clean process_cran_updates and apply
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2 changed files with 8 additions and 41 deletions
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@ -14,7 +14,7 @@ matrix:
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# - PLATFORM: ubuntu-2204
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# BLOCK: 20099:21169
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- PLATFORM: alpine-320
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BLOCK: 1100:21169
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BLOCK: 1115:21169
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steps:
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- name: 'Build binaries (${PLATFORM}: ${BLOCK})'
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secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT]
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@ -10,6 +10,7 @@ matrix:
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- PLATFORM: redhat-8
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- PLATFORM: ubuntu-2404
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- PLATFORM: ubuntu-2204
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# - PLATFORM: alpine-320
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steps:
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- name: 'Processing Updates: (${PLATFORM})'
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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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@ -27,20 +28,15 @@ steps:
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- arm-binaries-r-dep-cache-${PLATFORM}:/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/arm64-r-binaries.git .
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- rm -rf /mnt/cache/R-pkgs/00LOCK-arm64-r-binaries /mnt/cache/R-pkgs/00LOCK-rBinaries
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# for some reason this one is often corrupt on redhat-9
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- rm -rf /mnt/cache/R-pkgs/RPostgres /mnt/cache/pkgcache/R/pkgcache
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- R -q -e 'devtools::install(); packageVersion("rBinaries")'
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- 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'
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# manually install some packages into the cache so that some builds don't fail
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# Hmisc -> ABCanalysis
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# - 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"))'
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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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- 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)'
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# 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
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- 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)'
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backend_options:
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kubernetes:
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### PROD
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@ -62,36 +58,7 @@ steps:
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nodeSelector:
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kubernetes.io/arch: 'arm64'
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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: Upload PACKAGES files
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# secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token]
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# image: docker.io/pats22/arm-binaries-r-ubi9
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# pull: true
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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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# volumes:
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# - arm-binaries-r-dep-cache-rhel9:/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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# - R -q -e 'pak::local_install(); packageVersion("rBinaries")'
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# - R -q -e 'pak::pak(c("dyfanjones/s3fs", "pat-s/desc@description-from-remote", "pat-s/cranlike@s3"))'
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# - cd /mnt/cache/packages
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# - R -q -e 'options(crayon.enabled = TRUE); library(rBinaries); upload_package_index()'
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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: 1000Mi
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# cpu: 0m
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# limits:
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# memory: 1300Mi
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# cpu: 1000m
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# nodeSelector:
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# kubernetes.io/arch: 'arm64'
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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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