138 lines
14 KiB
YAML
138 lines
14 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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# download latest package version (avoid having to rebuild image every time)
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# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
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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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# more complicated system dependencies which pak cannot resolve
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
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### Check
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# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
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# - Rglpk
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# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
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- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/arm64/alpine320/latest', CRAN = 'https://cloud.r-project.org'))); library(dplyr); library(bincraftR); cran_pkgs = tools::CRAN_package_db()[['Package']]; '%nin%' <- Negate('%in%'); foo = query_metadata_table() |> filter(platform == 'alpine-320', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('FrF2', 'FrF2.catlg128', 'galah', 'gRain', 'gRbase', 'IDPmisc', 'lcopula', 'LDABiplots', 'LDAShiny', 'LDATS', 'ldatuning', 'LDM', 'leafem', 'leafletZH', 'leafpop', 'leafR', 'LeArEst', 'LearnClust', 'LearningRlab', 'learnPopGen', 'LearnVizLMM', 'leidenAlg', 'leidenbase', 'letsR', 'lgcp', 'lgpr', 'Libra', 'libstable4u', 'lidaRtRee', 'lidR', 'LifemapR', 'limorhyde2', 'lingtypology', 'link2GI', 'linkcomm', 'linkspotter', 'LMoFit', 'LncPath', 'lnmixsurv', 'locits', 'locpolExpectile', 'lofifonts', 'lordif', 'LorMe', 'lpacf', 'lpda', 'LPDynR', 'LPKsample', 'LPmerge', 'LS2Wstat', 'LSAfun', 'LSDsensitivity', 'LSVAR', 'LTAR', 'lucas', 'LUCIDus', 'lulcc', 'lvnet', 'lwgeom', 'M3', 'macroBiome', 'macrosyntR', 'MadanText', 'MadanTextNetwork', 'Maeswrap', 'magick', 'magickGUI', 'MainExistingDatasets', 'makePalette', 'makepipe', 'malan', 'MAMS', 'mand', 'manet', 'MantaID', 'maotai', 'mapboxapi', 'mapchina', 'MapGAM', 'mapgl', 'mapindia', 'mapindiatools', 'mapiso', 'mapme.biodiversity', 'mapmisc', 'mapping', 'mapsf', 'mapsRinteractive', 'mapStats', 'maptiles', 'mapview', 'margaret', 'markets', 'marmap', 'MARMoT', 'mashr', 'massiveGST', 'mau', 'MaximinInfer', 'maxlike', 'maxmatching', 'MazamaLocationUtils', 'MazamaSpatialPlots', 'MazamaSpatialUtils', 'mazeGen', 'MBC', 'MBCbook', 'MBMethPred', 'mbr', 'mBvs', 'mcauchyd', 'MCDA', 'mcMST', 'mcrPioda', 'mcvis', 'mDAG', 'MDMAPR', 'MDSGUI', 'MDSMap', 'mdsr', 'meconetcomp', 'mecoturn', 'medfate', 'medfateland', 'MediaNews', 'Mega2R', 'MEGENA', 'meme', 'Mercator', 'mergedblocks', 'messy.cats', 'MetabolomicsBasics', 'MetaComp', 'metadynminer3d', 'metajam', 'MetaLandSim', 'MetaNet', 'metanetwork', 'metaRange', 'metasnf', 'meteo', 'meteoEVT', 'meteoForecast', 'meteoland', 'MethodOpt', 'MetricGraph', 'mgc', 'mggd', 'mglmn', 'mgwrhw', 'micd', 'microbial', 'MicrobiomeSurv', 