From 9b4f69a79a9e2cb3d950562a3254b71581527b03 Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 6 Dec 2024 18:11:14 +0100 Subject: [PATCH] build alpine-321 --- .woodpecker/build-alpine-320-amd64.yaml | 20 ++- .woodpecker/build-alpine-320-arm64.yaml | 22 ++- .woodpecker/build-alpine-321-amd64-1.yaml | 111 ++++++++++++++ .woodpecker/build-alpine-321-amd64-10.yaml | 111 ++++++++++++++ .woodpecker/build-alpine-321-amd64-2.yaml | 113 +++++++++++++++ .woodpecker/build-alpine-321-amd64-3.yaml | 113 +++++++++++++++ .woodpecker/build-alpine-321-amd64-4.yaml | 111 ++++++++++++++ .woodpecker/build-alpine-321-amd64-5.yaml | 111 ++++++++++++++ .woodpecker/build-alpine-321-amd64-6.yaml | 113 +++++++++++++++ .woodpecker/build-alpine-321-amd64-7.yaml | 113 +++++++++++++++ .woodpecker/build-alpine-321-amd64-8.yaml | 114 +++++++++++++++ .woodpecker/build-alpine-321-amd64-9.yaml | 111 ++++++++++++++ .woodpecker/build-alpine-321-arm64-1.yaml | 137 ++++++++++++++++++ .woodpecker/build-alpine-321-arm64-10.yaml | 137 ++++++++++++++++++ .woodpecker/build-alpine-321-arm64-2.yaml | 137 ++++++++++++++++++ .woodpecker/build-alpine-321-arm64-3.yaml | 137 ++++++++++++++++++ .woodpecker/build-alpine-321-arm64-4.yaml | 136 +++++++++++++++++ .woodpecker/build-alpine-321-arm64-5.yaml | 137 ++++++++++++++++++ .woodpecker/build-alpine-321-arm64-6.yaml | 137 ++++++++++++++++++ .woodpecker/build-alpine-321-arm64-7.yaml | 137 ++++++++++++++++++ .woodpecker/build-alpine-321-arm64-8.yaml | 137 ++++++++++++++++++ .woodpecker/build-alpine-321-arm64-9.yaml | 137 ++++++++++++++++++ .woodpecker/build-redhat-8-amd64.yaml | 20 ++- .woodpecker/build-redhat-8-arm64.yaml | 38 ++--- .woodpecker/build-redhat-9-amd64.yaml | 20 ++- .woodpecker/build-redhat-9-arm64.yaml | 20 ++- .woodpecker/build-ubuntu-2204-amd64.yaml | 22 ++- .woodpecker/build-ubuntu-2204-arm64.yaml | 18 ++- .woodpecker/build-ubuntu-2404-amd64.yaml | 20 ++- .woodpecker/build-ubuntu-2404-arm64.yaml | 20 ++- .../process-updates-alpine-320-amd64.yaml | 17 ++- .../process-updates-alpine-320-arm64.yaml | 18 ++- .../process-updates-redhat-8-amd64.yaml | 21 ++- .../process-updates-redhat-8-arm64.yaml | 18 ++- .../process-updates-redhat-9-amd64.yaml | 18 ++- .../process-updates-redhat-9-arm64.yaml | 18 ++- .../process-updates-ubuntu-2204-amd64.yaml | 18 ++- .../process-updates-ubuntu-2204-arm64.yaml | 18 ++- .../process-updates-ubuntu-2404-amd64.yaml | 18 ++- .../process-updates-ubuntu-2404-arm64.yaml | 18 ++- ...update-package-index-alpine-320-amd64.yaml | 16 +- ...update-package-index-alpine-320-arm64.yaml | 16 +- .../update-package-index-redhat-8-amd64.yaml | 16 +- .../update-package-index-redhat-8-arm64.yaml | 16 +- .../update-package-index-redhat-9-amd64.yaml | 16 +- .../update-package-index-redhat-9-arm64.yaml | 16 +- ...pdate-package-index-ubuntu-2204-amd64.yaml | 16 +- ...pdate-package-index-ubuntu-2204-arm64.yaml | 16 +- ...pdate-package-index-ubuntu-2404-amd64.yaml | 16 +- ...pdate-package-index-ubuntu-2404-arm64.yaml | 16 +- 50 files changed, 2922 insertions(+), 130 deletions(-) create mode 100644 .woodpecker/build-alpine-321-amd64-1.yaml create mode 100644 .woodpecker/build-alpine-321-amd64-10.yaml create mode 100644 .woodpecker/build-alpine-321-amd64-2.yaml create mode 100644 .woodpecker/build-alpine-321-amd64-3.yaml create mode 100644 .woodpecker/build-alpine-321-amd64-4.yaml create mode 100644 .woodpecker/build-alpine-321-amd64-5.yaml create mode 100644 .woodpecker/build-alpine-321-amd64-6.yaml create mode 100644 .woodpecker/build-alpine-321-amd64-7.yaml create mode 100644 .woodpecker/build-alpine-321-amd64-8.yaml create mode 100644 .woodpecker/build-alpine-321-amd64-9.yaml create mode 100644 .woodpecker/build-alpine-321-arm64-1.yaml create mode 100644 .woodpecker/build-alpine-321-arm64-10.yaml create mode 100644 .woodpecker/build-alpine-321-arm64-2.yaml create mode 100644 .woodpecker/build-alpine-321-arm64-3.yaml create mode 100644 .woodpecker/build-alpine-321-arm64-4.yaml create mode 100644 .woodpecker/build-alpine-321-arm64-5.yaml create mode 100644 .woodpecker/build-alpine-321-arm64-6.yaml create mode 100644 .woodpecker/build-alpine-321-arm64-7.yaml create mode 100644 .woodpecker/build-alpine-321-arm64-8.yaml create mode 100644 .woodpecker/build-alpine-321-arm64-9.yaml diff --git a/.woodpecker/build-alpine-320-amd64.yaml b/.woodpecker/build-alpine-320-amd64.yaml index 716335b..778544a 100644 --- a/.woodpecker/build-alpine-320-amd64.yaml +++ b/.woodpecker/build-alpine-320-amd64.yaml @@ -10,12 +10,24 @@ skip_clone: true steps: - 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/amd64-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 @@ -31,11 +43,9 @@ steps: # volumes: # - amd64-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 # Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd' diff --git a/.woodpecker/build-alpine-320-arm64.yaml b/.woodpecker/build-alpine-320-arm64.yaml index ef11b51..ab833e6 100644 --- a/.woodpecker/build-alpine-320-arm64.yaml +++ b/.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 diff --git a/.woodpecker/build-alpine-321-amd64-1.yaml b/.woodpecker/build-alpine-321-amd64-1.yaml new file mode 100644 index 0000000..de05279 --- /dev/null +++ b/.woodpecker/build-alpine-321-amd64-1.yaml @@ -0,0 +1,111 @@ +when: + - event: manual + evaluate: 'build == "all"' + - event: manual + evaluate: 'build == "alpine-321-amd64"' + - event: manual + evaluate: 'build == "alpine-321-amd64-1"' + - 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: 1 + BLOCK_END: 2200 + 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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-amd64-10.yaml b/.woodpecker/build-alpine-321-amd64-10.yaml new file mode 100644 index 0000000..3d51e1f --- /dev/null +++ b/.woodpecker/build-alpine-321-amd64-10.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-amd64-2.yaml b/.woodpecker/build-alpine-321-amd64-2.yaml new file mode 100644 index 0000000..186b699 --- /dev/null +++ b/.woodpecker/build-alpine-321-amd64-2.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-amd64-3.yaml b/.woodpecker/build-alpine-321-amd64-3.yaml new file mode 100644 index 0000000..96bc054 --- /dev/null +++ b/.woodpecker/build-alpine-321-amd64-3.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-amd64-4.yaml b/.woodpecker/build-alpine-321-amd64-4.yaml new file mode 100644 index 0000000..5d340c9 --- /dev/null +++ b/.woodpecker/build-alpine-321-amd64-4.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-amd64-5.yaml b/.woodpecker/build-alpine-321-amd64-5.yaml new file mode 100644 index 0000000..bb787a4 --- /dev/null +++ b/.woodpecker/build-alpine-321-amd64-5.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-amd64-6.yaml b/.woodpecker/build-alpine-321-amd64-6.yaml new file mode 100644 index 0000000..3462d0a --- /dev/null +++ b/.woodpecker/build-alpine-321-amd64-6.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-amd64-7.yaml b/.woodpecker/build-alpine-321-amd64-7.yaml new file mode 100644 index 0000000..244bdb3 --- /dev/null +++ b/.woodpecker/build-alpine-321-amd64-7.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-amd64-8.yaml b/.woodpecker/build-alpine-321-amd64-8.yaml new file mode 100644 index 0000000..036eff9 --- /dev/null +++ b/.woodpecker/build-alpine-321-amd64-8.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-amd64-9.yaml b/.woodpecker/build-alpine-321-amd64-9.yaml new file mode 100644 index 0000000..c8ed084 --- /dev/null +++ b/.woodpecker/build-alpine-321-amd64-9.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-arm64-1.yaml b/.woodpecker/build-alpine-321-arm64-1.yaml new file mode 100644 index 0000000..5b764eb --- /dev/null +++ b/.woodpecker/build-alpine-321-arm64-1.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-arm64-10.yaml b/.woodpecker/build-alpine-321-arm64-10.yaml new file mode 100644 index 0000000..0f5daf9 --- /dev/null +++ b/.woodpecker/build-alpine-321-arm64-10.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-arm64-2.yaml b/.woodpecker/build-alpine-321-arm64-2.yaml new file mode 100644 index 0000000..963a39e --- /dev/null +++ b/.woodpecker/build-alpine-321-arm64-2.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-arm64-3.yaml b/.woodpecker/build-alpine-321-arm64-3.yaml new file mode 100644 index 0000000..8319bc1 --- /dev/null +++ b/.woodpecker/build-alpine-321-arm64-3.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-arm64-4.yaml b/.woodpecker/build-alpine-321-arm64-4.yaml new file mode 100644 index 0000000..34a8aa3 --- /dev/null +++ b/.woodpecker/build-alpine-321-arm64-4.