diff --git a/.woodpecker/build.yaml b/.woodpecker/build.yaml index 937e649..1269983 100644 --- a/.woodpecker/build.yaml +++ b/.woodpecker/build.yaml @@ -73,7 +73,7 @@ steps: # 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 # - R -q -e 'options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs[${BLOCK}], c("biplotbootGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "TextMiningGUI", "later", "RclusTool", "Rcmdr", "RcmdrMisc", "RcmdrPlugin.aRnova", "RcmdrPlugin.BiclustGUI", "RcmdrPlugin.BWS1", "RcmdrPlugin.BWS2", "RcmdrPlugin.BWS3", "RcmdrPlugin.cpd", "RcmdrPlugin.DCCV", "RcmdrPlugin.DCE", "RcmdrPlugin.depthTools", "RcmdrPlugin.DoE", "RcmdrPlugin.EACSPIR", "RcmdrPlugin.EBM", "RcmdrPlugin.EcoVirtual", "RcmdrPlugin.Export", "RcmdrPlugin.EZR", "RcmdrPlugin.FactoMineR", "RcmdrPlugin.GWRM", "RcmdrPlugin.HH", "RcmdrPlugin.KMggplot2", "RcmdrPlugin.MA", "RcmdrPlugin.MPAStats", "RcmdrPlugin.NMBU", "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "sf", "StratigrapheR", "tcltk2", "TVMM", "uHMM", "RInno")); library(bincraftR); future::plan("${STRATEGY}", workers = ${NCPUS}, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); pkgs = foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "${PLATFORM}"))' ### Manual pkg builds - - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL); pkgs = c("av", "baorista", "bartCause", "bartMan", "BayesMallows", "bayesnec", "bdvis", "biblio", "bidask", "BifactorIndicesCalculator", "bigDM", "bigsnpr", "bimets", "BioM2", "biostat3", "biplotbootGUI", "bispdep", "biwavelet", "BKTR", "blme", "bnlearn", "boot", "boxcoxmix", "BranchGLM", "BRugs", "bscui", "bsvarSIGNs", "calendar", "CaPO4Sim", "caretEnsemble", "casebase", "cba", "celltrackR", "cffr", "circular", "ClassComparison", "clrng", "clustermq", "CLVTools", "cncaGUI", "collapse", "conrad", "contingencytables", "ConvertPar", "convevol", "CopernicusDEM", "cops", "copula", "corrplot", "CoTiMA", "countSTAR", "coursekata", "crandep", "CRE", "CrossCarry", "csquares", "CTD", "ctgdist", "ctsem", "cusp", "cv", "D3mirt", "DanielBiostatistics10th", "dartR", "dartR.base", "dartR.captive", "dartR.popgen", "dartR.sexlinked", "dartR.sim", "dartR.spatial", "datana", "datardis", "dbarts", "decp", "deepgp", "deeptime", "deeptrafo", "designmatch", "dfidx", "DFIT", "difR", "DIFshiny", "digest", "distr", "distrEllipse", "distrSim", "diveR", "dmm", "DPQmpfr", "DPTM", "drda", "dsmSearch", "duckdbfs", "DWDLargeR", "dyn.log", "dynaTree", "dynBiplotGUI", "dynr", "eaf", "EBcoBART", "ecocbo", "ecocomDP", "EcoEnsemble", "ecoreg", "eddington", "EFA.dimensions", "EMCluster", "emmeans", "EnrichIntersect", "envi", "envvar", "equateIRT", "equateMultiple", "EthSEQ", "evalITR", "EventDetectGUI", "exampletestr", "expm", "extremevalues", "faoutlier", "fastcpd", "fastDummies", "fastICA", "FastUtils", "fBasics", "fcl", "fdasrvf", "fdrtool", "filters", "finbif", "fio", "FjordLight", "flan", "flexsurv", "FLORAL", "flow", "flps", "fluidsynth", "fntl", "FoReco", "fragility", "FuzzyPovertyR", "galamm", "gamstransfer", "GAS", "gasfluxes", "gateR", "geofi", "geosimilarity", "geppe", "gert", "GET", "GetTDData", "GFDrmst", "ggpath", "ggrepel", "ghapps", "giacR", "GLCMTextures", "glmmPen", "glmmrBase", "googleAnalyticsR", "googletraffic", "GPCMlasso", "gpindex", "gpuR", "grates", "grattanInflators", "GRIDCOPULA", "gridGeometry", "groupTesting", "GRShiny", "gsw", "gwid", "gWidgets2tcltk", "GWmodel", "Haplin", "hce", "heteromixgm", "HierPortfolios", "highs", "HMC", "hmstimer", "HSAUR3", "hstats", "htsr", "httr2", "hunspell", "HydroPortailStats", "ibdsim2", "IceSat2R", "ichimoku", "iClusterVB", "icosa", "ilabelled", "ImputeRobust", "incubate", "indicspecies", "iNEXT.3D", "INLAspacetime", "IPEDSuploadables", "iplots", "ipolygrowth", "irtawsi", "irtGUI", "irtpwr", "irtQ", "irtreliability", "IsoriX", "iSTATS", "jagshelper", "jmvcore", "joyn", "jqr", "jrt", "jsmodule", "jstager", "KappaGUI", "kequate", "kernelshap", "kernlab", "kit", "klassR", "KoboconnectR", "KSgeneral", "L1pack", "LBI", "leaflet.extras", "lefko3", "lessR", "lgpr", "lingtypology", "lme4breeding", "loon", "loon.ggplot", "loon.shiny", "loon.tourr", "lordif", "LRTesteR", "MachineShop", "magickGUI", "makepipe", "malariaAtlas", "MALDIquant", "mathml", "matrixStats", "MazamaLocationUtils", "MBA", "mboost", "MCARtest", "mcb", "mco", "MCPModGeneral", "mdatools", "mdsr", "Mega2R", "metajam", "MethEvolSIM", "microsimulation", "minic", "miniGUI", "minqa", "mirai", "mirt", "mirtCAT", "mispitools", "missRanger", "mobr", "moc.gapbk", "modsem", "MPV", "mrbayes", "MSCquartets", "msm", "mstDIF", "MultBiplotR", "multibias", "multibiplotGUI", "multIntTestFunc", "mvs", "mxfda", "myClim", "nanonext", "ncdf4", "ndtv", "neotoma2", "nestedcv", "NetFACS", "nflplotR", "NGBVS", "nlgm", "NlinTS", "nlme", "nomnoml", "oce", "octopucs", "od", "omopgenerics", "opencpu", "OpenMx", "openssl", "openxlsx2", "optbdmaeAT", "optrcdmaeAT", "ordinal", "ordinalpattern", "outlierensembles", "pairwiseCI", "paramlink2", "party", "partykit", "pastboon", "patchDVI", "patterncausality", "pbdZMQ", "pcaPP", "pdR", "pedtools", "PerFit", "perms", "PFLR", "phonfieldwork", "piecepackr", "PKPDsim", "plfMA", "plotBart", "PMCMRplus", "PNAR", "PointedSDMs", "polmineR", "poweRbal", "PRA", "PRECAST", "prettifyAddins", "preventr", "PriceIndices", "priceR", "prior3D", "priorCON", "PROsetta", "proteomicsCV", "PubChemR", "pubh", "pubmed.mineR", "qcpm", "QTE.RD", "qtkit", "qtl", "qualtRics", "quanteda.textplots", "Racmacs", "rapiclient", "rapidsplithalf", "rassta", "ravetools", "rayrender", "Rbeast", "RblDataLicense", "Rblpapi", "RclusTool", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos", "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "Rcplex", "RcppCWB", "RcppMeCab", "RcppParallel", "readrba", "referenceIntervals", "refineR", "refseqR", "relMix", "resilience", "ResultModelManager", "revdbayes", "rfviz", "RGraphSpace", "riAFTBART", "rio", "rjags", "rjson", "Rlabkey", "rmarchingcubes", "rmcfs", "RmecabKo", "RMySQL", "rnpn", "robotstxt", "robsurvey", "robustbase", "ROI.plugin.cplex", "ROI.plugin.highs", "ROI.plugin.qpoases", "rollup", "rolog", "ROracle", "rplum", "RPointCloud", "Rpoppler", "rrcov", "Rsagacmd", "RSP", "rstpm2", "rswipl", "rtide", "rTwig", "rugarch", "rytstat", "s3fs", "saeHB.panel.beta", "sampcompR", "SAMtool", "scDIFtest", "sched", "secr", "servr", "SGP", "shiny.benchmark", "shinyIRT", "ShinyItemAnalysis", "shinytest2", "SIAmodules", "Signac", "SigTree", "simCAT", "SimDesign", "SimNPH", "simodels", "simplePHENOTYPES", "SingleCaseES", "skedastic", "skpr", "sna", "snplinkage", "SNSequate", "soptdmaeA", "spatstat.explore", "speakeasyR", "Spectran", "spTimer", "SSDforR", "stan4bart", "startupmsg", "statnet", "stats4teaching", "stcpR6", "streamDAG", "strvalidator", "surface", "switchboard", "tabledown", "tables", "tcltk2", "TestAnaAPP", "TextMiningGUI", "tfrmtbuilder", "tiledb", "tkImgR", "tmsens", "TreeDist", "TTAinterfaceTrendAnalysis", "TVMM", "uHMM", "voi", "vvtableau", "wbacon", "webshot2", "ymd", "YTAnalytics"); pkgs = setdiff(pkgs, c("biplotbootGUI", "cncaGUI", "dynBiplotGUI", "ade4TkGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "TextMiningGUI", "later", "RclusTool", "Rcmdr", "RcmdrMisc", "RcmdrPlugin.aRnova", "RcmdrPlugin.BiclustGUI", "RcmdrPlugin.BWS1", "RcmdrPlugin.BWS2", "RcmdrPlugin.BWS3", "RcmdrPlugin.cpd", "RcmdrPlugin.DCCV", "RcmdrPlugin.DCE", "RcmdrPlugin.depthTools", "RcmdrPlugin.DoE", "RcmdrPlugin.EACSPIR", "RcmdrPlugin.EBM", "RcmdrPlugin.EcoVirtual", "RcmdrPlugin.Export", "RcmdrPlugin.EZR", "RcmdrPlugin.FactoMineR", "RcmdrPlugin.GWRM", "RcmdrPlugin.HH", "RcmdrPlugin.KMggplot2", "RcmdrPlugin.MA", "RcmdrPlugin.MPAStats", "RcmdrPlugin.NMBU", "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "sf", "StratigrapheR", "tcltk2", "TVMM", "uHMM", "RInno")); library(bincraftR); future::plan("${STRATEGY}", workers = ${NCPUS}, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "${PLATFORM}"))' + - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL); pkgs = c("ConvertPar", "convevol", "CopernicusDEM", "cops", "copula", "corrplot", "CoTiMA", "countSTAR", "coursekata", "crandep", "CRE", "CrossCarry", "csquares", "CTD", "ctgdist", "cusp", "cv", "D3mirt", "DanielBiostatistics10th", "dartR", "dartR.base", "dartR.captive", "dartR.popgen", "dartR.sexlinked", "dartR.sim", "dartR.spatial", "datana", "datardis", "dbarts", "decp", "deepgp", "deeptime", "deeptrafo", "designmatch", "dfidx", "DFIT", "difR", "DIFshiny", "digest", "distr", "distrEllipse", "distrSim", "diveR", "dmm", "DPQmpfr", "DPTM", "drda", "dsmSearch", "duckdbfs", "DWDLargeR", "dyn.log", "dynaTree", "dynBiplotGUI", "dynr", "eaf", "EBcoBART", "ecocbo", "ecocomDP", "EcoEnsemble", "ecoreg", "eddington", "EFA.dimensions", "EMCluster", "emmeans", "EnrichIntersect", "envi", "envvar", "equateIRT", "equateMultiple", "EthSEQ", "evalITR", "EventDetectGUI", "exampletestr", "expm", "extremevalues", "faoutlier", "fastcpd", "fastDummies", "fastICA", "FastUtils", "fBasics", "fcl", "fdasrvf", "fdrtool", "filters", "finbif", "fio", "FjordLight", "flan", "flexsurv", "FLORAL", "flow", "flps", "fluidsynth", "fntl", "FoReco", "fragility", "FuzzyPovertyR", "galamm", "gamstransfer", "GAS", "gasfluxes", "gateR", "geofi", "geosimilarity", "geppe", "gert", "GET", "GetTDData", "GFDrmst", "ggpath", "ggrepel", "ghapps", "giacR", "GLCMTextures", "glmmPen", "glmmrBase", "googleAnalyticsR", "googletraffic", "GPCMlasso", "gpindex", "gpuR", "grates", "grattanInflators", "GRIDCOPULA", "gridGeometry", "groupTesting", "GRShiny", "gsw", "gwid", "gWidgets2tcltk", "GWmodel", "Haplin", "hce", "heteromixgm", "HierPortfolios", "highs", "HMC", "hmstimer", "HSAUR3", "hstats", "htsr", "httr2", "hunspell", "HydroPortailStats", "ibdsim2", "IceSat2R", "ichimoku", "iClusterVB", "icosa", "ilabelled", "ImputeRobust", "incubate", "indicspecies", "iNEXT.3D", "INLAspacetime", "IPEDSuploadables", "iplots", "ipolygrowth", "irtawsi", "irtGUI", "irtpwr", "irtQ", "irtreliability", "IsoriX", "iSTATS", "jagshelper", "jmvcore", "joyn", "jqr", "jrt", "jsmodule", "jstager", "KappaGUI", "kequate", "kernelshap", "kernlab", "kit", "klassR", "KoboconnectR", "KSgeneral", "L1pack", "LBI", "leaflet.extras", "lefko3", "lessR", "lgpr", "lingtypology", "lme4breeding", "loon", "loon.ggplot", "loon.shiny", "loon.tourr", "lordif", "LRTesteR", "MachineShop", "magickGUI", "makepipe", "malariaAtlas", "MALDIquant", "mathml", "matrixStats", "MazamaLocationUtils", "MBA", "mboost", "MCARtest", "mcb", "mco", "MCPModGeneral", "mdatools", "mdsr", "Mega2R", "metajam", "MethEvolSIM", "microsimulation", "minic", "miniGUI", "minqa", "mirai", "mirt", "mirtCAT", "mispitools", "missRanger", "mobr", "moc.gapbk", "modsem", "MPV", "mrbayes", "MSCquartets", "msm", "mstDIF", "MultBiplotR", "multibias", "multibiplotGUI", "multIntTestFunc", "mvs", "mxfda", "myClim", "nanonext", "ncdf4", "ndtv", "neotoma2", "nestedcv", "NetFACS", "nflplotR", "NGBVS", "nlgm", "NlinTS", "nlme", "nomnoml", "oce", "octopucs", "od", "omopgenerics", "opencpu", "OpenMx", "openssl", "openxlsx2", "optbdmaeAT", "optrcdmaeAT", "ordinal", "ordinalpattern", "outlierensembles", "pairwiseCI", "paramlink2", "party", "partykit", "pastboon", "patchDVI", "patterncausality", "pbdZMQ", "pcaPP", "pdR", "pedtools", "PerFit", "perms", "PFLR", "phonfieldwork", "piecepackr", "PKPDsim", "plfMA", "plotBart", "PMCMRplus", "PNAR", "PointedSDMs", "polmineR", "poweRbal", "PRA", "PRECAST", "prettifyAddins", "preventr", "PriceIndices", "priceR", "prior3D", "priorCON", "PROsetta", "proteomicsCV", "PubChemR", "pubh", "pubmed.mineR", "qcpm", "QTE.RD", "qtkit", "qtl", "qualtRics", "quanteda.textplots", "Racmacs", "rapiclient", "rapidsplithalf", "rassta", "ravetools", "rayrender", "Rbeast", "RblDataLicense", "Rblpapi", "RclusTool", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos", "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "Rcplex", "RcppCWB", "RcppMeCab", "RcppParallel", "readrba", "referenceIntervals", "refineR", "refseqR", "relMix", "resilience", "ResultModelManager", "revdbayes", "rfviz", "RGraphSpace", "riAFTBART", "rio", "rjags", "rjson", "Rlabkey", "rmarchingcubes", "rmcfs", "RmecabKo", "RMySQL", "rnpn", "robotstxt", "robsurvey", "robustbase", "ROI.plugin.cplex", "ROI.plugin.highs", "ROI.plugin.qpoases", "rollup", "rolog", "ROracle", "rplum", "RPointCloud", "Rpoppler", "rrcov", "Rsagacmd", "RSP", "rstpm2", "rswipl", "rtide", "rTwig", "rugarch", "rytstat", "s3fs", "saeHB.panel.beta", "sampcompR", "SAMtool", "scDIFtest", "sched", "secr", "servr", "SGP", "shiny.benchmark", "shinyIRT", "ShinyItemAnalysis", "shinytest2", "SIAmodules", "Signac", "SigTree", "simCAT", "SimDesign", "SimNPH", "simodels", "simplePHENOTYPES", "SingleCaseES", "skedastic", "skpr", "sna", "snplinkage", "SNSequate", "soptdmaeA", "spatstat.explore", "speakeasyR", "Spectran", "spTimer", "SSDforR", "stan4bart", "startupmsg", "statnet", "stats4teaching", "stcpR6", "streamDAG", "strvalidator", "surface", "switchboard", "tabledown", "tables", "tcltk2", "TestAnaAPP", "TextMiningGUI", "tfrmtbuilder", "tiledb", "tkImgR", "tmsens", "TreeDist", "TTAinterfaceTrendAnalysis", "TVMM", "uHMM", "voi", "vvtableau", "wbacon", "webshot2", "ymd", "YTAnalytics"); pkgs = setdiff(pkgs, c("biplotbootGUI", "cncaGUI", "dynBiplotGUI", "ade4TkGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "TextMiningGUI", "later", "RclusTool", "Rcmdr", "RcmdrMisc", "RcmdrPlugin.aRnova", "RcmdrPlugin.BiclustGUI", "RcmdrPlugin.BWS1", "RcmdrPlugin.BWS2", "RcmdrPlugin.BWS3", "RcmdrPlugin.cpd", "RcmdrPlugin.DCCV", "RcmdrPlugin.DCE", "RcmdrPlugin.depthTools", "RcmdrPlugin.DoE", "RcmdrPlugin.EACSPIR", "RcmdrPlugin.EBM", "RcmdrPlugin.EcoVirtual", "RcmdrPlugin.Export", "RcmdrPlugin.EZR", "RcmdrPlugin.FactoMineR", "RcmdrPlugin.GWRM", "RcmdrPlugin.HH", "RcmdrPlugin.KMggplot2", "RcmdrPlugin.MA", "RcmdrPlugin.MPAStats", "RcmdrPlugin.NMBU", "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "sf", "StratigrapheR", "tcltk2", "TVMM", "uHMM", "RInno")); library(bincraftR); future::plan("${STRATEGY}", workers = ${NCPUS}, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers(global = TRUE); progressr::handlers("cli"); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "${PLATFORM}"))' backend_options: kubernetes: ### PROD-parallel diff --git a/.woodpecker/process_cran_updates.yaml b/.woodpecker/process_cran_updates.yaml index 480205f..eeee4b7 100644 --- a/.woodpecker/process_cran_updates.yaml +++ b/.woodpecker/process_cran_updates.yaml @@ -55,7 +55,7 @@ steps: - 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 # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = "error", repos = structure(c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"))); pkgs = tools::CRAN_package_db()[[1]][${BLOCK}]; pkgs = setdiff(pkgs, c("biplotbootGUI", "cncaGUI", "dynBiplotGUI", "ade4TkGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "TextMiningGUI", "later", "RclusTool", "Rcmdr", "RcmdrMisc", "RcmdrPlugin.aRnova", "RcmdrPlugin.BiclustGUI", "RcmdrPlugin.BWS1", "RcmdrPlugin.BWS2", "RcmdrPlugin.BWS3", "RcmdrPlugin.cpd", "RcmdrPlugin.DCCV", "RcmdrPlugin.DCE", "RcmdrPlugin.depthTools", "RcmdrPlugin.DoE", "RcmdrPlugin.EACSPIR", "RcmdrPlugin.EBM", "RcmdrPlugin.EcoVirtual", "RcmdrPlugin.Export", "RcmdrPlugin.EZR", "RcmdrPlugin.FactoMineR", "RcmdrPlugin.GWRM", "RcmdrPlugin.HH", "RcmdrPlugin.KMggplot2", "RcmdrPlugin.MA", "RcmdrPlugin.MPAStats", "RcmdrPlugin.NMBU", "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA" , "RcmdrPlugin.WorldFlora", "sf", "StratigrapheR", "tcltk2", "TVMM", "uHMM")); library(bincraftR); future::plan("sequential"); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = lubridate::interval(lubridate::today() - 2, lubridate::today() - 2), platform = "${PLATFORM}", process_updated = TRUE, process_new = TRUE)' + - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = "error", repos = structure(c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"))); pkgs = tools::CRAN_package_db()[[1]][${BLOCK}]; pkgs = setdiff(pkgs, c("biplotbootGUI", "cncaGUI", "dynBiplotGUI", "ade4TkGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "TextMiningGUI", "later", "RclusTool", "Rcmdr", "RcmdrMisc", "RcmdrPlugin.aRnova", "RcmdrPlugin.BiclustGUI", "RcmdrPlugin.BWS1", "RcmdrPlugin.BWS2", "RcmdrPlugin.BWS3", "RcmdrPlugin.cpd", "RcmdrPlugin.DCCV", "RcmdrPlugin.DCE", "RcmdrPlugin.depthTools", "RcmdrPlugin.DoE", "RcmdrPlugin.EACSPIR", "RcmdrPlugin.EBM", "RcmdrPlugin.EcoVirtual", "RcmdrPlugin.Export", "RcmdrPlugin.EZR", "RcmdrPlugin.FactoMineR", "RcmdrPlugin.GWRM", "RcmdrPlugin.HH", "RcmdrPlugin.KMggplot2", "RcmdrPlugin.MA", "RcmdrPlugin.MPAStats", "RcmdrPlugin.NMBU", "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA" , "RcmdrPlugin.WorldFlora", "sf", "StratigrapheR", "tcltk2", "TVMM", "uHMM")); library(bincraftR); future::plan("sequential"); options(progressr.enable = TRUE); progressr::handlers("cli"); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = lubridate::interval(lubridate::today() - 2, lubridate::today() - 2), platform = "${PLATFORM}", process_updated = TRUE, process_new = TRUE)' backend_options: kubernetes: ### PROD diff --git a/docker/Dockerfile-alpine-320 b/docker/Dockerfile-alpine-320 index f0ac513..0882bb8 100644 --- a/docker/Dockerfile-alpine-320 +++ b/docker/Dockerfile-alpine-320 @@ -48,7 +48,7 @@ RUN R -q -e 'install.packages("remotes", repo = "cloud.r-project.org"); remotes: # FIXME: switch to pak after https://github.com/r-lib/pak/issues/628 # deps from pak::pkg_deps(".")