From fca8dd57c560ffb3f5f71922f43f33161417e1d7 Mon Sep 17 00:00:00 2001 From: pat-s Date: Tue, 3 Sep 2024 16:55:54 +0200 Subject: [PATCH] include alpine in update runs --- .woodpecker/process_cran_updates.yaml | 10 +++++----- .woodpecker/update-package-index.yaml | 8 ++++---- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.woodpecker/process_cran_updates.yaml b/.woodpecker/process_cran_updates.yaml index d728063..cca0aee 100644 --- a/.woodpecker/process_cran_updates.yaml +++ b/.woodpecker/process_cran_updates.yaml @@ -10,7 +10,7 @@ matrix: - PLATFORM: redhat-8 - PLATFORM: ubuntu-2404 - PLATFORM: ubuntu-2204 - # - PLATFORM: alpine-320 + - 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] @@ -29,14 +29,14 @@ steps: commands: # download latest package version (avoid having to rebuild image every time) - 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 + - rm -rf /mnt/cache/R-pkgs/00LOCK-arm64-r-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR - rm -rf /mnt/cache/R-pkgs/RPostgres /mnt/cache/pkgcache/R/pkgcache - - R -q -e 'devtools::install(); packageVersion("rBinaries")' + - R -q -e 'devtools::install(); packageVersion("bincraftR")' - 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' - 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 - - 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)' + - 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(bincraftR); 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 @@ -86,4 +86,4 @@ steps: cpu: 0m limits: memory: 300Mi - cpu: 200m \ No newline at end of file + cpu: 200m diff --git a/.woodpecker/update-package-index.yaml b/.woodpecker/update-package-index.yaml index fee298d..7b2d0d9 100644 --- a/.woodpecker/update-package-index.yaml +++ b/.woodpecker/update-package-index.yaml @@ -10,7 +10,7 @@ matrix: - PLATFORM: redhat-8 - PLATFORM: ubuntu-2404 - PLATFORM: ubuntu-2204 - # - PLATFORM: alpine-320 + - PLATFORM: alpine-320 steps: - name: Upload PACKAGES files secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] @@ -28,10 +28,10 @@ steps: # 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/packages/* - - R -q -e 'devtools::install(); packageVersion("rBinaries")' + - R -q -e 'devtools::install(); packageVersion("bincraftR")' - R -q -e 'pak::pak(c("pat-s/desc@description-from-remote", "pat-s/cranlike@s3"))' - cd /mnt/cache/packages - - R -q -e 'options(crayon.enabled = TRUE); library(rBinaries); future::plan("multisession", workers = 4); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()' + - R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession", workers = 4); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()' backend_options: kubernetes: resources: @@ -67,4 +67,4 @@ steps: cpu: 0m limits: memory: 300Mi - cpu: 200m \ No newline at end of file + cpu: 200m