image regressions

.woodpecker/build-alpine-320-amd64.yaml

@@ -40,7 +40,7 @@ steps:
       - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       # Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
       - 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))'
-      - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); pkgs = c('ABACUS', 'abmR', 'abn', 'abstr', 'abstractr', 'acdcR', 'ActCR',  'actel', 'activAnalyzer', 'actxps', 'adapt4pv', 'AdhereRViz',  'AirExposure', 'ajv', 'alcyon', 'AlleleShift', 'almanac', 'alookr',  'amadeus', 'anominate', 'AntMAN', 'APCalign', 'aPCoA', 'apisensr',  'appeears', 'AquaBEHER', 'archive', 'arcpbf', 'arealDB', 'asciicast',  'audrex', 'audubon', 'autoBagging', 'autostats', 'av', 'badgen',  'baguette', 'banter', 'bartCause', 'bartMan', 'base64', 'basemaps',  'bate', 'BayesOrdDesign', 'BayesXsrc', 'bdl', 'BED', 'BeeBDC',  'behaviorchange', 'bfboinet', 'bigGP', 'bigrquerystorage', 'biocompute',  'biopixR', 'BioPred', 'BiplotGUI', 'blackmarbler', 'blatr', 'BoolFilter',  'bpmnR', 'bRacatus', 'brickster', 'brsim', 'BRugs', 'bs4Dash',  'BSTZINB', 'C50', 'CAinterprTools', 'canadamaps', 'CaseBasedReasoning',  'CausalGPS', 'causalHyperGraph', 'causalPAF', 'cbl', 'CCd', 'cellularautomata',  'CensSpatial', 'centerline', 'CERFIT', 'Certara.RsNLME', 'cffr',  'chilemapas', 'chooseGCM', 'CIMTx', 'ClickHouseHTTP', 'clinDataReview',  'clrng', 'clustTMB', 'ClusVis', 'cmprskcoxmsm', 'cohorttools',  'colormap', 'CompositionalRF', 'concaveman', 'conmet', 'conos',  'constrainedKriging', 'conversim', 'CoTiMA', 'countSTAR', 'covalchemy',  'covid19india', 'cppcheckR', 'CRE', 'creditmodel', 'crimeutils',  'crumble', 'cshapes', 'csmpv', 'ctrdata', 'CTRing', 'd4storagehub4R',  'daff', 'dagitty', 'dagwood', 'dartR', 'dartR.base', 'dartR.captive',  'dartR.popgen', 'dartR.sexlinked', 'dartR.sim', 'dartR.spatial',  'datacleanr', 'dataone', 'datapack', 'datasetjson', 'dataspice',  'dbarts', 'dblr', 'ddml', 'DeepLearningCausal', 'dendroNetwork',  'depCensoring', 'DGP4LCF', 'DiagrammeRsvg', 'DICEM', 'diffdfs',  'diffeRenTES', 'DIFM', 'DImodelsVis', 'DIscBIO', 'disclosuR',  'DiSCos', 'disk.frame', 'dismo', 'dispeRse', 'dissever', 'diversitree',  'divraster', 'DMMF', 'do3PCA', 'DoE.wrapper', 'DominoDataR',  'doMPI', 'doolkit', 'doRedis', 'DOT', 'dots', 'DoubleML', 'doublIn',  'downscale', 'dpkg', 'DRHotNet', 'DR.SC', 'DrugSim2DR', 'DRviaSPCN',  'DSAM', 'dsims', 'dsmSearch', 'dssd', 'Dtableone', 'dtComb',  'dti', 'dtrackr', 'DWLS', 'dycdtools', 'dynamAedes', 'dynamicSDM',  'dynatopGIS', 'dynr', 'dySEM', 'DySS', 'easyNCDF', 'easySdcTable',  'EBcoBART', 'ebmc', 'ecdata', 'eCerto', 'ech', 'ecochange', 'ecocomDP',  'ecoCopula', 'econetwork', 'ecopower', 'ecospat', 'edgebundleR',  'ediblecity', 'eDITH', 'eemdARIMA', 'EEMDelm', 'EEMDlstm', 'eemdTDNN',  'EFAfactors', 'EIX', 'emailjsr', 'EmissV', 'emld', 'enerscape',  'ENMTools', 'envi', 'epicmodel', 'epidm', 'epilogi', 'epimdr2',  'EpiSemble', 'epitweetr', 'epiworldRShiny', 'epizootic', 'eSDM',  'eseis', 'espadon', 'EthSEQ', 'ETRep', 'evidence', 'evobiR',  'excel.link', 'eyetools', 'FaaSr', 'facmodTS', 'fangs', 'fanovaGraph',  'fcl', 'fdq', 'FedData', 'fgdr', 'fingerPro', 'finnts', 'fio',  'fishRman', 'florabr', 'fluidsynth', 'fmesher', 'fmf', 'forensIT',  'forestdynR', 'FORTLS', 'foundry', 'FrF2.catlg128', 'FSK2R',  'func2vis', 'galah', 'gbifdb', 'gdtools', 'GeneralisedCovarianceMeasure',  'GENLIB', 'GenoTriplo', 'geocomplexity', 'geodl', 'geodrawr',  'geofi', 'geogenr', 'geoheatmap', 'georob', 'geostan', 'GeoTox',  'GeoWeightedModel', 'geslaR', 'gfer', 'ggESDA', 'ggfacto', 'ggpattern',  'giacR', 'GISTools', 'glossa', 'gmDatabase', 'Goodreader', 'googletraffic',  'gpboost', 'GPCERF', 'gpuR', 'Greymodels', 'GRShiny', 'gsbDesign',  'gsDesign2', 'gtExtras', 'GTFSwizard', 'gto', 'gtreg', 'gwavr',  'gwid', 'GWmodel', 'gwpcormapper', 'GWSDAT', 'habtools', 'HAC',  'handwriterApp', 'handwriterRF', 'hdf5r', 'hdf5r.Extra', 'HDSpatialScan' ); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'alpine-320'))"
+      - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); pkgs = c('xgboost'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); 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

