diff --git a/.woodpecker/build-alpine-320-amd64.yaml b/.woodpecker/build-alpine-320-amd64.yaml index f79304f..6410e1d 100644 --- a/.woodpecker/build-alpine-320-amd64.yaml +++ b/.woodpecker/build-alpine-320-amd64.yaml @@ -38,7 +38,7 @@ steps: # 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::meta_update()' - - R CMD INSTALL . + - 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 @@ -46,7 +46,7 @@ steps: # - 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/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 == 'amd64') |> 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'))" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/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 == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('A3', 'AalenJohansen', 'AATtools', 'ABACUS', 'abasequence', 'abbreviate', 'ABCanalysis', 'abc.data', 'abclass', 'ABCoptim', 'ABCp2', 'ABC.RAP', 'abcrf', 'abcrlda', 'abctools', 'abd', 'abdiv', 'abe', 'aberrance', 'abess', 'abglasso', 'ABHgenotypeR', 'abind', 'abjData', 'abjutils', 'ablasso', 'ABM', 'abmR', 'abn', 'abnormality', 'abodOutlier', 'ABPS', 'abseil', 'absorber', 'abstr', 'abstractr', 'ABSurvTDC', 'abtest', 'abundant', 'Ac3net', 'AcademicThemes', 'academictwitteR', 'acc', 'acca', 'accelerometry', 'accelmissing', 'AccelStab', 'accept', 'AcceptanceSampling', 'AcceptReject', 'accessibility', 'accessr', 'accessrmd', 'accrual', 'accrualPlot', 'accSDA', 'accucor', 'accumulate', 'acdcquery', 'acdcR', 'ACDm', 'ace2fastq', 'acebayes', 'ACE.CoCo', 'aceEditor', 'acepack', 'ACEsearch', 'ACEsimFit', 'ACEt', 'acfMPeriod', 'Achilles', 'acid', 'acled.api', 'ACNE', 'acnr', 'acopula', 'acoRn', 'AcousticNDLCodeR', 'acp', 'acro', 'acroname', 'AcrossTic', 'acs', 'acss', 'acss.data', 'ACSSpack', 'ACSWR', 'act', 'ACTCD', 'ActCR', 'actel', 'ActFrag', 'actilifecounts', 'ActiSleep', 'activAnalyzer', 'activatr', 'ActiveDriver', 'activegp', 'ActivePathways', 'adapt4pv', 'ade4', 'aebdata', 'airt', 'AIscreenR', 'ALFAM2', 'AlleleShift', 'alookr', 'amadeus', 'Amelia', 'AntMAN', 'APCalign', 'archive', 'arkhe', 'audrex', 'autoBagging', 'autoFC', 'autostats', 'av', 'baguette', 'bartCause', 'bartMan', 'base64', 'basemaps', 'bayesMig', 'bayesTFR', 'BayesXsrc', 'bbotk', 'BED', 'BeeBDC', 'BiDAG', 'BifactorIndicesCalculator', 'bigD', 'bigGP', 'BINtools', 'biogrowth', 'BioPred', 'BiplotGUI', 'blackmarbler', 'blatr', 'BoolFilter', 'brickster', 'brsim', 'BRugs', 'bscui', 'bullseye', 'C50', 'CAinterprTools', 'CaseBasedReasoning', 'CausalGPS', 'cbl', 'CERFIT', 'CIMTx', 'ClickHouseHTTP', 'clrng', 'ClusVis', 'cmprskcoxmsm', 'conos', 'ConvertPar', 'CoTiMA', 'countSTAR', 'CRE', 'creditmodel', 'crumble', 'csmpv', 'ctgdist', 'CTRing', 'D3mirt', 'd4storagehub4R', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'dartR.sim', 'dartR.spatial', 'dataone', 'datapack', 'dataspice', 'dbarts', 'dblr', 'ddml', 'DeepLearningCausal', 'dendroNetwork', 'DFIT', 'DGP4LCF', 'DICEM', 'diffdfs', 'diffeRenTES', 'DImodelsVis', 'DIscBIO', 'disclosuR', 'DiSCos', 'disk.frame', 'dismo', 'disparityfilter', 'dispeRse', 'dissever', 'distinctiveness', 'diversitree', 'divraster', 'dm', 'DMMF', 'DNAmixturesLite', 'DNetFinder', 'do3PCA', 'doconv', 'DoE.wrapper', 'DominoDataR', 'doMPI', 'doolkit', 'doRedis', 'dots', 'DoubleML', 'doublIn', 'downscale', 'dowser', 'dpkg', 'drake', 'DRHotNet', 'DR.SC', 'DrugSim2DR', 'DRviaSPCN', 'DSAM', 'dsem', 'dsims', 'dsmSearch', 'dssd', 'Dtableone', 'dtComb', 'dti', 'DTSEA', 'DTSR', 'dupNodes', 'DWLasso', 'DWLS', 'dycdtools', 'dymo', 'dynamAedes', 'dynamicSDM', 'dynatopGIS', 'dynetNLAResistance', 'dyngen', 'dynr', 'dynwrap', 'easybgm', 'easyDifferentialGeneCoexpression', 'easyNCDF', 'easySdcTable', 'EBcoBART', 'ebdbNet', 'ebmc', 'eCerto', 'ech', 'ecochange', 'ecocomDP', 'ecoCopula', 'econet', 'EcoNetGen', 'econetwork', 'economiccomplexity', 'ecopower', 'ecospat', 'edgebundleR', 'ediblecity', 'eDITH', 'edmcr', 'EDOIF', 'eegkit', 'eemdARIMA', 'EEMDelm', 'EEMDlstm', 'eemdTDNN', 'EFA.dimensions', 'EFAfactors', 'egor', 'eHDPrep', 'ehymet', 'ei', 'EIX', 'eixport', 'eks', 'elastes', 'EloOptimized', 'EloSteepness', 'elsa', 'emailjsr', 'EMAS', 'EMbC', 'emdi', 'EmissV', 'EMJMCMC', 'emplikAUC', 'EMSS', 'emstreeR', 'eNchange', 'EnergyOnlineCPM', 'enerscape', 'ENMeval', 'enmpa', 'enmSdmX'); 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'))" ### 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 +77,7 @@ steps: # tfrmtbuilder -> V8 (alpine) # Rcmdr (alpine) # readstata13 (alpine) - # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "amd64"))' + # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, debug = FALSE, force = TRUE, platform = "amd64"))' backend_options: kubernetes: resources: diff --git a/.woodpecker/build-alpine-320-arm64.yaml b/.woodpecker/build-alpine-320-arm64.yaml index 0b3ce78..0a18436 100644 --- a/.woodpecker/build-alpine-320-arm64.yaml +++ b/.woodpecker/build-alpine-320-arm64.yaml @@ -62,7 +62,7 @@ steps: # 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::meta_update()' - - R CMD INSTALL . + - 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 @@ -70,10 +70,10 @@ steps: # - 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/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'))" + - 