clean workflow files
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1 changed files with 33 additions and 263 deletions
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@ -55,22 +55,15 @@ steps:
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volumes:
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- arm64-binaries-r-dep-cache-redhat-9:/mnt/cache
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commands:
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# download latest package version (avoid having to rebuild image every time)
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# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
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- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git .
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- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
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# for some reason paks pkgcache is often corrupt
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- rm -rf /mnt/cache/R-pkgs/pkgcache/ /mnt/cache/pkgcache/ /root/.cache/R/
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- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
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- R -q -e 'packageVersion("bincraftR")'
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# more complicated system dependencies which pak cannot resolve
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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# 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
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### Check
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# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
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# - Rglpk
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# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
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- 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')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'redhat-9'))"
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# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
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- 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'))"
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### Manual pkg builds
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# 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
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# RInno: Windows-only
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@ -104,7 +97,6 @@ steps:
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# - 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"))'
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backend_options:
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kubernetes:
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### PROD-parallel
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resources:
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requests:
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memory: 14Gi
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