99 lines
No EOL
13 KiB
YAML
99 lines
No EOL
13 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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- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/alpine320/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 == 'alpine-320', arch == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('doBy', 'DoE.base', 'DoE.wrapper', 'eha', 'FeedbackTS', 'fgdr', 'fgm', 'FGRepo', 'FIESTA', 'FIESTAutils', 'finch', 'fingerPro', 'finnsurveytext', 'finnts', 'fisheye', 'fishRman', 'fitbitViz', 'flan', 'flexCWM', 'FlexScan', 'flood', 'flow', 'fmdu', 'fmf', 'fnets', 'foodingraph', 'forecastLSW', 'ForecastTB', 'forensIT', 'forestecology', 'forestRK', 'FORTLS', 'fossilbrush', 'foundry', 'FPCdpca', 'fPortfolio', 'frailtyMMpen', 'FRAPO', 'FreeSortR', 'FrF2', 'FrF2.catlg128', 'fRLR', 'frontiles', 'frscore', 'fsbrain', 'FSK2R', 'fsn', 'fsr', 'fssemR', 'func2vis', 'funspace', 'FuzzyLP', 'FWRGB', 'GADAG', 'gamCopula', 'gasanalyzer', 'gateR', 'gatoRs', 'gbeta', 'gbifdb', 'gbm.auto', 'gdalcubes', 'gdalraster', 'gdalUtilities', 'gdiff', 'gdistance', 'gecko', 'gellipsoid', 'gemtc', 'gen3sis', 'GeneralisedCovarianceMeasure', 'GeneralizedWendland', 'GeNetIt', 'genlasso', 'GENLIB', 'GenoTriplo', 'gensphere', 'GeoAdjust', 'geodata', 'geodiv', 'geodrawr', 'geoelectrics', 'GeoFIS', 'geogrid', 'geojson', 'geojsonio', 'geomander', 'geomerge', 'geomod', 'geonapi', 'geonetwork', 'geonode4R', 'GeoRange', 'geosptdb', 'geostatsp', 'geotopbricks', 'geoTS', 'GeoWeightedModel', 'geppe', 'geslaR', 'gfcanalysis', 'ggaligner', 'ggalt', 'ggautomap', 'ggbrain', 'ggdag', 'ggESDA', 'ggfacto', 'ggfx', 'ggiraphExtra', 'ggmapinset', 'ggOceanMaps', 'GGoutlieR', 'ggraph', 'GGRidge', 'ggseg', 'ggspatial', 'giacR', 'gifski', 'GIFT', 'gimme', 'GIMMEgVAR', 'gimms', 'GiniDistance', 'GInSARCorW', 'GISINTEGRATION', 'GISSB', 'gittargets', 'GJRM', 'GLCMTextures', 'gllvm', 'glmtoolbox', 'glober', 'glossa', 'glpkAPI', 'gmDatabase', 'gmp', 'GMPro', 'GNAR', 'GOCompare', 'gofcat', 'gofCopula', 'GoodFibes', 'GoodFitSBM', 'gor', 'gosset', 'GOxploreR', 'gp', 'GPBayes', 'gpboost', 'GPCERF', 'gpg', 'GPGame', 'GPoM', 'gps.track', 'GPSeqClus', 'gpuR', 'gRain', 'grainscape', 'graphclust', 'graphicalVAR', 'graphkernels', 'graphsim', 'graticule', 'gRaven', 'gRbase', 'gRc', 'GREENeR', 'GREMLINS', 'Greymodels', 'gRim', 'gromovlab', 'grPipe', 'GRShiny', 'GSD', 'GSEMA', 'gsl', 'gslnls', 'gtfs2gps', 'gumboot', 'gunit', 'gwavr', 'gwid', 'GWpcor', 'gwpcormapper', 'GWSDAT', 'gyro', 'h3jsr', 'habCluster', 'handwriter', 'haplotypes', 'happign', 'HCTDesign', 