.woodpecker/build-redhat-8-amd64.yaml

@@ -41,7 +41,7 @@ steps:
       - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       # biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
       # Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
-      - 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('later', 'lazysf', 'lconnect', 'leafem',  'leafpm', 'leafpop', 'leafR', 'leastcostpath', 'leidenbase',  'letsR', 'lgcp', 'lgpr', 'lidaRtRee', 'lidR', 'LipidomicsR',  'LMoFit', 'locpolExpectile', 'loewesadditivity', 'LorMe', 'LPDynR',  'LS2Wstat', 'lucas', 'lwgeom', 'M3', 'MainExistingDatasets',  'malariaAtlas', 'mapboxapi', 'mapchina', 'mapedit', 'MapGAM',  'mapi', 'mapiso', 'mapmixture', 'mapping', 'mapsapi', 'mapscanner',  'mapSpain', 'mapsRinteractive', 'mapStats', 'mapview', 'Markovchart',  'MassWateR', 'mathml', 'matRiks', 'MazamaLocationUtils', 'MazamaSpatialPlots',  'mbr', 'mcradds', 'MDSGUI', 'medfate', 'medfateland', 'MediaNews',  'metaGE', 'metajam', 'meteo', 'meteoland', 'meteospain', 'MetricGraph',  'MetSizeR', 'mfpp', 'mgwrhw', 'micd', 'miceRanger', 'MigConnectivity',  'minired', 'misuvi', 'mixgb', 'mixpoissonreg', 'MLE', 'mlmts',  'MMOC', 'MN', 'moc.gapbk', 'modgo', 'ModTools', 'momentuHMM',  'monographaR', 'MonoPhy', 'morphomap', 'Morphoscape', 'motif',  'move2', 'movecost', 'movegroup', 'mregions2', 'MTA', 'mvcauchy',  'mvcor', 'mvhtests', 'naive', 'nebula', 'negligible', 'neo4jshell',  'nesRdata', 'nestedcv', 'NetFACS', 'NetSci', 'NGBVS', 'NGCHM',  'nlgm', 'nlmixr2', 'nlmixr2plot', 'nmrrr', 'npcurePK', 'oaqc',  'obfuscatoR', 'OpenCL', 'outliers.ts.oga', 'parTimeROC', 'Patterns',  'pbANOVA', 'pcaL1', 'pcds.ugraph', 'pchc', 'PCRA', 'pgKDEsphere',  'phylotypr', 'phylter', 'plumberDeploy', 'PNAR', 'polyhedralCubature',  'popstudy', 'PoweREST', 'PPbigdata', 'ppsbm', 'practicalSigni',  'PRTree', 'qspray', 'qsub', 'QUALYPSO', 'R2PPT', 'R2wd', 'RandomWalker',  'RankAggSIgFUR', 'RAppArmor', 'RationalMatrix', 'ratioOfQsprays',  'ravetools', 'raymolecule', 'rcaiman', 'Rcatch22', 'rcccd', 'rcompanion',  'rcontroll', 'Rcplex', 'RcppCWB', 'RcppMagicEnum', 'rdflib',  'RDM', 'redland', 'regda', 'resultant', 'Rfast2', 'rFUSION',  'RInno', 'rmapzen', 'Rmpi', 'robin', 'RobRegression', 'RODBC',  'ROI.models.globalOptTests', 'ROI.plugin.cplex', 'ROI.plugin.neos',  'ROI.plugin.symphony', 'rollinglda', 'ROracle', 'rotor', 'Rpadrino',  