chore: reorganize CI workflow files
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24 changed files with 2486 additions and 436 deletions
136
.woodpecker/build-alpine-320-amd64.yaml
Normal file
136
.woodpecker/build-alpine-320-amd64.yaml
Normal file
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@ -0,0 +1,136 @@
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when:
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- event: manual
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evaluate: 'build == "all"'
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- event: manual
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evaluate: 'build == "alpine-320-amd64"'
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skip_clone: true
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steps:
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- name: 'Warming up'
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image: busybox:latest
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failure: ignore
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commands:
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- sleep 300
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- echo "Warmed Up"
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backend_options:
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kubernetes:
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resources:
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requests:
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memory: 29Gi
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cpu: 4000m
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limits:
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memory: 29Gi
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cpu: 4000m
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nodeSelector:
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kubernetes.io/arch: amd64
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node.kubernetes.io/instance-type: cpx51
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tolerations:
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- key: 'CI'
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operator: 'Equal'
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value: 'true'
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effect: 'NoSchedule'
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- name: 'Build binaries'
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secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT]
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image: docker.io/devxygmbh/amd64-binaries-r-alpine-320
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pull: true
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# to ensure the PACKAGES upload step is being executed
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failure: ignore
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environment:
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GIT_USER: pat-s
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# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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R_LIBS_USER: /mnt/cache/R-pkgs
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CCACHE_DIR: /mnt/cache/ccache
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PLATFORM: alpine-320
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BLOCK: 21424:length(pkgs)
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ARCH: amd64
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NCPUS: 2
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MEMORY: 29Gi
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INSTANCE_TYPE: cpx51
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STRATEGY: multisession
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volumes:
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- amd64-binaries-r-dep-cache-alpine-320:/mnt/cache
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commands:
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# download latest package version (avoid having to rebuild image every time)
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# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
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- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git .
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- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
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# for some reason paks pkgcache is often corrupt
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- rm -rf /mnt/cache/R-pkgs/pkgcache/ /mnt/cache/pkgcache/ /root/.cache/R/
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- R -q -e 'pak::meta_update()'
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- R CMD INSTALL .
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# more complicated system dependencies which pak cannot resolve
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
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### Check
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# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
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# - Rglpk
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# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
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- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$STRATEGY', workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'alpine-320'))"
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### Manual pkg builds
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# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
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# RInno: Windows-only
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# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
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# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
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# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
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# ROracle: sysdep missing -> create rule
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# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
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# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
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# RmecabKo: fatal error: mecab.h: No such file or directory
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# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
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# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
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# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
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# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
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# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
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# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
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# Racmacs -> rmarchingcubes
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# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
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# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
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# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
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# clrng -> gpuR
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# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
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# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
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# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
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# magickGUI, biplotbootGUI
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# ymd (alpine, voi)
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# tfrmtbuilder -> V8 (alpine)
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# Rcmdr (alpine)
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# readstata13 (alpine)
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# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "amd64"))'
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backend_options:
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kubernetes:
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### PROD-parallel
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resources:
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requests:
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memory: 29Gi
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cpu: 4000m
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limits:
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memory: 29Gi
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cpu: 4000m
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### PROD-sequential
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# resources:
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# requests:
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# memory: 29Gi
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# cpu: 2000m
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# limits:
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# memory: 29Gi
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# cpu: 4000m
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# DEBUG
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# resources:
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# requests:
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# memory: 4Gi
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# cpu: 2000m
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# limits:
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# memory: 4Gi
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# cpu: 2000m
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nodeSelector:
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kubernetes.io/arch: amd64
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node.kubernetes.io/instance-type: cpx51
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tolerations:
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- key: 'CI'
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operator: 'Equal'
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value: 'true'
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effect: 'NoSchedule'
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136
.woodpecker/build-alpine-320-arm64.yaml
Normal file
136
.woodpecker/build-alpine-320-arm64.yaml
Normal file
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@ -0,0 +1,136 @@
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when:
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- event: manual
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evaluate: 'build == "all"'
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- event: manual
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evaluate: 'build == "alpine-320-arm64"'
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skip_clone: true
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steps:
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- name: 'Warming up'
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image: busybox:latest
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failure: ignore
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commands:
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- sleep 300
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- echo 'Warmed Up'
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backend_options:
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kubernetes:
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resources:
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requests:
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memory: 29Gi
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cpu: 4000m
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limits:
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memory: 29Gi
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cpu: 4000m
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nodeSelector:
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kubernetes.io/arch: arm64
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node.kubernetes.io/instance-type: cax41
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tolerations:
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- key: 'CI'
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operator: 'Equal'
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value: 'true'
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effect: 'NoSchedule'
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- name: 'Build binaries'
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secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT]
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image: docker.io/devxygmbh/arm64-binaries-r-alpine-320
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pull: true
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# to ensure the PACKAGES upload step is being executed
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failure: ignore
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environment:
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GIT_USER: pat-s
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# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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R_LIBS_USER: /mnt/cache/R-pkgs
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CCACHE_DIR: /mnt/cache/ccache
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PLATFORM: alpine-320
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BLOCK: 20896:length(pkgs)
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ARCH: arm64
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NCPUS: 2
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MEMORY: 29Gi
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INSTANCE_TYPE: cax41
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STRATEGY: multisession
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volumes:
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- arm64-binaries-r-dep-cache-alpine-320:/mnt/cache
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commands:
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# download latest package version (avoid having to rebuild image every time)
|
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# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
|
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- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git .
