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-8:/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/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 == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('excel.link', 'facmodTS', 'fastFMM', 'FIESTA', 'FIESTAutils', 'filters', 'finch', 'fitbitViz', 'fitlandr', 'forestdata', 'FORTLS', 'FPCdpca', 'frscore', 'fsbrain', 'fsn', 'FTSgof', 'FuzzyImputationTest', 'geoidep', 'geojson', 'geojsonio', 'geppe', 'gerbil', 'ggfacto', 'ggpicrust2', 'glmtoolbox', 'googletraffic', 'gp', 'gpg', 'gpuR', 'handwriterApp', 'handwriterRF', 'HDiR', 'highd2means', 'hillshader', 'HLAtools', 'hypergeo2', 'imbalanceDatRel', 'IMIFA', 'InteRD', 'interpolation', 'irtQ', 'jack', 'kDGLM', 'KeyboardSimulator', 'KMD', 'KPC', 'KSgeneral', 'lgpr', 'LipidomicsR', 'LorMe', 'mapping', 'mathml', 'matRiks', 'mbr', 'mcradds', 'MDSGUI', 'MediaNews', 'mergedblocks', 'metaGE', 'metajam', 'meteo', 'MetSizeR', 'mfpp', 'micd', 'miceRanger', 'minired', 'mixgb', 'mixpoissonreg', 'MLE', 'mlmts', 'MMOC', 'MN', 'moc.gapbk', 'modgo', 'ModTools', 'MonoPhy', 'morphomap', 'mregions2', 'multibiplotGUI', 'mvcauchy', 'mvcor', 'mvhtests', 'naive', 'nebula', 'negligible', 'neo4jshell', 'nesRdata', 'nestedcv', 'NetFACS', 'NetSci', 'nflverse', 'NGBVS', 'NGCHM', 'nlgm', 'nlmixr2', 'nlmixr2plot', 'nmrrr', 'npcurePK', 'obfuscatoR', 'OpenCL', 'parTimeROC', 'Patterns', 'pbANOVA', 'pcaL1', 'pcds.ugraph', 'pchc', 'PCRA', 'pgKDEsphere', 'phylotypr', 'phylter', 'plumberDeploy', 'PNAR', 'polyhedralCubature', 'popstudy', 'PoweREST', 'PPbigdata', 'ppsbm', 'praatpicture', 'practicalSigni', 'PRTree', 'qspray', 'qsub', 'QUALYPSO', 'R2PPT', 'R2wd', 'Racmacs', 'RandomWalker', 'RankAggSIgFUR', 'RAppArmor', 'RationalMatrix', 'ratioOfQsprays', 'ravetools', 'raymolecule', 'Rblpapi', 'Rcatch22', 'rcccd', 'rcompanion', 'rcontroll', 'Rcplex', 'RcppCWB', 'RcppMagicEnum', 'rdflib', 'Rdimtools', 'RDM', 'redland', 'regda', 'resultant', 'Rfast2', 'rFUSION', 'Riemann', 'RInno', 'rmapzen', 'rmarchingcubes', 'RmecabKo', 'Rmpi', 'robin', 'RobRegression', 'robustarima', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROracle', 'RPatternJoin', 'RQuantLib', 'RSP', 'RSquaredMI', 'rStrava', 'Rsymphony', 'rties', 'Rtropical', 'rvMF', 'RWinEdt', 'satdad', 'scDIFtest', 'scMappR', 'segen', 'SEIRfansy', 'SelectBoost', 'SEMdeep', 'sendigR', 'seq2R', 'sevenbridges2', 'SherlockHolmes', 'shiny.benchmark', 'shinyExprPortal', 'shinyIRT', 'shinylive', 'shinyMixR', 'shinyQueryBuilder', 'shinytest2', 'shrinkTVPVAR', 'SIAmodules', 'simCAT', 'simDAG', 'SimNPH', 'smartsnp', 'smcryptoR', 'smvgraph', 'SOMMD', 'SpaCCI', 'spaceNet', 'sparseCov', 'spaths', 'spectralR', 'Spectran', 'spectrino', 'Spectrum', 'splusTimeSeries', 'spStack', 'ssh', 'SSHAARP', 'stppSim', 'surveyvoi', 'symbolicQspray', 'T4cluster', 'tabxplor', 'tame', 'taskscheduleR', 'TDAkit', 'theft', 'theftdlc', 'tidyclust', 'tiledb', 'TML', 'Toothnroll', 'TreeDimensionTest', 'triptych', 'trtswitch', 'truh', 'TSCI', 'tsmarch', 'tspredit', 'twl', 'UBayFS', 'valhallr', 'voiceR', 'vvdoctor', 'WaverideR', 'WCluster', 'webglobe', 'WRI'); 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'))"