'RPatternJoin', 'RPEGLMEN', 'RPESE', 'RPointCloud', 'Rpoppler',  'rpyANTs', 'RQdeltaCT', 'RQuantLib', 'RRTCS', 'rsat', 'RSAtools',  'RSDK', 'RSquaredMI', 'rStrava', 'Rsymphony', 'rties', 'rTLsDeep',  'Rtropical', 'rvMF', 'RWinEdt', 'segen', 'SEIRfansy', 'SelectBoost',  'sendigR', 'sevenbridges2', 'shinyExprPortal', 'shinylive', 'shinyMixR',  'simDAG', 'smartsnp', 'smvgraph', 'spaceNet', 'sparseCov', 'spaths',  'spectralR', 'spectrino', 'Spectrum', 'ssh', 'SSHAARP', 'surveyvoi',  'symbolicQspray', 'tabxplor', 'tame', 'taskscheduleR', 'theft',  'theftdlc', 'tidyclust', 'TML', 'Toothnroll', 'TreeDimensionTest',  'triptych', 'trtswitch', 'truh', 'TSCI', 'tsgarch', 'tsmarch',  'TSS.RESTREND', 'tssim', 'TTCA', 'TukeyRegion', 'turkeyelections',  'tvgarch', 'tvReg', 'TwitterAutomatedTrading', 'twl', 'TwoArmSurvSim',  'txshift', 'uavRmp', 'UBayFS', 'UCSCXenaShiny', 'ufRisk', 'UnalR',  'unusualprofile', 'upndown', 'UpSetVP', 'upstartr', 'URooTab',  'ursa', 'utile.tables', 'UtilityFrailtyPH12', 'vaccine', 'vachette',  'valhallr', 'validateIt', 'valueSetCompare', 'varjmcm', 'vccp',  'vcr', 'vectorwavelet', 'vetiver', 'vhcub', 'viewpoly', 'viraldomain',  'VIRF', 'VisualDom', 'vivid', 'VLTimeCausality', 'vmeasur', 'voiceR',  'vol2birdR', 'voluModel', 'VOSONDash', 'vscc', 'vsmi', 'VsusP',  'vvauditor', 'vvcanvas', 'vvdoctor', 'W2CWM2C', 'wallace', 'WaveletETS',  'WaveletGBM', 'WaveletKNN', 'WaveletLSTM', 'WaveletMLbestFL',  'WaverideR', 'waves', 'WCluster', 'wdnr.gis', 'wearables', 'weatherOz',  'webglobe', 'webp', 'weed', 'WeibullFit', 'WeibullR.ALT', 'weightedCL',  'weightedGCM', 'weird', 'wiesbaden', 'winch', 'windows.pls',  'worcs', 'WRI', 'wrTopDownFrag', 'WVPlots', 'wyz.code.metaTesting',  'wyz.code.rdoc', 'wyz.code.testthat', 'xdcclarge', 'xega', 'xegaDerivationTrees',  'xegaDfGene', 'xegaGaGene', 'xegaGeGene', 'xegaGpGene', 'xegaPermGene',  'xegaPopulation', 'xhaz', 'xmpdf', 'xslt', 'yhat', 'ypssc', 'zooimage' ); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'later', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, 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(CRAN = 'https://cran.devxy.io/amd64/rhel8/latest'))); pkgs = c('rlang', 'bit', 'bit64', 'RSQLite', 'vctrs'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'later', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); 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

