build alpine-321

2024-12-06 18:11:14 +01:00 · 2024-12-06 18:11:14 +01:00 · 9b4f69a79a
commit 9b4f69a79a
parent 722e0477dd
1 changed files with 2922 additions and 130 deletions
--- a/.woodpecker/build-redhat-8-arm64.yaml
+++ b/.woodpecker/build-redhat-8-arm64.yaml
@ -34,12 +34,24 @@ steps:
            effect: 'NoSchedule'

  - name: 'Build binaries'
-    secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT]
    image: docker.io/devxygmbh/arm64-binaries-r-redhat-8
    pull: true
    # to ensure the PACKAGES upload step is being executed
    failure: ignore
    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
@ -55,15 +67,13 @@ steps:
    volumes:
      - arm64-binaries-r-dep-cache-redhat-8:/mnt/cache
    commands:
-      - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git .
+      - git clone https://pat-s:$$GIT_RO_TOKEN@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
-      - rm -rf /mnt/cache/R-pkgs/pkgcache/ /mnt/cache/pkgcache/ /root/.cache/R/
-      - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
+      # 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'
-      - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c('rubias', 'rucrdtw',  'rugarch', 'ruimtehol', 'runner', 'Runuran', 'ruv', 'rvalues',  'Rvcg', 'rvg', 'rviewgraph', 'rvinecopulib', 'Rwave', 'RWDataPlyr',  'RWeka', 'RWekajars', 'rwfec', 'RWiener', 'RWinEdt', 'RWNN',  'Rwofost', 'RxnSim', 'rxylib', 'Ryacas0', 'RZigZag', 'rzmq',  'RZooRoH', 's2', 's2net', 'saccadr', 'sads', 'saeczi', 'saeMSPE',  'saeRobust', 'SAGMM', 'SALES', 'salso', 'SAM', 'SAMGEP', 'samon',  'sampling', 'SamplingBigData', 'samplingVarEst', 'samplr', 'samurais',  'sanic', 'sanitizers', 'SANple', 'santoku', 'SANvi', 'SAPP',  'SAR', 'sarima', 'sarsop', 'sasfunclust', 'sass', 'satellite',  'SBCK', 'sbde', 'sbfc', 'sBIC', 'sbm', 'SBmedian', 'sbmSDP',  'sbo', 'sboost', 'sbrl', 'SC.MEB', 'scagnostics', 'Scalelink',  'ScaleSpikeSlab', 'scalpel', 'scar', 'ScatterDensity', 'scattermore',  'SCCI', 'scclust', 'sccore', 'scDHA', 'scellpam', 'SCEPtER',  'SCEPtERbinary', 'scINSIGHT', 'SCIntRuler', 'scistreer', 'scITD',  'scMappR', 'scModels', 'scoper', 'scorematchingad', 'scorepeak',  'scoringRules', 'SCORNET', 'scout', 'scquantum', 'scrm', 'scrypt',  'scs', 'sdcMicro', 'sdcTable', 'sde', 'sdetorus', 'sdmTMB', 'SDMtune',  'sdpdth', 'sdprisk', 'sdrt', 'sdwd', 'SearchTrees', 'seas', 'secretbase',  'secsse', 'secure', 'seededlda', 'segclust2d', 'segen', 'segmag',  'segmenTier', 'segmentr', 'segMGarch', 'seismicRoll', 'SEL',  'selectiveInference', 'SELF', 'SemiCompRisks', 'semidist', 'semver',  'sendigR', 'SensMap', 'SenSpe', 'sentencepiece', 'sentometrics',  'sentopics', 'SeqDetect', 'seqHMM', 'seqinr', 'SeqKat', 'seqminer',  'SeqNet', 'seqtrie', 'SequenceSpikeSlab', 'sequoia', 'serrsBayes',  'Seurat', 'SeuratObject', 'sfcr', 'sfcurve', 'sfheaders', 'SFS',  'SFSI', 'sgd', 'SGDinference', 'sgeostat', 'SGL', 'sglasso',  'sgolay', 'SGPR', 'shapes', 'shapr', 'sharpeRratio', 'sharpPen',  'SheetReader', 'shide', 'ShiftConvolvePoibin', 'shiftR', 'shinyExprPortal',  'shinylive', 'shinyMixR', 'shinyRGL', 'showtext', 'shp2graph',  'shrinkDSM', 'shrinkTVP', 'SHT', 'Sieve', 'sift', 'signal', 'signalHsmm',  'signnet', 'SigTree', 'SILGGM', 'SimBIID', 'simcdm', 'simcross',  'simecol', 'simer', 'simest', 'SimEUCartelLaw', 'simfam', 'simFrame',  'SimInf', 'SimJoint', 'simmer', 'simplace', 'simplexreg', 'simplextree',  'simPop', 'simputation', 'SimReg', 'simRestore', 'SiMRiv', 'simstudy',  'SimSurvNMarker', 'simtrial', 'simts', 'singR', 'SiPhyNetwork',  'SIRmcmc', 'sirt'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'redhat-8'))"