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-arm64-5.yaml b/.woodpecker/build-alpine-321-arm64-5.yaml new file mode 100644 index 0000000..c2311ab --- /dev/null +++ b/.woodpecker/build-alpine-321-arm64-5.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-arm64-6.yaml b/.woodpecker/build-alpine-321-arm64-6.yaml new file mode 100644 index 0000000..0500f71 --- /dev/null +++ b/.woodpecker/build-alpine-321-arm64-6.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-arm64-7.yaml b/.woodpecker/build-alpine-321-arm64-7.yaml new file mode 100644 index 0000000..b8bb4a5 --- /dev/null +++ b/.woodpecker/build-alpine-321-arm64-7.yaml @@ -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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-arm64-8.yaml b/.woodpecker/build-alpine-321-arm64-8.yaml new file mode 100644 index 0000000..7008cc8 --- /dev/null +++ b/.woodpecker/build-alpine-321-arm64-8.yaml @@ -0,0 +1,137 @@ +when: + - event: manual + evaluate: 'build == "all"' + - event: manual + evaluate: 'build == "alpine-321-arm64"' + - event: manual + evaluate: 'build == "alpine-321-arm64-8"' + - 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: 15401 + BLOCK_END: 17600 + 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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-alpine-321-arm64-9.yaml b/.woodpecker/build-alpine-321-arm64-9.yaml new file mode 100644 index 0000000..4b47f35 --- /dev/null +++ b/.woodpecker/build-alpine-321-arm64-9.yaml @@ -0,0 +1,137 @@ +when: + - event: manual + evaluate: 'build == "all"' + - event: manual + evaluate: 'build == "alpine-321-arm64"' + - event: manual + evaluate: 'build == "alpine-321-arm64-9"' + - 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: 17601 + BLOCK_END: 19800 + 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::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2 + # filters: -> 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} \ No newline at end of file diff --git a/.woodpecker/build-redhat-8-amd64.yaml b/.woodpecker/build-redhat-8-amd64.yaml index 4215e32..cc13379 100644 --- a/.woodpecker/build-redhat-8-amd64.yaml +++ b/.woodpecker/build-redhat-8-amd64.yaml @@ -10,12 +10,24 @@ skip_clone: true steps: - 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/amd64-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 @@ -31,11 +43,9 @@ steps: # volumes: # - amd64-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::meta_update()' + # for some reason paks pkgcache is often corrupt- R -q -e 'pak::meta_update()' - 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 diff --git a/.woodpecker/build-redhat-8-arm64.yaml b/.woodpecker/build-redhat-8-arm64.yaml index 5d4c80a..aa9fcc0 100644 --- 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 diff --git a/.woodpecker/build-redhat-9-amd64.yaml b/.woodpecker/build-redhat-9-amd64.yaml index 0716421..6acc7ae 100644 --- a/.woodpecker/build-redhat-9-amd64.yaml +++ b/.woodpecker/build-redhat-9-amd64.yaml @@ -10,12 +10,24 @@ skip_clone: true steps: - 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/amd64-binaries-r-redhat-9 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 @@ -30,11 +42,9 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-redhat-9:/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' diff --git a/.woodpecker/build-redhat-9-arm64.yaml b/.woodpecker/build-redhat-9-arm64.yaml index cb7a8a9..6e24733 100644 --- a/.woodpecker/build-redhat-9-arm64.yaml +++ b/.woodpecker/build-redhat-9-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-9 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 @@ -55,11 +67,9 @@ steps: volumes: - arm64-binaries-r-dep-cache-redhat-9:/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' diff --git a/.woodpecker/build-ubuntu-2204-amd64.yaml b/.woodpecker/build-ubuntu-2204-amd64.yaml index 3ed6854..573786d 100644 --- a/.woodpecker/build-ubuntu-2204-amd64.yaml +++ b/.woodpecker/build-ubuntu-2204-amd64.yaml @@ -10,12 +10,24 @@ skip_clone: true steps: - 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/amd64-binaries-r-ubuntu-2204 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 @@ -25,17 +37,13 @@ steps: BLOCK: 4223:4755 ARCH: amd64 NCPUS: 4 - # MEMORY: 