|
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- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
|
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# for some reason paks pkgcache is often corrupt
|
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- rm -rf /mnt/cache/R-pkgs/pkgcache/ /mnt/cache/pkgcache/ /root/.cache/R/
|
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- R -q -e 'pak::meta_update()'
|
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- R CMD INSTALL .
|
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# more complicated system dependencies which pak cannot resolve
|
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
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# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
### Check
|
||||
# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
|
||||
# - Rglpk
|
||||
# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$STRATEGY', workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'alpine-320'))"
|
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### Manual pkg builds
|
||||
# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
|
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# 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
|
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# 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:
|
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# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
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# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
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|
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# magickGUI, biplotbootGUI
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# ymd (alpine, voi)
|
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# tfrmtbuilder -> V8 (alpine)
|
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# Rcmdr (alpine)
|
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# readstata13 (alpine)
|
||||
# - 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, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'alpine-320'))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD-parallel
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
### PROD-sequential
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 29Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 29Gi
|
||||
# cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
136
.woodpecker/build-redhat-8-amd64.yaml
Normal file
136
.woodpecker/build-redhat-8-amd64.yaml
Normal file
|
|
@ -0,0 +1,136 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "redhat-8-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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/amd64-binaries-r-redhat-8
|
||||
pull: true
|
||||
# to ensure the PACKAGES upload step is being executed
|
||||
failure: ignore
|
||||
environment:
|
||||
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: redhat-8
|
||||
BLOCK: 20588:length(pkgs)
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
INSTANCE_TYPE: cpx51
|
||||
STRATEGY: multisession
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-redhat-8:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
# more complicated system dependencies which pak cannot resolve
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
### Check
|
||||
# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
|
||||
# - Rglpk
|
||||
# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$STRATEGY', workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, 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
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "amd64"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD-parallel
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
### PROD-sequential
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 29Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 29Gi
|
||||
# cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
136
.woodpecker/build-redhat-8-arm64.yaml
Normal file
136
.woodpecker/build-redhat-8-arm64.yaml
Normal file
|
|
@ -0,0 +1,136 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "redhat-8-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: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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:
|
||||
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: redhat-8
|
||||
BLOCK: 20327:length(pkgs)
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
INSTANCE_TYPE: cax41
|
||||
STRATEGY: multisession
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-redhat-8:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
# more complicated system dependencies which pak cannot resolve
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
### Check
|
||||
# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
|
||||
# - Rglpk
|
||||
# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$STRATEGY', workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, 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
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "arm64"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD-parallel
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
### PROD-sequential
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 29Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 29Gi
|
||||
# cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
136
.woodpecker/build-redhat-9-amd64.yaml
Normal file
136
.woodpecker/build-redhat-9-amd64.yaml
Normal file
|
|
@ -0,0 +1,136 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "redhat-9-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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/amd64-binaries-r-redhat-9
|
||||
pull: true
|
||||
# to ensure the PACKAGES upload step is being executed
|
||||
failure: ignore
|
||||
environment:
|
||||
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: redhat-9
|
||||
BLOCK: 19127:length(pkgs)
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
INSTANCE_TYPE: cpx51
|
||||
STRATEGY: multisession
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-redhat-9:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
# more complicated system dependencies which pak cannot resolve
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
### Check
|
||||
# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
|
||||
# - Rglpk
|
||||
# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$STRATEGY', workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'redhat-9'))"
|
||||
### Manual pkg builds
|
||||
# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "amd64"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD-parallel
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
### PROD-sequential
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 29Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 29Gi
|
||||
# cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
136
.woodpecker/build-redhat-9-arm64.yaml
Normal file
136
.woodpecker/build-redhat-9-arm64.yaml
Normal file
|
|
@ -0,0 +1,136 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "redhat-9-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: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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:
|
||||
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: redhat-9
|
||||
BLOCK: 19336:length(pkgs)
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
INSTANCE_TYPE: cax41
|
||||
STRATEGY: multisession
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-redhat-9:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
# more complicated system dependencies which pak cannot resolve
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
### Check
|
||||
# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
|
||||
# - Rglpk
|
||||
# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$STRATEGY', workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'redhat-9'))"
|
||||
### Manual pkg builds
|
||||
# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "arm64"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD-parallel
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
### PROD-sequential
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 29Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 29Gi
|
||||
# cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
141
.woodpecker/build-ubuntu-2204-amd64.yaml
Normal file
141
.woodpecker/build-ubuntu-2204-amd64.yaml
Normal file
|
|
@ -0,0 +1,141 @@
|
|||
when:
|
||||
# - event: manual
|
||||
# evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "ubuntu-2204-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
environment:
|
||||
PLATFORM: ubuntu-2204
|
||||
BLOCK: 21389:length(pkgs)
|
||||
NCPUS: 2
|
||||
STRATEGY: multisession
|
||||
commands:
|
||||
- sleep 1
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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/amd64-binaries-r-amd64
|
||||
pull: true
|
||||
# to ensure the PACKAGES upload step is being executed
|
||||
failure: ignore
|
||||
environment:
|
||||
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: ubuntu-2204
|
||||
BLOCK: 21389:length(pkgs)
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
INSTANCE_TYPE: cpx51
|
||||
STRATEGY: multisession
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-ubuntu-2204:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
# more complicated system dependencies which pak cannot resolve
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
### Check
|
||||
# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
|
||||
# - Rglpk
|
||||
# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$STRATEGY', workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'ubuntu-2204'))"
|
||||
### Manual pkg builds
|
||||
# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "amd64"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD-parallel
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
### PROD-sequential
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 29Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 29Gi
|
||||
# cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
136
.woodpecker/build-ubuntu-2204-arm64.yaml
Normal file
136
.woodpecker/build-ubuntu-2204-arm64.yaml
Normal file
|
|
@ -0,0 +1,136 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "ubuntu-2204-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: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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:
|
||||
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: ubuntu-2204
|
||||
BLOCK: 20653:length(pkgs)
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
INSTANCE_TYPE: cax41
|
||||
STRATEGY: multisession
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-ubuntu-2204:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
|
||||
- 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::meta_update()'
|
||||
- R CMD INSTALL .
|
||||
# more complicated system dependencies which pak cannot resolve
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
### Check
|
||||
# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
|
||||
# - Rglpk
|
||||
# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$STRATEGY', workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'ubuntu-2204'))"
|
||||
### Manual pkg builds
|
||||
# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "arm64"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD-parallel
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
### PROD-sequential
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 29Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 29Gi
|
||||
# cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
141
.woodpecker/build-ubuntu-2404-amd64.yaml
Normal file
141
.woodpecker/build-ubuntu-2404-amd64.yaml
Normal file
|
|
@ -0,0 +1,141 @@
|
|||
when:
|
||||
# - event: manual
|
||||
# evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "ubuntu-2404-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
environment:
|
||||
PLATFORM: ubuntu-2204
|
||||
BLOCK: 21389:length(pkgs)
|
||||
NCPUS: 2
|
||||
STRATEGY: multisession
|
||||
commands:
|
||||
- sleep 1
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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/amd64-binaries-r-ubuntu-2404
|
||||
pull: true
|
||||
# to ensure the PACKAGES upload step is being executed
|
||||
failure: ignore
|
||||
environment:
|
||||
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: ubuntu-2404
|
||||
BLOCK: 21389:length(pkgs)
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
INSTANCE_TYPE: cpx51
|
||||
STRATEGY: multisession
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-ubuntu-2404:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
# more complicated system dependencies which pak cannot resolve
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
### Check
|
||||
# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
|
||||
# - Rglpk
|
||||
# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
|
||||
- xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c("biplotbootGUI", "Rsymphony", "PortfolioAnalytics", "ROI.plugin.symphony", "adea", "RInno", "skedastic", "RPushbullet", "SimNPH", "SimDesign","simCAT", "SIAmodules", "shinytest2", "shinyIRT", "ShinyItemAnalysis", "shiny.benchmark", "scDIFtest", "RSP", "ROracle", "ROI.plugin.qpoases", "ROI.plugin.cplex", "RmecabKo", "rmarchingcubes", "RcppMeCab", "Rcplex", "ravetools", "Rbeast", "Rblpapi", "RcppEnsmallen", "qtkit", "priorCON", "prior3D", "PerFit", "outlierensembles", "nomnoml", "mxfda", "MultBiplotR", "mstDIF", "mdsr", "makepipe", "lordif", "KSgeneral", "kequate", "jstager", "jrt", "irtreliability", "irtQ", "irtpwr", "irtawsi", "GRShiny", "gpuR", "googletraffic", "giacR", "gamstransfer", "aflps", "flow", "filters", "faoutlier", "equateIRT", "EnrichIntersect", "EFA.dimensions", "DFIT", "D3mirt", "ctgdist", "CoTiMA", "ConvertPar", "clrng", "bscui", "BifactorIndicesCalculator", "autoFC", "airt")); library(bincraftR); future::plan("$STRATEGY", workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers("cli"); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "amd64"))'
|
||||
### Manual pkg builds
|
||||
# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "amd64"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD-parallel
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
### PROD-sequential
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 29Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 29Gi
|
||||
# cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
136
.woodpecker/build-ubuntu-2404-arm64.yaml
Normal file
136
.woodpecker/build-ubuntu-2404-arm64.yaml
Normal file
|
|
@ -0,0 +1,136 @@
|
|||
when:
|
||||
- event: manual
|
||||
