132 lines
12 KiB
YAML
132 lines
12 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 == "alpine-320-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-alpine-320
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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: alpine-320
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BLOCK: 20896: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-alpine-320:/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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- R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
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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); library(dplyr); library(bincraftR); pkgs = c('SignifReg', 'signnet', 'signs', 'SigOptR', 'sigora', 'sigQC', 'sigr', 'SigTree', 'SIHR', 'siie', 'siland', 'SILFS', 'SILGGM', 'silicate', 'SillyPutty', 'SILM', 'silp', 'sim.BA', 'Sim.DiffProc', 'Sim.PLFN', 'sim1000G', 'sim2Dpredictr', 'simaerep', 'SimBIID', 'simboot', 'simCAT', 'simcausal', 'simcdm', 'SimComp', 'SimCop', 'SimCorMultRes', 'SimCorrMix', 'simcross', 'simDAG', 'simdd', 'SimDesign', 'SimDissolution', 'simdistr', 'simDNAmixtures', 'simecol', 'simEd', 'SimEngine', 'simer', 'simest', 'simET', 'SimEUCartelLaw', 'simex', 'simexaft', 'simExam', 'SIMEXBoost', 'simfam', 'simfinapi', 'simfit', 'simFrame', 'simglm', 'simgof', 'SimHaz', 'simhelpers', 'SIMICO', 'simIDM', 'SimilarityMeasures', 'Simile', 'SimInf', 'simIReff', 'simitation', 'simITS', 'SimJoint', 'simlandr', 'SIMle', 'simmer', 'simmer.bricks', 'simmer.plot', 'simMetric', 'simml', 'simMP', 'simmr', 'SIMMS', 'simMSM', 'SimMultiCorrData', 'SimNPH', 'simode', 'simodels', 'simPH', 'simphony', 'simplace', 'simplanonym', 'SIMPLE.REGRESSION', 'simpleboot', 'simpleCache', 'simplecolors', 'simpleFDR', 'simplegraph', 'simplegraphdb', 'simpleMH', 'simpleMLP', 'simpleNeural', 'simplePHENOTYPES', 'simpleRCache', 'simplermarkdown', 'simpleSetup', 'simpletex', 'simplexreg', 'simplextree', 'SimplicialCubature', 'simplifyNet', 'SimplyAgree', 'SIMplyBee', 'simPop', 'simpr', 'simputation', 'simr', 'simrec', 'SimReg', 'simrel', 'simRestore', 'SiMRiv', 'sims', 'simsalapar', 'simsem', 'SimSeq', 'simsl', 'SimSST', 'simstandard', 'simstudy', 'simsurv', 'SimSurvey', 'SimSurvNMarker', 'simTargetCov', 'simtimer', 'SimTimeVar', 'simTool', 'simtrait', 'simts', 'simuclustfactor', 'simukde', 'simulariatools', 'simulator', 'simule', 'simulMGF', 'SimVitD', 'sinaplot', 'sinar', 'sindyr', 'sinew', 'singcar', 'SingleCaseES', 'singleCellHaystack', 'singR', 'sinib', 'SINRELEF.LD', 'SIPDIBGE', 'SIPETool', 'SiPhyNetwork', 'siplab', 'siqr', 'sirad', 'SIRE', 'SIRmcmc', 'sirt', 'SIRthresholded', 'sirus', 'SIS', 'SISIR', 'sisireg', 'sistec', 'sisti', 'sistmr', 'sisVIVE', 'SIT', 'sitar', 'sitepickR', 'siteymlgen', 'SITH', 'sitmo', 'sitools', 'sitree', 'sitreeE', 'sits', 'sivs', 'SixSigma', 'SizeEstimation', 'sizeMat', 'SiZer', 'sjdbc', 'sjlabelled', 'sjmisc', 'sjSDM', 'sjstats', 'sjtable2df', 'SK4FGA', 'SKAT', 'skater', 'skedastic', 'skeletor', 'skellam', 'sketch', 'sketcher', 'sketching', 'sketchy', 'SkewHyperbolic', 'skewlmm', 'skewMLRM', 'skewsamp', 'skewt', 'SKFCPD', 'Skillings.Mack', 'skilljaR', 'skimr', 'skipTrack', 'sklarsomega', 'skm', 'SKNN', 'skpr', 'skylight', 'skyscapeR', 'slackr', 'slanter', 'slap', 'slasso', 'SLBDD', 'SLCARE', 'slcm', 'sld', 'SLDAssay', 'sleekts', 'SleepCycles', 'sleepr', 'sleepwalk', 'SLEMI', 'Sleuth2', 'Sleuth3', 'slfm', 'SLFPCA', 'slgf', 'SLHD', 'SlicedLHD', 'slickR', 'SLIDE', 'slideview', 'SlidingWindows', 'slim', 'slimrec', 'slippymath', 'slm', 'SLModels', 'sloop', 'SLOPE', 'slouch', 'slowraker', 'slp', 'SLPresElection', 'slr', 'SLSEdesign', 'SLTCA', 'slurmR', 'sm', 'smaa', 'smacof', 'smacofx', 'smallarea', 'SmallCountRounding', 'smallsets', 'smallstuff', 'smam', 'SMARTbayesR', 'smartDesign', 'SmartEDA', 'SmarterPoland', 'smartmap', 'SmartMeterAnalytics', 'SMARTp', 'smartsheetr', 'smartsizer', 'smartsnp', 'SmartSVA', 'smatr', 'smbinning', 'SmCCNet', 'SMCRM', 'smcryptoR', 'smcure', 'smd', 'smdata', 'smdi', 'SMDIC', 'smdocker', 'smerc', 'smetlite', 'SMFilter', 'smfishHmrf', 'smfsb', 'smicd', 'smidm', 'smile', 'smiles', 'smirnov', 'SmithWilsonYieldCurve', 'SMITIDstruct', 'SMITIDvisu', 'SMLE', 'smlePH', 'smlmkalman', 'SMLoutliers', 'SMM', 'SMMA', 'SMME', 'smmR', 'SMMT', 'SMNCensReg', 'smoke', 'smoof', 'smooth', 'smoothAPC', 'smoothedLasso', 'smoother', 'SmoothHazard', 'smoothHR', 'smoothic', 'smoothmest', 'smoothr', 'smoothROCtime', 'smoothSurv', 'smoothtail', 'SmoothTensor', 'SmoothWin', 'smoothy', 'smoots', 'smosr', 'smotefamily', 'SMOTEWB', 'smovie', 'smpic', 'smplot2', 'SMPracticals', 'SMR', 'sms', 'sMSROC', 'smss', 'sMTL', 'SMUT', 'SMVar', 'smvgraph', 'sn', 'sna', 'snahelper', 'Snake', 'snakecase', 'SnakesAndLaddersAnalysis', 'snap', 'snapchatadsR', 'snapKrig', 'snapshot', 'SNBdata', 'snem', 'snfa', 'SNFtool', 'snha', 'snn', 'snow', 'SnowballC', 'snowboot', 'snowfall', 'snowflakes', 'snowFT', 'snowquery'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'doBy', 'DoE.base', 'DoE.wrapper', 'eha', 'FrF2', 'FrF2.catlg128', 'gRbase', 'gRain', 'IDPmisc', 'pbkrtest', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'spdep')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'alpine-320'))"
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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, MediaNews: 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 = 'alpine-320'))'
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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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