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'))" ### 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 + # RInno, MediaNews: Windows-only # skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1) # rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved # Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/ @@ -101,7 +101,7 @@ steps: # tfrmtbuilder -> V8 (alpine) # Rcmdr (alpine) # readstata13 (alpine) - # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( 'RcmdrPlugin.orloca', 'RcmdrPlugin.PcaRobust', 'RcmdrPlugin.RiskDemo', 'RcmdrPlugin.RMTCJags', 'RcmdrPlugin.ROC', 'RcmdrPlugin.sos' , 'RcmdrPlugin.survival', 'RcmdrPlugin.TeachingDemos', 'RcmdrPlugin.TeachStat', 'RcmdrPlugin.temis', 'RcmdrPlugin.UCA', 'RcmdrPlugin.WorldFlora', 'streamDAG', 'stan4bart', 'snplinkage', 'saeHB.panel.beta', 'rTwig', 'rswipl', 'RPointCloud', 'rPDBapi', 'rolog', 'rmcfs', 'rjags', 'ResultModelManager', 'RcppCWB', 'RcmdrPlugin.WorldFlora', 'RcmdrPlugin.UCA', 'RcmdrPlugin.temis', 'RcmdrPlugin.TeachStat', 'RcmdrPlugin.TeachingDemos', 'RcmdrPlugin.survival', 'RcmdrPlugin.sos', 'RcmdrPlugin.ROC', 'RcmdrPlugin.RMTCJags', 'RcmdrPlugin.RiskDemo', 'RcmdrPlugin.PcaRobust', 'RclusTool', 'Rbeast', 'rayrender', 'quanteda.textmodels', 'polmineR', 'plotBart', 'NlinTS', 'ndtv', 'overtureR', 'mathml', 'magickGUI', 'lgpr', 'KappaGUI', 'historicalborrow', 'GSODR', 'GRIDCOPULA', 'googleAnalyticsR', 'fluidsynth', 'EventDetectGUI', 'evalITR', 'EBcoBART', 'deeptrafo', 'dbarts', 'CRE', 'countSTAR', 'bartMan', 'bartCause', 'altmeta', 'EthSEQ', 'dartR.spatial', 'dartR.sim', 'gwid', 'Mega2R', 'priorCON', 'prior3D', 'MCARtest', 'designmatch', 'highs', 'ROI.plugin.highs', 'GPCMlasso'); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'alpine-320'))' + # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( 'RcmdrPlugin.orloca', 'RcmdrPlugin.PcaRobust', 'RcmdrPlugin.RiskDemo', 'RcmdrPlugin.RMTCJags', 'RcmdrPlugin.ROC', 'RcmdrPlugin.sos' , 'RcmdrPlugin.survival', 'RcmdrPlugin.TeachingDemos', 'RcmdrPlugin.TeachStat', 'RcmdrPlugin.temis', 'RcmdrPlugin.UCA', 'RcmdrPlugin.WorldFlora', 'streamDAG', 'stan4bart', 'snplinkage', 'saeHB.panel.beta', 'rTwig', 'rswipl', 'RPointCloud', 'rPDBapi', 'rolog', 'rmcfs', 'rjags', 'ResultModelManager', 'RcppCWB', 'RcmdrPlugin.WorldFlora', 'RcmdrPlugin.UCA', 'RcmdrPlugin.temis', 'RcmdrPlugin.TeachStat', 'RcmdrPlugin.TeachingDemos', 'RcmdrPlugin.survival', 'RcmdrPlugin.sos', 'RcmdrPlugin.ROC', 'RcmdrPlugin.RMTCJags', 'RcmdrPlugin.RiskDemo', 'RcmdrPlugin.PcaRobust', 'RclusTool', 'Rbeast', 'rayrender', 'quanteda.textmodels', 'polmineR', 'plotBart', 'NlinTS', 'ndtv', 'overtureR', 'mathml', 'magickGUI', 'lgpr', 'KappaGUI', 'historicalborrow', 'GSODR', 'GRIDCOPULA', 'googleAnalyticsR', 'fluidsynth', 'EventDetectGUI', 'evalITR', 'EBcoBART', 'deeptrafo', 'dbarts', 'CRE', 'countSTAR', 'bartMan', 'bartCause', 'altmeta', 'EthSEQ', 'dartR.spatial', 'dartR.sim', 'gwid', 'Mega2R', 'priorCON', 'prior3D', 'MCARtest', 'designmatch', 'highs', 'ROI.plugin.highs', 'GPCMlasso'); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, debug = FALSE, force = TRUE, platform = 'alpine-320'))' backend_options: kubernetes: ### PROD-parallel diff --git a/.woodpecker/build-redhat-8-amd64.yaml b/.woodpecker/build-redhat-8-amd64.yaml index 7cdfd0b..5c30526 100644 --- a/.woodpecker/build-redhat-8-amd64.yaml +++ b/.woodpecker/build-redhat-8-amd64.yaml @@ -38,7 +38,7 @@ steps: # 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::meta_update()' - - R CMD INSTALL . + - 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 @@ -46,7 +46,7 @@ steps: # - 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('Achilles', 'adass', 'adea', 'adelie', 'afex', 'afthd', 'ag5Tools', 'AgroReg', 'AgroTech', 'aIc'); 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 = 'redhat-8'))" + - 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('Achilles', 'adass', 'adea', 'adelie', 'afex', 'afthd', 'ag5Tools', 'AgroReg', 'AgroTech', 'aIc'); options(progressr.enable = TRUE); pkgs = c('adamethods', 'adaptIVPT', 'adass', 'adelie', 'AgroReg', 'aIc', 'alphashape3d', 'amadeus', 'ANOVAShiny', 'ANOVAShiny2', 'Anthropometry', 'Apollonius', 'appeears', 'archive', 'Arothron', 'atable', 'atom4R', 'autoMFA', 'babelmixr2', 'bayesdfa', 'BayesfMRI', 'bcROCsurface', 'bdlp', 'bfsMaps', 'bigGP', 'bigrquerystorage', 'biplotbootGUI', 'BiplotGUI', 'bivpois', 'blatr', 'bltm', 'bRacatus', 'bridger', 'BRugs', 'BSPADATA', 'BSSoverSpace', 'CAESAR.Suite', 'camtrapR', 'canadamaps', 'canadianmaps', 'canaper', 'capm', 'cartograflow', 'cartogram', 'cartogramR', 'cartographer', 'cartographr', 'CatastRo', 'catfun', 'cauchypca', 'CCAMLRGIS', 'CCd', 'cdrcR', 'CDSE', 'censable', 'centerline', 'centr', 'Certara.R', 'cffdrs', 'cft', 'cheem', 'chessboard', 'chilemapas', 'chirps', 'choosepc', 'cleangeo', 'cleanTS', 'clrng', 'ClusTCR2', 'clusterMI', 'ClusterStability', 'ClustGeo', 'cnmap', 'CoastlineFD', 'cols', 'comorosmaps', 'CompositionalML', 'CompositionalRF', 'concaveman', 'condor', 'conleyreg', 'constrainedKriging', 'CoOL', 'CoordinateCleaner', 'CopernicusDEM', 'CopernicusMarine', 'corona', 'corrfuns', 