131 lines
10 KiB
YAML
131 lines
10 KiB
YAML
when:
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- event: manual
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evaluate: 'build == "all"'
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- event: manual
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evaluate: 'build == "redhat-8-arm64"'
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- event: manual
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evaluate: 'build == "all-arm64"'
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skip_clone: true
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steps:
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- name: 'Warming up'
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image: busybox:latest
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failure: ignore
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commands:
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- sleep 300
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- echo "Warmed Up"
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backend_options:
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kubernetes:
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resources:
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requests:
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memory: 14Gi
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cpu: 3000m
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limits:
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memory: 14Gi
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cpu: 3000m
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nodeSelector:
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kubernetes.io/arch: arm64
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node.kubernetes.io/instance-type: cax31
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tolerations:
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- key: 'CI'
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operator: 'Equal'
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value: 'true'
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effect: 'NoSchedule'
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- name: 'Build binaries'
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secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT]
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image: docker.io/devxygmbh/arm64-binaries-r-redhat-8
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pull: true
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# to ensure the PACKAGES upload step is being executed
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failure: ignore
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environment:
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GIT_USER: pat-s
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# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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R_LIBS_USER: /mnt/cache/R-pkgs
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CCACHE_DIR: /mnt/cache/ccache
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PLATFORM: redhat-8
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BLOCK: 20500:length(pkgs)
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ARCH: arm64
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NCPUS: 2
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MEMORY: 14Gi
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INSTANCE_TYPE: cax31
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STRATEGY: multisession
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volumes:
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- arm64-binaries-r-dep-cache-redhat-8:/mnt/cache
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commands:
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- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git .
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- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
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# for some reason paks pkgcache is often corrupt
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- rm -rf /mnt/cache/R-pkgs/pkgcache/ /mnt/cache/pkgcache/ /root/.cache/R/
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- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
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- R -q -e 'packageVersion("bincraftR")'
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
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- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c('rubias', 'rucrdtw', 'rugarch', 'ruimtehol', 'runner', 'Runuran', 'ruv', 'rvalues', 'Rvcg', 'rvg', 'rviewgraph', 'rvinecopulib', 'Rwave', 'RWDataPlyr', 'RWeka', 'RWekajars', 'rwfec', 'RWiener', 'RWinEdt', 'RWNN', 'Rwofost', 'RxnSim', 'rxylib', 'Ryacas0', 'RZigZag', 'rzmq', 'RZooRoH', 's2', 's2net', 'saccadr', 'sads', 'saeczi', 'saeMSPE', 'saeRobust', 'SAGMM', 'SALES', 'salso', 'SAM', 'SAMGEP', 'samon', 'sampling', 'SamplingBigData', 'samplingVarEst', 'samplr', 'samurais', 'sanic', 'sanitizers', 'SANple', 'santoku', 'SANvi', 'SAPP', 'SAR', 'sarima', 'sarsop', 'sasfunclust', 'sass', 'satellite', 'SBCK', 'sbde', 'sbfc', 'sBIC', 'sbm', 'SBmedian', 'sbmSDP', 'sbo', 'sboost', 'sbrl', 'SC.MEB', 'scagnostics', 'Scalelink', 'ScaleSpikeSlab', 'scalpel', 'scar', 'ScatterDensity', 'scattermore', 'SCCI', 'scclust', 'sccore', 'scDHA', 'scellpam', 'SCEPtER', 'SCEPtERbinary', 'scINSIGHT', 'SCIntRuler', 'scistreer', 'scITD', 'scMappR', 'scModels', 'scoper', 'scorematchingad', 'scorepeak', 'scoringRules', 'SCORNET', 'scout', 'scquantum', 'scrm', 'scrypt', 'scs', 'sdcMicro', 'sdcTable', 'sde', 'sdetorus', 'sdmTMB', 'SDMtune', 'sdpdth', 'sdprisk', 'sdrt', 'sdwd', 'SearchTrees', 'seas', 'secretbase', 'secsse', 'secure', 'seededlda', 'segclust2d', 'segen', 'segmag', 'segmenTier', 'segmentr', 'segMGarch', 'seismicRoll', 'SEL', 'selectiveInference', 'SELF', 'SemiCompRisks', 'semidist', 'semver', 'sendigR', 'SensMap', 'SenSpe', 'sentencepiece', 'sentometrics', 'sentopics', 'SeqDetect', 'seqHMM', 'seqinr', 'SeqKat', 'seqminer', 'SeqNet', 'seqtrie', 'SequenceSpikeSlab', 'sequoia', 'serrsBayes', 'Seurat', 'SeuratObject', 'sfcr', 'sfcurve', 'sfheaders', 'SFS', 'SFSI', 'sgd', 'SGDinference', 'sgeostat', 'SGL', 'sglasso', 'sgolay', 'SGPR', 'shapes', 'shapr', 'sharpeRratio', 'sharpPen', 'SheetReader', 'shide', 'ShiftConvolvePoibin', 'shiftR', 'shinyExprPortal', 'shinylive', 'shinyMixR', 'shinyRGL', 'showtext', 'shp2graph', 'shrinkDSM', 'shrinkTVP', 'SHT', 'Sieve', 'sift', 'signal', 'signalHsmm', 'signnet', 'SigTree', 'SILGGM', 'SimBIID', 'simcdm', 'simcross', 'simecol', 'simer', 'simest', 'SimEUCartelLaw', 'simfam', 'simFrame', 'SimInf', 'SimJoint', 'simmer', 'simplace', 'simplexreg', 'simplextree', 'simPop', 'simputation', 'SimReg', 'simRestore', 'SiMRiv', 'simstudy', 'SimSurvNMarker', 'simtrial', 'simts', 'singR', 'SiPhyNetwork', 'SIRmcmc', 'sirt'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'redhat-8'))"
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### Manual pkg builds
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# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
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# RInno: Windows-only
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# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
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# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
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# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
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# ROracle: sysdep missing -> create rule
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# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
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# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
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# RmecabKo: fatal error: mecab.h: No such file or directory
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# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
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# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
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# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
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# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
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# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
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# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
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# Racmacs -> rmarchingcubes
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# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
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# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
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# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
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# clrng -> gpuR
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# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
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# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
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# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
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# magickGUI, biplotbootGUI
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# ymd (alpine, voi)
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# tfrmtbuilder -> V8 (alpine)
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# Rcmdr (alpine)
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# readstata13 (alpine)
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# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, debug = FALSE, force = TRUE, platform = "arm64"))'
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backend_options:
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kubernetes:
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### PROD-parallel
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resources:
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requests:
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memory: 14Gi
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cpu: 3000m
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limits:
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memory: 14Gi
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cpu: 3000m
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### PROD-sequential
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# resources:
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# requests:
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# memory: 14Gi
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# cpu: 2000m
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# limits:
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# memory: 14Gi
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# cpu: 3000m
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# DEBUG
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# resources:
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# requests:
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# memory: 4Gi
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# cpu: 2000m
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# limits:
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# memory: 4Gi
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# cpu: 2000m
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nodeSelector:
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kubernetes.io/arch: arm64
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node.kubernetes.io/instance-type: cax31
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tolerations:
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- key: 'CI'
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operator: 'Equal'
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value: 'true'
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effect: 'NoSchedule'
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