build missing packages
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1 changed files with 38 additions and 38 deletions
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@ -62,7 +62,7 @@ steps:
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# for some reason paks pkgcache is often corrupt
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- rm -rf /mnt/cache/R-pkgs/pkgcache/ /mnt/cache/pkgcache/ /root/.cache/R/
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- R -q -e 'pak::meta_update()'
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- R CMD INSTALL .
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- R -q -e 'packageVersion("bincraftR")'
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# more complicated system dependencies which pak cannot resolve
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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# 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
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@ -70,10 +70,10 @@ steps:
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# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
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# - Rglpk
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# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
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- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/arm64/alpine320/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 == 'alpine-320', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'alpine-320'))"
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- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/arm64/alpine320/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 == 'alpine-320', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE);pkgs = c('ABACUS', 'ABCanalysis', 'abc.data', 'abclass', 'ABCoptim', 'ABCp2', 'ABC.RAP', 'abcrf', 'abcrlda', 'abctools', 'abmR', 'abn', 'acdcR', 'ACNE', 'actel', 'actxps', 'acumos', 'adapt4pv', 'add2ggplot', 'adepro', 'adespatial', 'AdhereRViz', 'adw', 'aebdata', 'africamonitor', 'ag5Tools', 'agriwater', 'aIc', 'AirExposure', 'AIscreenR', 'ajv', 'alcyon', 'ALFAM2', 'AlleleShift', 'almanac', 'alookr', 'altR2', 'amadeus', 'Amelia', 'amt', 'angstroms', 'animalEKF', 'anipaths', 'AntMAN', 'APCalign', 'apcf', 'aPCoA', 'apisensr', 'Apollonius', 'appeears', 'AquaBEHER', 'arakno', 'arcgisgeocode', 'archive', 'arcpbf', 'areal', 'arealDB', 'arkhe', 'aroma.affymetrix', 'aroma.cn', 'aroma.core', 'ARPALData', 'arrangements', 'artfima', 'asciicast', 'assignR', 'atakrig', 'atom4R', 'atpolR', 'audrex', 'audubon', 'autoBagging', 'autostats', 'av', 'AVGAS', 'aws', 'aws.wrfsmn', 'b64', 'badgen', 'baguette', 'bamm', 'BANAM', 'bangladesh', 'banter', 'bartCause', 'bartMan', 'base64', 'basemaps', 'basf', 'basifoR', 'bate', 'BAwiR', 'BayesfMRI', 'bayesMig', 'BayesOrdDesign', 'bayesTFR', 'BayesVarSel', 'BayesXsrc', 'bbl', 'bbotk', 'bcdata', 'bdc', 'bdl', 'BED', 'BeeBDC', 'behaviorchange', 'bfboinet', 'bfsMaps', 'BIEN', 'bigD', 'bigDM', 'bigGP', 'bigrquerystorage', 'biogrowth', 'biopixR', 'BioPred', 'bioregion', 'BiplotGUI', 'blockCV', 'BoolFilter', 'boostingDEA', 'bootnet', 'Boptbd', 'bpca', 'bpmnR', 'bRacatus', 'brainGraph', 'brainKCCA', 'brainR', 'bratteli', 'BRBVS', 'brickster', 'brsim', 'BRugs', 'BRVM', 'BSPADATA', 'BSSoverSpace', 'btergm', 'c3net', 'C443', 'C50', 'CACIMAR', 'CAESAR.Suite', 'CAinterprTools', 'Cairo', 'calendRio', 'calmate', 'camcorder', 'CAMML', 'camtrapR', 'canadamaps', 'cancerGI', 'candisc', 'Canek', 'cape', 'capm', 'carbonate', 'cartograflow', 'cartogram', 'cartogramR', 'Cascade', 'cascsim', 'CaseBasedReasoning', 'cases', 'cati', 'catSurv', 'cauchypca', 'causact', 'causalDisco', 'causaleffect', 'CausalGPS', 'causalHyperGraph', 'causaloptim', 'causalPAF', 'caviarpd', 'CCAMLRGIS', 'cccd', 'ccrs', 'ccTensor', 'cdlTools', 'cds', 'CDsampling', 'CDSE', 'CEEMDANML', 'cellKey', 'censorcopula', 'CensSpatial', 'centiserve', 'CePa', 'ceramic', 'CERFIT', 'CeRNASeek', 'cffdrs', 'cffr', 'cft', 'cglasso', 'ChaosGame', 'chatAI4R', 'ChernoffDist', 'chilemapas', 'chirps', 'choosepc', 'CIARA', 'CIMTx', 'CINNA', 'circularEV', 