evaluate: 'build == "all"'
|
||||
- event: manual
|
||||
evaluate: 'build == "ubuntu-2404-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: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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:
|
||||
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: ubuntu-2404
|
||||
BLOCK: 20126:length(pkgs)
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
INSTANCE_TYPE: cax41
|
||||
STRATEGY: multisession
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-ubuntu-2404:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
# more complicated system dependencies which pak cannot resolve
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
### Check
|
||||
# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
|
||||
# - Rglpk
|
||||
# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$STRATEGY', workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'ubuntu-2404'))"
|
||||
### Manual pkg builds
|
||||
# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
|
||||
# RInno: Windows-only
|
||||
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||
# ROracle: sysdep missing -> create rule
|
||||
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||
# Racmacs -> rmarchingcubes
|
||||
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||
# clrng -> gpuR
|
||||
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
|
||||
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||
|
||||
# magickGUI, biplotbootGUI
|
||||
# ymd (alpine, voi)
|
||||
# tfrmtbuilder -> V8 (alpine)
|
||||
# Rcmdr (alpine)
|
||||
# readstata13 (alpine)
|
||||
# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "arm64"))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD-parallel
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
### PROD-sequential
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 29Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 29Gi
|
||||
# cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
117
.woodpecker/process-updates-alpine-320-amd64.yaml
Normal file
117
.woodpecker/process-updates-alpine-320-amd64.yaml
Normal file
|
|
@ -0,0 +1,117 @@
|
|||
when:
|
||||
- event: [cron]
|
||||
cron: process-cran-updates-alpine-320-amd64
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "all"'
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "alpine-320-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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/amd64-binaries-r-alpine-320
|
||||
pull: true
|
||||
environment:
|
||||
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-320
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
STRATEGY: multisession
|
||||
INSTANCE_TYPE: cpx51
|
||||
INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 40)
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-alpine-320:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'alpine-320', process_updated = TRUE, process_new = TRUE)"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: codeberg.org/l-x/woodpecker-ntfy:1.3.1
|
||||
when:
|
||||
- status: [failure]
|
||||
settings:
|
||||
url: https://ntfy.devxy.io/ci-builds
|
||||
token:
|
||||
from_secret: ntfy_token
|
||||
title: "CI '${CI_REPO}' failed"
|
||||
actions: view, Open build, ${CI_PIPELINE_URL}, clear=false;
|
||||
click: ${CI_BUILD_LINK}
|
||||
message: |
|
||||
Workflow: ${CI_WORKFLOW_NAME/\n//}
|
||||
Commit message: ${CI_COMMIT_MESSAGE/\n//}
|
||||
Commit Author: ${CI_COMMIT_AUTHOR/\n//}
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 100Mi
|
||||
cpu: 0m
|
||||
limits:
|
||||
memory: 300Mi
|
||||
cpu: 200m
|
||||
122
.woodpecker/process-updates-alpine-320-arm64.yaml
Normal file
122
.woodpecker/process-updates-alpine-320-arm64.yaml
Normal file
|
|
@ -0,0 +1,122 @@
|
|||
when:
|
||||
- event: [cron]
|
||||
cron: process-cran-updates
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "all"'
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "alpine-320-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
environment:
|
||||
PLATFORM: ubuntu-2204
|
||||
BLOCK: 21389:length(pkgs)
|
||||
NCPUS: 2
|
||||
STRATEGY: multisession
|
||||
commands:
|
||||
- sleep 1
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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-${PLATFORM}
|
||||
pull: true
|
||||
environment:
|
||||
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-320
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
STRATEGY: multisession
|
||||
INSTANCE_TYPE: cax41
|
||||
INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 31)
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-${PLATFORM}:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'alpine-320', process_updated = TRUE, process_new = TRUE)"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: codeberg.org/l-x/woodpecker-ntfy:1.3.1
|
||||
when:
|
||||
- status: [failure]
|
||||
settings:
|
||||
url: https://ntfy.devxy.io/ci-builds
|
||||
token:
|
||||
from_secret: ntfy_token
