build-cran-binaries/.crow/build-alpine-320-amd64-single.yaml

when:
  - event: manual
    evaluate: 'build == "all"'
  # - event: manual
  #   evaluate: 'build == "alpine-320-amd64"'
  - event: manual
    evaluate: 'build == "alpine-320-amd64-0"'
  - event: manual
    evaluate: 'build == "all-amd64"'

skip_clone: true

steps:
  - name: 'Build binaries'
    image: docker.io/devxygmbh/amd64-binaries-r-alpine-320
    pull: true
    environment:
      RED_HAT_DEV_PW:
        from_secret: RED_HAT_DEV_PW
      HETZNER_S3_ACCESS_KEY_K3S:
        from_secret: HETZNER_S3_ACCESS_KEY_K3S
      HETZNER_S3_SECRET_KEY_K3S:
        from_secret: HETZNER_S3_SECRET_KEY_K3S
      PGPASS:
        from_secret: PGPASS
      GIT_RO_TOKEN:
        from_secret: GIT_RO_TOKEN
      GITHUB_PAT:
        from_secret: GITHUB_PAT
      # normal env vars
      GIT_USER: pat-s
      NTFY_SERVER:
        from_secret: NTFY_SERVER
      NTFY_TOPIC:
        from_secret: NTFY_TOPIC
      NTFY_AUTH: TRUE
      NTFY_PASSWORD:
        from_secret: ntfy_token
      # set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
      R_LIBS_USER: /mnt/cache/R-pkgs
      CCACHE_DIR: /mnt/cache/ccache
      PLATFORM: alpine-320
      ARCH: amd64
      NCPUS: 2
      STRATEGY: sequential
    # volumes:
    #   - amd64-binaries-r-dep-cache-alpine-320:/mnt/cache
    commands:
      - git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
      - R -q -e 'packageVersion("bincraftR")'
      - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
      # Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'rFUSION', 'MediaNews'
      - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c('ieegio',  'integr', 'interpolation', 'intkrige', 'intRinsic', 'intSDM',  'IOLS', 'ipanema', 'ipdw', 'ipsecr', 'IRkernel', 'irtawsi', 'isocat',  'IsoriX', 'ISRaD', 'itcSegment', 'itsdm', 'ivdoctr', 'janus',  'jdenticon', 'JFM', 'jrSiCKLSNMF', 'kazaam', 'KeyboardSimulator',  'lgpr', 'MDSGUI', 'medfateland', 'MediaNews', 'Mega2R', 'MetabolomicsBasics',  'minired', 'moc.gapbk', 'ModTools', 'MolgenisArmadillo', 'mpae',  'MPCR', 'noisemodel', 'ODT', 'omsvg', 'onsvtables', 'OpenCL',  'openrouteservice', 'opinAr', 'overturemapsr', 'palaeoverse',  'parqr', 'parquetize', 'pastclim', 'pbdMPI', 'pbdSLAP', 'pcaL1',  'PCRA', 'pgenlibr', 'pheble', 'phonics', 'plot3Drgl', 'plotdap',  'plothelper', 'plumberDeploy', 'plusCode2', 'pmclust', 'pMEM',  'Poly4AT', 'polyhedralCubature', 'polymapR', 'pooledpeaks', 'PoPdesign',  'PopGenReport', 'populR', 'portfolio.optimization', 'postdoc',  'potential', 'povmap', 'poweRbal', 'PoweREST', 'PPbigdata', 'ppcSpatial',  'ppgm', 'PPMiss', 'PPRL', 'ppsbm', 'praatpicture', 'practicalSigni',  'predhy.GUI', 'predict3d', 'predicts', 'predtoolsTS', 'presenter',  'pressuRe', 'PrevMap', 'prevR', 'prior3D', 'priorCON', 'prioritizr',  'prism', 'PRISMA2020', 'prismjs', 'prisonbrief', 'profExtrema',  'proffer', 'ProfoundData', 'proj4', 'protolite', 'prqlr', 'prWarp',  'psBayesborrow', 'psgp', 'psSubpathway', 'qad', 'QF', 'qlcVisualize',  'qmd', 'QRAGadget', 'qrencoder', 'qrlabelr', 'QRM', 'qspray',  'qsub', 'qtlc', 'quadmesh', 'quadtree', 'qualmap', 'R2BayesX',  'R2PPT', 'R2wd', 'r4lineups', 'Racmacs', 'RAINBOWR', 'randomcoloR',  'RandomWalker', 'Rata', 'Rblpapi', 'rblt', 