.woodpecker/build-redhat-9-amd64.yaml

@@ -38,7 +38,7 @@ steps:
       - R -q -e 'packageVersion("bincraftR")'
       - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       # Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
-      - 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('later', 'MediaNews', 'RInno', 'sbmSDP', 'sbo', 'sboost', 'sbrl',  'SC.MEB', 'Scalelink', 'ScaleSpikeSlab', 'scalpel', 'scar', 'ScatterDensity',  'scattermore', 'SCBiclust', 'scCAN', 'SCCI', 'scclust', 'sccore',  'SCdeconR', 'scDHA', 'scellpam', 'SCEPtER', 'SCEPtERbinary',  'scGate', 'scGOclust', 'sched', 'scINSIGHT', 'SCIntRuler', 'scISR',  'scistreer', 'scITD', 'scMappR', 'scModels', 'scOntoMatch', 'scoper',  'scorematchingad', 'scorepeak', 'scoringRules', 'SCORNET', 'scout',  'scplot', 'scquantum', 'SCRIP', 'scrm', 'ScRNAIMM', 'scRNAtools',  'scrypt', 'scs', 'scTenifoldKnk', 'SCtools', 'SDAR', 'sdcMicro',  'sdcTable', 'sde', 'sdetorus', 'sdmTMB', 'SDMtune', 'sdpdth',  'sdprisk', 'sdpt3r', 'sdrt', 'sdwd', 'SEA', 'SearchTrees', 'seas',  'SECP', 'secretbase', 'secsse', 'sectorgap', 'secure', 'seededlda',  'SeedMatchR', 'seeker', 'seer', 'segclust2d', 'segmag', 'segmenTier',  'segmentr', 'segMGarch', 'seismicRoll', 'SEL', 'selectiveInference',  'selectspm', 'SELF', 'SemiCompRisks', 'semidist', 'semnar', 'semver',  'SenSpe', 'sentencepiece', 'sentiment.ai', 'sentometrics', 'sentopics',  'sephora', 'seq2R', 'SeqDetect', 'seqgendiff', 'seqHMM', 'seqinr',  'SeqKat', 'seqminer', 'SeqNet', 'seqtrie', 'SequenceSpikeSlab',  'SequentialDesign', 'sequoia', 'seriation', 'serocalculator',  'serrsBayes', 'Seurat', 'SeuratObject', 'sfcr', 'sfcurve', 'sfdct',  'sfheaders', 'sfhotspot', 'SFS', 'SFSI', 'sgd', 'SGDinference',  'sgeostat', 'SGL', 'sglasso', 'sgmodel', 'sgolay', 'SGPR', 'sgsR',  'shapr', 'shapviz', 'sharpeRratio', 'sharpPen', 'SheetReader',  'ShellChron', 'SherlockHolmes', 'shide', 'ShiftConvolvePoibin',  'shiftR', 'shiny.blueprint', 'shiny.fluent', 'shiny.reglog',  'shinyCohortBuilder', 'shinydbauth', 'shinyExprPortal', 'shinyKGode',  'ShinyLink', 'shinymanager', 'shinyMolBio', 'shinypivottabler',  'shinyQueryBuilder', 'shinyrecipes', 'shinyTime', 'skedastic',  'spectrino', 'surveyvoi', 'taskscheduleR', 'theft', 'theftdlc',  'trtswitch', 'ursa'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'later', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'redhat-9'))"
+      - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(CRAN = 'https://cran.devxy.io/$ARCH/rhel9/latest'))); pkgs = c('paws.common', 'paws.storage', 'rlang', 'bit', 'bit64', 'RSQLite', 'vctrs'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); 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

