diff --git a/.woodpecker/build-alpine-320-amd64.yaml b/.woodpecker/build-alpine-320-amd64.yaml index ab7003f..1d40db4 100644 --- a/.woodpecker/build-alpine-320-amd64.yaml +++ b/.woodpecker/build-alpine-320-amd64.yaml @@ -31,23 +31,16 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-alpine-320:/mnt/cache commands: - # 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 - ### 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 + # Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd' - 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('ABACUS', 'abmR', 'abn', 'abstr', 'abstractr', 'acdcR', 'ActCR', 'actel', 'activAnalyzer', 'actxps', 'adapt4pv', 'AdhereRViz', 'AirExposure', 'ajv', 'alcyon', 'AlleleShift', 'almanac', 'alookr', 'amadeus', 'anominate', 'AntMAN', 'APCalign', 'aPCoA', 'apisensr', 'appeears', 'AquaBEHER', 'archive', 'arcpbf', 'arealDB', 'asciicast', 'audrex', 'audubon', 'autoBagging', 'autostats', 'av', 'badgen', 'baguette', 'banter', 'bartCause', 'bartMan', 'base64', 'basemaps', 'bate', 'BayesOrdDesign', 'BayesXsrc', 'bdl', 'BED', 'BeeBDC', 'behaviorchange', 'bfboinet', 'bigGP', 'bigrquerystorage', 'biocompute', 'biopixR', 'BioPred', 'BiplotGUI', 'blackmarbler', 'blatr', 'BoolFilter', 'bpmnR', 'bRacatus', 'brickster', 'brsim', 'BRugs', 'bs4Dash', 'BSTZINB', 'C50', 'CAinterprTools', 'canadamaps', 'CaseBasedReasoning', 'CausalGPS', 'causalHyperGraph', 'causalPAF', 'cbl', 'CCd', 'cellularautomata', 'CensSpatial', 'centerline', 'CERFIT', 'Certara.RsNLME', 'cffr', 'chilemapas', 'chooseGCM', 'CIMTx', 'ClickHouseHTTP', 'clinDataReview', 'clrng', 'clustTMB', 'ClusVis', 'cmprskcoxmsm', 'cohorttools', 'colormap', 'CompositionalRF', 'concaveman', 'conmet', 'conos', 'constrainedKriging', 'conversim', 'CoTiMA', 'countSTAR', 'covalchemy', 'covid19india', 'cppcheckR', 'CRE', 'creditmodel', 'crimeutils', 'crumble', 'cshapes', 'csmpv', 'ctrdata', 'CTRing', 'd4storagehub4R', 'daff', 'dagitty', 'dagwood', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'dartR.sim', 'dartR.spatial', 'datacleanr', 'dataone', 'datapack', 'datasetjson', 'dataspice', 'dbarts', 'dblr', 'ddml', 'DeepLearningCausal', 'dendroNetwork', 'depCensoring', 'DGP4LCF', 'DiagrammeRsvg', 'DICEM', 'diffdfs', 'diffeRenTES', 'DIFM', 'DImodelsVis', 'DIscBIO', 'disclosuR', 'DiSCos', 'disk.frame', 'dismo', 'dispeRse', 'dissever', 'diversitree', 'divraster', 'DMMF', 'do3PCA', 'DoE.wrapper', 'DominoDataR', 'doMPI', 'doolkit', 'doRedis', 'DOT', 'dots', 'DoubleML', 'doublIn', 'downscale', 'dpkg', 'DRHotNet', 'DR.SC', 'DrugSim2DR', 'DRviaSPCN', 'DSAM', 'dsims', 'dsmSearch', 'dssd', 'Dtableone', 'dtComb', 'dti', 'dtrackr', 'DWLS', 'dycdtools', 'dynamAedes', 'dynamicSDM', 'dynatopGIS', 'dynr', 'dySEM', 'DySS', 'easyNCDF', 'easySdcTable', 'EBcoBART', 'ebmc', 'ecdata', 'eCerto', 'ech', 'ecochange', 'ecocomDP', 'ecoCopula', 'econetwork', 'ecopower', 'ecospat', 'edgebundleR', 'ediblecity', 'eDITH', 'eemdARIMA', 'EEMDelm', 'EEMDlstm', 'eemdTDNN', 'EFAfactors', 'EIX', 'emailjsr', 'EmissV', 'emld', 'enerscape', 'ENMTools', 'envi', 'epicmodel', 'epidm', 'epilogi', 'epimdr2', 'EpiSemble', 'epitweetr', 'epiworldRShiny', 'epizootic', 'eSDM', 'eseis', 'espadon', 'EthSEQ', 'ETRep', 'evidence', 'evobiR', 'excel.link', 'eyetools', 'FaaSr', 'facmodTS', 'fangs', 'fanovaGraph', 'fcl', 'fdq', 'FedData', 'fgdr', 'fingerPro', 'finnts', 'fio', 'fishRman', 'florabr', 'fluidsynth', 'fmesher', 'fmf', 'forensIT', 'forestdynR', 'FORTLS', 'foundry', 'FrF2.catlg128', 'FSK2R', 'func2vis', 'galah', 'gbifdb', 'gdtools', 'GeneralisedCovarianceMeasure', 'GENLIB', 'GenoTriplo', 'geocomplexity', 'geodl', 'geodrawr', 'geofi', 'geogenr', 'geoheatmap', 'georob', 'geostan', 'GeoTox', 'GeoWeightedModel', 'geslaR', 'gfer', 'ggESDA', 'ggfacto', 'ggpattern', 'giacR', 'GISTools', 'glossa', 'gmDatabase', 'Goodreader', 'googletraffic', 'gpboost', 'GPCERF', 'gpuR', 'Greymodels', 'GRShiny', 'gsbDesign', 'gsDesign2', 'gtExtras', 'GTFSwizard', 'gto', 'gtreg', 'gwavr', 'gwid', 'GWmodel', 'gwpcormapper', 'GWSDAT', 'habtools', 'HAC', 'handwriterApp', 'handwriterRF', 'hdf5r', 'hdf5r.Extra', 'HDSpatialScan' ); 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'))" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); pkgs = c('ABACUS', 'abmR', 'abn', 'abstr', 'abstractr', 'acdcR', 'ActCR', 'actel', 'activAnalyzer', 'actxps', 'adapt4pv', 'AdhereRViz', 'AirExposure', 'ajv', 'alcyon', 'AlleleShift', 'almanac', 'alookr', 'amadeus', 'anominate', 'AntMAN', 'APCalign', 'aPCoA', 'apisensr', 'appeears', 'AquaBEHER', 'archive', 'arcpbf', 'arealDB', 'asciicast', 'audrex', 'audubon', 'autoBagging', 'autostats', 'av', 'badgen', 'baguette', 'banter', 'bartCause', 'bartMan', 'base64', 'basemaps', 'bate', 'BayesOrdDesign', 'BayesXsrc', 'bdl', 'BED', 'BeeBDC', 'behaviorchange', 'bfboinet', 'bigGP', 'bigrquerystorage', 'biocompute', 'biopixR', 'BioPred', 'BiplotGUI', 'blackmarbler', 'blatr', 'BoolFilter', 'bpmnR', 'bRacatus', 'brickster', 'brsim', 'BRugs', 'bs4Dash', 'BSTZINB', 'C50', 'CAinterprTools', 'canadamaps', 'CaseBasedReasoning', 'CausalGPS', 'causalHyperGraph', 'causalPAF', 'cbl', 'CCd', 'cellularautomata', 'CensSpatial', 'centerline', 'CERFIT', 'Certara.RsNLME', 'cffr', 'chilemapas', 'chooseGCM', 'CIMTx', 'ClickHouseHTTP', 'clinDataReview', 'clrng', 'clustTMB', 'ClusVis', 'cmprskcoxmsm', 'cohorttools', 'colormap', 'CompositionalRF', 'concaveman', 'conmet', 'conos', 'constrainedKriging', 'conversim', 'CoTiMA', 'countSTAR', 'covalchemy', 'covid19india', 'cppcheckR', 'CRE', 'creditmodel', 'crimeutils', 'crumble', 'cshapes', 'csmpv', 'ctrdata', 'CTRing', 'd4storagehub4R', 'daff', 'dagitty', 'dagwood', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'dartR.sim', 'dartR.spatial', 'datacleanr', 'dataone', 'datapack', 'datasetjson', 'dataspice', 'dbarts', 'dblr', 'ddml', 'DeepLearningCausal', 'dendroNetwork', 'depCensoring', 'DGP4LCF', 'DiagrammeRsvg', 'DICEM', 'diffdfs', 'diffeRenTES', 'DIFM', 'DImodelsVis', 'DIscBIO', 'disclosuR', 'DiSCos', 'disk.frame', 'dismo', 'dispeRse', 'dissever', 'diversitree', 'divraster', 'DMMF', 'do3PCA', 'DoE.wrapper', 'DominoDataR', 'doMPI', 'doolkit', 'doRedis', 'DOT', 'dots', 'DoubleML', 'doublIn', 'downscale', 'dpkg', 'DRHotNet', 'DR.SC', 'DrugSim2DR', 'DRviaSPCN', 'DSAM', 'dsims', 'dsmSearch', 'dssd', 'Dtableone', 'dtComb', 'dti', 'dtrackr', 'DWLS', 'dycdtools', 'dynamAedes', 'dynamicSDM', 'dynatopGIS', 'dynr', 'dySEM', 'DySS', 'easyNCDF', 'easySdcTable', 'EBcoBART', 'ebmc', 'ecdata', 'eCerto', 'ech', 'ecochange', 'ecocomDP', 'ecoCopula', 'econetwork', 'ecopower', 'ecospat', 'edgebundleR', 'ediblecity', 'eDITH', 'eemdARIMA', 'EEMDelm', 'EEMDlstm', 'eemdTDNN', 'EFAfactors', 'EIX', 'emailjsr', 'EmissV', 'emld', 'enerscape', 'ENMTools', 'envi', 'epicmodel', 'epidm', 'epilogi', 'epimdr2', 'EpiSemble', 'epitweetr', 'epiworldRShiny', 'epizootic', 'eSDM', 'eseis', 'espadon', 'EthSEQ', 'ETRep', 'evidence', 'evobiR', 'excel.link', 'eyetools', 'FaaSr', 'facmodTS', 'fangs', 'fanovaGraph', 'fcl', 'fdq', 'FedData', 'fgdr', 'fingerPro', 'finnts', 'fio', 'fishRman', 'florabr', 'fluidsynth', 'fmesher', 'fmf', 'forensIT', 'forestdynR', 'FORTLS', 'foundry', 'FrF2.catlg128', 'FSK2R', 'func2vis', 'galah', 'gbifdb', 'gdtools', 'GeneralisedCovarianceMeasure', 'GENLIB', 'GenoTriplo', 'geocomplexity', 'geodl', 'geodrawr', 'geofi', 'geogenr', 'geoheatmap', 'georob', 'geostan', 'GeoTox', 'GeoWeightedModel', 'geslaR', 'gfer', 'ggESDA', 'ggfacto', 'ggpattern', 'giacR', 'GISTools', 'glossa', 'gmDatabase', 'Goodreader', 'googletraffic', 'gpboost', 'GPCERF', 'gpuR', 'Greymodels', 'GRShiny', 'gsbDesign', 'gsDesign2', 