build alpine-321
This commit is contained in:
parent
722e0477dd
commit
9b4f69a79a
GPG key ID:
3C6318841EF78925
50 changed files with 2922 additions and 130 deletions
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@ -10,12 +10,24 @@ 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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RED_HAT_DEV_PW:
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from_secret: red_hat_dev_pw
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AWS_ACCESS_KEY_ID:
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from_secret: aws_access_key_id
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AWS_SECRET_ACCESS_KEY:
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from_secret: aws_secret_access_key
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PGPASS:
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from_secret: pgpass
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GIT_RO_TOEN:
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from_secret: git_ro_token
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GITHUB_PAT:
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from_secret: github_pat
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# normal env vars
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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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@ -31,11 +43,9 @@ steps:
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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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- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git .
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- git clone https://pat-s:$$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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# for some reason paks pkgcache is often corrupt- 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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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
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@ -34,12 +34,24 @@ steps:
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effect: 'NoSchedule'
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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/arm64-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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RED_HAT_DEV_PW:
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from_secret: red_hat_dev_pw
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AWS_ACCESS_KEY_ID:
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from_secret: aws_access_key_id
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AWS_SECRET_ACCESS_KEY:
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from_secret: aws_secret_access_key
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PGPASS:
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from_secret: pgpass
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GIT_RO_TOEN:
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from_secret: git_ro_token
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GITHUB_PAT:
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from_secret: github_pat
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# normal env vars
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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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@ -55,16 +67,14 @@ steps:
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volumes:
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- arm64-binaries-r-dep-cache-alpine-320:/mnt/cache
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commands:
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- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git .
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- git clone https://pat-s:$$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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# for some reason paks pkgcache is often corrupt- 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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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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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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# 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); library(dplyr); library(bincraftR); pkgs = c('SignifReg', 'signnet', 'signs', 'SigOptR', 'sigora', 'sigQC', 'sigr', 'SigTree', 'SIHR', 'siie', 'siland', 'SILFS', 'SILGGM', 'silicate', 'SillyPutty', 'SILM', 'silp', 'sim.BA', 'Sim.DiffProc', 'Sim.PLFN', 'sim1000G', 'sim2Dpredictr', 'simaerep', 'SimBIID', 'simboot', 'simCAT', 'simcausal', 'simcdm', 'SimComp', 'SimCop', 'SimCorMultRes', 'SimCorrMix', 'simcross', 'simDAG', 'simdd', 'SimDesign', 'SimDissolution', 'simdistr', 'simDNAmixtures', 'simecol', 'simEd', 'SimEngine', 'simer', 'simest', 'simET', 'SimEUCartelLaw', 'simex', 