|
||||
title: "CI '${CI_REPO}' failed"
|
||||
actions: view, Open build, ${CI_PIPELINE_URL}, clear=false;
|
||||
click: ${CI_BUILD_LINK}
|
||||
message: |
|
||||
Workflow: ${CI_WORKFLOW_NAME/\n//}
|
||||
Commit message: ${CI_COMMIT_MESSAGE/\n//}
|
||||
Commit Author: ${CI_COMMIT_AUTHOR/\n//}
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 100Mi
|
||||
cpu: 0m
|
||||
limits:
|
||||
memory: 300Mi
|
||||
cpu: 200m
|
||||
117
.woodpecker/process-updates-redhat-8-amd64.yaml
Normal file
117
.woodpecker/process-updates-redhat-8-amd64.yaml
Normal file
|
|
@ -0,0 +1,117 @@
|
|||
when:
|
||||
- event: [cron]
|
||||
cron: process-cran-updates-redhat-8-amd64
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "all"'
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "redhat-8-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 1
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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/amd64-binaries-r-redhat-8
|
||||
pull: true
|
||||
environment:
|
||||
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: redhat-8
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
STRATEGY: multisession
|
||||
INSTANCE_TYPE: cpx51
|
||||
INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3)
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-redhat-8:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = TRUE)"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: codeberg.org/l-x/woodpecker-ntfy:1.3.1
|
||||
when:
|
||||
- status: [failure]
|
||||
settings:
|
||||
url: https://ntfy.devxy.io/ci-builds
|
||||
token:
|
||||
from_secret: ntfy_token
|
||||
title: "CI '${CI_REPO}' failed"
|
||||
actions: view, Open build, ${CI_PIPELINE_URL}, clear=false;
|
||||
click: ${CI_BUILD_LINK}
|
||||
message: |
|
||||
Workflow: ${CI_WORKFLOW_NAME/\n//}
|
||||
Commit message: ${CI_COMMIT_MESSAGE/\n//}
|
||||
Commit Author: ${CI_COMMIT_AUTHOR/\n//}
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 100Mi
|
||||
cpu: 0m
|
||||
limits:
|
||||
memory: 300Mi
|
||||
cpu: 200m
|
||||
122
.woodpecker/process-updates-redhat-8-arm64.yaml
Normal file
122
.woodpecker/process-updates-redhat-8-arm64.yaml
Normal file
|
|
@ -0,0 +1,122 @@
|
|||
when:
|
||||
- event: [cron]
|
||||
cron: process-cran-updates
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "all"'
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "redhat-8-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
environment:
|
||||
PLATFORM: ubuntu-2204
|
||||
BLOCK: 21389:length(pkgs)
|
||||
NCPUS: 2
|
||||
STRATEGY: multisession
|
||||
commands:
|
||||
- sleep 1
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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-${PLATFORM}
|
||||
pull: true
|
||||
environment:
|
||||
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: redhat-8
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
STRATEGY: multisession
|
||||
INSTANCE_TYPE: cax41
|
||||
INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 31)
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-${PLATFORM}:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = TRUE)"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: codeberg.org/l-x/woodpecker-ntfy:1.3.1
|
||||
when:
|
||||
- status: [failure]
|
||||
settings:
|
||||
url: https://ntfy.devxy.io/ci-builds
|
||||
token:
|
||||
from_secret: ntfy_token
|
||||
title: "CI '${CI_REPO}' failed"
|
||||
actions: view, Open build, ${CI_PIPELINE_URL}, clear=false;
|
||||
click: ${CI_BUILD_LINK}
|
||||
message: |
|
||||
Workflow: ${CI_WORKFLOW_NAME/\n//}
|
||||
Commit message: ${CI_COMMIT_MESSAGE/\n//}
|
||||
Commit Author: ${CI_COMMIT_AUTHOR/\n//}
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 100Mi
|
||||
cpu: 0m
|
||||
limits:
|
||||
memory: 300Mi
|
||||
cpu: 200m
|
||||
117
.woodpecker/process-updates-redhat-9-amd64.yaml
Normal file
117
.woodpecker/process-updates-redhat-9-amd64.yaml
Normal file
|
|
@ -0,0 +1,117 @@
|
|||
when:
|
||||
- event: [cron]
|
||||
cron: process-cran-updates-redhat-9-amd64
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "all"'
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "redhat-9-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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/amd64-binaries-r-redhat-9
|
||||
pull: true
|
||||
environment:
|
||||
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: redhat-9
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
STRATEGY: multisession
|
||||
INSTANCE_TYPE: cpx51
|
||||
INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3)
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-redhat-9:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE)"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: codeberg.org/l-x/woodpecker-ntfy:1.3.1
|
||||
when:
|
||||
- status: [failure]
|
||||
settings:
|
||||
url: https://ntfy.devxy.io/ci-builds
|
||||
token:
|
||||
from_secret: ntfy_token
|
||||
title: "CI '${CI_REPO}' failed"
|
||||
