build-cran-binaries/.woodpecker/build-alpine-320-amd64.yaml

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

skip_clone: true

steps:
  - name: 'Build binaries'
    image: docker.io/devxygmbh/amd64-binaries-r-alpine-320
    pull: true
    # to ensure the PACKAGES upload step is being executed
    failure: ignore
    environment:
      RED_HAT_DEV_PW:
        from_secret: red_hat_dev_pw
      AWS_ACCESS_KEY_ID:
        from_secret: aws_access_key_id
      AWS_SECRET_ACCESS_KEY:
        from_secret: aws_secret_access_key
      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
      # 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
      BLOCK: 2991:2993
      ARCH: amd64
      NCPUS: 4
      STRATEGY: sequential
    # volumes:
    #   - amd64-binaries-r-dep-cache-alpine-320:/mnt/cache
    commands:
      - git clone https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/r-pkg-binaries.git .
      - rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR /mnt/cache/R-pkgs/00LOCK-pak /mnt/cache/pkgcache/R/pkgcache /mnt/cache/pkgcache/R/pkgcache /mnt/cache/R-pkgs/pkgcache
      - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.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'
      - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); pkgs = c('actel', 'AdhereRViz', 'ajv', 'AlleleShift', 'almanac', 'AntMAN',  'aPCoA', 'apisensr', 'appeears', 'asciicast', 'audubon', 'autoslider.core',  'autostats', 'badgen', 'baguette', 'bartCause', 'bartMan', 'base64',  'bate', 'BayesXsrc', 'bdl', 'behaviorchange', 'bigGP', 'biocompute',  'BiplotGUI', 'blackmarbler', 'blatr', 'bpmnR', 'bRacatus', 'BRugs',  'C50', 'canadamaps', 'CaseBasedReasoning', 'causalHyperGraph',  'causalPAF', 'centerline', 'cffr', 'chilemapas', 'cisp', 'clrng',  'countSTAR', 'CRE', 'CTRing', 'dartR', 'dartR.base', 'dartR.captive',  'dartR.popgen', 'dartR.sexlinked', 'dartR.sim', 'dartR.spatial',  'DGP4LCF', 'DoE.wrapper', 'doMPI', 'EBcoBART', 'ebmc', 'ecocomDP',  'eDITH', 'EFAfactors', 'enerscape', 'epidm', 'epizootic', 'EthSEQ',  'excel.link', 'eyetools', 'fangs', 'fingerPro', 'fmf', 'FrF2.catlg128',  'GENLIB', 'ggESDA', 'glossa', 'gpuR', 'GTFSwizard', 'gto', 'gtreg',  'gwid', 'habtools', 'hdf5r', 'hdf5r.Extra', 'hwig', 'ical', 'ieegio',  'imbalanceDatRel', 'intamapInteractive', 'integr', 'intRinsic',  'intSDM', 'jrSiCKLSNMF', 'js', 'JSconsole', 'jsonld', 'jsonNormalize',  'jsonvalidate', 'juicedown', 'juicyjuice', 'katex', 'kazaam',  'KeyboardSimulator', 'lgpr', 'LPDynR', 'lucas', 'mapping', 'MazamaLocationUtils',  'MazamaSpatialPlots', 'MazamaSpatialUtils', 'MDSGUI', 'medfateland',  'MediaNews', 'Mega2R', 'MetabolomicsBasics', 'metajam', 'midoc',  'minired', 'MMOC', 'moc.gapbk', 'ModTools', 'Morphoscape', 'movegroup',  'MPCR', 'nfl4th', 'nflverse', 'noisemodel', 'OpenCL', 'palaeoverse',  'pastclim', 'pbdMPI', 'pbdSLAP', 'pcaL1', 'pgenlibr', 'pheble',  'phonics', 'plotBart', 'pmclust', 'postdoc', 'PPRL', 'praatpicture',  'predhy.GUI', 'presenter', 'PRISMA2020', 'prismjs', 'R2PPT',  'R2wd', 'Racmacs', 'randomcoloR', 'ravetools', 'Rblpapi', 'rblt',  'RcmdrPlugin.cpd', 'RcmdrPlugin.GWRM', 'RcmdrPlugin.TeachStat',  'RcmdrPlugin.WorldFlora', 'Rcplex', 'RcppCWB', 'RcppMeCab', 'readNSx',  'redatamx', 'ReSurv', 'rFUSION', 'riAFTBART', 'rjade', 'rless',  'rliger', 'rmapshaper', 'rmapzen', 'RmecabKo', 'Rmpi', 'ROI.plugin.cplex',  'ROI.plugin.symphony', 'ROracle', 'Rpoppler', 'RQuantLib', 'rsofun',  'RSP', 'Rsymphony', 'rWCVP', 'RWinEdt', 'SANple', 'sarsop', 'Scalelink',  'secsse', 'SEMdeep', 'SEMgraph', 'SHAPforxgboost', 'shapviz',  'shiny.benchmark', 'shinytest2', 'shrinkTVPVAR', 'simplePHENOTYPES',  'SiMRiv', 'snplinkage', 'spectrino', 'stan4bart', 'stratastats',  'StratifiedRF', 'sugarbag', 'surveyvoi', 'tableschema.r', 'taskscheduleR',  'tern.rbmi', 'tesseract', 'tfrmtbuilder', 'TidyConsultant', 'tiledb',  'TKCat', 'tkImgR', 'tkRplotR', 'twdtw', 'tweetcheck', 'uaparserjs',  'V8', 'valhallr', 'voi', 'vol2birdR', 'vtree', 'xRing'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = '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, platform = "amd64"))'
    backend_options:
      kubernetes:
        resources:
          requests:
            memory: 5Gi
            cpu: 2000m
          limits:
            memory: 20Gi
            cpu: 3000m
        nodeSelector:
          kubernetes.io/arch: amd64
          node.kubernetes.io/instance-type: AX42
        tolerations:
          - key: 'CI'
            operator: 'Equal'
            value: 'true'
            effect: 'NoSchedule'