'gtExtras', 'GTFSwizard', 'gto', 'gtreg', 'gwavr', 'gwid', 'GWmodel', 'gwpcormapper', 'GWSDAT', 'habtools', 'HAC', 'handwriterApp', 'handwriterRF', 'hdf5r', 'hdf5r.Extra', 'HDSpatialScan' ); 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 diff --git a/.woodpecker/build-alpine-320-arm64.yaml b/.woodpecker/build-alpine-320-arm64.yaml index 61ecd45..b94aa55 100644 --- a/.woodpecker/build-alpine-320-arm64.yaml +++ b/.woodpecker/build-alpine-320-arm64.yaml @@ -13,7 +13,7 @@ steps: image: busybox:latest failure: ignore commands: - # - sleep 300 + - sleep 300 - echo 'Warmed Up' backend_options: kubernetes: @@ -55,18 +55,16 @@ steps: volumes: - arm64-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 - 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); library(dplyr); library(bincraftR); pkgs = c('FrF2', 'FrF2.catlg128', 'gRain', 'gRbase', 'IDPmisc', 'MediaNews', 'pbkrtest', 'psychonetrics', 'PWIR', 'qad', 'qdap', 'QF', 'qlcVisualize', 'qmd', 'qMRI', 'QRAGadget', 'qrencoder', 'qrlabelr', 'QRM', 'qspray', 'qsub', 'qtkit', 'qtlc', 'qtlnet', 'quadmesh', 'quadtree', 'qualmap', 'quantities', 'R2BayesX', 'R2PPT', 'R2wd', 'r4lineups', 'R6causal', 'Racmacs', 'radiant.basics', 'radiant.design', 'radiant.model', 'radiant.multivariate', 'rags2ridges', 'RAINBOWR', 'randomcoloR', 'RandomWalker', 'rangeMapper', 'rangeModelMetadata', 'rapidphylo', 'RAppArmor', 'raptr', 'Raquifer', 'rasterDT', 'rasterKernelEstimates', 'rasterList', 'rasterVis', 'Rata', 'ratematrix', 'RationalMatrix', 'ratioOfQsprays', 'RavenR', 'ravetools', 'rayshader', 'raytracing', 'rbgm', 'rbi', 'rbi.helpers', 'Rblpapi', 'rblt', 'RCA', 'rcaiman', 'Rcatch22', 'rcausim', 'rcccd', 'rccola', 'rcdd', 'RCDT', 'RCGLS', 'RchivalTag', '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', 'rCNV', 'rcontroll', 'RCPA', 'Rcplex', 'RcppBigIntAlgos', 'RcppCWB', 'RcppEnsmallen', 'RcppGSL', 'RcppMeCab', 'RcppZiggurat', 'rcrimeanalysis', 'rcssci', 'RCTrep', 'rdflib', 'RDieHarder', 'RDM', 'rdwplus', 'ReadDIM', 'readNSx', 'rechaRge', 'Recocrop', 'recolorize', 'red', 'redcas', 'redist', 'redistverse', 'redland', 'redlistr', 'redux', 'ref.ICAR', 'refreg', 'regda', 'regrrr', 'Relectoral', 'remote', 'reproj', 'rerddap', 'rerddapXtracto', 'reslife', 'restoptr', 'resultant', 'ReSurv', 'ReviewR', 'revtools', 'Rfast2', 'rflexscan', 'rflsgen', 'RFOC', 'rFUSION', 'RGCxGC', 'RGENERATEPREC', 'rgeopat2', 'rglplus', 'rgplates', 'riAFTBART', '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', 'Rnest', 'rnetcarto', 'RNetCDF', 'RockFab', 'ROCpsych', 'RODBC', 'RODBCDBI', 'ROI.models.miplib', 'ROI.plugin.cplex', 'ROI.plugin.glpk', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROMDB', 'ROracle', 'roseRF', 'rPAex', 'Rpdb', 'RPhosFate', 'RPointCloud', 'Rpoppler', 'rpostgis', 'RProtoBuf', 'RPushbullet', 'rpyANTs', 'rqti', 'Rquake', 'RQuantLib', 'rsat', 'rsi', 'rsocialwatcher', 'RSP', 'rSPARCS', 'RSquaredMI', 'RStoolbox', 'rsvg', 'Rsymphony', 'rtdists', 'rtiktoken', 'RTLknitr', 'rTLsDeep', 'rtmpt', 'rtodoist', 'Rtrack', 'Rtropical', 'rts', 'rtsdata', 'RVAideMemoire', 'rvMF', 'rwc', 'rWCVP', 'RWinEdt', 'RWmisc', 'rworldmap', 'rzmq', 's2dv', 'sabre', 'saeSim', 'saeTrafo', 'SAEval', 'salso', 'samadb', 'samc', 'sampbias', 'SangerTools', 'SANple', 'saotd', 'sara4r', 'sarsop', 'satdad', 'satellite', 'satin', 'SBdecomp', 'sbrl', 'Scalelink', 'SCDA', 'scDIFtest', 'SchoolDataIT', 'scMappR', 'scModels', 'scperturbR', 'scplot', 'SDGdetector', 'SDLfilter', 'sdm', 'sdmpredictors', 'SDMtune', 'sdmvspecies', 'SDPDmod', 'SEAHORS', 'SeaVal', 'secrdesign', 'secrlinear', 'secsse', 'SeedMatchR', 'seewave', 'segen', 'SegEnvIneq', 'SelectBoost', 'SELF', 'SEMdeep', 'SEMgraph', 'semicmprskcoxmsm', 'SemiCompRisks', 'SemiPar.depCens', 'semnar', 'sentiment.ai', 'SenTinMixt', 'sephora', 'sf', 'sfadv', 'sfarrow', 'sfcentral', 'sfdct', 'sfdep', 'sfhotspot', 'sfnetworks', 'sftime', 'sftrack', 'SGPdata', 'sgPLS', 'SGPR', 'sgpv', 'sgr', 'sgraph', 'sgsR', 'sgstar', 'sgt', 'shades', 'shadowr', 'shadowtext', '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', 'ShellChron', 'shelltrace', 'shelter', 'sherlock', 'SherlockHolmes', 'shidashi', 'shide', 'ShiftConvolvePoibin', 'shiftR', 'ShiftShareSE', 'shinipsum', 'shiny.benchmark', 'shiny.blueprint', 'shiny.destroy', 'shiny.emptystate', 'shiny.exe', 'shiny.fluent', 'shiny.i18n', 'shiny.info', 'shiny.pwa', 'shiny.react', 'shiny.reglog', 'shiny.router', 'shiny.semantic', 'shiny.tailwind', 'shiny.telemetry', 'shinyAce', 'shinyaframe', 'shinyalert', 'shinyanimate', 'shinyauthr', 'shinybrms', 'shinybrowser', 'shinyBS', 'shinybusy', 'shinyChakraSlider', 'shinyChakraUI', 'shinyChatR', 'shinyCohortBuilder', 'shinyCox', 'shinycroneditor', 'shinycssloaders', 'shinycustomloader', 'shinyCyJS', 'shinydashboard', 'shinydashboardPlus', 'shinyDatetimePickers', 'shinydbauth', 'shinydisconnect', 'shinydlplot', 'shinyDND', 'shinydrive', 'shinyEffects', 'shinyExprPortal', 'shinyFeedback', 'shinyFiles', 'shinyfilter', 'shinyfullscreen', 'shinyGizmo', 'shinyglide', 'shinyHeatmaply', 'shinyhelper', 'shinyhttr', 'shinyHugePlot', 'shinyInvoice', 'shinyIRT', 'ShinyItemAnalysis', 'shinyjqui', 'shinyjs', 'shinyKGode', 'shinyKnobs', 'shinylight', 'ShinyLink', 'shinyloadtest', 'shinylogs', 'shinyLottie', 'shinyLP', 'shinymanager', 'shinymaterial', 'shinyMatrix', 'shinyMergely', 'shinymeta', 'shinymgr', 'shinyML', 'shinyMobile', 'shinymodels', 'shinyMolBio', 'shinyMonacoEditor', 'shinyNORRRM', 'shinyNotes', 'shinyobjects', 'shinypanel', 'shinypanels', 'shinypivottabler', 'shinyPredict', 'shinyQueryBuilder', 'ShinyQuickStarter', 'shinyquiz', 'shinyRadioMatrix', 'shinyRatings', 'shinyrecipes', 'shinyreforms', 'shinyRGL', 'shinySbm'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'doBy', 'DoE.base', 'DoE.wrapper', 'eha', 'FrF2', 'FrF2.catlg128', 'gRbase', 'gRain', 'IDPmisc', 'pbkrtest')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'alpine-320'))" + # 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('FrF2', 'FrF2.catlg128', 'gRain', 'gRbase', 'IDPmisc', 'MediaNews', 'pbkrtest', 'psychonetrics', 'PWIR', 'qad', 'qdap', 'QF', 'qlcVisualize', 'qmd', 'qMRI', 'QRAGadget', 'qrencoder', 'qrlabelr', 'QRM', 'qspray', 'qsub', 'qtkit', 'qtlc', 'qtlnet', 'quadmesh', 'quadtree', 'qualmap', 'quantities', 'R2BayesX', 'R2PPT', 'R2wd', 'r4lineups', 'R6causal', 'Racmacs', 'radiant.basics', 'radiant.design', 'radiant.model', 'radiant.multivariate', 'rags2ridges', 'RAINBOWR', 'randomcoloR', 'RandomWalker', 'rangeMapper', 'rangeModelMetadata', 'rapidphylo', 'RAppArmor', 'raptr', 'Raquifer', 'rasterDT', 'rasterKernelEstimates', 'rasterList', 'rasterVis', 'Rata', 'ratematrix', 'RationalMatrix', 'ratioOfQsprays', 'RavenR', 'ravetools', 'rayshader', 'raytracing', 'rbgm', 'rbi', 'rbi.helpers', 'Rblpapi', 'rblt', 'RCA', 'rcaiman', 'Rcatch22', 'rcausim', 'rcccd', 'rccola', 'rcdd', 'RCDT', 'RCGLS', 'RchivalTag', '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', 'rCNV', 'rcontroll', 'RCPA', 'Rcplex', 'RcppBigIntAlgos', 'RcppCWB', 'RcppEnsmallen', 'RcppGSL', 'RcppMeCab', 'RcppZiggurat', 'rcrimeanalysis', 'rcssci', 'RCTrep', 'rdflib', 'RDieHarder', 'RDM', 'rdwplus', 'ReadDIM', 'readNSx', 'rechaRge', 'Recocrop', 'recolorize', 'red', 'redcas', 'redist', 'redistverse', 'redland', 'redlistr', 'redux', 'ref.ICAR', 'refreg', 'regda', 'regrrr', 'Relectoral', 'remote', 'reproj', 'rerddap', 'rerddapXtracto', 'reslife', 'restoptr', 'resultant', 'ReSurv', 'ReviewR', 'revtools', 'Rfast2', 'rflexscan', 'rflsgen', 'RFOC', 'rFUSION', 'RGCxGC', 'RGENERATEPREC', 'rgeopat2', 'rglplus', 'rgplates', 'riAFTBART', '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', 