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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/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 == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('excel.link', 'facmodTS', 'fastFMM', 'FIESTA', 'FIESTAutils', 'filters', 'finch', 'fitbitViz', 'fitlandr', 'forestdata', 'FORTLS', 'FPCdpca', 'frscore', 'fsbrain', 'fsn', 'FTSgof', 'FuzzyImputationTest', 'geoidep', 'geojson', 'geojsonio', 'geppe', 'gerbil', 'ggfacto', 'ggpicrust2', 'glmtoolbox', 'googletraffic', 'gp', 'gpg', 'gpuR', 'handwriterApp', 'handwriterRF', 'HDiR', 'highd2means', 'hillshader', 'HLAtools', 'hypergeo2', 'imbalanceDatRel', 'IMIFA', 'InteRD', 'interpolation', 'irtQ', 'jack', 'kDGLM', 'KeyboardSimulator', 'KMD', 'KPC', 'KSgeneral', 'lgpr', 'LipidomicsR', 'LorMe', 'mapping', 'mathml', 'matRiks', 'mbr', 'mcradds', 'MDSGUI', 'MediaNews', 'mergedblocks', 'metaGE', 'metajam', 'meteo', 'MetSizeR', 'mfpp', 'micd', 'miceRanger', 'minired', 'mixgb', 'mixpoissonreg', 'MLE', 'mlmts', 'MMOC', 'MN', 'moc.gapbk', 'modgo', 'ModTools', 'MonoPhy', 'morphomap', 'mregions2', 'multibiplotGUI', 'mvcauchy', 'mvcor', 'mvhtests', 'naive', 'nebula', 'negligible', 'neo4jshell', 'nesRdata', 'nestedcv', 'NetFACS', 'NetSci', 'nflverse', 'NGBVS', 'NGCHM', 'nlgm', 'nlmixr2', 'nlmixr2plot', 'nmrrr', 'npcurePK', 'obfuscatoR', 'OpenCL', 'parTimeROC', 'Patterns', 'pbANOVA', 'pcaL1', 'pcds.ugraph', 'pchc', 'PCRA', 'pgKDEsphere', 'phylotypr', 'phylter', 'plumberDeploy', 'PNAR', 'polyhedralCubature', 'popstudy', 'PoweREST', 'PPbigdata', 'ppsbm', 'praatpicture', 'practicalSigni', 'PRTree', 'qspray', 'qsub', 'QUALYPSO', 'R2PPT', 'R2wd', 'Racmacs', 'RandomWalker', 'RankAggSIgFUR', 'RAppArmor', 'RationalMatrix', 'ratioOfQsprays', 'ravetools', 'raymolecule', 'Rblpapi', 'Rcatch22', 'rcccd', 'rcompanion', 'rcontroll', 'Rcplex', 'RcppCWB', 'RcppMagicEnum', 'rdflib', 'Rdimtools', 'RDM', 'redland', 'regda', 'resultant', 'Rfast2', 'rFUSION', 'Riemann', 'RInno', 'rmapzen', 'rmarchingcubes', 'RmecabKo', 'Rmpi', 'robin', 'RobRegression', 'robustarima', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROracle', 'RPatternJoin', 'RQuantLib', 'RSP', 'RSquaredMI', 'rStrava', 'Rsymphony', 'rties', 'Rtropical', 'rvMF', 'RWinEdt', 'satdad', 'scDIFtest', 'scMappR', 'segen', 'SEIRfansy', 'SelectBoost', 'SEMdeep', 'sendigR', 'seq2R', 'sevenbridges2', 'SherlockHolmes', 'shiny.benchmark', 'shinyExprPortal', 'shinyIRT', 'shinylive', 'shinyMixR', 'shinyQueryBuilder', 'shinytest2', 'shrinkTVPVAR', 'SIAmodules', 'simCAT', 'simDAG', 'SimNPH', 'smartsnp', 'smcryptoR', 'smvgraph', 'SOMMD', 'SpaCCI', 'spaceNet', 'sparseCov', 'spaths', 'spectralR', 'Spectran', 'spectrino', 'Spectrum', 'splusTimeSeries', 'spStack', 'ssh', 'SSHAARP', 'stppSim', 'surveyvoi', 'symbolicQspray', 'T4cluster', 'tabxplor', 'tame', 'taskscheduleR', 'TDAkit', 'theft', 'theftdlc', 'tidyclust', 'tiledb', 'TML', 'Toothnroll', 'TreeDimensionTest', 'triptych', 'trtswitch', 'truh', 'TSCI', 'tsmarch', 'tspredit', 'twl', 'UBayFS', 'valhallr', 'voiceR', 'vvdoctor', 'WaverideR', 'WCluster', 'webglobe', 'WRI'); 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-8'))"
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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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