+      - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c('sirus',  'sisireg', 'SIT', 'SITH', 'sitmo', 'sits', 'sjdbc', 'SK4FGA',  'SKAT', 'sketching', 'SKFCPD', 'sklarsomega', 'skm', 'skpr',  'slasso', 'SLBDD', 'slcm', 'sld', 'sleev', 'slfm', 'SLHD', 'slider',  'SLOPE', 'slp', 'smaa', 'smacof', 'smam', 'smfishHmrf', 'smfsb',  'smile', 'SMITIDvisu', 'SMMA', 'SMME', 'smmR', 'smoof', 'smooth',  'smoothAPC', 'SmoothHazard', 'smoothSurv', 'SMUT', 'smvgraph',  'sna', 'SnowballC', 'SNPknock', 'snplist', 'snpsettest', 'SNSeg',  'SobolSequence', 'socceR', 'social', 'sodium', 'SoftBart', 'softImpute',  'som', 'sorcering', 'SoundexBR', 'sourcetools', 'sp', 'spAbundance',  'spacefillr', 'SpaceTimeBSS', 'SpaCOAP', 'SpaDES.tools', 'spam',  'spam64', 'spaMM', 'sparcl', 'SparseChol', 'sparseDFM', 'sparsegl',  'sparseHessianFD', 'sparseinv', 'SparseLPM', 'sparseLTSEigen',  'SparseM', 'SPARSEMODr', 'sparsereg', 'sparseSEM', 'sparsesvd',  'sparseSVM', 'SparseTSCGM', 'sparsevb', 'sparsevctrs', 'sparsio',  'sparta', 'sparvaride', 'spass', 'spate', 'spatgraphs', 'spaths',  'spatial', 'SpatialBSS', 'SpatialEpi', 'SpatialExtremes', 'SpatialfdaR',  'SpatialGEV', 'spatialising', 'SpatialKDE', 'SpatialKWD', 'SpatialPack',  'spatialrisk', 'SpatialTools', 'spatialwarnings', 'spatialwidget',  'SpatMCA', 'SpaTopic', 'SpatPCA', 'spatstat.explore', 'spatstat.Knet',  'spatstat.random', 'spatstat.sparse', 'spbal', 'spBayes', 'spBayesSurv',  'spBFA', 'Spbsampling', 'spc', 'spcosa', 'spCP', 'spcr', 'spduration',  'speakeasyR', 'SPECIES', 'specklestar', 'specs', 'SpecsVerification',  'spectralGraphTopology', 'spectralR', 'spectre', 'spectrino',  'sped', 'speedytax', 'spfa', 'spFW', 'spGARCH', 'spgs', 'spgwr',  'sphereplot', 'sphunif', 'spiderbar', 'spikeslab', 'spikeSlabGAM',  'spinBayes', 'splancs', 'SPlit', 'SplitGLM', 'SplitReg', 'splmm',  'splusTimeDate', 'spMC', 'spNNGP', 'spOccupancy', 'sport', 'spray',  'spreadr', 'springer', 'sprintr', 'SPSP', 'spsurv', 'spTDyn',  'SpTe2M', 'spTimer', 'squat', 'srm', 'SRTsim', 'ssh', 'Sshaped',  'SSLR', 'ssMousetrack', 'SSN2', 'SSOSVM', 'sspse', 'stable',  'staggered', 'stan4bart', 'StanMoMo', 'STAREG', 'starma', 'starsExtra',  'STARTdesign', 'starvz', 'statcomp', 'StatDA', 'statgenIBD',  'statgenQTLxT', 'statip', 'STB', 'stcos', 'stcpR6', 'stdvectors',  'steepness', 'stelfi', 'stepPlr', 'stepR', 'steps', 'StepSignalMargiLike',  'stepSplitReg', 'StepwiseTest', 'stfit', 'stima', 'stlplus',  'StochBlock', 'stochQN', 'stockR', 'stocks', 'stopp', 'stops',  'stosim', 'stpm', 'stpp', 'stpphawkes', 'surveyvoi', 'symbolicDA',  'symbolicQspray', 'T4cluster', 'taskscheduleR', 'TDAkit', 'tessellation',  'TestGardener', 'thames', 'TML', 'Toothnroll', 'TPMplt', 'traineR',  'treats', 'trinROC', 'triptych', 'TSclust', 'TSCS', 'tsmarch',  'TUFLOWR', 'TukeyRegion', 'uavRmp', 'UBayFS', 'ucie', 'UCSCXenaShiny',  'UnalR', 'valhallr', 'valueSetCompare', 'vegan3d', 'vennplot',  'VICatMix', 'viewpoly', 'VIRF', 'vivid', 'voiceR', 'VOSONDash',  'vvdoctor', 'wallace', 'WaveletLSTM', 'WaverideR', 'WCluster',  'webglobe', 'x3ptools'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'redhat-8'))"
      ### 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
@ -105,22 +115,6 @@ steps:
          limits:
            memory: 14Gi
            cpu: 3000m
-        ### PROD-sequential
-        # resources:
-        #   requests:
-        #     memory: 14Gi
-        #     cpu: 2000m
-        #   limits:
-        #     memory: 14Gi
-        #     cpu: 3000m
-        # DEBUG
-        # resources:
-        #   requests:
-        #     memory: 4Gi
-        #     cpu: 2000m
-        #   limits:
-        #     memory: 4Gi
-        #     cpu: 2000m
        nodeSelector:
          kubernetes.io/arch: arm64
          node.kubernetes.io/instance-type: cax31