'Rnest', 'rnetcarto', 'RNetCDF', 'RockFab', 'ROCpsych', 'RODBC', 'RODBCDBI', 'ROI.models.miplib', 'ROI.plugin.cplex', 'ROI.plugin.glpk', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROMDB', 'ROracle', 'roseRF', 'rPAex', 'Rpdb', 'RPhosFate', 'RPointCloud', 'Rpoppler', 'rpostgis', 'RProtoBuf', 'RPushbullet', 'rpyANTs', 'rqti', 'Rquake', 'RQuantLib', 'rsat', 'rsi', 'rsocialwatcher', 'RSP', 'rSPARCS', 'RSquaredMI', 'RStoolbox', 'rsvg', 'Rsymphony', 'rtdists', 'rtiktoken', 'RTLknitr', 'rTLsDeep', 'rtmpt', 'rtodoist', 'Rtrack', 'Rtropical', 'rts', 'rtsdata', 'RVAideMemoire', 'rvMF', 'rwc', 'rWCVP', 'RWinEdt', 'RWmisc', 'rworldmap', 'rzmq', 's2dv', 'sabre', 'saeSim', 'saeTrafo', 'SAEval', 'salso', 'samadb', 'samc', 'sampbias', 'SangerTools', 'SANple', 'saotd', 'sara4r', 'sarsop', 'satdad', 'satellite', 'satin', 'SBdecomp', 'sbrl', 'Scalelink', 'SCDA', 'scDIFtest', 'SchoolDataIT', 'scMappR', 'scModels', 'scperturbR', 'scplot', 'SDGdetector', 'SDLfilter', 'sdm', 'sdmpredictors', 'SDMtune', 'sdmvspecies', 'SDPDmod', 'SEAHORS', 'SeaVal', 'secrdesign', 'secrlinear', 'secsse', 'SeedMatchR', 'seewave', 'segen', 'SegEnvIneq', 'SelectBoost', 'SELF', 'SEMdeep', 'SEMgraph', 'semicmprskcoxmsm', 'SemiCompRisks', 'SemiPar.depCens', 'semnar', 'sentiment.ai', 'SenTinMixt', 'sephora', 'sf', 'sfadv', 'sfarrow', 'sfcentral', 'sfdct', 'sfdep', 'sfhotspot', 'sfnetworks', 'sftime', 'sftrack', 'SGPdata', 'sgPLS', 'SGPR', 'sgpv', 'sgr', 'sgraph', 'sgsR', 'sgstar', 'sgt', 'shades', 'shadowr', 'shadowtext', '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', 'ShellChron', 'shelltrace', 'shelter', 'sherlock', 'SherlockHolmes', 'shidashi', 'shide', 'ShiftConvolvePoibin', 'shiftR', 'ShiftShareSE', 'shinipsum', 'shiny.benchmark', 'shiny.blueprint', 'shiny.destroy', 'shiny.emptystate', 'shiny.exe', 'shiny.fluent', 'shiny.i18n', 'shiny.info', 'shiny.pwa', 'shiny.react', 'shiny.reglog', 'shiny.router', 'shiny.semantic', 'shiny.tailwind', 'shiny.telemetry', 'shinyAce', 'shinyaframe', 'shinyalert', 'shinyanimate', 'shinyauthr', 'shinybrms', 'shinybrowser', 'shinyBS', 'shinybusy', 'shinyChakraSlider', 'shinyChakraUI', 'shinyChatR', 'shinyCohortBuilder', 'shinyCox', 'shinycroneditor', 'shinycssloaders', 'shinycustomloader', 'shinyCyJS', 'shinydashboard', 'shinydashboardPlus', 'shinyDatetimePickers', 'shinydbauth', 'shinydisconnect', 'shinydlplot', 'shinyDND', 'shinydrive', 'shinyEffects', 'shinyExprPortal', 'shinyFeedback', 'shinyFiles', 'shinyfilter', 'shinyfullscreen', 'shinyGizmo', 'shinyglide', 'shinyHeatmaply', 'shinyhelper', 'shinyhttr', 'shinyHugePlot', 'shinyInvoice', 'shinyIRT', 'ShinyItemAnalysis', 'shinyjqui', 'shinyjs', 'shinyKGode', 'shinyKnobs', 'shinylight', 'ShinyLink', 'shinyloadtest', 'shinylogs', 'shinyLottie', 'shinyLP', 'shinymanager', 'shinymaterial', 'shinyMatrix', 'shinyMergely', 'shinymeta', 'shinymgr', 'shinyML', 'shinyMobile', 'shinymodels', 'shinyMolBio', 'shinyMonacoEditor', 'shinyNORRRM', 'shinyNotes', 'shinyobjects', 'shinypanel', 'shinypanels', 'shinypivottabler', 'shinyPredict', 'shinyQueryBuilder', 'ShinyQuickStarter', 'shinyquiz', 'shinyRadioMatrix', 'shinyRatings', 'shinyrecipes', 'shinyreforms', 'shinyRGL', 'shinySbm'); 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')); 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 diff --git a/.woodpecker/build-redhat-8-amd64.yaml b/.woodpecker/build-redhat-8-amd64.yaml index 4a3a4cb..6bcfdb2 100644 --- a/.woodpecker/build-redhat-8-amd64.yaml +++ b/.woodpecker/build-redhat-8-amd64.yaml @@ -31,8 +31,6 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-redhat-8:/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 @@ -40,14 +38,10 @@ steps: - R -q -e 'pak::meta_update()' - 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 - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/rhel8/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-8', arch == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); pkgs = c('later', 'lazysf', 'lconnect', 'leafem', 'leafpm', 'leafpop', 'leafR', 'leastcostpath', 'leidenbase', 'letsR', 'lgcp', 'lgpr', 'lidaRtRee', 'lidR', 'LipidomicsR', 'LMoFit', 'locpolExpectile', 'loewesadditivity', 'LorMe', 'LPDynR', 'LS2Wstat', 'lucas', 'lwgeom', 'M3', 'MainExistingDatasets', 'malariaAtlas', 'mapboxapi', 'mapchina', 'mapedit', 'MapGAM', 'mapi', 'mapiso', 'mapmixture', 'mapping', 'mapsapi', 'mapscanner', 'mapSpain', 'mapsRinteractive', 'mapStats', 'mapview', 'Markovchart', 'MassWateR', 'mathml', 'matRiks', 'MazamaLocationUtils', 'MazamaSpatialPlots', 'mbr', 'mcradds', 'MDSGUI', 'medfate', 'medfateland', 'MediaNews', 'metaGE', 'metajam', 'meteo', 'meteoland', 'meteospain', 'MetricGraph', 'MetSizeR', 'mfpp', 'mgwrhw', 'micd', 'miceRanger', 'MigConnectivity', 'minired', 'misuvi', 'mixgb', 'mixpoissonreg', 'MLE', 'mlmts', 'MMOC', 'MN', 'moc.gapbk', 'modgo', 'ModTools', 'momentuHMM', 'monographaR', 'MonoPhy', 'morphomap', 'Morphoscape', 'motif', 'move2', 'movecost', 'movegroup', 'mregions2', 'MTA', 'mvcauchy', 'mvcor', 'mvhtests', 'naive', 'nebula', 'negligible', 'neo4jshell', 'nesRdata', 'nestedcv', 'NetFACS', 'NetSci', 'NGBVS', 'NGCHM', 'nlgm', 'nlmixr2', 'nlmixr2plot', 'nmrrr', 'npcurePK', 'oaqc', 'obfuscatoR', 'OpenCL', 'outliers.ts.oga', 'parTimeROC', 'Patterns', 'pbANOVA', 'pcaL1', 'pcds.ugraph', 'pchc', 'PCRA', 'pgKDEsphere', 'phylotypr', 'phylter', 'plumberDeploy', 'PNAR', 'polyhedralCubature', 'popstudy', 'PoweREST', 'PPbigdata', 'ppsbm', 'practicalSigni', 'PRTree', 'qspray', 'qsub', 'QUALYPSO', 'R2PPT', 'R2wd', 'RandomWalker', 'RankAggSIgFUR', 'RAppArmor', 'RationalMatrix', 'ratioOfQsprays', 'ravetools', 'raymolecule', 'rcaiman', 'Rcatch22', 'rcccd', 'rcompanion', 'rcontroll', 'Rcplex', 'RcppCWB', 'RcppMagicEnum', 'rdflib', 'RDM', 'redland', 'regda', 'resultant', 'Rfast2', 'rFUSION', 'RInno', 'rmapzen', 'Rmpi', 'robin', 'RobRegression', 'RODBC', 'ROI.models.globalOptTests', 'ROI.plugin.cplex', 'ROI.plugin.neos', 'ROI.plugin.symphony', 'rollinglda', 'ROracle', 'rotor', 'Rpadrino', 'RPatternJoin', 'RPEGLMEN', 'RPESE', 'RPointCloud', 'Rpoppler', 'rpyANTs', 'RQdeltaCT', 'RQuantLib', 'RRTCS', 'rsat', 'RSAtools', 'RSDK', 'RSquaredMI', 'rStrava', 'Rsymphony', 'rties', 'rTLsDeep', 'Rtropical', 'rvMF', 'RWinEdt', 'segen', 'SEIRfansy', 'SelectBoost', 'sendigR', 'sevenbridges2', 'shinyExprPortal', 'shinylive', 'shinyMixR', 'simDAG', 'smartsnp', 'smvgraph', 'spaceNet', 'sparseCov', 'spaths', 'spectralR', 'spectrino', 'Spectrum', 'ssh', 'SSHAARP', 'surveyvoi', 'symbolicQspray', 'tabxplor', 'tame', 'taskscheduleR', 'theft', 'theftdlc', 'tidyclust', 'TML', 'Toothnroll', 'TreeDimensionTest', 'triptych', 'trtswitch', 'truh', 'TSCI', 'tsgarch', 'tsmarch', 'TSS.RESTREND', 'tssim', 'TTCA', 'TukeyRegion', 'turkeyelections', 'tvgarch', 'tvReg', 'TwitterAutomatedTrading', 'twl', 'TwoArmSurvSim', 'txshift', 'uavRmp', 'UBayFS', 'UCSCXenaShiny', 'ufRisk', 'UnalR', 'unusualprofile', 'upndown', 'UpSetVP', 'upstartr', 'URooTab', 'ursa', 'utile.tables', 'UtilityFrailtyPH12', 'vaccine', 'vachette', 'valhallr', 'validateIt', 'valueSetCompare', 'varjmcm', 'vccp', 'vcr', 'vectorwavelet', 'vetiver', 'vhcub', 'viewpoly', 'viraldomain', 'VIRF', 'VisualDom', 'vivid', 'VLTimeCausality', 'vmeasur', 'voiceR', 'vol2birdR', 'voluModel', 'VOSONDash', 'vscc', 'vsmi', 'VsusP', 'vvauditor', 'vvcanvas', 'vvdoctor', 'W2CWM2C', 'wallace', 'WaveletETS', 'WaveletGBM', 'WaveletKNN', 'WaveletLSTM', 'WaveletMLbestFL', 'WaverideR', 'waves', 'WCluster', 'wdnr.gis', 'wearables', 'weatherOz', 'webglobe', 'webp', 'weed', 'WeibullFit', 'WeibullR.ALT', 'weightedCL', 