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' 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-alpine-320 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: alpine-320 BLOCK: 2991:2993 ARCH: amd64 NCPUS: 4 # memory: 20Gi # INSTANCE_TYPE: ccx23 STRATEGY: sequential # volumes: # - amd64-binaries-r-dep-cache-alpine-320:/mnt/cache commands: # download latest package version (avoid having to rebuild image every time) # rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169 - 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")' # more complicated system dependencies which pak cannot resolve - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # 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 ### Check # - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists) # - Rglpk # biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run # doBy: hangs on alpine # later: hangs on ubuntu - 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))' - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); pkgs = c('doBy', 'DoE.base', 'DoE.wrapper', 'eha', 'FrF2', 'FrF2.catlg128', 'gRain', 'gRbase', 'IDPmisc', 'MediaNews', 'pbkrtest', 'RInno', 'RVAideMemoire', 'seewave', 'SEMdeep', 'semicmprskcoxmsm', 'SemiCompRisks', 'SemiPar.depCens', 'semnar', 'sentiment.ai', 'sephora', 'sfarrow', 'sfcentral', 'sfdct', 'sfhotspot', 'sfnetworks', 'sftrack', 'sgsR', 'ShapePattern', 'shapes', 'ShapeSelectForest', 'SHAPforxgboost', 'shapviz', 'ShellChron', 'shelter', 'shiny.benchmark', 'shinybrms', 'shinyCohortBuilder', 'shinyIRT', 'ShinyItemAnalysis', 'shinyRGL', 'shinytest2', 'shrinkDSM', 'SIAmodules', 'SIGN', 'siland', 'simCAT', 'SimDesign', 'SimInf', 'SimNPH', 'simplePHENOTYPES', 'simplexreg', 'SimRDS', 'SimSurvey', 'simulariatools', 'sirad', 'sisireg', 'sits', 'SLBDD', 'slideview', 'smartmap', 'smcryptoR', 'SMDIC', 'smile', 'SMITIDstruct', 'smlmkalman', 'smoothAPC', 'smosr', 'snplinkage', 'sociome', 'sodium', 'SoilSaltIndex', 'spacejamr', 'SpaDES', 'SpaDES.core', 'SpaDES.tools', 'spANOVA', 'sparrpowR', 'sparseCov', 'SPARSEMODr', 'SpatGC', 'SpatGRID', 'spatialEco', 'SpatialEpi', 'SpatialfdaR', 'SpatialGraph', 'SpatialKDE', 'SpatialPosition', 'spatialreg', 'SpatialRegimes', 'SpaTopic', 'spatsurv', 'spbal', 'spDates', 'spdynmod', 'spectacles', 'spectator', 'spectralR', 'spectrino', 'Spectrum', 'speech', 'spemd', 'spex', 'spGARCH', 'sphereplot', 'sphet', 'spidR', 'spldv', 'splm', 'spm', 'spm2', 'spsur', 'spup', 'SQL', 'SQRL', 'SRTsim', 'ssdGSA', 'SSDM', 'ssfa', 'ssh', 'SSIMmap', 'SSN2', 'SSNbayes', 'SSNbler', 'sta', 'stacomiR', 'stacomirtools', 'stampr', 'stan4bart', 'stars', 'starsExtra', 'starsTileServer', 'StatDA', 'statgenMPP', 'stcos', 'stelfi', 'stepgbm', 'steprf', 'steps', 'stfit', 'stopp', 'stops', 'stpphawkes', 'stppSim', 'strand', 'stratbr', 'StratifiedRF', 'StreamMetabolism', 'streetscape', 'string2path', 'stxplore', 'SubTS', 'SubtypeDrug', 'SUNGEO', 'SurfaceTortoise', 'SurrogateRsq', 'surrosurv', 'surveyPrev', 'surveyvoi', 'survivalMPLdc', 'survSNP', 'svars', 'swaRmverse', 'swfscAirDAS', 'swfscDAS', 'SWMPrExtension', 'symbolicDA', 'symbolicQspray', 'symengine', 'SymTS', 'T4cluster', 'tabularaster', 'tailDepFun', 'track2KBA', 'trackeRapp', 'traineR', 'transformr', 'transfR', 'traveltimeR', 'trigpoints', 'tripEstimation', 'TroublemakeR', 'trtswitch', 'truh', 'TSCI', 'TUFLOWR', 'tvthemes', 'twangMediation', 'twangRDC', 'uavRmp', 'udunits2', 'ugatsdb', 'ulex', 'ultrapolaRplot', 'UnalR', 'UniprotR', 'units', 'upstartr', 'ursa', 'usdm', 'valuemap', 'VancouvR', 'vapour', 'VBLPCM', 'VC2copula', 'vein', 'versioning', 'vines', 'virtualspecies', 'virtuoso', 'visaOTR', 'visStatistics', 'visualpred', 'visvow', 'vivid', 'vmeasur', 'voi', 'vol2birdR', 'voluModel', 'vvauditor', 'wactor', 'wallace', 'warabandi', 'washr', 'WaveletMLbestFL', 'waver', 'waves', 'WCluster', 'wdnr.gis', 'wdpar', 'weatherOz', 'webglobe', 'webSDM', 'WEGE', 'weightedGCM', 'wiesbaden', 'wildlifeDI', 'windAC', 'WMAP', 'WQM', 'xgb2sql', 'xgboost', 'xrf', 'xRing', 'xslt', 'zcurve', 'zonebuilder', 'zoomerjoin' ); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave')); 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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 # filters: -> 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'