'simexaft', 'simExam', 'SIMEXBoost', 'simfam', 'simfinapi', 'simfit', 'simFrame', 'simglm', 'simgof', 'SimHaz', 'simhelpers', 'SIMICO', 'simIDM', 'SimilarityMeasures', 'Simile', 'SimInf', 'simIReff', 'simitation', 'simITS', 'SimJoint', 'simlandr', 'SIMle', 'simmer', 'simmer.bricks', 'simmer.plot', 'simMetric', 'simml', 'simMP', 'simmr', 'SIMMS', 'simMSM', 'SimMultiCorrData', 'SimNPH', 'simode', 'simodels', 'simPH', 'simphony', 'simplace', 'simplanonym', 'SIMPLE.REGRESSION', 'simpleboot', 'simpleCache', 'simplecolors', 'simpleFDR', 'simplegraph', 'simplegraphdb', 'simpleMH', 'simpleMLP', 'simpleNeural', 'simplePHENOTYPES', 'simpleRCache', 'simplermarkdown', 'simpleSetup', 'simpletex', 'simplexreg', 'simplextree', 'SimplicialCubature', 'simplifyNet', 'SimplyAgree', 'SIMplyBee', 'simPop', 'simpr', 'simputation', 'simr', 'simrec', 'SimReg', 'simrel', 'simRestore', 'SiMRiv', 'sims', 'simsalapar', 'simsem', 'SimSeq', 'simsl', 'SimSST', 'simstandard', 'simstudy', 'simsurv', 'SimSurvey', 'SimSurvNMarker', 'simTargetCov', 'simtimer', 'SimTimeVar', 'simTool', 'simtrait', 'simts', 'simuclustfactor', 'simukde', 'simulariatools', 'simulator', 'simule', 'simulMGF', 'SimVitD', 'sinaplot', 'sinar', 'sindyr', 'sinew', 'singcar', 'SingleCaseES', 'singleCellHaystack', 'singR', 'sinib', 'SINRELEF.LD', 'SIPDIBGE', 'SIPETool', 'SiPhyNetwork', 'siplab', 'siqr', 'sirad', 'SIRE', 'SIRmcmc', 'sirt', 'SIRthresholded', 'sirus', 'SIS', 'SISIR', 'sisireg', 'sistec', 'sisti', 'sistmr', 'sisVIVE', 'SIT', 'sitar', 'sitepickR', 'siteymlgen', 'SITH', 'sitmo', 'sitools', 'sitree', 'sitreeE', 'sits', 'sivs', 'SixSigma', 'SizeEstimation', 'sizeMat', 'SiZer', 'sjdbc', 'sjlabelled', 'sjmisc', 'sjSDM', 'sjstats', 'sjtable2df', 'SK4FGA', 'SKAT', 'skater', 'skedastic', 'skeletor', 'skellam', 'sketch', 'sketcher', 'sketching', 'sketchy', 'SkewHyperbolic', 'skewlmm', 'skewMLRM', 'skewsamp', 'skewt', 'SKFCPD', 'Skillings.Mack', 'skilljaR', 'skimr', 'skipTrack', 'sklarsomega', 'skm', 'SKNN', 'skpr', 'skylight', 'skyscapeR', 'slackr', 'slanter', 'slap', 'slasso', 'SLBDD', 'SLCARE', 'slcm', 'sld', 'SLDAssay', 'sleekts', 'SleepCycles', 'sleepr', 'sleepwalk', 'SLEMI', 'Sleuth2', 'Sleuth3', 'slfm', 'SLFPCA', 'slgf', 'SLHD', 'SlicedLHD', 'slickR', 'SLIDE', 'slideview', 'SlidingWindows', 'slim', 'slimrec', 'slippymath', 'slm', 'SLModels', 'sloop', 'SLOPE', 'slouch', 'slowraker', 'slp', 'SLPresElection', 'slr', 'SLSEdesign', 'SLTCA', 'slurmR', 'sm', 'smaa', 'smacof', 'smacofx', 'smallarea', 'SmallCountRounding', 'smallsets', 'smallstuff', 'smam', 'SMARTbayesR', 'smartDesign', 'SmartEDA', 'SmarterPoland', 'smartmap', 'SmartMeterAnalytics', 'SMARTp', 'smartsheetr', 'smartsizer', 'smartsnp', 'SmartSVA', 'smatr', 'smbinning', 'SmCCNet', 'SMCRM', 'smcryptoR', 'smcure', 'smd', 'smdata', 'smdi', 'SMDIC', 'smdocker', 'smerc', 'smetlite', 'SMFilter', 'smfishHmrf', 'smfsb', 'smicd', 'smidm', 'smile', 'smiles', 'smirnov', 'SmithWilsonYieldCurve', 'SMITIDstruct', 'SMITIDvisu', 'SMLE', 'smlePH', 'smlmkalman', 'SMLoutliers', 'SMM', 'SMMA', 'SMME', 'smmR', 'SMMT', 'SMNCensReg', 'smoke', 'smoof', 'smooth', 'smoothAPC', 'smoothedLasso', 'smoother', 'SmoothHazard', 'smoothHR', 'smoothic', 'smoothmest', 'smoothr', 'smoothROCtime', 'smoothSurv', 'smoothtail', 'SmoothTensor', 'SmoothWin', 'smoothy', 'smoots', 'smosr', 'smotefamily', 'SMOTEWB', 'smovie', 'smpic', 'smplot2', 'SMPracticals', 'SMR', 'sms', 'sMSROC', 'smss', 'sMTL', 'SMUT', 'SMVar', 'smvgraph', 'sn', 'sna', 'snahelper', 'Snake', 'snakecase', 'SnakesAndLaddersAnalysis', 'snap', 'snapchatadsR', 'snapKrig', 'snapshot', 'SNBdata', 'snem', 'snfa', 'SNFtool', 'snha', 'snn', 'snow', 'SnowballC', 'snowboot', 'snowfall', 'snowflakes', 'snowFT', 'snowquery'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'doBy', 'DoE.base', 'DoE.wrapper', 'eha', 'FrF2', 'FrF2.catlg128', 'gRbase', 'gRain', 'IDPmisc', 'pbkrtest', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'spdep')); 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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- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); library(dplyr); library(bincraftR); pkgs = c('snpAIMeR', 'SNPannotator', 'SNPfiltR', 'SNPknock', 'snplinkage', 'snplist', 'sNPLS', 'snpReady', 'snpsettest', 'sns', 'SNSchart', 'SNSeg', 'SNSequate', 'SNSFdatasets', 'snSMART', 'snvecR', 'SNVLFDR', 'SOAR', 'SOAs', 'sobolnp', 'SobolSequence', 'soc.ca', 'socceR', 'social', 'socialh', 'socialmixr', 'socialranking', 'socialrisk', 'sociome', 'socviz', 'sodavis', 'sodium', 'sofa', 'Sofi', 'SOFIA', 'SoftBart', 'softbib', 'SoftClustering', 'softImpute', 'SOHPIE', 'SOIL', 'soilchemistry', 'SoilConservation', 'SoilFDA', 'soilfoodwebs', 'SoilFunctionality', 'SoilHyP', 'soilhypfit', 'SoilManageR', 'soilphysics', 'SoilR', 'SoilSaltIndex', 'SoilTaxonomy', 'soiltestcorr', 'SoilTesting', 'soiltexture', 'soilwater', 'Sojourn.Data', 'sokoban', 'solaR', 'solaR2', 'solarPos', 'solitude', 'solrad', 'solrium', 'solvebio', 'SolveSAPHE', 'som', 'som.nn', 'soma', 'SomaDataIO', 'somaticflags', 'SOMbrero', 'someMTP', 'SOMEnv', 'SOMMD', 