when: - event: [cron] cron: process-cran-updates - event: manual evaluate: 'task == "process-cran-updates"' skip_clone: true depends_on: - warm_up_process_cran_updates matrix: include: ### ARM # - PLATFORM: redhat-9 # ARCH: arm64 # NCPUS: 2 # MEMORY: 29Gi # STRATEGY: multisession # - PLATFORM: redhat-8 # ARCH: arm64 # NCPUS: 2 # MEMORY: 29Gi # STRATEGY: multisession # - PLATFORM: ubuntu-2404 # ARCH: arm64 # NCPUS: 2 # MEMORY: 29Gi # STRATEGY: multisession # - PLATFORM: ubuntu-2204 # ARCH: arm64 # NCPUS: 2 # MEMORY: 29Gi # STRATEGY: multisession # ### AMD # - PLATFORM: redhat-9 # ARCH: amd64 # NCPUS: 2 # MEMORY: 29Gi # STRATEGY: multisession # - PLATFORM: redhat-8 # ARCH: amd64 # NCPUS: 2 # MEMORY: 29Gi # STRATEGY: multisession # - PLATFORM: ubuntu-2404 # ARCH: amd64 # NCPUS: 2 # MEMORY: 29Gi # STRATEGY: multisession - PLATFORM: ubuntu-2204 ARCH: amd64 NCPUS: 2 MEMORY: 29Gi STRATEGY: multisession INSTANCE_TYPE: cpx51 INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 31) # - PLATFORM: alpine-320 # ARCH: amd64 # NCPUS: 2 # MEMORY: 29Gi # STRATEGY: multisession steps: - name: 'Processing Updates: (${PLATFORM})' secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] image: docker.io/devxygmbh/${ARCH}-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 volumes: - ${ARCH}-binaries-r-dep-cache-${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 = ${INTERVAL}, platform = "${PLATFORM}", process_updated = TRUE, process_new = TRUE)' backend_options: kubernetes: ### PROD resources: requests: memory: ${MEMORY} cpu: 4000m limits: memory: ${MEMORY} cpu: 4000m # DEBUG # resources: # requests: # memory: 4Gi # cpu: 2000m # limits: # memory: 4Gi # cpu: 2000m nodeSelector: kubernetes.io/arch: '${ARCH}' node.kubernetes.io/instance-type: '${INSTANCE_TYPE}' tolerations: - key: 'CI' operator: 'Equal' value: 'true' effect: 'NoSchedule' - name: 'ntfy' image: codeberg.org/l-x/woodpecker-ntfy:1.3.1 when: - status: [failure] settings: url: https://ntfy.devxy.io/ci-builds token: from_secret: ntfy_token title: "CI '${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