100 lines
No EOL
11 KiB
YAML
100 lines
No EOL
11 KiB
YAML
when:
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- event: manual
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evaluate: 'build == "all"'
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- event: manual
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evaluate: 'build == "alpine-320-amd64"'
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- event: manual
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evaluate: 'build == "all-amd64"'
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skip_clone: true
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steps:
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- name: 'Build binaries'
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secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT]
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image: docker.io/devxygmbh/amd64-binaries-r-alpine-320
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pull: true
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# to ensure the PACKAGES upload step is being executed
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failure: ignore
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environment:
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GIT_USER: pat-s
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# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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R_LIBS_USER: /mnt/cache/R-pkgs
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CCACHE_DIR: /mnt/cache/ccache
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PLATFORM: alpine-320
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BLOCK: 2991:2993
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ARCH: amd64
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NCPUS: 4
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# memory: 20Gi
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# INSTANCE_TYPE: ccx23
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STRATEGY: sequential
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# volumes:
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# - amd64-binaries-r-dep-cache-alpine-320:/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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# doBy: hangs on alpine
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# later: hangs on ubuntu
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- 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))'
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- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); pkgs = c('seewave', 'segen', 'SelectBoost', 'SELF', 'SEMdeep', 'semicmprskcoxmsm', 'SemiCompRisks', 'SemiPar.depCens', 'semnar', 'sentiment.ai', 'sephora', 'sfarrow', 'sfcentral', 'sfdct', 'sfhotspot', 'sfnetworks', 'sftrack', 'sgsR', 'ShapePattern', 'shapes', 'ShapeSelectForest', 'SHAPforxgboost', 'shapviz', 'ShellChron', 'shelter', 'shiny.benchmark', 'shinybrms', 'shinyCohortBuilder', 'shinyIRT', 'ShinyItemAnalysis', 'shinyRGL', 'shinytest2', 'shrinkDSM', 'SIAmodules', 'SIGN', 'siland', 'simCAT', 'SimDesign', 'SimInf', 'SimNPH', 'simplePHENOTYPES', 'simplexreg', 'SimRDS', 'SimSurvey', 'simulariatools', 'sirad', 'sisireg', 'sits', 'SLBDD', 'slideview', 'smartmap', 'smcryptoR', 'SMDIC', 'smile', 'SMITIDstruct', 'smlmkalman', 'smoothAPC', 'smosr', 'snplinkage', 'sociome', 'sodium', 'SoilSaltIndex', 'spacejamr', 'SpaDES', 'SpaDES.core', 'SpaDES.tools', 'spANOVA', 'sparrpowR', 'sparseCov', 'SPARSEMODr', 'SpatGC', 'SpatGRID', 'spatialEco', 'SpatialEpi', 'SpatialfdaR', 'SpatialGraph', 'SpatialKDE', 'SpatialPosition', 'spatialreg', 'SpatialRegimes', 'SpaTopic', 'spatsurv', 'spbal', 'spDates', 'spdynmod', 'spectacles', 'spectator', 'spectralR', 'spectrino', 'Spectrum', 'speech', 'spemd', 'spex', 'spGARCH', 'sphereplot', 'sphet', 'spidR', 'spldv', 'splm', 'spm', 'spm2', 'spsur', 'spup', 'SQL', 'SQRL', 'SRTsim', 'ssdGSA', 'SSDM', 'ssfa', 'ssh', 'SSIMmap', 'SSN2', 'SSNbayes', 'SSNbler', 'sta', 'stacomiR', 'stacomirtools', 'stampr', 'stan4bart', 'stars', 'starsExtra', 'starsTileServer', 'StatDA', 'statgenMPP', 'stcos', 'stelfi', 'stepgbm', 'steprf', 'steps', 'stfit', 'stopp', 'stops', 'stpphawkes', 'stppSim', 'strand', 'stratbr', 'StratifiedRF', 'StreamMetabolism', 'streetscape', 'string2path', 'stxplore', 'SubTS', 'SubtypeDrug', 'SUNGEO', 'SurfaceTortoise', 'SurrogateRsq', 'surrosurv', 'surveyPrev', 'surveyvoi', 'survivalMPLdc', 'survSNP', 'svars', 'swaRmverse', 'swfscAirDAS', 'swfscDAS', 'SWMPrExtension', 'symbolicDA', 'symbolicQspray', 'symengine', 'SymTS', 'T4cluster', 'tabularaster', 'tailDepFun', 'tanaka', 'taskscheduleR', 'tcpl', 'TDAkit', 'TDLM', 'tealeaves', 'tectonicr', 'telefit', 'TensorTools', 'terra', 'terrainr', 'tessellation', 'tesseract', 'TestGardener', 'texor', 'texPreview', 'TextForecast', 'textshaping', 'tfevents', 'tggd', 'thames', 'theft', 'theftdlc', 'threeBrain', 'tidybins', 'tidycensus', 'TidyConsultant', 'tidygeoRSS', 'tidync', 'tidyplots', 'tidyrgee', 'tidysdm', 'tidyterra', 