'sommer', 'SOMnmR', 'somspace', 'sonar', 'SongEvo', 'sonicLength', 'sonicscrewdriver', 'sonify', 'SOP', 'SOPC', 'SOPIE', 'soptdmaeA', 'soql', 'SOR', 'sorcering', 'sorocs', 'SorptionAnalysis', 'sortable', 'SortedEffects', 'sorvi', 'sos', 'sotkanet', 'sotu', 'sound', 'soundClass', 'soundecology', 'SoundexBR', 'soundgen', 'SoupX', 'SouthParkRshiny', 'sovereign', 'SoyNAM', 'SoyURT', 'sp', 'SP2000', 'sp23design', 'spaa', 'spAbundance', 'SpaCCI', 'spacefillr', 'spacejamr', 'spaceNet', 'spacesXYZ', 'spacetime', 'SpaceTimeBSS', 'SpaCOAP', 'spacyr', 'SPADAR', 'spAddins', 'SpadeR', 'SpaDES', 'SpaDES.core', 'SpaDES.tools', 'spaero', 'spagmix', 'spam', 'spam64', 'spaMM', 'spanish', 'spANOVA', 'sparcl', 'spark.sas7bdat', 'sparkavro', 'sparkbq', 'sparkhail', 'sparkline', 'sparklyr', 'sparklyr.flint', 'sparklyr.nested', 'sparktex', 'sparktf', 'sparkwarc', 'sparkxgb', 'sparr', 'sparrpowR', 'sparseBC', 'SparseBiplots', 'SparseChol', 'sparseCov', 'SparseDC', 'sparseDFM', 'sparsediscrim', 'sparseEigen', 'sparseFLMM', 'SparseFunClust', 'sparsegl', 'SparseGrid', 'sparseHessianFD', 'sparseIndexTracking', 'sparseinv', 'sparseLDA', 'SparseLPM', 'sparseLRMatrix', 'sparseLTSEigen', 'SparseM', 'sparseMatEst', 'SparseMDC', 'SPARSEMODr', 'SparseMSE', 'sparseMVN', 'sparsepca', 'sparsepp', 'sparseR', 'sparsereg', 'sparsestep', 'sparsesvd', 'sparseSVM', 'SparseTSCGM', 'sparsevar', 'sparsevb', 'sparsevctrs', 'SparseVFC', 'sparsio', 'SPARTAAS', 'sparvaride', 'SPAS', 'spass', 'spate', 'SpatEntropy', 'SPAtest', 'SpatFD', 'SpatGC', 'spatgeom', 'spatgraphs', 'SpatGRID', 'spaths', 'spatial', 'SpatialAcc', 'SpatialBSS', 'spatialCovariance', 'SpatialDDLS', 'spatialEco', 'SpatialEpi', 'SpatialExtremes', 'SpatialfdaR', 'SpatialGEV', 'SpatialGraph', 'spatialising', 'SpatialKDE', 'SpatialKWD', 'SpatialML', 'SpatialNP', 'SpatialPack', 'SpatialPOP', 'SpatialPosition', 'spatialprobit', 'SpatialRDD', 'SpatialRegimes', 'spatialRF', 'spatialrisk', 'SpatialRoMLE', 'spatialsample', 'spatialTIME', 'SpatialTools', 'SpatialVS', 'spatialwarnings', 'spatialwidget', 'SpatMCA', 'SpaTopic', 'SpatPCA', 'SpATS', 'spatsoc', 'spatstat.explore', 'spatstat.gui', 'spatstat.Knet', 'spatstat.local', 'spatstat.random', 'spatstat.sparse', 'spatsurv', 'SPB', 'spbabel', 'spbal', 'spBayes', 'spBayesSurv', 'spBFA', 'Spbsampling', 'spc', 'spc4sts', 'spcadjust', 'SPCALDA', 'SPCAvRP', 'SPCDAnalyze', 'SPCompute', 'spcosa', 'spcov', 'spCP', 'spcr', 'spd', 'spData', 'spDates', 'spectrino', 'stan4bart', 'StratifiedRF', 'surveyvoi', 'taskscheduleR', 'tern.rbmi', 'tesseract', 'tiledb', 'tkImgR', 'tkRplotR', 'valhallr', 'vchartr', 'voi', 'vol2birdR', 'xRing'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'doBy', 'DoE.base', 'DoE.wrapper', 'eha', 'FrF2', 'FrF2.catlg128', 'gRbase', 'gRain', 'IDPmisc', 'pbkrtest', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'spdep')); 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, MediaNews: Windows-only
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111
.woodpecker/build-alpine-321-amd64-1.yaml
Normal file
111
.woodpecker/build-alpine-321-amd64-1.yaml
Normal file
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@ -0,0 +1,111 @@
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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-321-amd64"'
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- event: manual
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evaluate: 'build == "alpine-321-amd64-1"'
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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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image: docker.io/devxygmbh/amd64-binaries-r-alpine-321
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pull: true
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environment:
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RED_HAT_DEV_PW:
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from_secret: red_hat_dev_pw
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AWS_ACCESS_KEY_ID:
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from_secret: aws_access_key_id
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AWS_SECRET_ACCESS_KEY:
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from_secret: aws_secret_access_key
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PGPASS:
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from_secret: pgpass
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GIT_RO_TOEN:
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from_secret: git_ro_token
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GITHUB_PAT:
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from_secret: github_pat
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# normal env vars
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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-321
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BLOCK_START: 1
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BLOCK_END: 2200
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ARCH: amd64