'corrViz', 'covatest', 'covid19sf', 'covidcast', 'CPC', 'cpmr', 'cppcontainers', 'cpss', 'CptNonPar', 'cropDemand', 'CropScapeR', 'cropZoning', 'crsuggest', 'CRTspat', 'crumble', 'CruzPlot', 'crwbmetareg', 'cryptography', 'cshapes', 'CSHShydRology', 'csodata', 'csquares', 'ctmm', 'ctpm', 'cubble', 'cvap', 'CvmortalityMult', 'cyclestreets', 'D3mirt', 'dafishr', 'damAOI', 'dataone', 'datapack', 'dataspice', 'datazoom.amazonia', 'DCluster', 'dcortools', 'dcorVS', 'deepMOU', 'densityarea', 'DescrTab2', 'DescToolsAddIns', 'DFD', 'DGEAR', 'dggridR', 'DIFM', 'DImodelsVis', 'dirttee', 'disaggregation', 'disclosuR', 'dispeRse', 'distanceto', 'divseg', 'divvy', 'DNLC', 'doMPI', 'doolkit', 'dots', 'DrDimont', 'DRHotNet', 'drugprepr', 'dsims', 'dsmSearch', 'dssd', 'Dtableone', 'dtComb', 'dwp', 'dynamicSDM', 'DynForest', 'EasyDescribe', 'ebirdst', 'ebvcube', 'ech', 'ecochange', 'ecocomDP', 'ediblecity', 'eDITH', 'EFDR', 'eiExpand', 'eixport', 'eks', 'EMbC', 'emdi', 'EmiR', 'EmissV', 'emstreeR', 'ENMTools', 'epiCo', 'epifitter', 'epilogi', 'EpiStats', 'epm', 'EQUALrepeat', 'EQUALSTATS', 'eSDM', 'ETRep', 'evapoRe', 'EventDetectGUI', 'EventPredInCure', 'evian', 'EvidenceSynthesis', 'evident', 'evinf', 'evola', 'evolMap', 'Evomorph', 'evoper', 'EvoPhylo', 'evoTS', 'evreg', 'EWSmethods', 'exactextractr', 'exams2learnr', 'exams2sakai', 'exams.forge', 'exams.mylearn', 'ExcelFunctionsR', 'excel.link', 'excluder', 'exdqlm', 'executablePackeR', 'expDB', 'expectreg', 'ExpertChoice', 'explainer', 'ExplainPrediction', 'explor', 'exploratory', 'expowo', 'extRatum', 'ezmmek', 'fable.ata', 'fableCount', 'facmodCS', 'facmodTS', 'factset.protobuf.stach.v2', 'FADPclust', 'fakemake', 'fakir', 'FAMetA', 'familial', 'fangs', 'fanovaGraph', 'fasstr', 'fastadi', 'FastCUB', 'fastFMM', 'fastglmpca', 'FAST.R', 'fat2Lpoly', 'FAVAR', 'fbati', 'fcaR', 'fcfdr', 'fcl', 'fcr', 'FCVAR', 'fdq', 'fect', 'fedstatAPIr', 'feltr', 'ferrn', 'fgdr', 'fgeo', 'fgeo.analyze', 'fgeo.plot', 'fgm', 'FIESTA', 'FIESTAutils', 'filters', 'finch', 'findSVI', 'fisheye', 'fishRman', 'fitbitViz', 'fitlandr', 'flexpolyline', 'FlexScan', 'flightplot', 'FLightR', 'fluidsynth', 'forestdata', 'forestecology', 'ForestTools', 'FORTLS', 'frscore', 'fsn', 'fsr', 'fude', 'FuzzyImputationTest', 'gamblers.ruin.gameplay', 'gatoRs', 'gaussplotR', 'gbm.auto', 'gdalUtilities', 'GeNetIt', 'GeoAdjust', 'geoAr', 'geobr', 'geocausal', 'geocmeans', 'geodimension', 'geodiv', 'geodrawr', 'geofi', 'GeoFIS', 'geogenr', 'geogrid', 'geoheatmap', 'geoidep', 'geojson', 'geojsonio'); 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'))" ### 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 +77,7 @@ steps: # tfrmtbuilder -> V8 (alpine) # Rcmdr (alpine) # readstata13 (alpine) - # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "amd64"))' + # - 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 diff --git a/.woodpecker/build-redhat-8-arm64.yaml b/.woodpecker/build-redhat-8-arm64.yaml index 1947ac4..a2e471c 100644 --- a/.woodpecker/build-redhat-8-arm64.yaml +++ b/.woodpecker/build-redhat-8-arm64.yaml @@ -62,7 +62,7 @@ steps: # 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::meta_update()' - - R CMD INSTALL . + - 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 @@ -70,7 +70,7 @@ steps: # - 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); 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 = 'redhat-8'))" + - 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('adamethods', 'adaptIVPT', 'adass', 'adelie', 'AFM', 'AgroReg', 'aIc', 'alphashape3d', 'amadeus', 'ANOVAShiny', 'ANOVAShiny2', 'Anthropometry', 'Apollonius', 'appeears', 'archeoViz', 'archive', 'aroma.core', 'Arothron', 'atable', 'atom4R', 'autoMFA', 'babelmixr2', 'BAwiR', 'bcROCsurface', 'bfsMaps', 'bigGP', 'bigrquerystorage', 'biplotbootGUI', 'BiplotGUI', 'bivpois', 'blatr', 'bltm', 'bpca', 'bRacatus', 'brainKCCA', 'brainR', 'bratteli', 'BRugs', 'CAESAR.Suite', 'calendRio', 'camcorder', 'candisc', 'catfun', 'cauchypca', 'CCd', 'Certara.R', 'ChaosGame', 'cheem', 'choosepc', 'circularEV', 'ClaimsProblems', 'clrng', 'ClusROC', 'ClusTCR2', 'clusterMI', 'ClusterStability', 'cncaGUI', 'cols', 'CompositionalML', 'CompositionalRF', 'concom', 'condor', 'ConfidenceEllipse', 'ConsRank', 'ConsRankClass', 'controlfunctionIV', 'cops', 'corrfuns', 'CovTools', 'CPC', 'cpmr', 'cppcontainers', 'cpss', 'CptNonPar', 'crumble', 'crwbmetareg', 'cryptography', 'cubing', 'curvHDR', 'D3mirt', 'dataone', 'datapack', 'dataspice', 'dbcsp', 'dcortools', 'dcorVS', 'deepMOU', 'DescrTab2', 'DescToolsAddIns', 'DGEAR', 'DIDmultiplegtDYN', 'do3PCA', 'doMPI', 'doolkit', 'DrDimont', 'drugprepr', 'dymo', 'DynForest', 'EasyDescribe', 'ecocomDP', 'eDITH', 'eegkit', 'emstreeR', 'epifitter', 'epilogi', 'EQUALrepeat', 'EQUALSTATS', 'esback', 'eSDM', 'eseis', 'eselect', 'esmisc', 'espadon', 'ETASbootstrap', 'etree', 'ETRep', 'Euclimatch', 'Eunomia', 'eurocordexr', 'evapoRe', 'EvidenceSynthesis', 'Evomorph', 'exactextractr', 'excel.link', 'export', 'expowo', 'ExtractTrainData', 'ExtremalDep', 'ExtremeRisks', 'FaaSr', 'fabisearch', 'facmodTS', 'factset.protobuf.stach.v2', 'fangs', 'fasterize', 'fastFMM', 'FastRWeb', 'fcl', 