'tigris', 'tiledb', 'timeLineGraphics', 'TimeVizPro', 'tkImgR', 'tkRplotR', 'tmap', 'tmaptools', 'TML', 'TOC', 'togglr', 'tongfen', 'Toothnroll', 'topicdoc', 'topicmodels', 'topoDistance', 'toxSummary', 'TPMplt', 'track2KBA', 'trackeRapp', 'traineR', 'transformr', 'transfR', 'traveltimeR', 'trigpoints', 'tripEstimation', 'TroublemakeR', 'trtswitch', 'truh', 'TSCI', 'TUFLOWR', 'tvthemes', 'twangMediation', 'twangRDC', 'uavRmp', 'udunits2', 'ugatsdb', 'ulex', 'ultrapolaRplot', 'UnalR', 'UniprotR', 'units', 'upstartr', 'ursa', 'usdm', 'valuemap', 'VancouvR', 'vapour', 'VBLPCM', 'VC2copula', 'vein', 'versioning', 'vines', 'virtualspecies', 'virtuoso', 'visaOTR', 'visStatistics', 'visualpred', 'visvow', 'vivid', 'vmeasur', 'voi', 'vol2birdR', 'voluModel', 'vvauditor', 'wactor', 'wallace', 'warabandi', 'washr', 'WaveletMLbestFL', 'waver', 'waves', 'WCluster', 'wdnr.gis', 'wdpar', 'weatherOz', 'webglobe', 'webSDM', 'WEGE', 'weightedGCM', 'wiesbaden', 'wildlifeDI', 'windAC', 'WMAP', 'WQM', 'xgb2sql', 'xgboost', 'xrf', 'xRing', 'xslt', 'zcurve', 'zonebuilder', 'zoomerjoin'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'alpine-320'))"
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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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# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
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# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
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# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
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# ROracle: sysdep missing -> create rule
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# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
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# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
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# RmecabKo: fatal error: mecab.h: No such file or directory
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# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
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# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
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# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
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# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
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# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
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# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
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# Racmacs -> rmarchingcubes
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# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
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# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
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# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
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# clrng -> gpuR
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# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
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# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
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# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
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# magickGUI, biplotbootGUI
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# ymd (alpine, voi)
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# tfrmtbuilder -> V8 (alpine)
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# Rcmdr (alpine)
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# readstata13 (alpine)
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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 = "amd64"))'
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backend_options:
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kubernetes:
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resources:
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requests:
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memory: 5Gi
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cpu: 2000m
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limits:
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memory: 20Gi
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cpu: 3000m
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nodeSelector:
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kubernetes.io/arch: amd64
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node.kubernetes.io/instance-type: AX42
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tolerations:
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- key: 'CI'
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operator: 'Equal'
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value: 'true'
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effect: 'NoSchedule' |