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build missing packages

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This commit is contained in:
Patrick Schratz 2024-11-21 19:06:04 +01:00
commit f86acf0869
Signed by: pat-s
GPG key ID: 3C6318841EF78925
1 changed files with 38 additions and 38 deletions
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6
.woodpecker/build-redhat-8-amd64.yaml
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@ -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