.woodpecker/build-redhat-9-arm64.yaml

@@ -63,7 +63,7 @@ steps:
       - R -q -e 'packageVersion("bincraftR")'
       - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       # Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
-      - 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('bnRep', 'bootwar', 'BoundaryStats', 'bratteli', 'CAESAR.Suite',  'calendRio', 'camcorder', 'carbonate', 'Cascade', 'cdcatR', 'cdmTools',  'CEDA', 'cheem', 'christmas', 'chronochrt', 'clarabel', 'clustermole',  'CohortGenerator', 'colocr', 'colorizer', 'compositeReliabilityInNestedDesigns',  'conmet', 'conversim', 'CopSens', 'coveR2', 'coxphm', 'cropcircles',  'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked',  'dartR.sim', 'dartR.spatial', 'databraryr', 'datacleanr', 'EDCimport',  'leidenbase', 'MediaNews', 'MonoPhy', 'nesRdata', 'NGCHM', 'OpenCL',  'paleopop', 'Path.Analysis', 'Patterns', 'pcaL1', 'PCRA', 'ph2bye',  'pikchr', 'R2PPT', 'R2wd', 'Racmacs', 'RAppArmor', 'ravetools',  'Rblpapi', 'Rcatch22', 'Rcplex', 'RcppCWB', 'rdflib', 'redland',  'rFUSION', 'RInno', 'rmarchingcubes', 'RmecabKo', 'Rmpi', 'RobustPrediction',  'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROI.plugin.symphony',  'ROracle', 'RQuantLib', 'Rsymphony', 'RWinEdt', 'shinyMixR',  'sivirep', 'spectrino', 'surveyvoi', 'taskscheduleR', 'TFM',  'theft', 'theftdlc', 'tiledb', 'traineR', 'trtswitch', 'TukeyRegion',  'ursa', 'VecDep', 'visvaR'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, 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(CRAN = 'https://cran.devxy.io/arm64/rhel9/latest'))); pkgs = c('paws.common', 'paws.storage', 'rlang', 'bit', 'bit64', 'RSQLite', 'vctrs'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); 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

.woodpecker/build-ubuntu-2204-arm64.yaml

@@ -63,7 +63,7 @@ steps:
       - R -q -e 'packageVersion("bincraftR")'
       - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       # Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
-      - 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('compositeReliabilityInNestedDesigns', 'conversim', 'coxphm',  'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked',  'diathor', 'DIFshiny', 'do3PCA', 'GeoThinneR', 'leidenbase',  'literanger', 'MediaNews', 'oaqc', 'Rcatch22', 'RcppCWB', 'rFUSION',  'RInno', 'rmarchingcubes', 'RmecabKo', 'ROI.plugin.cplex', 'ROI.plugin.qpoases',  'ROracle', 'RSP', 'RWinEdt', 'rworkflows', 'scDIFtest', 'shiny.benchmark',  'shinyIRT', 'shinytest2', 'SIAmodules', 'simCAT', 'SimNPH', 'spectrino',  'taskscheduleR', 'theft', 'theftdlc', 'tiledb', 'trtswitch',  'ursa'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, 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(CRAN = 'https://cran.devxy.io/arm64/jammy/latest'))); pkgs = c('rlang', 'bit', 'bit64', 'RSQLite', 'vctrs'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); 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

.woodpecker/build-ubuntu-2404-amd64.yaml

@@ -39,7 +39,7 @@ steps:
       - R -q -e 'packageVersion("bincraftR")'
       - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       # Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
-      - 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('CoTiMA', 'later', 'leidenbase', 'lgpr', 'literanger', 'MDSGUI',  'MediaNews', 'MonoPhy', 'MPCR', 'oaqc', 'ondisc', 'R2PPT', 'R2wd',  'ravetools', 'Rcatch22', 'Rcplex', 'RcppCWB', 'rFUSION', 'RInno',  'rmarchingcubes', 'RmecabKo', 'ROI.plugin.cplex', 'ROI.plugin.qpoases',  'ROI.plugin.symphony', 'ROracle', 'Rsymphony', 'RWinEdt', 'rworkflows',  'SegEnvIneq', 'skedastic', 'spectrino', 'taskscheduleR', 'TaxaNorm',  'theft', 'theftdlc', 'trtswitch', 'ursa', 'verbaliseR'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'CoTiMA', 'later', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, 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(CRAN = 'https://cran.devxy.io/amd64/noble/latest'))); pkgs = c('future'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'CoTiMA', 'later', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); 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