actions: view, Open build, ${CI_PIPELINE_URL}, clear=false;
|
||||
click: ${CI_BUILD_LINK}
|
||||
message: |
|
||||
Workflow: ${CI_WORKFLOW_NAME/\n//}
|
||||
Commit message: ${CI_COMMIT_MESSAGE/\n//}
|
||||
Commit Author: ${CI_COMMIT_AUTHOR/\n//}
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 100Mi
|
||||
cpu: 0m
|
||||
limits:
|
||||
memory: 300Mi
|
||||
cpu: 200m
|
||||
122
.woodpecker/process-updates-redhat-9-arm64.yaml
Normal file
122
.woodpecker/process-updates-redhat-9-arm64.yaml
Normal file
|
|
@ -0,0 +1,122 @@
|
|||
when:
|
||||
- event: [cron]
|
||||
cron: process-cran-updates
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "all"'
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "redhat-9-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
environment:
|
||||
PLATFORM: ubuntu-2204
|
||||
BLOCK: 21389:length(pkgs)
|
||||
NCPUS: 2
|
||||
STRATEGY: multisession
|
||||
commands:
|
||||
- sleep 1
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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-${PLATFORM}
|
||||
pull: true
|
||||
environment:
|
||||
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: redhat-9
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
STRATEGY: multisession
|
||||
INSTANCE_TYPE: cax41
|
||||
INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 31)
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-${PLATFORM}:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE)"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: codeberg.org/l-x/woodpecker-ntfy:1.3.1
|
||||
when:
|
||||
- status: [failure]
|
||||
settings:
|
||||
url: https://ntfy.devxy.io/ci-builds
|
||||
token:
|
||||
from_secret: ntfy_token
|
||||
title: "CI '${CI_REPO}' failed"
|
||||
actions: view, Open build, ${CI_PIPELINE_URL}, clear=false;
|
||||
click: ${CI_BUILD_LINK}
|
||||
message: |
|
||||
Workflow: ${CI_WORKFLOW_NAME/\n//}
|
||||
Commit message: ${CI_COMMIT_MESSAGE/\n//}
|
||||
Commit Author: ${CI_COMMIT_AUTHOR/\n//}
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 100Mi
|
||||
cpu: 0m
|
||||
limits:
|
||||
memory: 300Mi
|
||||
cpu: 200m
|
||||
117
.woodpecker/process-updates-ubuntu-2204-amd64.yaml
Normal file
117
.woodpecker/process-updates-ubuntu-2204-amd64.yaml
Normal file
|
|
@ -0,0 +1,117 @@
|
|||
when:
|
||||
- event: [cron]
|
||||
cron: process-cran-updates-ubuntu-2204-amd64
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "all"'
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "ubuntu-2204-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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/amd64-binaries-r-ubuntu-2204
|
||||
pull: true
|
||||
environment:
|
||||
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: ubuntu-2204
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
STRATEGY: multisession
|
||||
INSTANCE_TYPE: cpx51
|
||||
INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3)
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-ubuntu-2204:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = TRUE)"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: codeberg.org/l-x/woodpecker-ntfy:1.3.1
|
||||
when:
|
||||
- status: [failure]
|
||||
settings:
|
||||
url: https://ntfy.devxy.io/ci-builds
|
||||
token:
|
||||
from_secret: ntfy_token
|
||||
title: "CI '${CI_REPO}' failed"
|
||||
actions: view, Open build, ${CI_PIPELINE_URL}, clear=false;
|
||||
click: ${CI_BUILD_LINK}
|
||||
message: |
|
||||
Workflow: ${CI_WORKFLOW_NAME/\n//}
|
||||
Commit message: ${CI_COMMIT_MESSAGE/\n//}
|
||||
Commit Author: ${CI_COMMIT_AUTHOR/\n//}
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 100Mi
|
||||
cpu: 0m
|
||||
limits:
|
||||
memory: 300Mi
|
||||
cpu: 200m
|
||||
117
.woodpecker/process-updates-ubuntu-2204-arm64.yaml
Normal file
117
.woodpecker/process-updates-ubuntu-2204-arm64.yaml
Normal file
|
|
@ -0,0 +1,117 @@
|
|||
when:
|
||||
- event: [cron]
|
||||
cron: process-cran-updates-ubuntu-2204-arm64
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "all"'
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "ubuntu-2204-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: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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:
|
||||
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: ubuntu-2204
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
STRATEGY: multisession
|
||||
INSTANCE_TYPE: cax41
|
||||
INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3)
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-ubuntu-2204:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = TRUE)"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: codeberg.org/l-x/woodpecker-ntfy:1.3.1
|
||||
when:
|
||||
- status: [failure]
|
||||
settings:
|
||||
url: https://ntfy.devxy.io/ci-builds
|
||||
token:
|
||||
from_secret: ntfy_token
|
||||
title: "CI '${CI_REPO}' failed"
|
||||
actions: view, Open build, ${CI_PIPELINE_URL}, clear=false;
|
||||
click: ${CI_BUILD_LINK}