'hdf5r', 'hdf5r.Extra', 'HDiR', 'hdmed', 'HDSpatialScan', 'healthyverse', 'HellCor', 'hellorust', 'helsinki', 'hemispheR', 'heterogen', 'HeteroGGM', 'heteromixgm', 'hexSticker', 'hglasso', 'hilldiv', 'hillshader', 'himach', 'HMMcopula', 'HOasso', 'hosm', 'HospitalNetwork', 'hspm', 'htmldf', 'HTT', 'huge', 'HUM', 'HybridMicrobiomes', 'hydroloom', 'hyfo', 'hyper.fit', 'HyperG', 'hypergeo2', 'HypergeoMat', 'hypervolume', 'hypsoLoop', 'hySAINT', 'IAcsSPCR', 'IATscores', 'ibmdbR', 'icardaFIGSr', 'ICDS', 'IceSat2R', 'icesConnect', 'icesDatsu', 'icesDatsuQC', 'icesSD', 'icosa', 'ICSClust', 'IDE', 'IDEATools', 'iDINGO', 'IDMIR', 'idopNetwork', 'IDPmisc', 'ieegio', 'ife', 'igraphinshiny', 'iGraphMatch', 'igraphtosonia', 'igraphwalshdata', 'iimi', 'image.binarization', 'image.textlinedetector', 'imagerExtra', 'imageseg', 'imbalanceDatRel', 'ImHD', 'IMIFA', 'immcp', 'immuneSIM', 'ImportExport', 'imsig', 'indelmiss', 'ineAtlas', 'inferCSN', 'influential', 'Infusion', 'INLABMA', 'intamap', 'intamapInteractive', 'integr', 'interpolation', 'intkrige', 'intRinsic', 'intSDM', 'IOLS', 'ipADMIXTURE', 'ipanema', 'IPCAPS', 'ipdw', 'iPRISM', 'ipsecr', 'irboost', 'IRexamples', 'IRkernel', 'irtawsi', 'irtpwr', 'irtQ', 'irtreliability', 'IsingFit', 'isocat', 'ISRaD', 'iSTATS', 'itcSegment', 'itsdm', 'ivdoctr', 'ixplorer', 'jdenticon', 'Jdmbs', 'jeek', 'jewel', 'JFM', 'JGL', 'jmastats', 'jmBIG', 'jpgrid', 'jpmesh', 'jrSiCKLSNMF', 'jrt', 'jSDM', 'jstager', 'Karen', 'kazaam', 'kDGLM', 'kehra', 'kequate', 'kernhaz', 'KernSmoothIRT', 'KeyboardSimulator', 'kgraph', 'KinMixLite', 'kissmig', 'kknn', 'kml3d', 'KMLtoSHAPE', 'kpcaIG', 'kpcalg', 'L1centrality', 'l1spectral', 'LabourMarketAreas', 'LAGOSNE', 'lagsarlmtree', 'LAIr', 'lakemorpho', 'landform', 'landsepi', 'lar', 'lavaan.shiny', 'lazysf', 'LBPG', 'LCMCR', 'lcopula', 'LDABiplots', 'LDAShiny', 'LDATS', 'LDM', 'leafem', 'leafpop', 'leafR', 'LeArEst', 'LearnClust', 'LearningRlab', 'learnPopGen', 'leidenAlg', 'leidenbase', 'letsR', 'lgcp', 'lgpr', 'Libra', 'libstable4u', 'lidaRtRee', 'lidR', 'LifemapR', 'limorhyde2', 'lingtypology', 'link2GI', 'linkcomm', 'linkspotter', 'LipidomicsR', 'LMoFit', 'LncPath', 'lnmixsurv', 'locits', 'lofifonts', 'lordif', 'lpacf', 'lpda', 'LPKsample', 'LPmerge', 'LS2Wstat', 'LSAfun', 'LSVAR', 'LTAR', 'lucas', 'LUCIDus', 'lulcc', 'lvnet', 'lwgeom', 'M3', 'macroBiome', 'macrosyntR', 'MadanText', 'MadanTextNetwork', 'Maeswrap', 'magick', 'MainExistingDatasets'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy')); 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' |