14Gi - # INSTANCE_TYPE: ccx23 STRATEGY: sequential # volumes: # - amd64-binaries-r-dep-cache-ubuntu-2204:/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/ - - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages + # for some reason paks pkgcache is often corrupt- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'packageVersion("bincraftR")' # Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd' diff --git a/.woodpecker/build-ubuntu-2204-arm64.yaml b/.woodpecker/build-ubuntu-2204-arm64.yaml index aa95517..30169c0 100644 --- a/.woodpecker/build-ubuntu-2204-arm64.yaml +++ b/.woodpecker/build-ubuntu-2204-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-ubuntu-2204 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 @@ -55,10 +67,8 @@ steps: volumes: - arm64-binaries-r-dep-cache-ubuntu-2204:/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 /mnt/cache/R-pkgs/gert - # 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")' - R -q -e 'packageVersion("bincraftR")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages diff --git a/.woodpecker/build-ubuntu-2404-amd64.yaml b/.woodpecker/build-ubuntu-2404-amd64.yaml index 615246f..a12bfec 100644 --- a/.woodpecker/build-ubuntu-2404-amd64.yaml +++ b/.woodpecker/build-ubuntu-2404-amd64.yaml @@ -10,12 +10,24 @@ skip_clone: true steps: - 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/amd64-binaries-r-ubuntu-2404 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 @@ -31,11 +43,9 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-ubuntu-2404:/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' diff --git a/.woodpecker/build-ubuntu-2404-arm64.yaml b/.woodpecker/build-ubuntu-2404-arm64.yaml index 8c9ccee..bd70a85 100644 --- a/.woodpecker/build-ubuntu-2404-arm64.yaml +++ b/.woodpecker/build-ubuntu-2404-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-ubuntu-2404 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 @@ -55,11 +67,9 @@ steps: volumes: - arm64-binaries-r-dep-cache-ubuntu-2404:/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' diff --git a/.woodpecker/process-updates-alpine-320-amd64.yaml b/.woodpecker/process-updates-alpine-320-amd64.yaml index 832caf2..905d6d7 100644 --- a/.woodpecker/process-updates-alpine-320-amd64.yaml +++ b/.woodpecker/process-updates-alpine-320-amd64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: 'Processing Updates' - secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] image: docker.io/devxygmbh/amd64-binaries-r-alpine-320 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 @@ -27,10 +39,9 @@ steps: # volumes: # - amd64-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 /mnt/cache/R-pkgs/00LOCK-RPostgres # 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")' - R -q -e 'packageVersion("bincraftR")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages diff --git a/.woodpecker/process-updates-alpine-320-arm64.yaml b/.woodpecker/process-updates-alpine-320-arm64.yaml index d51f306..64b5cfe 100644 --- a/.woodpecker/process-updates-alpine-320-arm64.yaml +++ b/.woodpecker/process-updates-alpine-320-arm64.yaml @@ -34,10 +34,22 @@ steps: effect: 'NoSchedule' - name: 'Processing Updates' - 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 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 @@ -53,10 +65,8 @@ 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 /mnt/cache/R-pkgs/00LOCK-RPostgres - # 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")' - R -q -e 'packageVersion("bincraftR")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages diff --git a/.woodpecker/process-updates-redhat-8-amd64.yaml b/.woodpecker/process-updates-redhat-8-amd64.yaml index b6d31b1..a07616a 100644 --- a/.woodpecker/process-updates-redhat-8-amd64.yaml +++ b/.woodpecker/process-updates-redhat-8-amd64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: 'Processing Updates' - secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] image: docker.io/devxygmbh/amd64-binaries-r-redhat-8 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 @@ -27,11 +39,8 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-redhat-8:/mnt/cache commands: - - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . - - rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR /mnt/cache/R-pkgs/00LOCK-RPostgres - # for some reason paks pkgcache is often corrupt - - rm -rf /mnt/cache/R-pkgs/pkgcache/ /mnt/cache/pkgcache/ /root/.cache/R/ - - R -q -e 'pak::meta_update()' + - git clone https://pat-s:$$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 /mnt/cache/R-pkgs/00LOCK-RPostgres- R -q -e 'pak::meta_update()' - 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 diff --git a/.woodpecker/process-updates-redhat-8-arm64.yaml b/.woodpecker/process-updates-redhat-8-arm64.yaml index 4ac22c6..9b3ef9d 100644 --- a/.woodpecker/process-updates-redhat-8-arm64.yaml +++ b/.woodpecker/process-updates-redhat-8-arm64.yaml @@ -34,10 +34,22 @@ steps: effect: 'NoSchedule' - name: 'Processing Updates' - 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 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 @@ -53,10 +65,8 @@ 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 /mnt/cache/R-pkgs/00LOCK-RPostgres - # 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")' - R -q -e 'packageVersion("bincraftR")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages diff --git a/.woodpecker/process-updates-redhat-9-amd64.yaml b/.woodpecker/process-updates-redhat-9-amd64.yaml index 434cd1b..d211948 100644 --- a/.woodpecker/process-updates-redhat-9-amd64.yaml +++ b/.woodpecker/process-updates-redhat-9-amd64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: 'Processing Updates' - secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] image: docker.io/devxygmbh/amd64-binaries-r-redhat-9 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 @@ -28,10 +40,8 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-redhat-9:/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 /mnt/cache/R-pkgs/00LOCK-RPostgres - # 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")' - R -q -e 'packageVersion("bincraftR")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages diff --git a/.woodpecker/process-updates-redhat-9-arm64.yaml b/.woodpecker/process-updates-redhat-9-arm64.yaml index e799787..fd1c55a 100644 --- a/.woodpecker/process-updates-redhat-9-arm64.yaml +++ b/.woodpecker/process-updates-redhat-9-arm64.yaml @@ -34,10 +34,22 @@ steps: effect: 'NoSchedule' - name: 'Processing Updates' - 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-9 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 @@ -53,10 +65,8 @@ steps: volumes: - arm64-binaries-r-dep-cache-redhat-9:/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 /mnt/cache/R-pkgs/00LOCK-RPostgres - # 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")' - R -q -e 'packageVersion("bincraftR")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages diff --git a/.woodpecker/process-updates-ubuntu-2204-amd64.yaml b/.woodpecker/process-updates-ubuntu-2204-amd64.yaml index 50d0c84..4e6a3e7 100644 --- a/.woodpecker/process-updates-ubuntu-2204-amd64.yaml +++ b/.woodpecker/process-updates-ubuntu-2204-amd64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: 'Processing Updates' - secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] image: docker.io/devxygmbh/amd64-binaries-r-ubuntu-2204 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 @@ -28,10 +40,8 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-ubuntu-2204:/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 /mnt/cache/R-pkgs/00LOCK-RPostgres - # 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")' - R -q -e 'packageVersion("bincraftR")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages diff --git a/.woodpecker/process-updates-ubuntu-2204-arm64.yaml b/.woodpecker/process-updates-ubuntu-2204-arm64.yaml index cf4ca18..1cdfe7d 100644 --- a/.woodpecker/process-updates-ubuntu-2204-arm64.yaml +++ b/.woodpecker/process-updates-ubuntu-2204-arm64.yaml @@ -34,10 +34,22 @@ steps: effect: 'NoSchedule' - name: 'Processing Updates' - 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-ubuntu-2204 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 @@ -53,10 +65,8 @@ steps: volumes: - arm64-binaries-r-dep-cache-ubuntu-2204:/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 /mnt/cache/R-pkgs/00LOCK-RPostgres - # 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")' - R -q -e 'packageVersion("bincraftR")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages