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process all package updates since build start

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This commit is contained in:
Patrick Schratz 2024-08-28 18:38:25 +02:00
commit d4d95e1a4a
Signed by: pat-s
GPG key ID: 3C6318841EF78925
2 changed files with 9 additions and 10 deletions
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14
.woodpecker/process_cran_updates.yaml
View file

@ -7,9 +7,9 @@ skip_clone: true
matrix:
include:
- PLATFORM: redhat-9
# - PLATFORM: redhat-8
# - PLATFORM: ubuntu-2404
# - PLATFORM: ubuntu-2204
- PLATFORM: redhat-8
- PLATFORM: ubuntu-2404
- PLATFORM: ubuntu-2204
steps:
- name: 'Processing Updates: (${PLATFORM})'
secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT]
@ -41,17 +41,17 @@ steps:
# more complicated system dependencies which pak cannot resolve
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
- R -q -e 'options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = "error", repos = structure(c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"))); pkgs = tools::CRAN_package_db()[[1]][${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"); process_cran_updates(interval = lubridate::today() - 2, platform = "${PLATFORM}")'
- R -q -e 'options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = "error", repos = structure(c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"))); pkgs = tools::CRAN_package_db()[[1]][${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"); process_cran_updates(interval = lubridate::interval(lubridate::today() - 28, lubridate::today() - 1), platform = "${PLATFORM}")'
backend_options:
kubernetes:
### PROD
resources:
requests:
memory: 4Gi
memory: 10Gi
cpu: 1000m
limits:
memory: 13Gi
cpu: 1000m
memory: 14Gi
cpu: 4000m
# DEBUG
# resources:
# requests:

5
R/process_cran_updates.R
View file

@ -31,7 +31,7 @@ process_cran_updates <- function(
all_pkgs <- dplyr::bind_rows(updated_pkgs, new_pkgs)
# purrr::walk2(all_pkgs$name, all_pkgs$version, ~ build_binary_package(.x, .y, platform = platform))
purrr::walk2(all_pkgs$name, all_pkgs$version, ~ build_binary_package(.x, .y, platform = platform))
if (prune) {
removed_pkgs <- get_removed_cran_packages(interval)
@ -60,11 +60,10 @@ process_cran_updates <- function(
files_filtered <- grep(sprintf("%s_", .x), files, value = TRUE)
if (length(files_filtered > 0)) {
s3fs::s3_file_delete(files_filtered)
cli::cli_alert_success("{.fun process_cran_updates}: Successfully removed {.pkg {basename(files_filtered)}} from S3.")
} else {
cli::cli_alert("{.fun process_cran_updates}: No tarballs found for package {.pkg {.x}} - already removed?")
}
cli::cli_alert_success("{.fun process_cran_updates}: Successfully removed {.pkg {basename(files_filtered)}} from S3.")
})
}
}