'weightedGCM', 'weird', 'wiesbaden', 'winch', 'windows.pls', 'worcs', 'WRI', 'wrTopDownFrag', 'WVPlots', 'wyz.code.metaTesting', 'wyz.code.rdoc', 'wyz.code.testthat', 'xdcclarge', 'xega', 'xegaDerivationTrees', 'xegaDfGene', 'xegaGaGene', 'xegaGeGene', 'xegaGpGene', 'xegaPermGene', 'xegaPopulation', 'xhaz', 'xmpdf', 'xslt', 'yhat', 'ypssc', 'zooimage' ); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'later')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'redhat-8'))" + # 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/rhel8/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-8', arch == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); pkgs = c('later', 'lazysf', 'lconnect', 'leafem', 'leafpm', 'leafpop', 'leafR', 'leastcostpath', 'leidenbase', 'letsR', 'lgcp', 'lgpr', 'lidaRtRee', 'lidR', 'LipidomicsR', 'LMoFit', 'locpolExpectile', 'loewesadditivity', 'LorMe', 'LPDynR', 'LS2Wstat', 'lucas', 'lwgeom', 'M3', 'MainExistingDatasets', 'malariaAtlas', 'mapboxapi', 'mapchina', 'mapedit', 'MapGAM', 'mapi', 'mapiso', 'mapmixture', 'mapping', 'mapsapi', 'mapscanner', 'mapSpain', 'mapsRinteractive', 'mapStats', 'mapview', 'Markovchart', 'MassWateR', 'mathml', 'matRiks', 'MazamaLocationUtils', 'MazamaSpatialPlots', 'mbr', 'mcradds', 'MDSGUI', 'medfate', 'medfateland', 'MediaNews', 'metaGE', 'metajam', 'meteo', 'meteoland', 'meteospain', 'MetricGraph', 'MetSizeR', 'mfpp', 'mgwrhw', 'micd', 'miceRanger', 'MigConnectivity', 'minired', 'misuvi', 'mixgb', 'mixpoissonreg', 'MLE', 'mlmts', 'MMOC', 'MN', 'moc.gapbk', 'modgo', 'ModTools', 'momentuHMM', 'monographaR', 'MonoPhy', 'morphomap', 'Morphoscape', 'motif', 'move2', 'movecost', 'movegroup', 'mregions2', 'MTA', 'mvcauchy', 'mvcor', 'mvhtests', 'naive', 'nebula', 'negligible', 'neo4jshell', 'nesRdata', 'nestedcv', 'NetFACS', 'NetSci', 'NGBVS', 'NGCHM', 'nlgm', 'nlmixr2', 'nlmixr2plot', 'nmrrr', 'npcurePK', 'oaqc', 'obfuscatoR', 'OpenCL', 'outliers.ts.oga', 'parTimeROC', 'Patterns', 'pbANOVA', 'pcaL1', 'pcds.ugraph', 'pchc', 'PCRA', 'pgKDEsphere', 'phylotypr', 'phylter', 'plumberDeploy', 'PNAR', 'polyhedralCubature', 'popstudy', 'PoweREST', 'PPbigdata', 'ppsbm', 'practicalSigni', 'PRTree', 'qspray', 'qsub', 'QUALYPSO', 'R2PPT', 'R2wd', 'RandomWalker', 'RankAggSIgFUR', 'RAppArmor', 'RationalMatrix', 'ratioOfQsprays', 'ravetools', 'raymolecule', 'rcaiman', 'Rcatch22', 'rcccd', 'rcompanion', 'rcontroll', 'Rcplex', 'RcppCWB', 'RcppMagicEnum', 'rdflib', 'RDM', 'redland', 'regda', 'resultant', 'Rfast2', 'rFUSION', 'RInno', 'rmapzen', 'Rmpi', 'robin', 'RobRegression', 'RODBC', 'ROI.models.globalOptTests', 'ROI.plugin.cplex', 'ROI.plugin.neos', 'ROI.plugin.symphony', 'rollinglda', 'ROracle', 'rotor', 'Rpadrino', 'RPatternJoin', 'RPEGLMEN', 'RPESE', 'RPointCloud', 'Rpoppler', 'rpyANTs', 'RQdeltaCT', 'RQuantLib', 'RRTCS', 'rsat', 'RSAtools', 'RSDK', 'RSquaredMI', 'rStrava', 'Rsymphony', 'rties', 'rTLsDeep', 'Rtropical', 'rvMF', 'RWinEdt', 'segen', 'SEIRfansy', 'SelectBoost', 'sendigR', 'sevenbridges2', 'shinyExprPortal', 'shinylive', 'shinyMixR', 'simDAG', 'smartsnp', 'smvgraph', 'spaceNet', 'sparseCov', 'spaths', 'spectralR', 'spectrino', 'Spectrum', 'ssh', 'SSHAARP', 'surveyvoi', 'symbolicQspray', 'tabxplor', 'tame', 'taskscheduleR', 'theft', 'theftdlc', 'tidyclust', 'TML', 'Toothnroll', 'TreeDimensionTest', 'triptych', 'trtswitch', 'truh', 'TSCI', 'tsgarch', 'tsmarch', 'TSS.RESTREND', 'tssim', 'TTCA', 'TukeyRegion', 'turkeyelections', 'tvgarch', 'tvReg', 'TwitterAutomatedTrading', 'twl', 'TwoArmSurvSim', 'txshift', 'uavRmp', 'UBayFS', 'UCSCXenaShiny', 'ufRisk', 'UnalR', 'unusualprofile', 'upndown', 'UpSetVP', 'upstartr', 'URooTab', 'ursa', 'utile.tables', 'UtilityFrailtyPH12', 'vaccine', 'vachette', 'valhallr', 'validateIt', 'valueSetCompare', 'varjmcm', 'vccp', 'vcr', 'vectorwavelet', 'vetiver', 'vhcub', 'viewpoly', 'viraldomain', 'VIRF', 'VisualDom', 'vivid', 'VLTimeCausality', 'vmeasur', 'voiceR', 'vol2birdR', 'voluModel', 'VOSONDash', 'vscc', 'vsmi', 'VsusP', 'vvauditor', 'vvcanvas', 'vvdoctor', 'W2CWM2C', 'wallace', 'WaveletETS', 'WaveletGBM', 'WaveletKNN', 'WaveletLSTM', 'WaveletMLbestFL', 'WaverideR', 'waves', 'WCluster', 'wdnr.gis', 'wearables', 'weatherOz', 'webglobe', 'webp', 'weed', 'WeibullFit', 'WeibullR.ALT', 'weightedCL', 'weightedGCM', 'weird', 'wiesbaden', 'winch', 'windows.pls', 'worcs', 'WRI', 'wrTopDownFrag', 'WVPlots', 'wyz.code.metaTesting', 'wyz.code.rdoc', 'wyz.code.testthat', 'xdcclarge', 'xega', 'xegaDerivationTrees', 'xegaDfGene', 'xegaGaGene', 'xegaGeGene', 'xegaGpGene', 'xegaPermGene', 'xegaPopulation', 'xhaz', 'xmpdf', 'xslt', 'yhat', 'ypssc', 'zooimage' ); 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-8'))" ### 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 diff --git a/.woodpecker/build-redhat-8-arm64.yaml b/.woodpecker/build-redhat-8-arm64.yaml index b18d10b..54f36bf 100644 --- a/.woodpecker/build-redhat-8-arm64.yaml +++ b/.woodpecker/build-redhat-8-arm64.yaml @@ -55,22 +55,15 @@ steps: volumes: - arm64-binaries-r-dep-cache-redhat-8:/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 - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/arm64/rhel8/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-8', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('excel.link', 'facmodTS', 'fastFMM', 'FIESTA', 'FIESTAutils', 'filters', 'finch', 'fitbitViz', 'fitlandr', 'forestdata', 'FORTLS', 'FPCdpca', 'frscore', 'fsbrain', 'fsn', 'FTSgof', 'FuzzyImputationTest', 'geoidep', 'geojson', 'geojsonio', 'geppe', 'gerbil', 'ggfacto', 'ggpicrust2', 'glmtoolbox', 'googletraffic', 'gp', 'gpg', 'gpuR', 'handwriterApp', 'handwriterRF', 'HDiR', 'highd2means', 'hillshader', 'HLAtools', 'hypergeo2', 'imbalanceDatRel', 'IMIFA', 'InteRD', 'interpolation', 'irtQ', 'jack', 'kDGLM', 'KeyboardSimulator', 'KMD', 'KPC', 'KSgeneral', 'lgpr', 'LipidomicsR', 'LorMe', 'mapping', 'mathml', 'matRiks', 'mbr', 'mcradds', 'MDSGUI', 'MediaNews', 'mergedblocks', 'metaGE', 'metajam', 'meteo', 'MetSizeR', 'mfpp', 'micd', 'miceRanger', 'minired', 'mixgb', 'mixpoissonreg', 'MLE', 'mlmts', 'MMOC', 'MN', 'moc.gapbk', 'modgo', 'ModTools', 'MonoPhy', 'morphomap', 'mregions2', 'multibiplotGUI', 'mvcauchy', 'mvcor', 'mvhtests', 'naive', 'nebula', 'negligible', 'neo4jshell', 'nesRdata', 'nestedcv', 'NetFACS', 'NetSci', 'nflverse', 'NGBVS', 'NGCHM', 'nlgm', 'nlmixr2', 'nlmixr2plot', 'nmrrr', 'npcurePK', 'obfuscatoR', 'OpenCL', 'parTimeROC', 'Patterns', 'pbANOVA', 'pcaL1', 'pcds.ugraph', 'pchc', 'PCRA', 'pgKDEsphere', 'phylotypr', 'phylter', 'plumberDeploy', 'PNAR', 'polyhedralCubature', 'popstudy', 'PoweREST', 'PPbigdata', 'ppsbm', 'praatpicture', 'practicalSigni', 'PRTree', 'qspray', 'qsub', 'QUALYPSO', 'R2PPT', 'R2wd', 'Racmacs', 'RandomWalker', 'RankAggSIgFUR', 'RAppArmor', 'RationalMatrix', 'ratioOfQsprays', 'ravetools', 'raymolecule', 'Rblpapi', 'Rcatch22', 'rcccd', 'rcompanion', 'rcontroll', 'Rcplex', 'RcppCWB', 'RcppMagicEnum', 'rdflib', 'Rdimtools', 'RDM', 'redland', 'regda', 'resultant', 'Rfast2', 'rFUSION', 'Riemann', 'RInno', 'rmapzen', 'rmarchingcubes', 'RmecabKo', 'Rmpi', 'robin', 'RobRegression', 'robustarima', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROracle', 'RPatternJoin', 'RQuantLib', 'RSP', 'RSquaredMI', 'rStrava', 'Rsymphony', 'rties', 'Rtropical', 'rvMF', 'RWinEdt', 'satdad', 'scDIFtest', 'scMappR', 'segen', 'SEIRfansy', 'SelectBoost', 'SEMdeep', 'sendigR', 'seq2R', 'sevenbridges2', 'SherlockHolmes', 'shiny.benchmark', 'shinyExprPortal', 'shinyIRT', 'shinylive', 'shinyMixR', 'shinyQueryBuilder', 'shinytest2', 'shrinkTVPVAR', 'SIAmodules', 