build alpine-321

.woodpecker/build-alpine-320-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-alpine-320
     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
@@ -55,16 +67,14 @@ steps:
     volumes:
       - arm64-binaries-r-dep-cache-alpine-320:/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
       - 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))'
       # 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); 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'))"
+      - 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'))"
       ### 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, MediaNews: Windows-only