when: - event: manual evaluate: 'build == "all"' - event: manual evaluate: 'build == "alpine-320-arm64"' - event: manual evaluate: 'build == "all-arm64"' skip_clone: true steps: - name: 'Warming up' image: busybox:latest failure: ignore commands: - sleep 300 - echo 'Warmed Up' backend_options: kubernetes: resources: requests: memory: 14Gi cpu: 3000m limits: memory: 14Gi cpu: 3000m nodeSelector: kubernetes.io/arch: arm64 node.kubernetes.io/instance-type: cax31 tolerations: - key: 'CI' operator: 'Equal' value: 'true' effect: 'NoSchedule' - 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/arm64-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: 20896:length(pkgs) ARCH: arm64 NCPUS: 2 MEMORY: 14Gi INSTANCE_TYPE: cax31 STRATEGY: multisession volumes: - arm64-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 # 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 - 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))' # 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); library(dplyr); library(bincraftR); pkgs = c('AlleleShift', 'AntMAN', 'aPCoA', 'apisensr', 'autoslider.core', 'baguette', 'bartCause', 'bartMan', 'base64', 'BayesXsrc', 'bdl', 'bigGP', 'BiplotGUI', 'blackmarbler', 'blatr', 'BLCOP', 'blender', 'Blendstat', 'blindrecalc', 'blindreview', 'blink', 'bliss', 'blm', 'blme', 'blmeco', 'BLModel', 'blob', 'blockcluster', 'BlockCov', 'blockForest', 'blocklength', 'blockmatrix', 'BlockMissingData', 'blockmodeling', 'BlockmodelingGUI', 'blockmodels', 'blockrand', 'blocksdesign', 'blocs', 'blogdown', 'BLOQ', 'BLPestimatoR', 'BLR', 'blrm', 'BLRPM', 'BLRShiny', 'BLRShiny2', 'blsBandit', 'blscrapeR', 'BLSM', 'blsR', 'bltm', 'bluebike', 'BlythStillCasellaCI', 'BMA', 'bmabasket', 'BMAmevt', 'bmass', 'BMconcor', 'bmem', 'bmemLavaan', 'bmet', 'bmgarch', 'bmggum', 'BMisc', 'bmixture', 'bmlm', 'bmm', 'bmp', 'BMRBr', 'BMRMM', 'BMS', 'bmscstan', 'bmstdr', 'BMT', 'BMTAR', 'bnclassify', 'bndesr', 'bndovb', 'bnlearn', 'bnma', 'bnmonitor', 'bnnSurvival', 'bnpa', 'BNPdensity', 'BNPmix', 'bnpsd', 'BNPTSclust', 'BNrich', 'BNSL', 'BNSP', 'bnstruct', 'bnviewer', 'boa', 'BoardGames', 'bodenmiller', 'Bodi', 'bodsr', 'bodycomp', 'bodycompref', 'boggy', 'boilerpipeR', 'BOIN', 'boinet', 'boiwsa', 'BOJ', 'bolasso', 'bolsec', 'Bolstad2', 'BoltzMM', 'bondAnalyst', 'BondValuation', 'BoneProfileR', 'BonEV', 'bonn', 'bonsai', 'bonsaiforest', 'BRugs', 'bscui', 'C50', 'CaseBasedReasoning', 'causalHyperGraph', 'clrng', 'ConvertPar', 'CoTiMA', 'countSTAR', 'CRE', 'ctgdist', 'CTRing', 'D3mirt', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'dartR.sim', 'dartR.spatial', 'DFIT', 'DGP4LCF', 'DoE.wrapper', 'doMPI', 'EBcoBART', 'ebmc', 'ecocomDP', 'eDITH', 'EFA.dimensions', 'EFAfactors', 'enerscape', 'epidm', 'epizootic', 'equateIRT', 'EthSEQ', 'excel.link', 'eyetools', 'fangs', 'faoutlier', 'filters', 'fingerPro', 'flow', 'fmf', 'FrF2.catlg128', 'GENLIB', 'ggESDA', 'giacR', 'glossa', 'gpuR', 'GTFSwizard', 'gwid', 'habtools', 'hdf5r', 'hdf5r.Extra', 'ieegio', 'imbalanceDatRel', 'intRinsic', 'intSDM', 'jrSiCKLSNMF', 'kazaam', 'KeyboardSimulator', 'lgpr', 'mapping', 'MazamaSpatialPlots', 'MDSGUI', 'medfateland', 'MediaNews', 'Mega2R', 'MetabolomicsBasics', 'midoc', 'minired', 'moc.gapbk', 'ModTools', 'movegroup', 'MPCR', 'nfl4th', 'nflverse', 'noisemodel', 'OpenCL', 'pastclim', 'pbdMPI', 'pbdSLAP', 'pcaL1', 'pgenlibr', 'pheble', 'phonics', 'plotBart', 'pmclust', 'PPRL', 'praatpicture', 'predhy.GUI', 'R2PPT', 'R2wd', 'ravetools', 'Rbeast', 'Rblpapi', 'rblt', 'RcmdrPlugin.cpd', 'RcmdrPlugin.GWRM', 'RcmdrPlugin.TeachStat', 'RcmdrPlugin.WorldFlora', 'Rcplex', 'RcppCWB', 'RcppMeCab', 'readNSx', 'redatamx', 'ReSurv', 'rFUSION', 'riAFTBART', 'RInno', 'rliger', 'rmarchingcubes', 'RmecabKo', 'Rmpi', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROracle', 'Rpoppler', 'RPushbullet', 'RQuantLib', 'rsofun', 'RSP', 'Rsymphony', 'rWCVP', 'RWinEdt', 'SANple', 'sarsop', 'Scalelink', 'scDIFtest', 'secsse', 'sfadv', 'SGPdata', 'sgPLS', 'SGPR', 'sgpv', 'sgr', 'sgraph', 'sgsR', 'sgstar', 'sgt', 'shades', 'shadowr', 'shadowtext', 'shannon', 'ShapDoE', 'shape', 'ShapeChange', 'shapefiles', 'shapeNA', 'ShapePattern', 'shapeR', 'shapes', 'ShapeSelectForest', 'SHAPforxgboost', 'shapley', 'ShapleyOutlier', 'ShapleyValue', 'shapper', 'shapr', 'shapviz', 'shar', 'SharkDemography', 'sharp', 'sharpData', 'SharpeR', 'sharpeRratio', 'sharpPen', 'sharpr2', 'sharpshootR', 'sharx', 'shattering', 'shazam', 'SheetReader', 'SHELF', 'ShellChron', 'shelltrace', 'sherlock', 'SherlockHolmes', 'shidashi', 'shide', 'ShiftConvolvePoibin', 'shiftR'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'doBy', 'DoE.base', 'DoE.wrapper', 'eha', 'FrF2', 'FrF2.catlg128', 'gRbase', 'gRain', 'IDPmisc', 'pbkrtest', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'spdep')); 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, MediaNews: 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 = 'alpine-320'))' backend_options: kubernetes: ### PROD-parallel resources: requests: memory: 14Gi cpu: 3000m limits: memory: 14Gi cpu: 3000m ### PROD-sequential # resources: # requests: # memory: 14Gi # cpu: 2000m # limits: # memory: 14Gi # cpu: 3000m # DEBUG # resources: # requests: # memory: 4Gi # cpu: 2000m # limits: # memory: 4Gi # cpu: 2000m nodeSelector: kubernetes.io/arch: arm64 node.kubernetes.io/instance-type: cax31 tolerations: - key: 'CI' operator: 'Equal' value: 'true' effect: 'NoSchedule'