'fdaPDE', 'FIESTA', 'FIESTAutils', 'filters', 'finch', 'fingerPro', 'fitbitViz', 'fitlandr', 'fluidsynth', 'fmdu', 'forestdata', 'FORTLS', 'FPCdpca', 'FreeSortR', 'frontiles', 'frscore', 'fsbrain', 'fsn', 'FTSgof', 'FuzzyImputationTest', 'gellipsoid', 'gensphere', 'geoelectrics', 'geoheatmap', 'geoidep', 'geojson', 'geojsonio', 'geomorph', 'georob', 'geppe', 'gerbil', 'ggfacto', 'ggpicrust2', 'glmtoolbox', 'GoodFibes', 'googletraffic', 'gp', 'gpg', 'GPGame', 'GPoM', 'gpuR', 'Greymodels', 'gyro', 'handwriterApp', 'handwriterRF', 'HDiR', 'hellorust', 'hermiter', 'hesim', 'heterogen', 'hetGP', 'heumilkr', 'heuristicsmineR', 'hexDensity', 'hgm', 'hhsmm', 'hibayes', 'HiClimR', 'HiddenMarkov', 'HiDimDA', 'hierarchicalSets', 'hierNet', 'highd2means', 'highfrequency', 'highlight', 'highOrderPortfolios', 'highs', 'higlasso', 'hilbert', 'hilbertSimilarity', 'hillshader', 'hint', 'hipread', 'HiResTEC', 'hisse', 'histmdl', 'historicalborrowlong', 'hitandrun', 'hive', 'hkevp', 'HLAtools', 'hlt', 'HMB', 'hmcdm', 'hmm.discnp', 'HMMEsolver', 'HMMextra0s', 'HMMmlselect', 'hmmTMB', 'hommel', 'hopit', 'hpa', 'hqreg', 'hrqglas', 'hrt', 'hSDM', 'hsphase', 'hsrecombi', 'hsstan', 'htetree', 'HTLR', 'HTT', 'httk', 'httpgd', 'httpuv', 'hubEnsembles', 'huge', 'HUM', 'humaniformat', 'humanleague', 'hunspell', 'HybridMicrobiomes', 'hydflood', 'hydrotoolbox', 'hyper2', 'hyper.fit', 'hypergeo2', 'ICSClust', 'imbalanceDatRel', 'IMIFA', 'InteRD', 'interpolation', 'IOLS', 'irtQ', 'iSTATS', 'ivdoctr', 'jack', 'JFM', 'JSDNE', 'karel', 'kDGLM', 'kernhaz', 'KernSmoothIRT', 'KeyboardSimulator', 'KMD', 'kml3d', 'KPC', 'kpcaIG', 'KSgeneral', 'lgpr', 'LipidomicsR', 'LorMe', 'LSAfun', 'Maeswrap', 'maicplus', 'maotai', 'mapping', 'mathml', 'matRiks', 'mbr', 'mcauchyd', 'mcradds', 'MDSGUI', 'MDSMap', 'MediaNews', 'mergedblocks', 'metadynminer3d', 'metaGE', 'metajam', 'meteo', 'MetSizeR', 'mfpp'); 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'))" ### 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 @@ -101,7 +101,7 @@ steps: # tfrmtbuilder -> V8 (alpine) # Rcmdr (alpine) # readstata13 (alpine) - # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "arm64"))' + # - 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 diff --git a/.woodpecker/build-redhat-9-amd64.yaml b/.woodpecker/build-redhat-9-amd64.yaml index 1ff85cf..88772a2 100644 --- a/.woodpecker/build-redhat-9-amd64.yaml +++ b/.woodpecker/build-redhat-9-amd64.yaml @@ -61,7 +61,7 @@ steps: # 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::meta_update()' - - R CMD INSTALL . + - 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 @@ -69,7 +69,7 @@ steps: # - 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); 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 = 'redhat-9'))" + - 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('adamethods', 'adaptIVPT', 'AFM', 'alphashape3d', 'Anthropometry', 'Apollonius', 'archeoViz', 'Arothron', 'atom4R', 'bigGP', 'BiplotGUI', 'blatr', 'BRugs', 'ConvertPar', 'crumble', 'D3mirt', 'DALSM', 'dataone', 'datapack', 'doMPI', 'dsmSearch', 'ETRep', 'excel.link', 'facmodTS', 'FeatureHashing', 'fect', 'fedmatch', 'fedstatAPIr', 'ff', 'fftw', 'fftwtools', 'fGarch', 'fgdr', 'fgeo', 'fgeo.analyze', 'fgeo.plot', 'FGLMtrunc', 'fgm', 'FHDI', 'fHMM', 'fido', 'fields', 'FieldSimR', 'fiery', 'FIESTA', 'FIESTAutils', 'filelock', 'FILEST', 'filling', 'finalsize', 'finbipartite', 'fingerPro', 'fingraph', 'finiteruinprob', 'finity', 'finreportr', 'fio', 'fipp', 'FiRE', 'first', 'fishMod', 'FishPhyloMaker', 'FisPro', 'FIT', 'fitbitViz', 'fitlandr', 'fixest', 'FKF', 'FKSUM', 'flam', 'flamingos', 'flan', 'flashClust', 'flashier', 'flashlight', 'flashr', 'flexclust', 'flexCWM', 'flexiblas', 'flexpolyline', 'FlexReg', 'flexrsurv', 'FlexScan', 'FlexVarJM', 'flifo', 'flintyR', 'float', 'flock', 'FLOPART', 'FLORAL', 'flowml', 'flowTraceR', 'flsa', 'FLSSS', 'fluidsynth', 'flying', 'FlyingR', 'FMC', 'FMCCSD', 'fmdu', 'FME', 'fmerPack', 'fmf', 'fmri', 'fmriqa', 'fMRIscrub', 'FMStable', 'fmx', 'FNN', 'fNonlinear', 'footprint', 'forecast', 'ForecastComb', 'forecastLSW', 'forecastSNSTS', 'ForecastTB', 'foreign', 'forensIT', 'forestControl', 'forestecology', 'forestly', 'forestRK', 'ForestTools', 'formods', 'FORTLS', 'FossilSimShiny', 'fourierin', 'fourPNO', 'fpeek', 'fplot', 'fpop', 'fpopw', 'fpow', 'fpp', 'fpp2', 'fqacalc', 'frab', 'fracdiff', 'fractional', 'fracture', 'frailtyEM', 'frailtyMMpen', 'frailtySurv', 'FRCC', 'frechet', 'free', 'freealg', 'freebird', 'FREEtree', 'frequentistSSDBinary', 'FRESHD', 'FRK', 'fRLR', 'frontier', 'frontiles', 'froth', 'fsbrain', 'FSelectorRcpp', 'FSInteract', 'fso', 'fssemR', 'FSSF', 'fst', 'fstcore', 'FuncDiv', 'fUnitRoots', 'funLBM', 'funmediation', 'funspace', 'funtimes', 'fusen', 'fuser', 'fuzzyRankTests', 'FuzzySimRes', 'FVDDPpkg', 'fwsim', 'fy', 'GADAG', 'gadget2', 'gafit', 'GAGAs', 'galamm', 'galigor', 'GALLO', 'gam', 'gamesGA', 'gamlr', 'gamlss.dist', 'gamlss.ggplots', 'gamlssx', 'gamma', 'gammSlice', 'gamreg', 'gamsel', 'gamselBayes', 'ganDataModel', 'ganGenerativeData', 'GANPA', 'gap', 'gapfill', 'GAS', 'gaselect', 'GaSP', 'gasper', 'gastempt', 'gaston', 'gateR', 'GauPro', 'gausscov', 