build-cran-binaries/.woodpecker/build-redhat-9-amd64.yaml

when:
  - event: manual
    evaluate: 'build == "all"'
  - event: manual
    evaluate: 'build == "redhat-9-amd64"'
  - event: manual
    evaluate: 'build == "all-amd64"'

skip_clone: true

steps:
  - name: 'Build binaries'
    secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT]
    image: docker.io/devxygmbh/amd64-binaries-r-redhat-9
    pull: true
    # to ensure the PACKAGES upload step is being executed
    failure: ignore
    environment:
      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: redhat-9
      BLOCK: 2394:2428
      ARCH: amd64
      NCPUS: 4
      INSTANCE_TYPE: AX42
      STRATEGY: sequential
    # volumes:
    #   - amd64-binaries-r-dep-cache-redhat-9:/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
      # for some reason paks pkgcache is often corrupt
      - rm -rf /mnt/cache/R-pkgs/pkgcache/ /mnt/cache/pkgcache/ /root/.cache/R/
      - 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, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/rhel9/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 == 'redhat-9', arch == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('later', 'MediaNews', 'RInno', 'sbmSDP', 'sbo', 'sboost', 'sbrl',  'SC.MEB', 'Scalelink', 'ScaleSpikeSlab', 'scalpel', 'scar', 'ScatterDensity',  'scattermore', 'SCBiclust', 'scCAN', 'SCCI', 'scclust', 'sccore',  'SCdeconR', 'scDHA', 'scellpam', 'SCEPtER', 'SCEPtERbinary',  'scGate', 'scGOclust', 'sched', 'scINSIGHT', 'SCIntRuler', 'scISR',  'scistreer', 'scITD', 'scMappR', 'scModels', 'scOntoMatch', 'scoper',  'scorematchingad', 'scorepeak', 'scoringRules', 'SCORNET', 'scout',  'scplot', 'scquantum', 'SCRIP', 'scrm', 'ScRNAIMM', 'scRNAtools',  'scrypt', 'scs', 'scTenifoldKnk', 'SCtools', 'SDAR', 'sdcMicro',  'sdcTable', 'sde', 'sdetorus', 'sdmTMB', 'SDMtune', 'sdpdth',  'sdprisk', 'sdpt3r', 'sdrt', 'sdwd', 'SEA', 'SearchTrees', 'seas',  'SECP', 'secretbase', 'secsse', 'sectorgap', 'secure', 'seededlda',  'SeedMatchR', 'seeker', 'seer', 'segclust2d', 'segmag', 'segmenTier',  'segmentr', 'segMGarch', 'seismicRoll', 'SEL', 'selectiveInference',  'selectspm', 'SELF', 'SemiCompRisks', 'semidist', 'semnar', 'semver',  'SenSpe', 'sentencepiece', 'sentiment.ai', 'sentometrics', 'sentopics',  'sephora', 'seq2R', 'SeqDetect', 'seqgendiff', 'seqHMM', 'seqinr',  'SeqKat', 'seqminer', 'SeqNet', 'seqtrie', 'SequenceSpikeSlab',  'SequentialDesign', 'sequoia', 'seriation', 'serocalculator',  'serrsBayes', 'Seurat', 'SeuratObject', 'sfcr', 'sfcurve', 'sfdct',  'sfheaders', 'sfhotspot', 'SFS', 'SFSI', 'sgd', 'SGDinference',  'sgeostat', 'SGL', 'sglasso', 'sgmodel', 'sgolay', 'SGPR', 'sgsR',  'shapr', 'shapviz', 'sharpeRratio', 'sharpPen', 'SheetReader',  'ShellChron', 'SherlockHolmes', 'shide', 'ShiftConvolvePoibin',  'shiftR', 'shiny.blueprint', 'shiny.fluent', 'shiny.reglog',  'shinyCohortBuilder', 'shinydbauth', 'shinyExprPortal', 'shinyKGode',  'ShinyLink', 'shinymanager', 'shinyMolBio', 'shinypivottabler',  'shinyQueryBuilder', 'shinyrecipes', 'shinyTime', 'skedastic',  'spectrino', 'surveyvoi', 'taskscheduleR', 'theft', 'theftdlc',  'trtswitch', 'ursa'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'later', '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-9'))"
      ### 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'