$package -RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi","s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "pat-s/cranlike@s3", "pat-s/desc@description-from-remote"))' +RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi", "s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress"))' COPY . . # remove secrets from COPY diff --git a/docker/Dockerfile-redhat-8 b/docker/Dockerfile-redhat-8 index 57e0654..fee3bc9 100644 --- a/docker/Dockerfile-redhat-8 +++ b/docker/Dockerfile-redhat-8 @@ -38,7 +38,7 @@ RUN bash -c 'echo -e "PKG_SYSREQS = TRUE\nPKG_SYSREQS_VERBOSE = TRUE" > /root/.R # FIXME: switch to pak after https://github.com/r-lib/pak/issues/628 # deps from pak::pkg_deps(".")$package -RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "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", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "pat-s/cranlike@s3", "pat-s/desc@description-from-remote"))' +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"))' COPY . . # remove secrets from COPY diff --git a/docker/Dockerfile-redhat-9 b/docker/Dockerfile-redhat-9 index ed8c803..a9245c7 100644 --- a/docker/Dockerfile-redhat-9 +++ b/docker/Dockerfile-redhat-9 @@ -35,9 +35,9 @@ RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCC=ccache gcc\nCPP=c # R repos RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile' -COPY . . +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"))' -RUN R -q -e 'pak::local_install_deps()' +COPY . . # remove secrets from COPY RUN touch /.Renviron /.envrc && rm /.Renviron /.envrc RUN R CMD INSTALL . && rm -rf r-pkg-binaries diff --git a/docker/Dockerfile-ubuntu-2204 b/docker/Dockerfile-ubuntu-2204 index dc31d4d..2d6d17f 100644 --- a/docker/Dockerfile-ubuntu-2204 +++ b/docker/Dockerfile-ubuntu-2204 @@ -33,9 +33,9 @@ RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCC=ccache gcc\nCPP=c # R repos RUN bash -c 'echo -e "options(pkg.sysreqs_verbose = TRUE, crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > ~/.Rprofile' -COPY . . +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"))' -RUN R -q -e 'pak::local_install_deps()' +COPY . . # remove secrets from COPY RUN touch /.Renviron /.envrc && rm /.Renviron /.envrc RUN R CMD INSTALL . && rm -rf r-pkg-binaries diff --git a/docker/Dockerfile-ubuntu-2404 b/docker/Dockerfile-ubuntu-2404 index 1d433db..983f35d 100644 --- a/docker/Dockerfile-ubuntu-2404 +++ b/docker/Dockerfile-ubuntu-2404 @@ -33,9 +33,9 @@ RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCC=ccache gcc\nCPP=c # R repos RUN bash -c 'echo -e "options(pkg.sysreqs_verbose = TRUE, crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > ~/.Rprofile' -COPY . . +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"))' -RUN R -q -e 'pak::local_install_deps()' +COPY . . # remove secrets from COPY RUN touch /.Renviron /.envrc && rm /.Renviron /.envrc RUN R CMD INSTALL . && rm -rf r-pkg-binaries