'GaussSuppression', 'gb', 'GB2group', 'gbeta', 'GBJ', 'gbm', 'gbm.auto', 'gbp', 'gCat', 'gcdnet', 'gcKrig', 'gclm', 'gcmr', 'GCPBayes', 'GCPM', 'GCSM', 'gcTensor', 'gcxgclab', 'gdalcubes', 'gdalraster', 'GDELTtools', 'GDILM.ME', 'GDINA', 'gdpc', 'GE', 'GeDS', 'gee', 'GEEaSPU', 'geepack', 'geigen', 'gelnet', 'glpkAPI', 'imbalanceDatRel', 'IMIFA', 'KeyboardSimulator', 'leafR', 'lgpr', 'lidaRtRee', 'lidR', 'mcrPioda', 'MDSGUI', 'MediaNews', 'metajam', 'minired', 'moc.gapbk', 'mregions2', 'MVA', 'mvabund', 'mvctm', 'mvDFA', 'mvgam', 'mvLSW', 'mvLSWimpute', 'mvMAPIT', 'mvMORPH', 'mvna', 'mvnfast', 'mvnimpute', 'mvnmle', 'mvord', 'mvp', 'MVR', 'mvrsquared', 'mvSLOUCH', 'mvst', 'MVT', 'mwa', 'mwcsr', 'mwTensor', 'mxsem', 'n1qn1', 'N2R', 'nabor', 'NADA2', 'nadiv', 'NAIR', 'NAM', 'nametagger', 'nandb', 'nanoarrow', 'nanoparquet', 'nanostringr', 'naryn', 'natcpp', 'nat.nblast', 'natstrat', 'nat.templatebrains', 'natural', 'navigation', 'NBDesign', 'nbfar'); 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'))" ### 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 @@ -100,7 +100,7 @@ steps: # tfrmtbuilder -> V8 (alpine) # Rcmdr (alpine) # readstata13 (alpine) - # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "amd64"))' + # - 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 diff --git a/.woodpecker/build-redhat-9-arm64.yaml b/.woodpecker/build-redhat-9-arm64.yaml index 57ee3bc..6716201 100644 --- a/.woodpecker/build-redhat-9-arm64.yaml +++ b/.woodpecker/build-redhat-9-arm64.yaml @@ -62,7 +62,7 @@ steps: # 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::meta_update()' - - R CMD INSTALL . + - 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 @@ -70,7 +70,7 @@ steps: # - 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); 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 = 'redhat-9'))" + - 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('adamethods', 'adaptIVPT', 'AFM', 'aIc', 'alphashape3d', 'Anthropometry', 'Apollonius', 'archeoViz', 'Arothron', 'atom4R', 'bigGP', 'bio.infer', 'BiplotGUI', 'blatr', 'BNSP', 'bpca', 'brainKCCA', 'brainR', 'BRugs', 'candisc', 'ChaosGame', 'choosepc', 'circularEV', 'ClaimsProblems', 'clintrialx', 'clrng', 'ClusROC', 'cncaGUI', 'concom', 'ConfidenceEllipse', 'ConsRank', 'ConsRankClass', 'controlfunctionIV', 'cops', 'CovTools', 'crumble', 'cubing', 'curvHDR', 'dataone', 'datapack', 'dbcsp', 'dcortools', 'dcorVS', 'deductive', 'deepgp', 'deform', 'deformula', 'degreenet', 'Delaporte', 'deldir', 'demu', 'DendSer', 'denim', 'densEstBayes', 'depcache', 'depcoeff', 'DepthProc', 'descr', 'deseats', 'desla', 'deSolve', 'detectRUNS', 'DetMCD', 'DetR', 'detrendr', 'devEMF', 'devoid', 'dexter', 'dexterMST', 'dfcomb', 'dfms', 'dfmta', 'dfphase1', 'dfsaneacc', 'dggridR', 'dglars', 'DGM', 'dgof', 'DGP4LCF', 'dgumbel', 'diagis', 'DiceDesign', 'DiceKriging', 'diceR', 'didimputation', 'DIDmultiplegtDYN', 'diffIRT', 'diffmatchpatch', 'diffobj', 'diffudist', 'DIFM', 'digest', 'DIME', 'dina', 'dipm', 'dipsaus', 'diptest', 'Dire', 'DIRECT', 'DirichletReg', 'DirStats', 'disaggregation', 'disbayes', 'disclapmix2', 'DiSCos', 'DiscreteDists', 'discretefit', 'disk.frame', 'dismo', 'dispeRse', 'distances', 'distcomp', 'distops', 'distory', 'divDyn', 'diveR', 'diversitree', 'diversityForest', 'divest', 'divo', 'dixon', 'dixonTest', 'do3PCA', 'doMPI', 'doolkit', 'dti', 'dymo', 'eDITH', 'eegkit', 'espadon', 'ETRep', 'Evomorph', 'excel.link', 'export', 'fabisearch', 'facmodTS', 'fdaPDE', 'filters', 'fingerPro', 'fitbitViz', 'fmdu', 'FPCdpca', 'fsbrain', 'gellipsoid', 'gensphere', 'geoelectrics', 'GoodFibes', 'GPGame', 'GPoM', 'gpuR', 'Greymodels', 'gyro', 'HDiR', 'hillshader', 'HUM', 'HybridMicrobiomes', 'hyper.fit', 'icosa', 'ICSClust', 'IOLS', 'ivdoctr', 'JFM', 'JSDNE', 'kernhaz', 'KernSmoothIRT', 'KeyboardSimulator', 'kml3d', 'kpcaIG', 'KSgeneral', 'lgpr', 'LSAfun', 'Maeswrap', 'maotai', 'mcauchyd', 'MDSGUI', 'MDSMap', 'MediaNews', 'metadynminer3d', 'metajam', 'mggd', 'minired', 'MLE', 'moc.gapbk', 'molaR', 'morph', 'Morpho', 'morphomap', 'MorphoTools2', 'mregions2', 'mstudentd', 'mully', 'multibiplotGUI', 'MultiscaleDTM', 'MultivariateAnalysis', 'mvhist', 'mvinfluence', 'mvmesh', 'nat', 'nat.nblast', 'nat.templatebrains', 'nesRdata', 'NGCHM', 'nltm', 'Nmix', 'nmixgof', 'nmslibR', 'nnet', 'nnlib2Rcpp', 'nnls', 'nodeSub', 'noisysbmGGM', 'noncompliance', 'nonlinearTseries', 'nonmem2rx', 'nonneg.cg', 'nonprobsvy', 'nopaco', 'norm', 'NormPsy', 'nortestARMA', 'not', 'np', 'NPBayesImputeCat', 'npcp', 'npcure', 'NPflow', 'npregfast', 'nprobust', 'npROCRegression', 'npsf', 'npsp', 'NScluster', 'nse', 'numbat', 'numberofalleles', 'Numero', 'numOSL', 'NUSS', 'nvmix', 'o2geosocial', 'o2plsda', 'obliqueRSF', 'OBsMD', 'oc', 'oce', 'OceanView', 'ocf', 'OCNet', 'odbc', 'odeGUTS', 'ODRF', 'oeli', 'oem', 'offlineChange', 'ohenery', 'ohoegdm', 'olctools', 'OncoBayes2', 'oncomsm', 'ondisc', 'oneclust', 'onehot', 'onemap', 'onion', 'onlineCOV', 'onlineforecast', 'onlinePCA', 'ontologySimilarity', 'opa', 'OpenCL', 'openCR', 'opencv', 'OpenImageR', 'OpenMx', 'openssl', 'openxlsx', 'oppr', 'Opt5PL', 'OptCirClust', 'OptGS', 'OptHedging', 'optimization', 'optiSel', 