'simCAT', 'simDAG', 'SimNPH', 'smartsnp', 'smcryptoR', 'smvgraph', 'SOMMD', 'SpaCCI', 'spaceNet', 'sparseCov', 'spaths', 'spectralR', 'Spectran', 'spectrino', 'Spectrum', 'splusTimeSeries', 'spStack', 'ssh', 'SSHAARP', 'stppSim', 'surveyvoi', 'symbolicQspray', 'T4cluster', 'tabxplor', 'tame', 'taskscheduleR', 'TDAkit', 'theft', 'theftdlc', 'tidyclust', 'tiledb', 'TML', 'Toothnroll', 'TreeDimensionTest', 'triptych', 'trtswitch', 'truh', 'TSCI', 'tsmarch', 'tspredit', 'twl', 'UBayFS', 'valhallr', 'voiceR', 'vvdoctor', 'WaverideR', 'WCluster', 'webglobe', 'WRI'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'redhat-8'))" + # 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/arm64/rhel8/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-8', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('excel.link', 'facmodTS', 'fastFMM', 'FIESTA', 'FIESTAutils', 'filters', 'finch', 'fitbitViz', 'fitlandr', 'forestdata', 'FORTLS', 'FPCdpca', 'frscore', 'fsbrain', 'fsn', 'FTSgof', 'FuzzyImputationTest', 'geoidep', 'geojson', 'geojsonio', 'geppe', 'gerbil', 'ggfacto', 'ggpicrust2', 'glmtoolbox', 'googletraffic', 'gp', 'gpg', 'gpuR', 'handwriterApp', 'handwriterRF', 'HDiR', 'highd2means', 'hillshader', 'HLAtools', 'hypergeo2', 'imbalanceDatRel', 'IMIFA', 'InteRD', 'interpolation', 'irtQ', 'jack', 'kDGLM', 'KeyboardSimulator', 'KMD', 'KPC', 'KSgeneral', 'lgpr', 'LipidomicsR', 'LorMe', 'mapping', 'mathml', 'matRiks', 'mbr', 'mcradds', 'MDSGUI', 'MediaNews', 'mergedblocks', 'metaGE', 'metajam', 'meteo', 'MetSizeR', 'mfpp', 'micd', 'miceRanger', 'minired', 'mixgb', 'mixpoissonreg', 'MLE', 'mlmts', 'MMOC', 'MN', 'moc.gapbk', 'modgo', 'ModTools', 'MonoPhy', 'morphomap', 'mregions2', 'multibiplotGUI', 'mvcauchy', 'mvcor', 'mvhtests', 'naive', 'nebula', 'negligible', 'neo4jshell', 'nesRdata', 'nestedcv', 'NetFACS', 'NetSci', 'nflverse', 'NGBVS', 'NGCHM', 'nlgm', 'nlmixr2', 'nlmixr2plot', 'nmrrr', 'npcurePK', 'obfuscatoR', 'OpenCL', 'parTimeROC', 'Patterns', 'pbANOVA', 'pcaL1', 'pcds.ugraph', 'pchc', 'PCRA', 'pgKDEsphere', 'phylotypr', 'phylter', 'plumberDeploy', 'PNAR', 'polyhedralCubature', 'popstudy', 'PoweREST', 'PPbigdata', 'ppsbm', 'praatpicture', 'practicalSigni', 'PRTree', 'qspray', 'qsub', 'QUALYPSO', 'R2PPT', 'R2wd', 'Racmacs', 'RandomWalker', 'RankAggSIgFUR', 'RAppArmor', 'RationalMatrix', 'ratioOfQsprays', 'ravetools', 'raymolecule', 'Rblpapi', 'Rcatch22', 'rcccd', 'rcompanion', 'rcontroll', 'Rcplex', 'RcppCWB', 'RcppMagicEnum', 'rdflib', 'Rdimtools', 'RDM', 'redland', 'regda', 'resultant', 'Rfast2', 'rFUSION', 'Riemann', 'RInno', 'rmapzen', 'rmarchingcubes', 'RmecabKo', 'Rmpi', 'robin', 'RobRegression', 'robustarima', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROracle', 'RPatternJoin', 'RQuantLib', 'RSP', 'RSquaredMI', 'rStrava', 'Rsymphony', 'rties', 'Rtropical', 'rvMF', 'RWinEdt', 'satdad', 'scDIFtest', 'scMappR', 'segen', 'SEIRfansy', 'SelectBoost', 'SEMdeep', 'sendigR', 'seq2R', 'sevenbridges2', 'SherlockHolmes', 'shiny.benchmark', 'shinyExprPortal', 'shinyIRT', 'shinylive', 'shinyMixR', 'shinyQueryBuilder', 'shinytest2', 'shrinkTVPVAR', 'SIAmodules', 'simCAT', 'simDAG', 'SimNPH', 'smartsnp', 'smcryptoR', 'smvgraph', 'SOMMD', 'SpaCCI', 'spaceNet', 'sparseCov', 'spaths', 'spectralR', 'Spectran', 'spectrino', 'Spectrum', 'splusTimeSeries', 'spStack', 'ssh', 'SSHAARP', 'stppSim', 'surveyvoi', 'symbolicQspray', 'T4cluster', 'tabxplor', 'tame', 'taskscheduleR', 'TDAkit', 'theft', 'theftdlc', 'tidyclust', 'tiledb', 'TML', 'Toothnroll', 'TreeDimensionTest', 'triptych', 'trtswitch', 'truh', 'TSCI', 'tsmarch', 'tspredit', 'twl', 'UBayFS', 'valhallr', 'voiceR', 'vvdoctor', 'WaverideR', 'WCluster', 'webglobe', 'WRI'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', '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-8'))" ### 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 diff --git a/.woodpecker/build-redhat-9-amd64.yaml b/.woodpecker/build-redhat-9-amd64.yaml index a5e5e4f..e281026 100644 --- a/.woodpecker/build-redhat-9-amd64.yaml +++ b/.woodpecker/build-redhat-9-amd64.yaml @@ -9,30 +9,6 @@ when: 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: 2000m - # limits: - # memory: 14Gi - # cpu: 2000m - # nodeSelector: - # kubernetes.io/arch: amd64 - # node.kubernetes.io/instance-type: ccx23 - # 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/amd64-binaries-r-redhat-9 @@ -54,22 +30,15 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-redhat-9:/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 - - 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')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'redhat-9'))" + # 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 @@ -103,7 +72,6 @@ steps: # - 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: - ### PROD-parallel resources: requests: memory: 5Gi @@ -111,22 +79,6 @@ steps: limits: memory: 20Gi 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: amd64 node.kubernetes.io/instance-type: AX42 diff --git a/.woodpecker/build-redhat-9-arm64.yaml b/.woodpecker/build-redhat-9-arm64.yaml index c6b48ec..356598a 100644 --- a/.woodpecker/build-redhat-9-arm64.yaml +++ b/.woodpecker/build-redhat-9-arm64.yaml @@ -55,22 +55,15 @@ steps: volumes: - arm64-binaries-r-dep-cache-redhat-9:/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 - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/arm64/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 == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('bnRep', 'bootwar', 'BoundaryStats', 'bratteli', 'CAESAR.Suite', 'calendRio', 'camcorder', 'carbonate', 'Cascade', 'cdcatR', 'cdmTools', 'CEDA', 'cheem', 'christmas', 'chronochrt', 'clarabel', 'clustermole', 'CohortGenerator', 'colocr', 'colorizer', 'compositeReliabilityInNestedDesigns', 'conmet', 'conversim', 'CopSens', 'coveR2', 'coxphm', 'cropcircles', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'dartR.sim', 'dartR.spatial', 'databraryr', 'datacleanr', 'EDCimport', 'leidenbase', 'MediaNews', 'MonoPhy', 'nesRdata', 'NGCHM', 'OpenCL', 'paleopop', 'Path.Analysis', 'Patterns', 'pcaL1', 'PCRA', 'ph2bye', 'pikchr', 'R2PPT', 'R2wd', 'Racmacs', 'RAppArmor', 'ravetools', 'Rblpapi', 'Rcatch22', 'Rcplex', 'RcppCWB', 'rdflib', 'redland', 'rFUSION', 'RInno', 'rmarchingcubes', 'RmecabKo', 'Rmpi', 'RobustPrediction', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROracle', 'RQuantLib', 'Rsymphony', 'RWinEdt', 'shinyMixR', 'sivirep', 'spectrino', 'surveyvoi', 'taskscheduleR', 'TFM', 'theft', 'theftdlc', 'tiledb', 'traineR', 'trtswitch', 'TukeyRegion', 'ursa', 'VecDep', 'visvaR'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'redhat-9'))" + # 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/arm64/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 == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('bnRep', 'bootwar', 'BoundaryStats', 'bratteli', 'CAESAR.Suite', 'calendRio', 'camcorder', 'carbonate', 'Cascade', 'cdcatR', 'cdmTools', 'CEDA', 'cheem', 'christmas', 'chronochrt', 'clarabel', 'clustermole', 'CohortGenerator', 'colocr', 'colorizer', 'compositeReliabilityInNestedDesigns', 'conmet', 'conversim', 'CopSens', 'coveR2', 'coxphm', 'cropcircles', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'dartR.sim', 'dartR.spatial', 'databraryr', 'datacleanr', 'EDCimport', 'leidenbase', 'MediaNews', 'MonoPhy', 'nesRdata', 'NGCHM', 'OpenCL', 'paleopop', 'Path.Analysis', 'Patterns', 'pcaL1', 'PCRA', 'ph2bye', 'pikchr', 'R2PPT', 'R2wd', 'Racmacs', 'RAppArmor', 'ravetools', 'Rblpapi', 'Rcatch22', 'Rcplex', 'RcppCWB', 'rdflib', 