diff --git a/.woodpecker/process-updates-ubuntu-2404-amd64.yaml b/.woodpecker/process-updates-ubuntu-2404-amd64.yaml index b4b1798..d910a81 100644 --- a/.woodpecker/process-updates-ubuntu-2404-amd64.yaml +++ b/.woodpecker/process-updates-ubuntu-2404-amd64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: 'Processing Updates' - secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] image: docker.io/devxygmbh/amd64-binaries-r-ubuntu-2404 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 @@ -27,10 +39,8 @@ steps: # volumes: # - amd64-binaries-r-dep-cache-ubuntu-2404:/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 /mnt/cache/R-pkgs/00LOCK-RPostgres - # 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")' - R -q -e 'packageVersion("bincraftR")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages diff --git a/.woodpecker/process-updates-ubuntu-2404-arm64.yaml b/.woodpecker/process-updates-ubuntu-2404-arm64.yaml index 3537bcb..f8f8e15 100644 --- a/.woodpecker/process-updates-ubuntu-2404-arm64.yaml +++ b/.woodpecker/process-updates-ubuntu-2404-arm64.yaml @@ -34,10 +34,22 @@ steps: effect: 'NoSchedule' - name: 'Processing Updates' - 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-ubuntu-2404 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 @@ -53,10 +65,8 @@ steps: volumes: - arm64-binaries-r-dep-cache-ubuntu-2404:/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 /mnt/cache/R-pkgs/00LOCK-RPostgres - # 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")' - R -q -e 'packageVersion("bincraftR")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages diff --git a/.woodpecker/update-package-index-alpine-320-amd64.yaml b/.woodpecker/update-package-index-alpine-320-amd64.yaml index 5f4e434..8789d72 100644 --- a/.woodpecker/update-package-index-alpine-320-amd64.yaml +++ b/.woodpecker/update-package-index-alpine-320-amd64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: Upload PACKAGES files - secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] image: docker.io/devxygmbh/amd64-binaries-r-alpine-320 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 @@ -21,7 +33,7 @@ steps: volumes: - amd64-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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'packageVersion("bincraftR")' diff --git a/.woodpecker/update-package-index-alpine-320-arm64.yaml b/.woodpecker/update-package-index-alpine-320-arm64.yaml index eab3bc5..82589f0 100644 --- a/.woodpecker/update-package-index-alpine-320-arm64.yaml +++ b/.woodpecker/update-package-index-alpine-320-arm64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: Upload PACKAGES files - 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 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 @@ -21,7 +33,7 @@ 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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'pak::pak("pat-s/cranlike@s3")' diff --git a/.woodpecker/update-package-index-redhat-8-amd64.yaml b/.woodpecker/update-package-index-redhat-8-amd64.yaml index 1a62a11..675981a 100644 --- a/.woodpecker/update-package-index-redhat-8-amd64.yaml +++ b/.woodpecker/update-package-index-redhat-8-amd64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: Upload PACKAGES files - secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] image: docker.io/devxygmbh/amd64-binaries-r-redhat-8 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 @@ -21,7 +33,7 @@ steps: volumes: - amd64-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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'pak::pak("pat-s/cranlike@s3")' diff --git a/.woodpecker/update-package-index-redhat-8-arm64.yaml b/.woodpecker/update-package-index-redhat-8-arm64.yaml index 63f7c1c..8216d63 100644 --- a/.woodpecker/update-package-index-redhat-8-arm64.yaml +++ b/.woodpecker/update-package-index-redhat-8-arm64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: Upload PACKAGES files - 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 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 @@ -21,7 +33,7 @@ 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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'pak::pak("pat-s/cranlike@s3")' diff --git a/.woodpecker/update-package-index-redhat-9-amd64.yaml b/.woodpecker/update-package-index-redhat-9-amd64.yaml index 0dc67bb..c6533aa 100644 --- a/.woodpecker/update-package-index-redhat-9-amd64.yaml +++ b/.woodpecker/update-package-index-redhat-9-amd64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: Upload PACKAGES files - secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] image: docker.io/devxygmbh/amd64-binaries-r-redhat-9 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 @@ -21,7 +33,7 @@ steps: volumes: - amd64-binaries-r-dep-cache-redhat-9:/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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'pak::pak("pat-s/cranlike@s3")' diff --git a/.woodpecker/update-package-index-redhat-9-arm64.yaml b/.woodpecker/update-package-index-redhat-9-arm64.yaml index 646bac8..84ea10e 100644 --- a/.woodpecker/update-package-index-redhat-9-arm64.yaml +++ b/.woodpecker/update-package-index-redhat-9-arm64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: Upload PACKAGES files - 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-9 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 @@ -21,7 +33,7 @@ steps: volumes: - arm64-binaries-r-dep-cache-redhat-9:/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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'pak::pak("pat-s/cranlike@s3")' diff --git a/.woodpecker/update-package-index-ubuntu-2204-amd64.yaml b/.woodpecker/update-package-index-ubuntu-2204-amd64.yaml index b8b7729..1c03980 100644 --- a/.woodpecker/update-package-index-ubuntu-2204-amd64.yaml +++ b/.woodpecker/update-package-index-ubuntu-2204-amd64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: Upload PACKAGES files - secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] image: docker.io/devxygmbh/amd64-binaries-r-ubuntu-2204 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 @@ -21,7 +33,7 @@ steps: volumes: - amd64-binaries-r-dep-cache-ubuntu-2204:/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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'pak::pak("pat-s/cranlike@s3")' diff --git a/.woodpecker/update-package-index-ubuntu-2204-arm64.yaml b/.woodpecker/update-package-index-ubuntu-2204-arm64.yaml index d435a73..538e8b6 100644 --- a/.woodpecker/update-package-index-ubuntu-2204-arm64.yaml +++ b/.woodpecker/update-package-index-ubuntu-2204-arm64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: Upload PACKAGES files - 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-ubuntu-2204 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 @@ -21,7 +33,7 @@ steps: volumes: - arm64-binaries-r-dep-cache-ubuntu-2204:/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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'pak::pak("pat-s/cranlike@s3")' diff --git a/.woodpecker/update-package-index-ubuntu-2404-amd64.yaml b/.woodpecker/update-package-index-ubuntu-2404-amd64.yaml index cfaa552..f622ee7 100644 --- a/.woodpecker/update-package-index-ubuntu-2404-amd64.yaml +++ b/.woodpecker/update-package-index-ubuntu-2404-amd64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: Upload PACKAGES files - secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] image: docker.io/devxygmbh/amd64-binaries-r-ubuntu-2404 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 @@ -21,7 +33,7 @@ steps: volumes: - amd64-binaries-r-dep-cache-ubuntu-2404:/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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'pak::pak("pat-s/cranlike@s3")' diff --git a/.woodpecker/update-package-index-ubuntu-2404-arm64.yaml b/.woodpecker/update-package-index-ubuntu-2404-arm64.yaml index aa766cb..40a50c0 100644 --- a/.woodpecker/update-package-index-ubuntu-2404-arm64.yaml +++ b/.woodpecker/update-package-index-ubuntu-2404-arm64.yaml @@ -10,10 +10,22 @@ skip_clone: true steps: - name: Upload PACKAGES files - 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-ubuntu-2404 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 @@ -21,7 +33,7 @@ steps: volumes: - arm64-binaries-r-dep-cache-ubuntu-2404:/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/packages/* - R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")' - R -q -e 'pak::pak("pat-s/cranlike@s3")'