'cit', 'CITMIC', 'Claddis', 'ClaimsProblems', 'clarabel', 'cld3', 'cleangeo', 'cleanTS', 'clhs', 'ClickHouseHTTP', 'clickstream', 'climateStability', 'CLimd', 'climetrics', 'clinDataReview', 'ClusROC', 'clustAnalytics', 'clusterMI', 'clustermole', 'clustNet', 'clustree', 'clustringr', 'clustTMB', 'ClusVis', 'CLVTools', 'cmprskcoxmsm', 'cmsaf', 'cmsafops', 'cncaGUI', 'cnmap', 'CNVScope', 'coalescentMCMC', 'CoastlineFD', 'CoClust', 'CoDiNA', 'cohorttools', 'CoImp', 'colocr', 'colorfindr', 'colorist', 'colorizer', 'colormap', 'cols', 'comato', 'comorosmaps', 'compareMCMCs', 'CompareMultipleModels', 'Compositional', 'CompositionalML', 'concaveman', 'concom', 'ConcordanceTest', 'ConfidenceEllipse', 'CoNI', 'conmet', 'ConNEcT', 'conos', 'ConsRank', 'ConsRankClass', 'constrainedKriging', 'ContaminatedMixt', 'controlfunctionIV', 'conversim', 'convevol', 'cooltools', 'CoordinateCleaner', 'CooRTweet', 'CopCTS', 'CopernicusDEM', 'cops', 'CopulaCenR', 'copulaedas', 'corclass', 'coreCT', 'corHMM', 'corkscrew', 'corrfuns', 'corrViz', 'cosso', 'COST', 'countSTAR', 'coveR2', 'covid19india', 'CovTools', 'Coxmos', 'CPC', 'cpmr', 'cppcheckR', 'cpss', 'crandep', 'cranly', 'CRE', 'creditmodel', 'crimeutils'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); 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 = 'alpine-320'))"
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### Manual pkg builds
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# 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
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# RInno: Windows-only
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# RInno, MediaNews: Windows-only
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# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
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# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
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# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
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@ -101,7 +101,7 @@ steps:
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# tfrmtbuilder -> V8 (alpine)
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# Rcmdr (alpine)
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# readstata13 (alpine)
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# - 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, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'alpine-320'))'
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# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( 'RcmdrPlugin.orloca', 'RcmdrPlugin.PcaRobust', 'RcmdrPlugin.RiskDemo', 'RcmdrPlugin.RMTCJags', 'RcmdrPlugin.ROC', 'RcmdrPlugin.sos' , 'RcmdrPlugin.survival', 'RcmdrPlugin.TeachingDemos', 'RcmdrPlugin.TeachStat', 'RcmdrPlugin.temis', 'RcmdrPlugin.UCA', 'RcmdrPlugin.WorldFlora', 'streamDAG', 'stan4bart', 'snplinkage', 'saeHB.panel.beta', 'rTwig', 'rswipl', 'RPointCloud', 'rPDBapi', 'rolog', 'rmcfs', 'rjags', 'ResultModelManager', 'RcppCWB', 'RcmdrPlugin.WorldFlora', 'RcmdrPlugin.UCA', 'RcmdrPlugin.temis', 'RcmdrPlugin.TeachStat', 'RcmdrPlugin.TeachingDemos', 'RcmdrPlugin.survival', 'RcmdrPlugin.sos', 'RcmdrPlugin.ROC', 'RcmdrPlugin.RMTCJags', 'RcmdrPlugin.RiskDemo', 'RcmdrPlugin.PcaRobust', 'RclusTool', 'Rbeast', 'rayrender', 'quanteda.textmodels', 'polmineR', 'plotBart', 'NlinTS', 'ndtv', 'overtureR', 'mathml', 'magickGUI', 'lgpr', 'KappaGUI', 'historicalborrow', 'GSODR', 'GRIDCOPULA', 'googleAnalyticsR', 'fluidsynth', 'EventDetectGUI', 'evalITR', 'EBcoBART', 'deeptrafo', 'dbarts', 'CRE', 'countSTAR', 'bartMan', 'bartCause', 'altmeta', 'EthSEQ', 'dartR.spatial', 'dartR.sim', 'gwid', 'Mega2R', 'priorCON', 'prior3D', 'MCARtest', 'designmatch', 'highs', 'ROI.plugin.highs', 'GPCMlasso'); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, debug = FALSE, force = TRUE, platform = 'alpine-320'))'
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backend_options:
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kubernetes:
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### PROD-parallel
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