'redland', 'rFUSION', 'RInno', 'rmarchingcubes', 'RmecabKo', 'Rmpi', 'RobustPrediction', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROracle', 'RQuantLib', 'Rsymphony', 'RWinEdt', 'shinyMixR', 'sivirep', 'spectrino', 'surveyvoi', 'taskscheduleR', 'TFM', 'theft', 'theftdlc', 'tiledb', 'traineR', 'trtswitch', 'TukeyRegion', 'ursa', 'VecDep', 'visvaR'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', '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 @@ -104,7 +97,6 @@ steps: # - 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 = "arm64"))' backend_options: kubernetes: - ### PROD-parallel resources: requests: memory: 14Gi diff --git a/.woodpecker/build-ubuntu-2204-amd64.yaml b/.woodpecker/build-ubuntu-2204-amd64.yaml index 980183c..5bdc95a 100644 --- a/.woodpecker/build-ubuntu-2204-amd64.yaml +++ b/.woodpecker/build-ubuntu-2204-amd64.yaml @@ -1,6 +1,6 @@ when: - # - event: manual - # evaluate: 'build == "all"' + - event: manual + evaluate: 'build == "all"' - event: manual evaluate: 'build == "ubuntu-2204-amd64"' - event: manual @@ -31,7 +31,6 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-ubuntu-2204:/mnt/cache commands: - # 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 @@ -39,11 +38,8 @@ steps: - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'packageVersion("bincraftR")' - ### 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 - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(CRAN = 'https://cran.devxy.io/amd64/jammy/latest'))); pkgs = c('BiplotGUI', 'KeyboardSimulator', 'MDSGUI', 'R2PPT', 'R2wd', 'RWinEdt', 'Rveg', 'blatr', 'excel.link', 'leidenbase', 'mpathr', 'spectrino', 'taskscheduleR'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'CoTiMA', 'later')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'ubuntu-2204'))" + # 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))); pkgs = c('BiplotGUI', 'KeyboardSimulator', 'MDSGUI', 'R2PPT', 'R2wd', 'RWinEdt', 'Rveg', 'blatr', 'excel.link', 'leidenbase', 'mpathr', 'spectrino', 'taskscheduleR'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'CoTiMA', '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 = 'ubuntu-2204'))" ### 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 @@ -77,7 +73,6 @@ steps: # - 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: - ### PROD-parallel resources: requests: memory: 5Gi @@ -85,22 +80,6 @@ steps: limits: memory: 20Gi 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: amd64 node.kubernetes.io/instance-type: AX42 diff --git a/.woodpecker/build-ubuntu-2204-arm64.yaml b/.woodpecker/build-ubuntu-2204-arm64.yaml index 7350929..19f3c13 100644 --- a/.woodpecker/build-ubuntu-2204-arm64.yaml +++ b/.woodpecker/build-ubuntu-2204-arm64.yaml @@ -55,22 +55,15 @@ steps: volumes: - arm64-binaries-r-dep-cache-ubuntu-2204:/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 /mnt/cache/R-pkgs/gert # 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 - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/arm64/jammy/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 == 'ubuntu-2204', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('compositeReliabilityInNestedDesigns', 'conversim', 'coxphm', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'diathor', 'DIFshiny', 'do3PCA', 'GeoThinneR', 'leidenbase', 'literanger', 'MediaNews', 'oaqc', 'Rcatch22', 'RcppCWB', 'rFUSION', 'RInno', 'rmarchingcubes', 'RmecabKo', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROracle', 'RSP', 'RWinEdt', 'rworkflows', 'scDIFtest', 'shiny.benchmark', 'shinyIRT', 'shinytest2', 'SIAmodules', 'simCAT', 'SimNPH', 'spectrino', 'taskscheduleR', 'theft', 'theftdlc', 'tiledb', 'trtswitch', 'ursa'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'ubuntu-2204'))" + # 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/arm64/jammy/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 == 'ubuntu-2204', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('compositeReliabilityInNestedDesigns', 'conversim', 'coxphm', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'diathor', 'DIFshiny', 'do3PCA', 'GeoThinneR', 'leidenbase', 'literanger', 'MediaNews', 'oaqc', 'Rcatch22', 'RcppCWB', 'rFUSION', 'RInno', 'rmarchingcubes', 'RmecabKo', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROracle', 'RSP', 'RWinEdt', 'rworkflows', 'scDIFtest', 'shiny.benchmark', 'shinyIRT', 'shinytest2', 'SIAmodules', 'simCAT', 'SimNPH', 'spectrino', 'taskscheduleR', 'theft', 'theftdlc', 'tiledb', 'trtswitch', 'ursa'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', '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 = 'ubuntu-2204'))" ### 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 @@ -104,7 +97,6 @@ steps: # - 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 = "arm64"))' backend_options: kubernetes: - ### PROD-parallel resources: requests: memory: 14Gi @@ -112,22 +104,6 @@ steps: 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 diff --git a/.woodpecker/build-ubuntu-2404-amd64.yaml b/.woodpecker/build-ubuntu-2404-amd64.yaml index 20f5b06..ce6f849 100644 --- a/.woodpecker/build-ubuntu-2404-amd64.yaml +++ b/.woodpecker/build-ubuntu-2404-amd64.yaml @@ -1,6 +1,6 @@ when: - # - event: manual - # evaluate: 'build == "all"' + - event: manual + evaluate: 'build == "all"' - event: manual evaluate: 'build == "ubuntu-2404-amd64"' - event: manual @@ -31,22 +31,15 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-ubuntu-2404:/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 - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/noble/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 == 'ubuntu-2404', arch == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('CoTiMA', 'later', 'leidenbase', 'lgpr', 'literanger', 'MDSGUI', 'MediaNews', 'MonoPhy', 'MPCR', 'oaqc', 'ondisc', 'R2PPT', 'R2wd', 'ravetools', 'Rcatch22', 'Rcplex', 'RcppCWB', 'rFUSION', 'RInno', 'rmarchingcubes', 'RmecabKo', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROracle', 'Rsymphony', 'RWinEdt', 'rworkflows', 'SegEnvIneq', 'skedastic', 'spectrino', 'taskscheduleR', 'TaxaNorm', 'theft', 'theftdlc', 'trtswitch', 'ursa', 'verbaliseR'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'CoTiMA', 'later')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'ubuntu-2404'))" + # 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/noble/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 == 'ubuntu-2404', arch == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('CoTiMA', 'later', 'leidenbase', 'lgpr', 'literanger', 'MDSGUI', 'MediaNews', 'MonoPhy', 'MPCR', 'oaqc', 'ondisc', 'R2PPT', 'R2wd', 'ravetools', 'Rcatch22', 'Rcplex', 'RcppCWB', 'rFUSION', 'RInno', 'rmarchingcubes', 'RmecabKo', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROracle', 'Rsymphony', 'RWinEdt', 'rworkflows', 'SegEnvIneq', 'skedastic', 'spectrino', 'taskscheduleR', 'TaxaNorm', 'theft', 'theftdlc', 'trtswitch', 'ursa', 'verbaliseR'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'CoTiMA', '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 = 'ubuntu-2404'))" ### 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 @@ -80,7 +73,6 @@ steps: # - 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: - ### PROD-parallel resources: requests: memory: 5Gi @@ -88,22 +80,6 @@ steps: limits: memory: 20Gi 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: amd64 node.kubernetes.io/instance-type: AX42 diff --git a/.woodpecker/build-ubuntu-2404-arm64.yaml b/.woodpecker/build-ubuntu-2404-arm64.yaml index c738b59..4a32f86 100644 --- a/.woodpecker/build-ubuntu-2404-arm64.yaml +++ b/.woodpecker/build-ubuntu-2404-arm64.yaml @@ -55,22 +55,15 @@ steps: volumes: - arm64-binaries-r-dep-cache-ubuntu-2404:/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 - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/arm64/noble/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 == 'ubuntu-2404', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('BoundaryStats', 'Colossus', 'compositeReliabilityInNestedDesigns', 'conversim', 'coxphm', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'diathor', 'DIFshiny', 'leidenbase', 'MediaNews', 'MonoPhy', 'oaqc', 'Rcatch22', 'RInno', 'rmarchingcubes', 'RmecabKo', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROracle', 'RSP', 'scDIFtest', 'shiny.benchmark', 'shinyIRT', 'shinytest2', 'SIAmodules', 'simCAT', 'SimNPH', 'theft', 'theftdlc', 'trtswitch', 'ursa'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'ubuntu-2404'))" + # 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/arm64/noble/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 == 'ubuntu-2404', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('BoundaryStats', 'Colossus', 'compositeReliabilityInNestedDesigns', 'conversim', 'coxphm', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'diathor', 'DIFshiny', 'leidenbase', 'MediaNews', 'MonoPhy', 'oaqc', 'Rcatch22', 'RInno', 'rmarchingcubes', 'RmecabKo', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROracle', 'RSP', 'scDIFtest', 'shiny.benchmark', 'shinyIRT', 'shinytest2', 'SIAmodules', 'simCAT', 'SimNPH', 'theft', 'theftdlc', 'trtswitch', 'ursa'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', '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 = 'ubuntu-2404'))" ### 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 @@ -104,7 +97,6 @@ steps: # - 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 = "arm64"))' backend_options: kubernetes: - ### PROD-parallel resources: requests: memory: 14Gi diff --git a/.woodpecker/process-updates-alpine-320-amd64.yaml b/.woodpecker/process-updates-alpine-320-amd64.yaml index 95a24cd..832caf2 100644 --- a/.woodpecker/process-updates-alpine-320-amd64.yaml +++ b/.woodpecker/process-updates-alpine-320-amd64.yaml @@ -27,7 +27,6 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-alpine-320:/mnt/cache commands: - # download latest package version (avoid having to rebuild image every time) - 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-RPostgres # for some reason paks pkgcache is often corrupt @@ -35,12 +34,10 @@ steps: - 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 - # 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 # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'alpine-320', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); bincraftR::process_cran_updates(interval = $INTERVAL, platform = 'alpine-320', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: - ### PROD resources: requests: memory: 18Gi diff --git a/.woodpecker/process-updates-alpine-320-arm64.yaml b/.woodpecker/process-updates-alpine-320-arm64.yaml index a79081b..d51f306 100644 --- a/.woodpecker/process-updates-alpine-320-arm64.yaml +++ b/.woodpecker/process-updates-alpine-320-arm64.yaml @@ -53,7 +53,6 @@ steps: volumes: - arm64-binaries-r-dep-cache-alpine-320:/mnt/cache commands: - # download latest package version (avoid having to rebuild image every time) - 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-RPostgres # for some reason paks pkgcache is often corrupt @@ -61,9 +60,8 @@ steps: - 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 - # 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 # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'alpine-320', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); bincraftR::process_cran_updates(interval = $INTERVAL, platform = 'alpine-320', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: ### PROD diff --git a/.woodpecker/process-updates-redhat-8-amd64.yaml b/.woodpecker/process-updates-redhat-8-amd64.yaml index 35ee198..b6d31b1 100644 --- a/.woodpecker/process-updates-redhat-8-amd64.yaml +++ b/.woodpecker/process-updates-redhat-8-amd64.yaml @@ -9,30 +9,6 @@ when: skip_clone: true steps: - # - name: 'Warming up' - # image: busybox:latest - # failure: ignore - # commands: - # - sleep 300 - # - echo "Warmed Up" - # backend_options: - # kubernetes: - # resources: - # requests: - # memory: 18Gi - # cpu: 3000m - # limits: - # memory: 18Gi - # cpu: 3000m - # nodeSelector: - # kubernetes.io/arch: amd64 - # node.kubernetes.io/instance-type: AX42 - # tolerations: - # - key: 'CI' - # operator: 'Equal' - # value: 'true' - # effect: 'NoSchedule' - - name: 'Processing Updates' 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-8 @@ -46,14 +22,11 @@ steps: PLATFORM: redhat-8 ARCH: amd64 NCPUS: 2 - # MEMORY: 18Gi STRATEGY: sequential - # INSTANCE_TYPE: cpx41 INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3) # volumes: # - amd64-binaries-r-dep-cache-redhat-8:/mnt/cache commands: - # download latest package version (avoid having to rebuild image every time) - 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-RPostgres # for some reason paks pkgcache is often corrupt @@ -62,12 +35,10 @@ steps: - 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 - # 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 # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); bincraftR::process_cran_updates(interval = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: - ### PROD resources: requests: memory: 18Gi diff --git a/.woodpecker/process-updates-redhat-9-amd64.yaml b/.woodpecker/process-updates-redhat-9-amd64.yaml index 524a50e..434cd1b 100644 --- a/.woodpecker/process-updates-redhat-9-amd64.yaml +++ b/.woodpecker/process-updates-redhat-9-amd64.yaml @@ -28,7 +28,6 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-redhat-9:/mnt/cache commands: - # download latest package version (avoid having to rebuild image every time) - 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-RPostgres # for some reason paks pkgcache is often corrupt @@ -36,12 +35,10 @@ steps: - 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 - # 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 # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); bincraftR::process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: - ### PROD resources: requests: memory: 18Gi diff --git a/.woodpecker/process-updates-redhat-9-arm64.yaml b/.woodpecker/process-updates-redhat-9-arm64.yaml index d31972d..e799787 100644 --- a/.woodpecker/process-updates-redhat-9-arm64.yaml +++ b/.woodpecker/process-updates-redhat-9-arm64.yaml @@ -53,7 +53,6 @@ steps: volumes: - arm64-binaries-r-dep-cache-redhat-9:/mnt/cache commands: - # download latest package version (avoid having to rebuild image every time) - 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-RPostgres # for some reason paks pkgcache is often corrupt @@ -61,12 +60,10 @@ steps: - 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 - # 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 # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); bincraftR::process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: - ### PROD resources: requests: memory: 14Gi @@ -74,14 +71,6 @@ steps: 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 diff --git a/.woodpecker/process-updates-ubuntu-2204-amd64.yaml b/.woodpecker/process-updates-ubuntu-2204-amd64.yaml index bd27498..50d0c84 100644 --- a/.woodpecker/process-updates-ubuntu-2204-amd64.yaml +++ b/.woodpecker/process-updates-ubuntu-2204-amd64.yaml @@ -24,12 +24,10 @@ steps: NCPUS: 2 MEMORY: 18Gi STRATEGY: sequential - # INSTANCE_TYPE: ccx23 INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3) # volumes: # - amd64-binaries-r-dep-cache-ubuntu-2204:/mnt/cache commands: - # download latest package version (avoid having to rebuild image every time) - 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-RPostgres # for some reason paks pkgcache is often corrupt @@ -37,12 +35,10 @@ steps: - 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 - # 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 # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); bincraftR::process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: - ### PROD resources: requests: memory: 18Gi diff --git a/.woodpecker/process-updates-ubuntu-2404-amd64.yaml b/.woodpecker/process-updates-ubuntu-2404-amd64.yaml index fe33273..b4b1798 100644 --- a/.woodpecker/process-updates-ubuntu-2404-amd64.yaml +++ b/.woodpecker/process-updates-ubuntu-2404-amd64.yaml @@ -27,7 +27,6 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-ubuntu-2404:/mnt/cache commands: - # download latest package version (avoid having to rebuild image every time) - 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-RPostgres # for some reason paks pkgcache is often corrupt @@ -35,12 +34,10 @@ steps: - 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 - # 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 # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); bincraftR::process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: - ### PROD resources: requests: memory: 18Gi diff --git a/.woodpecker/update-package-index-alpine-320-amd64.yaml b/.woodpecker/update-package-index-alpine-320-amd64.yaml index 5ba6062..6d06672 100644 --- a/.woodpecker/update-package-index-alpine-320-amd64.yaml +++ b/.woodpecker/update-package-index-alpine-320-amd64.yaml @@ -21,14 +21,12 @@ steps: 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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'packageVersion("bincraftR")' - cd /mnt/cache/packages - - R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession", workers = future::availableCores()); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()' + - R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession", workers = 4); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()' backend_options: kubernetes: resources: diff --git a/.woodpecker/update-package-index-alpine-320-arm64.yaml b/.woodpecker/update-package-index-alpine-320-arm64.yaml index a655216..5c40cb4 100644 --- a/.woodpecker/update-package-index-alpine-320-arm64.yaml +++ b/.woodpecker/update-package-index-alpine-320-arm64.yaml @@ -21,8 +21,6 @@ steps: volumes: - arm64-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:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . - rm -rf /mnt/cache/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' diff --git a/.woodpecker/update-package-index-redhat-8-amd64.yaml b/.woodpecker/update-package-index-redhat-8-amd64.yaml index 8ac5e82..b8c7fdb 100644 --- a/.woodpecker/update-package-index-redhat-8-amd64.yaml +++ b/.woodpecker/update-package-index-redhat-8-amd64.yaml @@ -21,8 +21,6 @@ steps: volumes: - amd64-binaries-r-dep-cache-redhat-8:/mnt/cache commands: - # download latest package version (avoid having to rebuild image every time) - # rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169 - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . - rm -rf /mnt/cache/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' diff --git a/.woodpecker/update-package-index-redhat-8-arm64.yaml b/.woodpecker/update-package-index-redhat-8-arm64.yaml index 628eaec..ca2794f 100644 --- a/.woodpecker/update-package-index-redhat-8-arm64.yaml +++ b/.woodpecker/update-package-index-redhat-8-arm64.yaml @@ -21,8 +21,6 @@ steps: volumes: - arm64-binaries-r-dep-cache-redhat-8:/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:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . - rm -rf /mnt/cache/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' diff --git a/.woodpecker/update-package-index-redhat-9-amd64.yaml b/.woodpecker/update-package-index-redhat-9-amd64.yaml index 2e19851..7456d83 100644 --- a/.woodpecker/update-package-index-redhat-9-amd64.yaml +++ b/.woodpecker/update-package-index-redhat-9-amd64.yaml @@ -21,8 +21,6 @@ steps: volumes: - amd64-binaries-r-dep-cache-redhat-9:/mnt/cache commands: - # download latest package version (avoid having to rebuild image every time) - # rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169 - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . - rm -rf /mnt/cache/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' diff --git a/.woodpecker/update-package-index-redhat-9-arm64.yaml b/.woodpecker/update-package-index-redhat-9-arm64.yaml index 9bf5db6..acfdb32 100644 --- a/.woodpecker/update-package-index-redhat-9-arm64.yaml +++ b/.woodpecker/update-package-index-redhat-9-arm64.yaml @@ -21,8 +21,6 @@ steps: volumes: - arm64-binaries-r-dep-cache-redhat-9:/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:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . - rm -rf /mnt/cache/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' diff --git a/.woodpecker/update-package-index-ubuntu-2204-amd64.yaml b/.woodpecker/update-package-index-ubuntu-2204-amd64.yaml index 0ed5a41..e810c3a 100644 --- a/.woodpecker/update-package-index-ubuntu-2204-amd64.yaml +++ b/.woodpecker/update-package-index-ubuntu-2204-amd64.yaml @@ -21,8 +21,6 @@ steps: volumes: - amd64-binaries-r-dep-cache-ubuntu-2204:/mnt/cache commands: - # download latest package version (avoid having to rebuild image every time) - # rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169 - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . - rm -rf /mnt/cache/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' diff --git a/.woodpecker/update-package-index-ubuntu-2204-arm64.yaml b/.woodpecker/update-package-index-ubuntu-2204-arm64.yaml index 4c02b17..d42ddde 100644 --- a/.woodpecker/update-package-index-ubuntu-2204-arm64.yaml +++ b/.woodpecker/update-package-index-ubuntu-2204-arm64.yaml @@ -21,8 +21,6 @@ steps: volumes: - arm64-binaries-r-dep-cache-ubuntu-2204:/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:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . - rm -rf /mnt/cache/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' diff --git a/.woodpecker/update-package-index-ubuntu-2404-amd64.yaml b/.woodpecker/update-package-index-ubuntu-2404-amd64.yaml index 4f5de8b..2d54576 100644 --- a/.woodpecker/update-package-index-ubuntu-2404-amd64.yaml +++ b/.woodpecker/update-package-index-ubuntu-2404-amd64.yaml @@ -21,8 +21,6 @@ steps: volumes: - amd64-binaries-r-dep-cache-ubuntu-2404:/mnt/cache commands: - # download latest package version (avoid having to rebuild image every time) - # rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169 - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . - rm -rf /mnt/cache/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' diff --git a/.woodpecker/update-package-index-ubuntu-2404-arm64.yaml b/.woodpecker/update-package-index-ubuntu-2404-arm64.yaml index 39d6e79..c345588 100644 --- a/.woodpecker/update-package-index-ubuntu-2404-arm64.yaml +++ b/.woodpecker/update-package-index-ubuntu-2404-arm64.yaml @@ -21,8 +21,6 @@ steps: volumes: - arm64-binaries-r-dep-cache-ubuntu-2404:/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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'