build missing packages

2024-11-21 19:06:04 +01:00 · 2024-11-21 19:06:04 +01:00 · f86acf0869
commit f86acf0869
parent a9a2e95712
1 changed files with 38 additions and 38 deletions
--- 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