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-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