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NCPUS: 2
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STRATEGY: sequential
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volumes:
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- amd64-binaries-r-dep-cache-alpine-321:/mnt/cache
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commands:
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- git clone https://pat-s:$$GIT_RO_TOEN@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- 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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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
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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(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
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### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 5Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 20Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: AX42
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
111
.woodpecker/build-alpine-321-amd64-10.yaml
Normal file
111
.woodpecker/build-alpine-321-amd64-10.yaml
Normal file
|
|
@ -0,0 +1,111 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64-10"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/amd64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 19801
|
||||
BLOCK_END: 22000
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- 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))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 5Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 20Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: AX42
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
113
.woodpecker/build-alpine-321-amd64-2.yaml
Normal file
113
.woodpecker/build-alpine-321-amd64-2.yaml
Normal file
|
|
@ -0,0 +1,113 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64-2"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/amd64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 2201
|
||||
BLOCK_END: 4400
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- 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))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 5Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 20Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: AX42
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
113
.woodpecker/build-alpine-321-amd64-3.yaml
Normal file
113
.woodpecker/build-alpine-321-amd64-3.yaml
Normal file
|
|
@ -0,0 +1,113 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64-3"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/amd64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 4401
|
||||
BLOCK_END: 6600
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 5Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 20Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: AX42
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
111
.woodpecker/build-alpine-321-amd64-4.yaml
Normal file
111
.woodpecker/build-alpine-321-amd64-4.yaml
Normal file
|
|
@ -0,0 +1,111 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64-4"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/amd64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 6601
|
||||
BLOCK_END: 8800
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- 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))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 5Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 20Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: AX42
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
111
.woodpecker/build-alpine-321-amd64-5.yaml
Normal file
111
.woodpecker/build-alpine-321-amd64-5.yaml
Normal file
|
|
@ -0,0 +1,111 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64-5"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/amd64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 8801
|
||||
BLOCK_END: 11000
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- 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))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 5Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 20Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: AX42
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
113
.woodpecker/build-alpine-321-amd64-6.yaml
Normal file
113
.woodpecker/build-alpine-321-amd64-6.yaml
Normal file
|
|
@ -0,0 +1,113 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64-6"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/amd64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 11001
|
||||
BLOCK_END: 13200
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- 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))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 5Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 20Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: AX42
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
113
.woodpecker/build-alpine-321-amd64-7.yaml