.woodpecker/images.yaml

@@ -29,7 +29,7 @@ steps:
   - name: 'Build image'
     image: docker.io/thegeeklab/wp-docker-buildx:6.0.1
     settings:
-      mtu: 1400
+      mtu: 1350
       platforms: linux/${ARCH}
       Containerfile: docker/Containerfile-${PLATFORM}
       experimental: true

docker/Containerfile-alpine-320

@@ -12,6 +12,8 @@ FROM alpine:3.20.3 AS final
 ARG R_VERSION=4.4.2
 ENV PATH=/opt/R/${R_VERSION}/bin:$PATH
 ENV TZ="Europe/Berlin"
+ENV R_LIBS_USER=/mnt/cache/R-pkgs
+ENV R_PKG_CACHE_DIR=/mnt/cache/pkgcache
 
 ARG ARCH=arm64
 ENV NCPUS=2
@@ -39,13 +41,16 @@ RUN apk del lapack lapack-dev
 RUN apk add -q --no-cache R-dev curl ca-certificates bash g++ tzdata openjdk17 tar sed patch openblas-dev pkgconfig linux-headers ccache libxml2-dev libgit2-dev libpq-dev pkgconfig fftw-dev automake autoconf libtool elfutils-dev
 # - Chromium should be auto-installed once pkgdepends merges the latest system-requirements rule changes
 RUN apk add -q --no-cache chromium
+# FIXME: https://github.com/dmlc/xgboost/issues/8595
+RUN apk add --no-cache --update --repository=https://dl-cdn.alpinelinux.org/alpine/v3.16/main/ libexecinfo-dev
 
 # https://github.com/RcppCore/Rcpp/issues/448#issuecomment-220148774
 # LDFLAGS+=-fPIC -> arrow (https://github.com/r-hub/r-minimal/blob/main/examples/arrow/Dockerfile)
 # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66)
 # CXXFLAGS: -> Rcpp 
+# -DDMLC_USE_FOPEN64=0 -> xgboost (https://github.com/dmlc/xgboost/issues/8595)
 # can't set ccache for gfortran because of https://gitlab.com/roigrp/solver/highs/-/issues/4
-RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCXXFLAGS=-D__MUSL__\nCPPFLAGS=-D__MUSL__\nCFLAGS += -flax-vector-conversions\nLDFLAGS+=-fPIC\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=gfortran\nFC=gfortran" > /root/.R/Makevars'
+RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCXXFLAGS=-D__MUSL__ -DDMLC_USE_FOPEN64=0\nCPPFLAGS=-D__MUSL__ -DDMLC_USE_FOPEN64=0\nCFLAGS += -flax-vector-conversions\nLDFLAGS+=-fPIC\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=gfortran\nFC=gfortran" > /root/.R/Makevars'
 
 # R repos
 RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cran.devxy.io/$ARCH/alpine320/latest\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile'
@@ -57,6 +62,9 @@ RUN apk add --allow-untrusted "r-${R_VERSION}_1_$(arch).apk" && rm "r-${R_VERSIO
 
 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))'
 
+# these dirs will later be used by the CI with existing mounts
+RUN mkdir -p /mnt/cache/packages /mnt/cache/pkgcache /mnt/cache/R-pkgs
+
 # FIXME: switch to pak after https://github.com/r-lib/pak/issues/628
 # deps from pak::pkg_deps(".")$package
 RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi", "s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress", "future.callr", "dbplyr"))'

docker/Containerfile-redhat-8

@@ -17,6 +17,8 @@ ARG R_VERSION=4.4.2
 ARG RED_HAT_DEV_PW
 ENV PATH=/opt/R/${R_VERSION}/bin:$PATH
 ENV TZ="Europe/Berlin"
+ENV R_LIBS_USER=/mnt/cache/R-pkgs
+ENV R_PKG_CACHE_DIR=/mnt/cache/pkgcache
 