'rccola', 'RcmdrMisc',  'RcmdrPlugin.aRnova', 'RcmdrPlugin.BiclustGUI', 'RcmdrPlugin.BWS1',  'RcmdrPlugin.BWS2', 'RcmdrPlugin.BWS3', 'RcmdrPlugin.cpd', 'RcmdrPlugin.DCCV',  'RcmdrPlugin.DCE', 'RcmdrPlugin.depthTools', 'RcmdrPlugin.DoE',  'RcmdrPlugin.EACSPIR', 'RcmdrPlugin.EBM', 'RcmdrPlugin.EcoVirtual',  'RcmdrPlugin.Export', 'RcmdrPlugin.EZR', 'RcmdrPlugin.FactoMineR',  'RcmdrPlugin.GWRM', 'RcmdrPlugin.HH', 'RcmdrPlugin.KMggplot2',  'RcmdrPlugin.MA', 'RcmdrPlugin.MPAStats', 'RcmdrPlugin.NMBU',  'RcmdrPlugin.orloca', 'RcmdrPlugin.PcaRobust', 'RcmdrPlugin.RiskDemo',  'RcmdrPlugin.RMTCJags', 'RcmdrPlugin.ROC', 'RcmdrPlugin.sos',  'RcmdrPlugin.survival', 'RcmdrPlugin.TeachingDemos', 'RcmdrPlugin.TeachStat',  'RcmdrPlugin.temis', 'RcmdrPlugin.UCA', 'RcmdrPlugin.WorldFlora',  'Rcplex', 'RcppCWB', 'RcppMeCab', 'RDM', 'rdwplus', 'ReadDIM',  'readNSx', 'rechaRge', 'Recocrop', 'recolorize', 'red', 'redist',  'redistverse', 'redland', 'redlistr', 'redux', 'ref.ICAR', 'refreg',  'Relectoral', 'remote', 'reproj', 'rerddapXtracto', 'restoptr',  'resultant', 'RevGadgets', 'ReviewR', 'revtools', 'rflexscan',  'rflsgen', 'RFOC', 'rFUSION', 'RGCxGC', 'RGENERATEPREC', 'rgeopat2',  'rgl2gltf', 'rglplus', 'rgplates', 'RIdeogram', 'Riemann', 'RInno',  'RiskMap', 'riverdist', 'rivnet', 'rjade', 'RKHSMetaMod', 'rKIN',  'RKorAPClient', 'rleafmap', 'rless', 'rLFT', 'Rlibeemd', 'Rlibkdv',  'rliger', 'rmacrostrat', 'rmapshaper', 'rmapzen', 'rmarchingcubes',  'RMariaDB', 'RmecabKo', 'RMOPI', 'Rmpfr', 'Rmpi', 'Rmst', 'RMySQL',  'rnaturalearth', 'rnmamod', 'RockFab', 'RODBCDBI', 'ROI.models.miplib',  'ROI.plugin.clarabel', 'ROI.plugin.cplex', 'ROI.plugin.glpk',  'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROMDB', 'ROracle',  'rPAex', 'Rpdb', 'RPhosFate', 'RPointCloud', 'Rpolyhedra', 'RProtoBuf',  'rqti', 'Rquake', 'RQuantLib', 'rsat', 'rsi', 'rsocialwatcher',  'RSP', 'rSPARCS', 'Rsymphony', 'RTLknitr', 'rTLsDeep', 'rWCVP',  'RWinEdt', 'SANple', 'sarsop', 'Scalelink', 'scoredec', 'scplot',  'secsse', 'SEMdeep', 'SEMgraph', 'sf', 'sfarrow', 'sfcentral',  'sfdep', 'sfhotspot', 'sftime', 'sftrack', 'shapes', 'ShapeSelectForest',  'ShellChron', 'shiny.benchmark', 'shinyMixR', 'shinyRGL', 'shinytest',  'shinytest2', 'shrinkDSM', 'shrinkTVPVAR', 'SIGN', 'siland',  'SimInf', 'simplePHENOTYPES', 'simplexreg', 'SiMRiv', 'SimSurvey',  'simulariatools', 'sirad', 'sits', 'SLBDD', 'slideview', 'smartmap',  'smcryptoR', 'smdi', 'SMDIC', 'smile', 'SMITIDstruct', 'smoothAPC',  'smosr', 'snplinkage', 'sociome', 'SoilSaltIndex', 'spacejamr',  'SpaDES', 'SpaDES.core', 'SpaDES.tools', 'spANOVA', 'sparrpowR',  'sparseCov', 'SPARSEMODr', 'sparsevb', 'SpatGC', 'SpatGRID',  'SpatialDDLS', 'spatialEco', 'SpatialEpi', 'SpatialfdaR', 'SpatialGraph',  'SpatialKDE', 'SpatialPosition', 'SpatialRegimes', 'SpaTopic',  'spatsurv', 'spbal', 'spectralR', 'Spectran', 'spectrino', 'Spectrum',  'SQL', 'SRTsim', 'stratastats', 'StratifiedRF', 'stRoke', 'sugarbag',  'SUNGEO', 'surveyexplorer', 'surveyvoi', 'swaprinc', 'SymTS',  'tableschema.r', 'taskscheduleR', 'tfrmt', 'tfrmtbuilder', 'tidyCDISC',  'tidycmprsk', 'TidyConsultant', 'tiledb', 'tinyscholar', 'TKCat',  'tkImgR', 'tkRplotR', 'TML', 'trackeRapp', 'TSCI', 'twdtw', 'tweetcheck',  'uaparserjs', 'UnalR', 'V8', 