Normal file
113
.woodpecker/build-alpine-321-amd64-7.yaml
Normal file
|
|
@ -0,0 +1,113 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64-7"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/amd64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 13201
|
||||
BLOCK_END: 15400
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 5Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 20Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: AX42
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
114
.woodpecker/build-alpine-321-amd64-8.yaml
Normal file
114
.woodpecker/build-alpine-321-amd64-8.yaml
Normal file
|
|
@ -0,0 +1,114 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64-8"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/amd64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 15401
|
||||
BLOCK_END: 17600
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
# -
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- 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))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 5Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 20Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: AX42
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
111
.woodpecker/build-alpine-321-amd64-9.yaml
Normal file
111
.woodpecker/build-alpine-321-amd64-9.yaml
Normal file
|
|
@ -0,0 +1,111 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-amd64-9"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/amd64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 17601
|
||||
BLOCK_END: 19800
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- 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))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 5Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 20Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: AX42
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
137
.woodpecker/build-alpine-321-arm64-1.yaml
Normal file
137
.woodpecker/build-alpine-321-arm64-1.yaml
Normal file
|
|
@ -0,0 +1,137 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64-1"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo 'Warmed Up'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
limits:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/arm64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 1
|
||||
BLOCK_END: 2200
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- 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))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 10Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 14Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
137
.woodpecker/build-alpine-321-arm64-10.yaml
Normal file
137
.woodpecker/build-alpine-321-arm64-10.yaml
Normal file
|
|
@ -0,0 +1,137 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64-10"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo 'Warmed Up'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
limits:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/arm64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 19801
|
||||
BLOCK_END: 22000
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 10Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 14Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
137
.woodpecker/build-alpine-321-arm64-2.yaml
Normal file
137
.woodpecker/build-alpine-321-arm64-2.yaml
Normal file
|
|
@ -0,0 +1,137 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64-2"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo 'Warmed Up'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
limits:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/arm64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 2201
|
||||
BLOCK_END: 4400
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- 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))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 10Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 14Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
137
.woodpecker/build-alpine-321-arm64-3.yaml
Normal file
137
.woodpecker/build-alpine-321-arm64-3.yaml
Normal file
|
|
@ -0,0 +1,137 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64-3"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo 'Warmed Up'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
limits:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/arm64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 4401
|
||||
BLOCK_END: 6600
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 10Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 14Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
136
.woodpecker/build-alpine-321-arm64-4.yaml
Normal file
136
.woodpecker/build-alpine-321-arm64-4.yaml
Normal file
|
|
@ -0,0 +1,136 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64-4"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo 'Warmed Up'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
limits:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/arm64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 6601