 ENV ARCH=arm64
 ENV NCPUS=2
@@ -31,7 +33,7 @@ RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.n
 # ImageMagick-c++-devel ImageMagick-devel: boths are not auto-installed via pak sysreqs
 # mecab-devel: RcppMeCab -> no autodetection yet
 # libfftw3-dev: ravetools -> actually auto-detect but somehow doesn't work in container?
-RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb ImageMagick-c++-devel ImageMagick-devel xz pkg-config mecab-devel fftw-devel tk-devel automake
+RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb ImageMagick-c++-devel ImageMagick-devel xz pkg-config mecab-devel fftw-devel tk-devel automake readline-devel
 
 ### CUSTOM DEPENDENCIES 
 # These usually are not packaged in OS repositories and need to be installed from source
@@ -54,6 +56,9 @@ RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vect
 RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cran.devxy.io/$ARCH/rhel8/latest\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile'
 RUN bash -c 'echo -e "PKG_SYSREQS = TRUE\nPKG_SYSREQS_VERBOSE = TRUE\nPKG_SYSREQS_PLATFORM=\"redhat-8\"" > /root/.Renviron'
 
+# these dirs will later be used by the CI with existing mounts
+RUN mkdir -p /mnt/cache/packages /mnt/cache/pkgcache /mnt/cache/R-pkgs
+
 # FIXME: switch to pak after https://github.com/r-lib/pak/issues/628
 # deps from pak::pkg_deps(".")$package
 RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi", "s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress", "future.callr", "dbplyr"))'

docker/Containerfile-redhat-9

@@ -17,6 +17,8 @@ ARG R_VERSION=4.4.2
 ARG RED_HAT_DEV_PW
 ENV PATH=/opt/R/${R_VERSION}/bin:$PATH
 ENV TZ="Europe/Berlin"
+ENV R_LIBS_USER=/mnt/cache/R-pkgs
+ENV R_PKG_CACHE_DIR=/mnt/cache/pkgcache
 
 ENV ARCH=arm64
 ENV NCPUS=2
@@ -31,7 +33,7 @@ RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.n
 # ImageMagick-c++-devel ImageMagick-devel: boths are not auto-installed via pak sysreqs
 # mecab-devel: RcppMeCab -> no autodetection yet
 # libfftw3-dev: ravetools -> actually auto-detect but somehow doesn't work in container?
-RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb ImageMagick-c++-devel ImageMagick-devel xz pkg-config mecab-devel fftw-devel tk-devel automake
+RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb ImageMagick-c++-devel ImageMagick-devel xz pkg-config mecab-devel fftw-devel tk-devel automake readline-devel
 
 ### CUSTOM DEPENDENCIES 
 # These usually are not packaged in OS repositories and need to be installed from source
@@ -41,7 +43,7 @@ RUN cd /JAGS-4.3.2 && make 2>&1 && make install 2>&1 >/dev/null && rm -rf JAGS-4
 RUN dnf install -y chromium
 
 ### INSTALL R
-RUN curl -O "https://devxy-r-builds.s3.eu-central-003.backblazeb2.com/el8/R-${R_VERSION}-1-1.$(arch).rpm"
+RUN curl -O "https://devxy-r-builds.s3.eu-central-003.backblazeb2.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/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
 
@@ -54,6 +56,9 @@ RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vect
 RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cran.devxy.io/$ARCH/rhel9/latest\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile'
 RUN bash -c 'echo -e "PKG_SYSREQS = TRUE\nPKG_SYSREQS_VERBOSE = TRUE\nPKG_SYSREQS_PLATFORM=\"redhat-9\"" > /root/.Renviron'
 
+# these dirs will later be used by the CI with existing mounts
+RUN mkdir -p /mnt/cache/packages /mnt/cache/pkgcache /mnt/cache/R-pkgs
+
 # FIXME: switch to pak after https://github.com/r-lib/pak/issues/628
 # deps from pak::pkg_deps(".")$package
 RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi", "s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress", "future.callr", "dbplyr"))'