46875},{"x":1773552243515,"y":2094.875},{"x":1773552248514,"y":2467.734375},{"x":1773552253514,"y":2813.84375},{"x":1773552258514,"y":2330.40625},{"x":1773552263514,"y":2116.78125},{"x":1773552268514,"y":2514.5625},{"x":1773552273514,"y":2329.328125},{"x":1773552278515,"y":2737.984375},{"x":1773552283512,"y":2200.15625},{"x":1773552288514,"y":2794.875},{"x":1773552293515,"y":2301.34375},{"x":1773552298514,"y":2796.546875},{"x":1773552303517,"y":2541.765625},{"x":1773552308516,"y":2406},{"x":1773552313515,"y":2244.515625},{"x":1773552318521,"y":2628.84375},{"x":1773552323514,"y":2663.09375},{"x":1773552328515,"y":2398.46875},{"x":1773552333523,"y":2452.90625},{"x":1773552338516,"y":2169.703125},{"x":1773552343514,"y":2715.84375},{"x":1773552348524,"y":2430.203125},{"x":1773552353514,"y":2556.609375},{"x":1773552358514,"y":2677.046875},{"x":1773552363513,"y":2340.6875},{"x":1773552368514,"y":2118.59375},{"x":1773552373519,"y":2031},{"x":1773552378512,"y":2497.484375},{"x":1773552383514,"y":2403.59375},{"x":1773552388525,"y":2192.5625},{"x":1773552393514,"y":1912.140625},{"x":1773552398524,"y":2487.90625},{"x":1773552403522,"y":2350.125},{"x":1773552408514,"y":2045.09375},{"x":1773552413514,"y":2409.625},{"x":1773552418520,"y":2451.796875},{"x":1773552423514,"y":2300.375},{"x":1773552428
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":1773551878518,"y":39.66697925482034},{"x":1773551883528,"y":44.36339522546419},{"x":1773551888515,"y":43.513513513513516},{"x":1773551893514,"y":43.79172229639519},{"x":1773551898514,"y":45.63624250499667},{"x":1773551903514,"y":50.233177881412395},{"x":1773551908520,"y":30.666666666666664},{"x":1773551913514,"y":28.198258539852645},{"x":1773551918515,"y":23.933333333333334},{"x":1773551923514,"y":17.84037558685446},{"x":1773551928520,"y":32.486631016042786},{"x":1773551933514,"y":22.259358288770052},{"x":1773551938513,"y":26.48037258815702},{"x":1773551943515,"y":23.77762893503014},{"x":1773551948515,"y":21.947965310206804},{"x":1773551953519,"y":9.827357237715804},{"x":1773551958514,"y":11.804158283031523},{"x":1773551963518,"y":20.613742494996664},{"x":1773551968515,"y":23.895582329317268},{"x":1773551973515,"y":23.082099596231494},{"x":1773551978515,"y":21.559322033898304},{"x":1773551983523,"y":13.01416048550236},{"x":1773551988527,"y":21.916890080428956},{"x":1773551993515,"y":39.312204989885366},{"x":1773551998514,"y":35.360962566844925},{"x":1773552003513,"y":46.82698730794923},{"x":1773552008514,"y":43.495663775850566},{"x":1773552013514,"y":33.042895442359246},{"x":1773552018514,"y":21.85430463576159},{"x":1773552023514,"y":14.24713031735314},{"x":1773552028515,"y":17.154255319148938},{"x":1773552033514,"y":18.51106639839034},{"x":1773552038514,"y":20.294708640321502},{"x":1773552043516,"y":15.587846763540291},{"x":1773552048515,"y":16.53116531165312},{"x":1773552053514,"y":35.160427807486634},{"x":1773552058514,"y":20.10688042752171},{"x":1773552063514,"y":44.843646041250835},{"x":1773552068516,"y":62.35842771485676},{"x":1773552073514,"y":50.835003340013365},{"x":1773552078514,"y":45.28552456839309},{"x":1773552083515,"y":56.19557937039518},{"x":1773552088514,"y":59.85303941215765},{"x":1773552093514,"y":63.53333333333333},{"x":1773552098515,"y":35.6283422459893},{"x":1773552103515,"y":17.011340893929287},{"x":1773552108523,"y":50.53333333333333},{"x":1773552113515,"y":56.78022712090849},{"x":1773552118514,"y":32.93172690763052},{"x":1773552123514,"y":12.072434607645874},{"x":1773552128515,"y":9.751176866173504},{"x":1773552133512,"y":12.013422818791947},{"x":1773552138516,"y":11.058981233243967},{"x":1773552143512,"y":10.991957104557642},{"x":1773552148514,"y":12.659075686537175},{"x":1773552153515,"y":11.697860962566844},{"x":1773552158514,"y":11.26005361930295},{"x":1773552163514,"y":12.541918175720992},{"x":1773552168516,"y":10.954301075268818},{"x":1773552173514,"y":8.46774193548387},{"x":1773552178514,"y":9.261744966442953},{"x":1773552183514,"y":9.036144578313253},{"x":1773552188514,"y":19.59731543624161},{"x":1773552193514,"y":9.456740442655935},{"x":1773552198514,"y":10.62542030934768},{"x":1773552203514,"y":8.316566063044936},{"x":1773552208514,"y":9.872397582269981},{"x":1773552213514,"y":10.073875083948959},{"x":1773552218514,"y":15.060240963855422},{"x":1773552223517,"y":26.118904475617903},{"x":1773552228512,"y":20.866666666666667},{"x":1773552233515,"y":25.987943737441395},{"x":1773552238514,"y":45.86666666666667},{"x":1773552243515,"y":49.83299933199733},{"x":1773552248514,"y":48.197596795727634},{"x":1773552253514,"y":53.835890593729154},{"x":1773552258514,"y":48.432288192128084},{"x":1773552263514,"y":60.280373831775705},{"x":1773552268514,"y":75.89880159786951},{"x":1773552273514,"y":66.71122994652407},{"x":1773552278515,"y":60.66666666666667},{"x":1773552283512,"y":33.88814913448735},{"x":1773552288514,"y":38.07615230460922},{"x":1773552293515,"y":30.887258172114745},{"x":1773552298514,"y":33.86666666666667},{"x":1773552303517,"y":35.6},{"x":1773552308516,"y":31.842456608811748},{"x":1773552313515,"y":32.266666666666666},{"x":1773552318521,"y":34.15446071904128},{"x":1773552323514,"y":32.219251336898395},{"x":1773552328515,"y":33.666666666666664},{"x":17735523335
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 ERRORs
macOS-latest (auto)
ignoring SIGPIPE signal
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, 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)
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)
dependency ‘BiocVersion’ is 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~L1UMXY.dockerbuild
135 KB
sha256:a3f80e75f03bb13b7a6a37432c08fdaf57dda8e062c4b4769f65c2cefcfc9d9b
macOS-biocversion-release-r-auto-results
7.57 MB
sha256:8462f31702b67537a9f7128b87160b3d07c505775770d6b3eda18bde6b57c0d7