'microinverterdata', 'micromap', 'micropan', 'midoc', 'MigConnectivity', 'mikropml', 'mineSweepR', 'minired', 'miRetrieve', 'MiscMetabar', 'missSBM', 'misuvi', 'mixcat', 'mixgb', 'mixhvg', 'mixKernel', 'mixpoissonreg', 'mkde', 'mlbplotR', 'MLCOPULA', 'MLE', 'mlmts', 'mlr3spatial', 'mlVAR', 'MMOC', 'mmod', 'mmpca', 'MN', 'mnet', 'MNS', 'moc.gapbk', 'ModelMap', 'modelSSE', 'modeltime', 'modeltime.ensemble', 'modeltime.resample', 'modgo', 'modisfast', 'modMax', 'modnets', 'modopt.matlab', 'ModStatR', 'ModTools', 'molaR', 'MolgenisArmadillo', 'momentuHMM', 'Momocs', 'mongolite', 'monographaR', 'MonoPhy', 'monoreg', 'moodef', 'moodleR', 'mop', 'morph', 'Morpho', 'morphomap', 'Morphoscape', 'MorphoTools2', 'motifcluster', 'move2', 'movecost', 'movegroup', 'moveWindSpeed', 'mpae', 'MPCR', 'mppR', 'MRG', 'MRPC', 'MRReg', 'MRS', 'MSclassifR', 'MSSQL', 'mstDIF', 'mstudentd', 'MTA', 'MtreeRing', 'mully', 'MultBiplotR', 'multibiplotGUI', 'multibridge', 'MultiGroupO', 'multimedia', 'multinma', 'multinomineq', 'MultiscaleDTM', 'MultivariateAnalysis', 'mvabund', 'mvcauchy', 'mvcor', 'mvhist', 'mvhtests', 'mvinfluence', 'mvmesh', 'mvMORPH', 'mvnormalTest', 'mvst', 'mwcsr', 'mwTensor', 'mxfda', 'N2R', 'NAIR', 'naive', 'nat', 'nat.nblast', 'nat.templatebrains', 'NCC', 'ncdf4', 'ncdfgeom', 'ncdump', 'ncmeta', 'NCSCopula', 'ndi', 'neatmaps', 'nebula', 'necountries', 'Neighboot', 'neotoma2', 'NEpiC', 'nesRdata', 'nestedcv', 'netassoc', 'netCoin', 'NetFACS', 'netgwas', 'NetLogoR', 'netmediate', 'NetOrigin', 'netplot', 'nets', 'NetSci', 'netseg', 'netSEM', 'netShiny', 'NetSwan', 'NetworkComparisonTest', 'NetworkDistance', 'networkGen', 'networktools', 'neuroimaGene', 'nfl4th', 'nflfastR', 'nflverse', 'NGBVS', 'nhdplusTools', 'nhdR', 'nichevol', 'NIMAA', 'nimble', 'nimbleAPT', 'nimbleCarbon', 'nimbleEcology', 'nimbleHMC', 'nimbleNoBounds', 'nimbleSCR', 'nimbleSMC', 'NipponMap', 'njgeo', 'nlgm', 'nlnet', 'NLPutils', 'nncc', 'nngeo', 'noaastormevents', 'node2vec', 'nodiv', 'noisemodel', 'noisysbmGGM', 'nomnoml', 'novelqualcodes', 'npbr', 'npcs', 'npphen', 'nsga3', 'nswgeo', 'numbat', 'nutriNetwork', 'oaqc', 'OasisR', 'occCite', 'oceanexplorer', 'oceanic', 'oceanis', 'oceanmap', 'OceanView', 'OCNet', 'odbc', 'ODT', 'oeli', 'ofpetrial', 'ohun', 'OmopSketch', 'omsvg', 'oncoPredict', 'oncrawlR', 'One4All', 'onelogin', 'onmaRg', 'onsvtables', 'ontophylo', 'OpenCL', 'openCR', 'opencv', 'opendatatoronto', 'OpenLand', 'OpenRepGrid.ic', 'openrouteservice', 'OpenStreetMap', 'opinAr', 'optbdmaeAT', 'optBiomarker', 'optimus', 'optiSolve', 'optrcdmaeAT', 'optrefine', 'Orcs', 'ORION', 'orthoDr', 'oRus', 'osc', 'OSMscale', 'OTrecod', 'outlierensembles', 'outliers.ts.oga', 'overturemapsr', 'OVtool', 'ows4R', 'pagoda2', 'palaeoverse', 'paleobioDB', 'paleopop', 'paleotree', 'palm', 'PAMmisc', 'PAMpal', 'PAMscapes', 'pannotator', 'pargasite', 'parma', 'parqr', 'parquetize', 'particle.swarm.optimisation', 'particles', 'PAsso', 'pastclim', 'paths', 'patternize'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'FrF2', 'FrF2.catlg128', 'gRbase', 'gRain', 'IDPmisc')); 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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