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use own cran repos

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This commit is contained in:
Patrick Schratz 2024-11-05 22:19:49 +01:00
commit 2abb903efa
Signed by: pat-s
GPG key ID: 3C6318841EF78925
1 changed files with 131 additions and 336 deletions
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46
.woodpecker/build-ubuntu-2204-amd64.yaml
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@ -9,30 +9,6 @@ when:
skip_clone: true
steps:
- name: 'Warming up'
image: busybox:latest
failure: ignore
commands:
- sleep 300
- echo "Warmed Up"
backend_options:
kubernetes:
resources:
requests:
memory: 14Gi
cpu: 2000m
limits:
memory: 14Gi
cpu: 2000m
nodeSelector:
kubernetes.io/arch: amd64
node.kubernetes.io/instance-type: ccx23
tolerations:
- key: 'CI'
operator: 'Equal'
value: 'true'
effect: 'NoSchedule'
- name: 'Build binaries'
secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT]
image: docker.io/devxygmbh/amd64-binaries-r-ubuntu-2204
@ -46,14 +22,14 @@ steps:
R_LIBS_USER: /mnt/cache/R-pkgs
CCACHE_DIR: /mnt/cache/ccache
PLATFORM: ubuntu-2204
BLOCK: 1913:4755
BLOCK: 2128:4755
ARCH: amd64
NCPUS: 2
MEMORY: 14Gi
INSTANCE_TYPE: ccx23
NCPUS: 4
# MEMORY: 14Gi
# INSTANCE_TYPE: ccx23
STRATEGY: sequential
volumes:
- amd64-binaries-r-dep-cache-ubuntu-2204:/mnt/cache
# volumes:
# - amd64-binaries-r-dep-cache-ubuntu-2204:/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
@ -70,7 +46,7 @@ steps:
# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
# - Rglpk
# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$STRATEGY', workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'ubuntu-2204'))"
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/jammy/latest', CRAN = 'https://cloud.r-project.org'))); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$STRATEGY', workers = $NCPUS, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs[$BLOCK], function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = 'ubuntu-2204'))"
### Manual pkg builds
# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
# RInno: Windows-only
@ -107,11 +83,11 @@ steps:
### PROD-parallel
resources:
requests:
memory: 14Gi
memory: 5Gi
cpu: 2000m
limits:
memory: 14Gi
cpu: 2000m
memory: 16Gi
cpu: 4000m
### PROD-sequential
# resources:
# requests:
@ -130,7 +106,7 @@ steps:
# cpu: 2000m
nodeSelector:
kubernetes.io/arch: amd64
node.kubernetes.io/instance-type: ccx23
node.kubernetes.io/instance-type: AX42
tolerations:
- key: 'CI'
operator: 'Equal'