'optmatch', 'optpart', 'opusminer', 'orca', 'Orcs', 'ordinalgmifs', 'ore', 'orf', 'ORION', 'orsk', 'orthoDr', 'osc', 'oscar', 'OSFD', 'oskeyring', 'osmdata', 'osqp'); 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'))" ### 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 @@ -101,7 +101,7 @@ steps: # tfrmtbuilder -> V8 (alpine) # Rcmdr (alpine) # readstata13 (alpine) - # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "arm64"))' + # - 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 diff --git a/.woodpecker/build-ubuntu-2204-amd64.yaml b/.woodpecker/build-ubuntu-2204-amd64.yaml index cbfbcbb..09eb900 100644 --- a/.woodpecker/build-ubuntu-2204-amd64.yaml +++ b/.woodpecker/build-ubuntu-2204-amd64.yaml @@ -38,7 +38,7 @@ steps: # 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::meta_update()' - - R CMD INSTALL . + - 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 @@ -46,7 +46,7 @@ steps: # - 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/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 == 'amd64') |> 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 = 'ubuntu-2204'))" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/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 == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('abmR', 'asremlPlus', 'assocInd', 'AST', 'atakrig', 'AtlasMaker', 'atmopt', 'atom4R', 'atpolR', 'audrex', 'audubon', 'augmentedRCBD', 'AurieLSHGaussian', 'auRoc', 'ausplotsR', 'autoEnsemble', 'autoharp', 'automap', 'autoMFA', 'AutoPipe', 'autoReg', 'autostats', 'autothresholdr', 'autoTS', 'AVGAS', 'avotrex', 'AWR.Kinesis', 'aws', 'aws.wrfsmn', 'AZIAD', 'b64', 'babette', 'BACCT', 'bacistool', 'backShift', 'badgen', 'baggr', 'baker', 'bakR', 'baldur', 'BallMapper', 'bamdit', 'bamm', 'BANAM', 'bang', 'bangladesh', 'BANOVA', 'banter', 'baorista', 'bartMachine', 'bartMachineJARs', 'bartMan', 'baRulho', 'basf', 'basifoR', 'BASiNET', 'BASiNETEntropy', 'basket', 'BasketballAnalyzeR', 'baskexact', 'basksim', 'bate', 'BAwiR', 'bayclumpr', 'Bayenet', 'bayes4psy', 'BayesCACE', 'bfw', 'BiBitR', 'BifactorIndicesCalculator', 'bigBits', 'bigGP', 'biocompute', 'biospear', 'BiplotGUI', 'blatr', 'BRugs', 'clrng', 'CoTiMA', 'deeptrafo', 'excel.link', 'FastRWeb', 'filters', 'gllvm', 'gpuR', 'highd2means', 'KeyboardSimulator', 'lgpr', 'MDSGUI', 'MediaNews', 'mixcat', 'MPCR', 'netShiny', 'nevada', 'NFCP', 'nfl4th', 'nflverse', 'NGCHM', 'NIMAA', 'nlcv', 'nlmixr2rpt', 'noaastormevents', 'NoviceDeveloperResources2', 'npcurePK', 'npi', 'nRegression', 'nucim', 'numbat', 'oceanmap', 'ondisc', 'One4All', 'onelogin', 'OpenCL', 'opencv', 'opendatatoronto', 'openmeteo', 'openVA', 'R2PPT', 'R2wd', 'ravetools', 'Rcplex', 'RcppCWB', 'rFUSION', 'RWinEdt', 'spectrino', 'taskscheduleR'); 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'))" ### 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 +77,7 @@ steps: # tfrmtbuilder -> V8 (alpine) # Rcmdr (alpine) # readstata13 (alpine) - # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "amd64"))' + # - 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 diff --git a/.woodpecker/build-ubuntu-2204-arm64.yaml b/.woodpecker/build-ubuntu-2204-arm64.yaml index 8ed9b5b..0abb27a 100644 --- a/.woodpecker/build-ubuntu-2204-arm64.yaml +++ b/.woodpecker/build-ubuntu-2204-arm64.yaml @@ -62,7 +62,7 @@ steps: # 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::meta_update()' - - R CMD INSTALL . + - 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 @@ -70,7 +70,7 @@ steps: # - 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); 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 = 'ubuntu-2204'))" + - 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('aIc', 'asremlPlus', 'assignR', 'BiplotGUI', 'blatr', 'BNSP', 'BRugs', 'clrng', 'deeptrafo', 'doconv', 'excel.link', 'fBasics', 'filters', 'gpuR', 'imbalanceDatRel', 'IMIFA', 'KeyboardSimulator', 'KSgeneral', 'lgpr', 'MDSGUI', 'MediaNews', 'minired', 'R2PPT', 'R2wd', 'Racmacs', 'ravetools', 'Rblpapi', 'Rcplex', 'RcppCWB', 'redatamx', 'rFUSION', 'Rmpi', 'RWinEdt', 'simplexreg', 'simplextree', 'simPop', 'simputation', 'SimReg', 'simRestore', 'SiMRiv', 'simStateSpace', 'simstudy', 'SimSurvNMarker', 'simts', 'singR', 'SiPhyNetwork', 'SIRmcmc', 'sirt', 'sirus', 'sisireg', 'SIT', 'SITH', 'sitmo', 'sits', 'SK4FGA', 'SKAT', 'sketching', 'SKFCPD', 'sklarsomega', 'skm', 'skpr', 'slasso', 'slcm', 'sld', 'sleev', 'slfm', 'SLHD', 'SLOPE', 'slp', 'smaa', 'smam', 'smartsnp', 'smcryptoR', 'smfishHmrf', 'smfsb', 'smile', 'SMITIDvisu', 'SMMA', 'SMME', 'smmR', 'smoof', 'smooth', 'SmoothHazard', 'smoothSurv', 'smurf', 'SMUT', 'sna', 'SnowballC', 'SNPknock', 'snplist', 'snpsettest', 'SNSeg', 'SobolSequence', 'socceR', 'social', 'sodium', 'SoftBart', 'softImpute', 'som', 'sorcering', 'SoundexBR', 'sourcetools', 'sox', 'sp', 'spAbundance', 'spacefillr', 'SpaceTimeBSS', 'SpaCOAP', 'SpaDES.tools', 'spam', 'spam64', 'spaMM', 'sparcl', 'SparseChol', 'sparseDFM', 'sparsegl', 'sparseHessianFD', 'sparseinv', 'SparseLPM', 'sparseLTSEigen', 'SparseM', 'SPARSEMODr', 'sparsereg', 'sparsesvd', 'sparseSVM', 'SparseTSCGM', 'sparsevb', 'sparsevctrs', 'sparsio', 'sparta', 