|
||||
BLOCK_END: 8800
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- 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))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 10Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 14Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
137
.woodpecker/build-alpine-321-arm64-5.yaml
Normal file
137
.woodpecker/build-alpine-321-arm64-5.yaml
Normal file
|
|
@ -0,0 +1,137 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64-5"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo 'Warmed Up'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
limits:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/arm64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 8801
|
||||
BLOCK_END: 11000
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 10Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 14Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
137
.woodpecker/build-alpine-321-arm64-6.yaml
Normal file
137
.woodpecker/build-alpine-321-arm64-6.yaml
Normal file
|
|
@ -0,0 +1,137 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64-6"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo 'Warmed Up'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
limits:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/arm64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 11001
|
||||
BLOCK_END: 13200
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- 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))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 10Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 14Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
137
.woodpecker/build-alpine-321-arm64-7.yaml
Normal file
137
.woodpecker/build-alpine-321-arm64-7.yaml
Normal file
|
|
@ -0,0 +1,137 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64"'
|
||||
- event: manual
|
||||
evaluate: 'build == "alpine-321-arm64-7"'
|
||||
- event: manual
|
||||
evaluate: 'build == "all-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo 'Warmed Up'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
limits:
|
||||
memory: 13Gi
|
||||
cpu: 3000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'Build binaries'
|
||||
image: docker.io/devxygmbh/arm64-binaries-r-alpine-321
|
||||
pull: true
|
||||
environment:
|
||||
RED_HAT_DEV_PW:
|
||||
from_secret: red_hat_dev_pw
|
||||
AWS_ACCESS_KEY_ID:
|
||||
from_secret: aws_access_key_id
|
||||
AWS_SECRET_ACCESS_KEY:
|
||||
from_secret: aws_secret_access_key
|
||||
PGPASS:
|
||||
from_secret: pgpass
|
||||
GIT_RO_TOEN:
|
||||
from_secret: git_ro_token
|
||||
GITHUB_PAT:
|
||||
from_secret: github_pat
|
||||
# normal env vars
|
||||
GIT_USER: pat-s
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
PLATFORM: alpine-321
|
||||
BLOCK_START: 13201
|
||||
BLOCK_END: 15400
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
STRATEGY: sequential
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-alpine-321:/mnt/cache
|
||||
commands:
|
||||
- git clone https://pat-s:$$GIT_RO_TOEN@git.devxy.io/devxy/r-pkg-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
||||
# for some reason paks pkgcache is often corrupt
|
||||
- export MAXWAIT=10; sleep $((RANDOM % MAXWAIT))
|
||||
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
|
||||
- R -q -e 'packageVersion("bincraftR")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd'
|
||||
- R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); if (file.exists(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')))) block_start = as.character(data.table::fread(sprintf('/mnt/cache/%s.txt', Sys.getenv('CI_WORKFLOW_NAME')), sep = '\t')) else block_start = Sys.getenv('BLOCK_START'); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[block_start:$BLOCK_END]; pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', '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 = 'alpine-321'))"
|
||||
### Manual pkg builds
|
||||
# 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
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# 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
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - 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"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 10Gi
|
||||
cpu: 1000m
|
||||
limits:
|
||||
memory: 14Gi
|
||||
cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax31
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: binwiederhier/ntfy:v2.11.0
|
||||
when:
|
||||
- status: [failure]
|
||||
environment:
|
||||
NTFY_TOKEN:
|
||||
from_secret: ntfy_token
|
||||
commands: |
|
||||
BUILD_INDEX=$(cat build_index.txt)
|
||||
ntfy publish --tags=no_entry_sign --token $NTFY_TOKEN -t "Run '${CI_REPO}' failed at $BUILD_INDEX" --click="${CI_PIPELINE_URL}" --actions="view, Open build, ${CI_PIPELINE_URL}, clear=true;" ntfy.devxy.io/ci-builds Workflow: ${CI_WORKFLOW_NAME} Commit message: ${CI_COMMIT_MESSAGE} Commit Author: ${CI_COMMIT_AUTHOR}
|
||||
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