97 lines
No EOL
11 KiB
YAML
97 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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- 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('A3', 'AalenJohansen', 'AATtools', 'ABACUS', 'abasequence', 'abbreviate', 'ABCanalysis', 'abc.data', 'abclass', 'ABCoptim', 'ABCp2', 'ABC.RAP', 'abcrf', 'abcrlda', 'abctools', 'abd', 'abdiv', 'abe', 'aberrance', 'abess', 'abglasso', 'ABHgenotypeR', 'abind', 'abjData', 'abjutils', 'ablasso', 'ABM', 'abmR', 'abn', 'abnormality', 'abodOutlier', 'ABPS', 'abseil', 'absorber', 'abstr', 'abstractr', 'ABSurvTDC', 'abtest', 'abundant', 'Ac3net', 'AcademicThemes', 'academictwitteR', 'acc', 'acca', 'accelerometry', 'accelmissing', 'AccelStab', 'accept', 'AcceptanceSampling', 'AcceptReject', 'accessibility', 'accessr', 'accessrmd', 'accrual', 'accrualPlot', 'accSDA', 'accucor', 'accumulate', 'acdcquery', 'acdcR', 'ACDm', 'ace2fastq', 'acebayes', 'ACE.CoCo', 'aceEditor', 'acepack', 'ACEsearch', 'ACEsimFit', 'ACEt', 'acfMPeriod', 'Achilles', 'acid', 'acled.api', 'ACNE', 'acnr', 'acopula', 'acoRn', 'AcousticNDLCodeR', 'acp', 'acro', 'acroname', 'AcrossTic', 'acs', 'acss', 'acss.data', 'ACSSpack', 'ACSWR', 'act', 'ACTCD', 'ActCR', 'actel', 'ActFrag', 'actilifecounts', 'ActiSleep', 'activAnalyzer', 'activatr', 'ActiveDriver', 'activegp', 'ActivePathways', 'adapt4pv', 'ade4', 'aebdata', 'airt', 'AIscreenR', 'ALFAM2', 'AlleleShift', 'alookr', 'amadeus', 'Amelia', 'AntMAN', 'APCalign', 'archive', 'arkhe', 'audrex', 'autoBagging', 'autoFC', 'autostats', 'av', 'baguette', 'bartCause', 'bartMan', 'base64', 'basemaps', 'bayesMig', 'bayesTFR', 'BayesXsrc', 'bbotk', 'BED', 'BeeBDC', 'BiDAG', 'BifactorIndicesCalculator', 'bigD', 'bigGP', 'BINtools', 'biogrowth', 'BioPred', 'BiplotGUI', 'blackmarbler', 'blatr', 'BoolFilter', 'brickster', 'brsim', 'BRugs', 'bscui', 'bullseye', 'C50', 'CAinterprTools', 'CaseBasedReasoning', 'CausalGPS', 'cbl', 'CERFIT', 'CIMTx', 'ClickHouseHTTP', 'clrng', 'ClusVis', 'cmprskcoxmsm', 'conos', 'ConvertPar', 'CoTiMA', 'countSTAR', 'CRE', 'creditmodel', 'crumble', 'csmpv', 'ctgdist', 'CTRing', 'D3mirt', 'd4storagehub4R', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'dartR.sim', 'dartR.spatial', 'dataone', 'datapack', 'dataspice', 'dbarts', 'dblr', 'ddml', 'DeepLearningCausal', 'dendroNetwork', 'DFIT', 'DGP4LCF', 'DICEM', 'diffdfs', 'diffeRenTES', 'DImodelsVis', 'DIscBIO', 'disclosuR', 'DiSCos', 'disk.frame', 'dismo', 'disparityfilter', 'dispeRse', 'dissever', 'distinctiveness', 'diversitree', 'divraster', 'dm', 'DMMF', 'DNAmixturesLite', 'DNetFinder', 'do3PCA', 'doconv', 'DoE.wrapper', 'DominoDataR', 'doMPI', 'doolkit', 'doRedis', 'dots', 'DoubleML', 'doublIn', 'downscale', 'dowser', 'dpkg', 'drake', 'DRHotNet', 'DR.SC', 'DrugSim2DR', 'DRviaSPCN', 'DSAM', 'dsem', 'dsims', 'dsmSearch', 'dssd', 'Dtableone', 'dtComb', 'dti', 'DTSEA', 'DTSR', 'dupNodes', 'DWLasso', 'DWLS', 'dycdtools', 'dymo', 'dynamAedes', 'dynamicSDM', 'dynatopGIS', 'dynetNLAResistance', 'dyngen', 'dynr', 'dynwrap', 'easybgm', 'easyDifferentialGeneCoexpression', 'easyNCDF', 'easySdcTable', 'EBcoBART', 'ebdbNet', 'ebmc', 'eCerto', 'ech', 'ecochange', 'ecocomDP', 'ecoCopula', 'econet', 'EcoNetGen', 'econetwork', 'economiccomplexity', 'ecopower', 'ecospat', 'edgebundleR', 'ediblecity', 'eDITH', 'edmcr', 'EDOIF', 'eegkit', 'eemdARIMA', 'EEMDelm', 'EEMDlstm', 'eemdTDNN', 'EFA.dimensions', 'EFAfactors', 'egor', 'eHDPrep', 'ehymet', 'ei', 'EIX', 'eixport', 'eks', 'elastes', 'EloOptimized', 'EloSteepness', 'elsa', 'emailjsr', 'EMAS', 'EMbC', 'emdi', 'EmissV', 'EMJMCMC', 'emplikAUC', 'EMSS', 'emstreeR', 'eNchange', 'EnergyOnlineCPM', 'enerscape', 'ENMeval', 'enmpa', 'enmSdmX'); 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 = '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' |