'valhallr', 'valuemap', 'vol2birdR',  'vtree', 'washr', 'webglobe', 'xRing'); pkgs = setdiff(pkgs, c('RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'rFUSION', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', 'compareGroups', 'pls', 'SNPassoc', 'spdep', 'surveillance')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, s3_endpoint = 'https://hel1.your-objectstorage.com', s3_region = 'hel1', s3_bucket = 'devxy-r-package-binaries-hel1', s3_access_key_id = Sys.getenv('HETZNER_S3_ACCESS_KEY_K3S'), s3_secret_access_key = Sys.getenv('HETZNER_S3_SECRET_KEY_K3S'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'alpine-320'))"
      ### Manual pkg builds
      # 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
      # RInno: Windows-only
      # skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
      # rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
      # Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
      # ROracle: sysdep missing -> create rule
      # ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
      # ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
      # RmecabKo: fatal error: mecab.h: No such file or directory
      # rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
      # RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
      # Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
      # Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
      # Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
      # ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
      # Racmacs -> rmarchingcubes
      # minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note:   template argument deduction/substitution failed:
      # KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
      # gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
      # clrng -> gpuR
      # BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
      # 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
      # filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
      # magickGUI, biplotbootGUI
      # ymd (alpine, voi)
      # tfrmtbuilder -> V8 (alpine)
      # Rcmdr (alpine)
      # readstata13 (alpine)
      # - 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, s3_endpoint = 'https://hel1.your-objectstorage.com', s3_region = 'hel1', s3_bucket = 'devxy-r-package-binaries-hel1', s3_access_key_id = Sys.getenv('HETZNER_S3_ACCESS_KEY_K3S'), s3_secret_access_key = Sys.getenv('HETZNER_S3_SECRET_KEY_K3S'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = "amd64"))'
    backend_options:
      kubernetes:
        resources:
          requests:
            memory: 5Gi
            cpu: 1000m
          limits:
            memory: 20Gi
            cpu: 2000m
        nodeSelector:
          kubernetes.io/arch: amd64
          node.kubernetes.io/instance-type: AX42
        tolerations:
          - key: 'CI'
            operator: 'Equal'
            value: 'true'
            effect: 'NoSchedule'

  - name: 'ntfy'
    image: binwiederhier/ntfy:v2.11.0
    when:
      - status: [failure]
    environment:
      NTFY_TOKEN:
        from_secret: ntfy_token
    commands: |
      BUILD_INDEX=$(cat build_index.txt)
      ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}