'sparvaride', 'spass', 'spate', 'spatgraphs', 'spaths', 'spatial', 'SpatialBSS', 'SpatialEpi', 'SpatialExtremes', 'SpatialGEV', 'spatialising', 'SpatialKDE', 'SpatialKWD', 'SpatialPack', 'spatialreg', 'spatialrisk', 'SpatialTools', 'spatialwarnings', 'spatialwidget', 'SpatMCA', 'SpaTopic', 'SpatPCA', 'spatstat.Knet', 'spatstat.linnet', 'spatstat.model', 'spatstat.random', 'spatstat.sparse', 'spbal', 'spBayes', 'spBayesSurv', 'spBFA', 'Spbsampling', 'spc', 'spCP', 'spcr', 'spdep', 'spduration', 'speakeasyR', 'SPECIES', 'specklestar', 'specs', 'SpecsVerification', 'spectralGraphTopology', 'Spectran', 'spectre', 'spectrino', 'sped', 'speedytax', 'spfa', 'spFW', 'spGARCH', 'spgs', 'spgwr', 'sphunif', 'spiderbar', 'spikeslab', 'spinBayes', 'splancs', 'SPlit', 'SplitGLM', 'SplitReg', 'splmm', 'splusTimeDate', 'splusTimeSeries', 'spMC', 'spNNGP', 'spOccupancy', 'sport', 'spray', 'spreadr', 'springer', 'sprintr', 'SPSP', 'spsurv', 'spTDyn', 'SpTe2M', 'spTimer', 'squat', 'srm', 'ssh', 'Sshaped', 'SSLR', 'ssMousetrack', 'SSN2', 'SSOSVM', 'sspse', 'sstvars', 'stable', 'staggered', 'stan4bart', 'StanMoMo', 'STAREG', 'starma', 'starsExtra', 'STARTdesign', 'starvz', 'statcomp', 'statgenIBD', 'statgenQTLxT', 'statip', 'STB', 'stcos', 'stcpR6', 'stdvectors', 'steepness', 'stelfi', 'stepPlr', 'steps', 'StepSignalMargiLike', 'stepSplitReg', 'StepwiseTest', 'stfit', 'stima', 'stlplus', 'StochBlock', 'stochQN', 'stockR', 'stocks', 'stosim', 'stpm', 'stpp', 'stpphawkes', 'strat', 'stratEst', 'StrathE2E2', 'stratification', 'strawr', 'stream', 'streambugs', 'strex', 'strider', 'string2path', 'stringdist', 'stringfish', 'stringi', 'stringmagic', 'striprtf', 'strucchangeRcpp', 'StuteTest', 'subplex', 'subrank', 'SubTite', 'SubTS', 'sumFREGAT', 'SummaryLasso', 'sumR', 'sumSome', 'supclust', 'supercells', 'SuperExactTest', 'SuperGauss', 'SuperpixelImageSegmentation', 'SuperRanker', 'SuppDists', 'surbayes', 'sureLDA', 'SurrogateBMA', 'SurrogateRegression', 'surtvep', 'survAUC', 'survC1', 'surveil', 'SurvEval', 'surveybootstrap', 'surveygraph', 'surveysd', 'surveyvoi', 'survIDINRI', 'survidm', 'survival'); 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'))" ### 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 @@ -101,7 +101,7 @@ steps: # tfrmtbuilder -> V8 (alpine) # Rcmdr (alpine) # readstata13 (alpine) - # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "arm64"))' + # - 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 diff --git a/.woodpecker/build-ubuntu-2404-amd64.yaml b/.woodpecker/build-ubuntu-2404-amd64.yaml index aac65e4..08946c7 100644 --- a/.woodpecker/build-ubuntu-2404-amd64.yaml +++ b/.woodpecker/build-ubuntu-2404-amd64.yaml @@ -38,7 +38,7 @@ steps: # 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::meta_update()' - - R CMD INSTALL . + - 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 @@ -46,7 +46,7 @@ steps: # - 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); 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 = 'ubuntu-2404'))" + - 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('abmR', 'adw', 'AgroTech', 'agua', 'AQEval', 'arakno', 'arcgisgeocode', 'arcgisutils', 'archeofrag', 'archeoViz', 'archetyper', 'arcpbf', 'arcpullr', 'ardl.nardl', 'areal', 'arealDB', 'arenar', 'ARGOS', 'ari', 'arlclustering', 'Arothron', 'ARPALData', 'arrangements', 'artfima', 'aslib', 'asremlPlus', 'Ball', 'Benchmarking', 'BiplotGUI', 'blatr', 'BRugs', 'clrng', 'CoTiMA', 'deeptrafo', 'disclosuR', 'doconv', 'ecoCopula', 'Eunomia', 'excel.link', 'filters', 'gpuR', 'KeyboardSimulator', 'lgpr', 'MDSGUI', 'MediaNews', 'MPCR', 'ondisc', 'R2PPT', 'R2wd', 'ravetools', 'Rcplex', 'RcppCWB', 'rFUSION', 'RWinEdt', 'spectrino', 'taskscheduleR', 'TaxaNorm', 'verbaliseR'); 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'))" ### 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 +77,7 @@ steps: # tfrmtbuilder -> V8 (alpine) # Rcmdr (alpine) # readstata13 (alpine) - # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "amd64"))' + # - 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 diff --git a/.woodpecker/build-ubuntu-2404-arm64.yaml b/.woodpecker/build-ubuntu-2404-arm64.yaml index 37068d8..040a2b8 100644 --- a/.woodpecker/build-ubuntu-2404-arm64.yaml +++ b/.woodpecker/build-ubuntu-2404-arm64.yaml @@ -62,7 +62,7 @@ steps: # 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::meta_update()' - - R CMD INSTALL . + - 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 @@ -70,7 +70,7 @@ steps: # - 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); 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 = 'ubuntu-2404'))" + - 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('abmR', 'aIc', 'asremlPlus', 'biplotbootGUI', 'BiplotGUI', 'blatr', 'bmstdr', 'BNSP', 'BRugs', 'clrng', 'deeptrafo', 'excel.link', 'filters', 'gpuR', 'jointNmix', 'KeyboardSimulator', 'KSgeneral', 'lgpr', 'mcrPioda', 'MDSGUI', 'MediaNews', 'minired', 'PytrendsLongitudinalR', 'R2PPT', 'R2wd', 'Racmacs', 'ravetools', 'Rblpapi', 'Rcplex', 'RcppCWB', 'redatamx', 'rFUSION', 'Rmpi', 'RWinEdt', 'spectrino', 'taskscheduleR', 'tiledb', 'truh', 'TSCI'); 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'))" ### 