|
||||
message: |
|
||||
Workflow: ${CI_WORKFLOW_NAME/\n//}
|
||||
Commit message: ${CI_COMMIT_MESSAGE/\n//}
|
||||
Commit Author: ${CI_COMMIT_AUTHOR/\n//}
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 100Mi
|
||||
cpu: 0m
|
||||
limits:
|
||||
memory: 300Mi
|
||||
cpu: 200m
|
||||
117
.woodpecker/process-updates-ubuntu-2404-amd64.yaml
Normal file
117
.woodpecker/process-updates-ubuntu-2404-amd64.yaml
Normal file
|
|
@ -0,0 +1,117 @@
|
|||
when:
|
||||
- event: [cron]
|
||||
cron: process-cran-updates-ubuntu-2404-amd64
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "all"'
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "ubuntu-2404-amd64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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/amd64-binaries-r-ubuntu-2404
|
||||
pull: true
|
||||
environment:
|
||||
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: ubuntu-2404
|
||||
ARCH: amd64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
STRATEGY: multisession
|
||||
INSTANCE_TYPE: cpx51
|
||||
INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3)
|
||||
volumes:
|
||||
- amd64-binaries-r-dep-cache-ubuntu-2404:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', process_updated = TRUE, process_new = TRUE)"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: amd64
|
||||
node.kubernetes.io/instance-type: cpx51
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: codeberg.org/l-x/woodpecker-ntfy:1.3.1
|
||||
when:
|
||||
- status: [failure]
|
||||
settings:
|
||||
url: https://ntfy.devxy.io/ci-builds
|
||||
token:
|
||||
from_secret: ntfy_token
|
||||
title: "CI '${CI_REPO}' failed"
|
||||
actions: view, Open build, ${CI_PIPELINE_URL}, clear=false;
|
||||
click: ${CI_BUILD_LINK}
|
||||
message: |
|
||||
Workflow: ${CI_WORKFLOW_NAME/\n//}
|
||||
Commit message: ${CI_COMMIT_MESSAGE/\n//}
|
||||
Commit Author: ${CI_COMMIT_AUTHOR/\n//}
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 100Mi
|
||||
cpu: 0m
|
||||
limits:
|
||||
memory: 300Mi
|
||||
cpu: 200m
|
||||
122
.woodpecker/process-updates-ubuntu-2404-arm64.yaml
Normal file
122
.woodpecker/process-updates-ubuntu-2404-arm64.yaml
Normal file
|
|
@ -0,0 +1,122 @@
|
|||
when:
|
||||
- event: [cron]
|
||||
cron: process-cran-updates-ubuntu-2404-arm64
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "all"'
|
||||
- event: manual
|
||||
evaluate: 'process_cran_updates == "ubuntu-2404-arm64"'
|
||||
|
||||
skip_clone: true
|
||||
|
||||
steps:
|
||||
- name: 'Warming up'
|
||||
image: busybox:latest
|
||||
failure: ignore
|
||||
environment:
|
||||
PLATFORM: ubuntu-2204
|
||||
BLOCK: 21389:length(pkgs)
|
||||
NCPUS: 2
|
||||
STRATEGY: multisession
|
||||
commands:
|
||||
- sleep 300
|
||||
- echo "Warmed Up"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: arm64
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
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:
|
||||
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: ubuntu-2404
|
||||
ARCH: arm64
|
||||
NCPUS: 2
|
||||
MEMORY: 29Gi
|
||||
STRATEGY: multisession
|
||||
INSTANCE_TYPE: cax41
|
||||
INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3)
|
||||
volumes:
|
||||
- arm64-binaries-r-dep-cache-ubuntu-2404:/mnt/cache
|
||||
commands:
|
||||
# download latest package version (avoid having to rebuild image every time)
|
||||
- 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()'
|
||||
- R CMD INSTALL .
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
|
||||
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
|
||||
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', process_updated = TRUE, process_new = TRUE)"
|
||||
backend_options:
|
||||
kubernetes:
|
||||
### PROD
|
||||
resources:
|
||||
requests:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
limits:
|
||||
memory: 29Gi
|
||||
cpu: 4000m
|
||||
# DEBUG
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
# limits:
|
||||
# memory: 4Gi
|
||||
# cpu: 2000m
|
||||
nodeSelector:
|
||||
kubernetes.io/arch: 'arm64'
|
||||
node.kubernetes.io/instance-type: cax41
|
||||
tolerations:
|
||||
- key: 'CI'
|
||||
operator: 'Equal'
|
||||
value: 'true'
|
||||
effect: 'NoSchedule'
|
||||
|
||||
- name: 'ntfy'
|
||||
image: codeberg.org/l-x/woodpecker-ntfy:1.3.1
|
||||
when:
|
||||
- status: [failure]
|
||||
settings:
|
||||
url: https://ntfy.devxy.io/ci-builds
|
||||
token:
|
||||
from_secret: ntfy_token
|
||||
title: "CI '${CI_REPO}' failed"
|
||||
actions: view, Open build, ${CI_PIPELINE_URL}, clear=false;
|
||||
click: ${CI_BUILD_LINK}
|
||||
message: |
|
||||
Workflow: ${CI_WORKFLOW_NAME/\n//}
|
||||
Commit message: ${CI_COMMIT_MESSAGE/\n//}
|
||||
Commit Author: ${CI_COMMIT_AUTHOR/\n//}
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 100Mi
|
||||
cpu: 0m
|
||||
limits:
|
||||
memory: 300Mi
|
||||
cpu: 200m
|
||||
Some files were not shown because too many files have changed in this diff Show more
Loading…
Reference in a new issue