From 1305f3fd359f206a88119f74c13623c9a88ceae5 Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 30 Aug 2024 10:24:13 +0200 Subject: [PATCH] clean process_cran_updates and apply --- .woodpecker/build.yaml | 2 +- .woodpecker/process_cran_updates.yaml | 47 ++++----------------------- 2 files changed, 8 insertions(+), 41 deletions(-) diff --git a/.woodpecker/build.yaml b/.woodpecker/build.yaml index aea4613..6e795ec 100644 --- a/.woodpecker/build.yaml +++ b/.woodpecker/build.yaml @@ -14,7 +14,7 @@ matrix: # - PLATFORM: ubuntu-2204 # BLOCK: 20099:21169 - PLATFORM: alpine-320 - BLOCK: 1100:21169 + BLOCK: 1115:21169 steps: - name: 'Build binaries (${PLATFORM}: ${BLOCK})' secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] diff --git a/.woodpecker/process_cran_updates.yaml b/.woodpecker/process_cran_updates.yaml index ea3a4a5..eee1718 100644 --- a/.woodpecker/process_cran_updates.yaml +++ b/.woodpecker/process_cran_updates.yaml @@ -10,6 +10,7 @@ matrix: - PLATFORM: redhat-8 - PLATFORM: ubuntu-2404 - PLATFORM: ubuntu-2204 + # - PLATFORM: alpine-320 steps: - name: 'Processing Updates: (${PLATFORM})' secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] @@ -27,20 +28,15 @@ steps: - arm-binaries-r-dep-cache-${PLATFORM}:/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/arm64-r-binaries.git . - rm -rf /mnt/cache/R-pkgs/00LOCK-arm64-r-binaries /mnt/cache/R-pkgs/00LOCK-rBinaries - # for some reason this one is often corrupt on redhat-9 - rm -rf /mnt/cache/R-pkgs/RPostgres /mnt/cache/pkgcache/R/pkgcache - R -q -e 'devtools::install(); packageVersion("rBinaries")' - mkdir -p /root/.R && /bin/bash -c 'echo -e "CXX_STD = CXX14\nCC=ccache gcc\nCPP=ccache gcc\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=ccache /usr/bin/gfortran\nFC=ccache /usr/bin/gfortran" > /root/.R/Makevars' - # manually install some packages into the cache so that some builds don't fail - # Hmisc -> ABCanalysis - # - R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE, PKG_SYSREQS_PLATFORM = "redhat-9"); pak::pak(c("Hmisc", "pls", "abd", "doRNG", "devtools"))' - # 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 - - 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]][${BLOCK}]; pkgs = setdiff(pkgs, c("biplotbootGUI", "cncaGUI", "dynBiplotGUI", "ade4TkGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "TextMiningGUI", "later", "RclusTool", "Rcmdr", "RcmdrMisc", "RcmdrPlugin.aRnova", "RcmdrPlugin.BiclustGUI", "RcmdrPlugin.BWS1", "RcmdrPlugin.BWS2", "RcmdrPlugin.BWS3", "RcmdrPlugin.cpd", "RcmdrPlugin.DCCV", "RcmdrPlugin.DCE", "RcmdrPlugin.depthTools", "RcmdrPlugin.DoE", "RcmdrPlugin.EACSPIR", "RcmdrPlugin.EBM", "RcmdrPlugin.EcoVirtual", "RcmdrPlugin.Export", "RcmdrPlugin.EZR", "RcmdrPlugin.FactoMineR", "RcmdrPlugin.GWRM", "RcmdrPlugin.HH", "RcmdrPlugin.KMggplot2", "RcmdrPlugin.MA", "RcmdrPlugin.MPAStats", "RcmdrPlugin.NMBU", "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA" , "RcmdrPlugin.WorldFlora", "sf", "StratigrapheR", "tcltk2", "TVMM", "uHMM")); library(rBinaries); future::plan("sequential"); options(future.globals.onReference = NULL); process_cran_updates(interval = lubridate::interval(lubridate::today() - 32, lubridate::today() - 2), platform = "${PLATFORM}", process_updated = FALSE, process_new = FALSE)' + # 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 + - 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]][${BLOCK}]; pkgs = setdiff(pkgs, c("biplotbootGUI", "cncaGUI", "dynBiplotGUI", "ade4TkGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "TextMiningGUI", "later", "RclusTool", "Rcmdr", "RcmdrMisc", "RcmdrPlugin.aRnova", "RcmdrPlugin.BiclustGUI", "RcmdrPlugin.BWS1", "RcmdrPlugin.BWS2", "RcmdrPlugin.BWS3", "RcmdrPlugin.cpd", "RcmdrPlugin.DCCV", "RcmdrPlugin.DCE", "RcmdrPlugin.depthTools", "RcmdrPlugin.DoE", "RcmdrPlugin.EACSPIR", "RcmdrPlugin.EBM", "RcmdrPlugin.EcoVirtual", "RcmdrPlugin.Export", "RcmdrPlugin.EZR", "RcmdrPlugin.FactoMineR", "RcmdrPlugin.GWRM", "RcmdrPlugin.HH", "RcmdrPlugin.KMggplot2", "RcmdrPlugin.MA", "RcmdrPlugin.MPAStats", "RcmdrPlugin.NMBU", "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA" , "RcmdrPlugin.WorldFlora", "sf", "StratigrapheR", "tcltk2", "TVMM", "uHMM")); library(rBinaries); future::plan("sequential"); options(future.globals.onReference = NULL); process_cran_updates(interval = lubridate::interval(lubridate::today() - 2, lubridate::today() - 2), platform = "${PLATFORM}", process_updated = TRUE, process_new = TRUE)' backend_options: kubernetes: ### PROD @@ -62,36 +58,7 @@ steps: nodeSelector: kubernetes.io/arch: 'arm64' tolerations: - - key: "CI" - operator: "Equal" - value: "true" - effect: "NoSchedule" - # - name: Upload PACKAGES files - # secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token] - # image: docker.io/pats22/arm-binaries-r-ubi9 - # 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 - # volumes: - # - arm-binaries-r-dep-cache-rhel9:/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 - # - R -q -e 'pak::local_install(); packageVersion("rBinaries")' - # - R -q -e 'pak::pak(c("dyfanjones/s3fs", "pat-s/desc@description-from-remote", "pat-s/cranlike@s3"))' - # - cd /mnt/cache/packages - # - R -q -e 'options(crayon.enabled = TRUE); library(rBinaries); upload_package_index()' - # backend_options: - # kubernetes: - # resources: - # requests: - # memory: 1000Mi - # cpu: 0m - # limits: - # memory: 1300Mi - # cpu: 1000m - # nodeSelector: - # kubernetes.io/arch: 'arm64' + - key: 'CI' + operator: 'Equal' + value: 'true' + effect: 'NoSchedule'