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 @@ -101,7 +101,7 @@ steps: # tfrmtbuilder -> V8 (alpine) # Rcmdr (alpine) # readstata13 (alpine) - # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "arm64"))' + # - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, debug = FALSE, force = TRUE, platform = "arm64"))' backend_options: kubernetes: ### PROD-parallel diff --git a/docker/Containerfile-alpine-320 b/docker/Containerfile-alpine-320 index afb9139..f358be4 100644 --- a/docker/Containerfile-alpine-320 +++ b/docker/Containerfile-alpine-320 @@ -44,7 +44,7 @@ RUN bash -c 'echo -e "PKG_SYSREQS=TRUE\nPKG_SYSREQS_VERBOSE=TRUE" > ~/.Renviron' RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/alpine320/r-${R_VERSION}_1_$(arch).apk" RUN apk add --allow-untrusted "r-${R_VERSION}_1_$(arch).apk" && rm "r-${R_VERSION}_1_$(arch).apk" -RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' +RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' # FIXME: switch to pak after https://github.com/r-lib/pak/issues/628 # deps from pak::pkg_deps(".")$package diff --git a/docker/Containerfile-redhat-8 b/docker/Containerfile-redhat-8 index caf8a83..d4fcd60 100644 --- a/docker/Containerfile-redhat-8 +++ b/docker/Containerfile-redhat-8 @@ -29,7 +29,7 @@ RUN dnf install -y chromium ### INSTALL R RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/el8/R-${R_VERSION}-1-1.$(arch).rpm" RUN dnf install -q -y "R-${R_VERSION}-1-1.$(arch).rpm" && rm "R-${R_VERSION}-1-1.$(arch).rpm" -RUN 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()$arch))' +RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) diff --git a/docker/Containerfile-redhat-9 b/docker/Containerfile-redhat-9 index d562a68..2d3385e 100644 --- a/docker/Containerfile-redhat-9 +++ b/docker/Containerfile-redhat-9 @@ -28,7 +28,7 @@ RUN dnf install -y chromium ### INSTALL R RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/el9/R-${R_VERSION}-1-1.$(arch).rpm" RUN dnf install -q -y "R-${R_VERSION}-1-1.$(arch).rpm" && rm "R-${R_VERSION}-1-1.$(arch).rpm" -RUN 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()$arch))' +RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) diff --git a/docker/Containerfile-shiny-app b/docker/Containerfile-shiny-app index a782c64..02432c6 100644 --- a/docker/Containerfile-shiny-app +++ b/docker/Containerfile-shiny-app @@ -1,7 +1,7 @@ FROM devxygmbh/r-alpine:4.4-3.20 AS build # ARG GITHUB_PAT -RUN 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()$arch))' +RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' COPY --link ./DESCRIPTION . COPY --link ./R ./R diff --git a/docker/Containerfile-ubuntu-2204 b/docker/Containerfile-ubuntu-2204 index 5b43e2f..0bad30b 100644 --- a/docker/Containerfile-ubuntu-2204 +++ b/docker/Containerfile-ubuntu-2204 @@ -14,7 +14,7 @@ ARG GITHUB_PAT # tcl tk tk-dev tk-table: must be available before running xvfb-run (i.e. starting the graphical session) # libmecab-dev: RcppMeCab -> no autodetection yet # libfftw3-dev: ravetools -> actually auto-detect but somehow doesn't work in container? -RUN apt update && apt install -y --no-install-recommends gdebi-core g++ gfortran libbz2-dev libblas-dev libicu-dev liblapack-dev liblzma-dev libpaper-utils libpcre2-dev libtcl8.6 libtk8.6 libxt6 unzip zip zlib1g-dev libpcre3-dev libopenblas-dev curl ca-certificates make ccache htop libgit2-dev git libpq-dev libxml2-dev libgit2-dev cmake xvfb libcurl4-openssl-dev xz-utils tcl tk tk-dev tk-table pkg-config libmecab-dev libfftw3-dev +RUN apt update && apt install -y --no-install-recommends gdebi-core g++ gfortran libbz2-dev libblas-dev libicu-dev liblapack-dev liblzma-dev libpaper-utils libpcre2-dev libtcl8.6 libtk8.6 libxt6 unzip zip zlib1g-dev libpcre3-dev libopenblas-dev curl ca-certificates make ccache htop libgit2-dev git libpq-dev libxml2-dev libgit2-dev cmake xvfb libcurl4-openssl-dev xz-utils tcl tk tk-dev tk-table pkg-config libmecab-dev libfftw3-dev automake ### CUSTOM DEPENDENCIES # These usually are not packaged in OS repositories and need to be installed from source @@ -29,7 +29,7 @@ RUN apt-get install -y software-properties-common && \ ### INSTALL R RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/2204/r-${R_VERSION}_1_$(dpkg --print-architecture).deb" RUN gdebi -n -qq "r-${R_VERSION}_1_$(dpkg --print-architecture).deb" && rm "r-${R_VERSION}_1_$(dpkg --print-architecture).deb" -RUN 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()$arch))' +RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) diff --git a/docker/Containerfile-ubuntu-2404 b/docker/Containerfile-ubuntu-2404 index dfcf1e1..a1b0403 100644 --- a/docker/Containerfile-ubuntu-2404 +++ b/docker/Containerfile-ubuntu-2404 @@ -29,7 +29,7 @@ RUN apt-get install -y software-properties-common && \ ### INSTALL R RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/2404/r-${R_VERSION}_1_$(dpkg --print-architecture).deb" RUN gdebi -n -qq "r-${R_VERSION}_1_$(dpkg --print-architecture).deb" && rm "r-${R_VERSION}_1_$(dpkg --print-architecture).deb" -RUN 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()$arch))' +RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66)