From 2abb903efa4f54c13e0911c1343bacc74e31e928 Mon Sep 17 00:00:00 2001 From: pat-s Date: Tue, 5 Nov 2024 22:19:49 +0100 Subject: [PATCH] use own cran repos --- .woodpecker/build-alpine-320-amd64.yaml | 46 +++--------- .woodpecker/build-alpine-320-arm64.yaml | 2 +- .woodpecker/build-redhat-8-amd64.yaml | 44 +++--------- .woodpecker/build-redhat-8-arm64.yaml | 2 +- .woodpecker/build-redhat-9-amd64.yaml | 6 +- .woodpecker/build-redhat-9-arm64.yaml | 2 +- .woodpecker/build-ubuntu-2204-amd64.yaml | 46 +++--------- .woodpecker/build-ubuntu-2204-arm64.yaml | 2 +- .woodpecker/build-ubuntu-2404-amd64.yaml | 42 +++-------- .woodpecker/build-ubuntu-2404-arm64.yaml | 2 +- .../process-updates-alpine-320-amd64.yaml | 46 ++---------- .../process-updates-alpine-320-arm64.yaml | 2 +- .../process-updates-redhat-8-amd64.yaml | 70 ++++++++----------- .../process-updates-redhat-8-arm64.yaml | 2 +- .../process-updates-redhat-9-amd64.yaml | 45 ++---------- .../process-updates-redhat-9-arm64.yaml | 2 +- .../process-updates-ubuntu-2204-amd64.yaml | 60 ++++++++-------- .../process-updates-ubuntu-2204-arm64.yaml | 2 +- .../process-updates-ubuntu-2404-amd64.yaml | 42 ++--------- .../process-updates-ubuntu-2404-arm64.yaml | 2 +- 20 files changed, 131 insertions(+), 336 deletions(-) diff --git a/.woodpecker/build-alpine-320-amd64.yaml b/.woodpecker/build-alpine-320-amd64.yaml index 2196c09..897f9b1 100644 --- a/.woodpecker/build-alpine-320-amd64.yaml +++ b/.woodpecker/build-alpine-320-amd64.yaml @@ -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-alpine-320 @@ -46,14 +22,14 @@ steps: R_LIBS_USER: /mnt/cache/R-pkgs CCACHE_DIR: /mnt/cache/ccache PLATFORM: alpine-320 - BLOCK: 1581:2993 + BLOCK: 1880:2993 ARCH: amd64 - NCPUS: 2 - MEMORY: 14Gi - INSTANCE_TYPE: ccx23 + NCPUS: 4 + # MEMORY: 18Gi + # INSTANCE_TYPE: ccx23 STRATEGY: sequential - volumes: - - amd64-binaries-r-dep-cache-alpine-320:/mnt/cache + # volumes: + # - amd64-binaries-r-dep-cache-alpine-320:/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 = 'alpine-320'))" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/alpine320/latest', CRAN = 'https://cloud.r-project.org'))); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$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 = 'alpine-320'))" ### 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 @@ -106,14 +82,14 @@ steps: kubernetes: resources: requests: - memory: 14Gi + memory: 5Gi cpu: 2000m limits: - memory: 14Gi - cpu: 2000m + memory: 18Gi + cpu: 4000m nodeSelector: kubernetes.io/arch: amd64 - node.kubernetes.io/instance-type: ccx23 + node.kubernetes.io/instance-type: AX42 tolerations: - key: 'CI' operator: 'Equal' diff --git a/.woodpecker/build-alpine-320-arm64.yaml b/.woodpecker/build-alpine-320-arm64.yaml index 6a31c71..aaae058 100644 --- a/.woodpecker/build-alpine-320-arm64.yaml +++ b/.woodpecker/build-alpine-320-arm64.yaml @@ -68,7 +68,7 @@ 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 = 'alpine-320'))" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$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 = 'alpine-320'))" ### 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 diff --git a/.woodpecker/build-redhat-8-amd64.yaml b/.woodpecker/build-redhat-8-amd64.yaml index 275b8c8..70182e3 100644 --- a/.woodpecker/build-redhat-8-amd64.yaml +++ b/.woodpecker/build-redhat-8-amd64.yaml @@ -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-redhat-8 @@ -46,14 +22,14 @@ steps: R_LIBS_USER: /mnt/cache/R-pkgs CCACHE_DIR: /mnt/cache/ccache PLATFORM: redhat-8 - BLOCK: 228:1833 + BLOCK: 737:1833 ARCH: amd64 - NCPUS: 2 - MEMORY: 14Gi - INSTANCE_TYPE: ccx23 + NCPUS: 4 + # MEMORY: 14Gi + # INSTANCE_TYPE: ccx23 STRATEGY: sequential - volumes: - - amd64-binaries-r-dep-cache-redhat-8:/mnt/cache + # volumes: + # - amd64-binaries-r-dep-cache-redhat-8:/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 = 'redhat-8'))" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/rhel8/latest', CRAN = 'https://cloud.r-project.org'))); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$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 = 'redhat-8'))" ### 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 + 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' diff --git a/.woodpecker/build-redhat-8-arm64.yaml b/.woodpecker/build-redhat-8-arm64.yaml index fbd58e4..b349bae 100644 --- a/.woodpecker/build-redhat-8-arm64.yaml +++ b/.woodpecker/build-redhat-8-arm64.yaml @@ -68,7 +68,7 @@ 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 = 'redhat-8'))" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$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 = 'redhat-8'))" ### 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 diff --git a/.woodpecker/build-redhat-9-amd64.yaml b/.woodpecker/build-redhat-9-amd64.yaml index f93cbbc..5016259 100644 --- a/.woodpecker/build-redhat-9-amd64.yaml +++ b/.woodpecker/build-redhat-9-amd64.yaml @@ -48,7 +48,7 @@ steps: PLATFORM: redhat-9 BLOCK: 715:2428 ARCH: amd64 - NCPUS: 2 + NCPUS: 4 MEMORY: 14Gi INSTANCE_TYPE: AX42 STRATEGY: sequential @@ -70,7 +70,7 @@ 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 = 'redhat-9'))" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/rhel9/latest', CRAN = 'https://cloud.r-project.org'))); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$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 = 'redhat-9'))" ### 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 @@ -111,7 +111,7 @@ steps: cpu: 2000m limits: memory: 14Gi - cpu: 2000m + cpu: 4000m ### PROD-sequential # resources: # requests: diff --git a/.woodpecker/build-redhat-9-arm64.yaml b/.woodpecker/build-redhat-9-arm64.yaml index 7e2ba09..1c5fb4b 100644 --- a/.woodpecker/build-redhat-9-arm64.yaml +++ b/.woodpecker/build-redhat-9-arm64.yaml @@ -68,7 +68,7 @@ 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 = 'redhat-9'))" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$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 = 'redhat-9'))" ### 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 diff --git a/.woodpecker/build-ubuntu-2204-amd64.yaml b/.woodpecker/build-ubuntu-2204-amd64.yaml index 44b6257..dc50a0d 100644 --- a/.woodpecker/build-ubuntu-2204-amd64.yaml +++ b/.woodpecker/build-ubuntu-2204-amd64.yaml @@ -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' diff --git a/.woodpecker/build-ubuntu-2204-arm64.yaml b/.woodpecker/build-ubuntu-2204-arm64.yaml index 2cafe1f..65c4a88 100644 --- a/.woodpecker/build-ubuntu-2204-arm64.yaml +++ b/.woodpecker/build-ubuntu-2204-arm64.yaml @@ -68,7 +68,7 @@ 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 = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$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 diff --git a/.woodpecker/build-ubuntu-2404-amd64.yaml b/.woodpecker/build-ubuntu-2404-amd64.yaml index 1fcfb5c..26d608e 100644 --- a/.woodpecker/build-ubuntu-2404-amd64.yaml +++ b/.woodpecker/build-ubuntu-2404-amd64.yaml @@ -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-2404 @@ -46,14 +22,14 @@ steps: R_LIBS_USER: /mnt/cache/R-pkgs CCACHE_DIR: /mnt/cache/ccache PLATFORM: ubuntu-2404 - BLOCK: 1813:4298 + BLOCK: 1886:4298 ARCH: amd64 - NCPUS: 2 + NCPUS: 4 MEMORY: 14Gi - INSTANCE_TYPE: ccx23 + # INSTANCE_TYPE: ccx23 STRATEGY: sequential - volumes: - - amd64-binaries-r-dep-cache-ubuntu-2404:/mnt/cache + # volumes: + # - amd64-binaries-r-dep-cache-ubuntu-2404:/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-2404'))" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/noble/latest', CRAN = 'https://cloud.r-project.org'))); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$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-2404'))" ### 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 + 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' diff --git a/.woodpecker/build-ubuntu-2404-arm64.yaml b/.woodpecker/build-ubuntu-2404-arm64.yaml index f92a504..d0e297d 100644 --- a/.woodpecker/build-ubuntu-2404-arm64.yaml +++ b/.woodpecker/build-ubuntu-2404-arm64.yaml @@ -68,7 +68,7 @@ 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-2404'))" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'redatam', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('$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-2404'))" ### 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 diff --git a/.woodpecker/process-updates-alpine-320-amd64.yaml b/.woodpecker/process-updates-alpine-320-amd64.yaml index 37f8e16..9379a07 100644 --- a/.woodpecker/process-updates-alpine-320-amd64.yaml +++ b/.woodpecker/process-updates-alpine-320-amd64.yaml @@ -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: 4000m - limits: - memory: 14Gi - cpu: 4000m - nodeSelector: - kubernetes.io/arch: amd64 - node.kubernetes.io/instance-type: cpx41 - tolerations: - - key: 'CI' - operator: 'Equal' - value: 'true' - effect: 'NoSchedule' - - name: 'Processing Updates' 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-alpine-320 @@ -46,12 +22,10 @@ steps: PLATFORM: alpine-320 ARCH: amd64 NCPUS: 2 - MEMORY: 14Gi STRATEGY: sequential - INSTANCE_TYPE: cpx41 INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3) - volumes: - - amd64-binaries-r-dep-cache-alpine-320:/mnt/cache + # volumes: + # - amd64-binaries-r-dep-cache-alpine-320:/mnt/cache commands: # download latest package version (avoid having to rebuild image every time) - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . @@ -63,28 +37,20 @@ steps: - 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 - - xvfb-run 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', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'alpine-320', process_updated = TRUE, process_new = TRUE)" + - xvfb-run 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', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'alpine-320', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: ### PROD resources: requests: memory: 14Gi - cpu: 4000m + cpu: 3000m limits: memory: 14Gi - cpu: 4000m - # DEBUG - # resources: - # requests: - # memory: 4Gi - # cpu: 2000m - # limits: - # memory: 4Gi - # cpu: 2000m + cpu: 3000m nodeSelector: kubernetes.io/arch: amd64 - node.kubernetes.io/instance-type: cpx41 + node.kubernetes.io/instance-type: AX42 tolerations: - key: 'CI' operator: 'Equal' diff --git a/.woodpecker/process-updates-alpine-320-arm64.yaml b/.woodpecker/process-updates-alpine-320-arm64.yaml index 1674920..322a3c0 100644 --- a/.woodpecker/process-updates-alpine-320-arm64.yaml +++ b/.woodpecker/process-updates-alpine-320-arm64.yaml @@ -63,7 +63,7 @@ steps: - 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 - - xvfb-run 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', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'alpine-320', process_updated = TRUE, process_new = TRUE)" + - xvfb-run 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', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'alpine-320', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: ### PROD diff --git a/.woodpecker/process-updates-redhat-8-amd64.yaml b/.woodpecker/process-updates-redhat-8-amd64.yaml index 9afaa87..53c1505 100644 --- a/.woodpecker/process-updates-redhat-8-amd64.yaml +++ b/.woodpecker/process-updates-redhat-8-amd64.yaml @@ -9,29 +9,29 @@ 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: 4000m - limits: - memory: 14Gi - cpu: 4000m - nodeSelector: - kubernetes.io/arch: amd64 - node.kubernetes.io/instance-type: cpx41 - tolerations: - - key: 'CI' - operator: 'Equal' - value: 'true' - effect: 'NoSchedule' + # - name: 'Warming up' + # image: busybox:latest + # failure: ignore + # commands: + # - sleep 300 + # - echo "Warmed Up" + # backend_options: + # kubernetes: + # resources: + # requests: + # memory: 14Gi + # cpu: 3000m + # limits: + # memory: 14Gi + # cpu: 3000m + # nodeSelector: + # kubernetes.io/arch: amd64 + # node.kubernetes.io/instance-type: AX42 + # tolerations: + # - key: 'CI' + # operator: 'Equal' + # value: 'true' + # effect: 'NoSchedule' - name: 'Processing Updates' secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] @@ -46,12 +46,12 @@ steps: PLATFORM: redhat-8 ARCH: amd64 NCPUS: 2 - MEMORY: 14Gi + # MEMORY: 14Gi STRATEGY: sequential - INSTANCE_TYPE: cpx41 + # INSTANCE_TYPE: cpx41 INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3) - volumes: - - amd64-binaries-r-dep-cache-redhat-8:/mnt/cache + # volumes: + # - amd64-binaries-r-dep-cache-redhat-8:/mnt/cache commands: # download latest package version (avoid having to rebuild image every time) - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . @@ -63,28 +63,20 @@ steps: - 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 - - xvfb-run 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', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: ### PROD resources: requests: memory: 14Gi - cpu: 4000m + cpu: 3000m limits: memory: 14Gi - cpu: 4000m - # DEBUG - # resources: - # requests: - # memory: 4Gi - # cpu: 2000m - # limits: - # memory: 4Gi - # cpu: 2000m + cpu: 3000m nodeSelector: kubernetes.io/arch: amd64 - node.kubernetes.io/instance-type: cpx41 + node.kubernetes.io/instance-type: AX42 tolerations: - key: 'CI' operator: 'Equal' diff --git a/.woodpecker/process-updates-redhat-8-arm64.yaml b/.woodpecker/process-updates-redhat-8-arm64.yaml index 6d325fe..94883de 100644 --- a/.woodpecker/process-updates-redhat-8-arm64.yaml +++ b/.woodpecker/process-updates-redhat-8-arm64.yaml @@ -63,7 +63,7 @@ steps: - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: ### PROD diff --git a/.woodpecker/process-updates-redhat-9-amd64.yaml b/.woodpecker/process-updates-redhat-9-amd64.yaml index 103037f..0084275 100644 --- a/.woodpecker/process-updates-redhat-9-amd64.yaml +++ b/.woodpecker/process-updates-redhat-9-amd64.yaml @@ -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: 4000m - limits: - memory: 14Gi - cpu: 4000m - nodeSelector: - kubernetes.io/arch: amd64 - node.kubernetes.io/instance-type: cpx41 - tolerations: - - key: 'CI' - operator: 'Equal' - value: 'true' - effect: 'NoSchedule' - - name: 'Processing Updates' 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-redhat-9 @@ -48,10 +24,9 @@ steps: NCPUS: 2 MEMORY: 14Gi STRATEGY: sequential - INSTANCE_TYPE: cpx41 INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3) - volumes: - - amd64-binaries-r-dep-cache-redhat-9:/mnt/cache + # volumes: + # - amd64-binaries-r-dep-cache-redhat-9:/mnt/cache commands: # download latest package version (avoid having to rebuild image every time) - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . @@ -63,28 +38,20 @@ steps: - 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 - - xvfb-run 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', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE)" + - xvfb-run 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', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: ### PROD resources: requests: memory: 14Gi - cpu: 4000m + cpu: 3000m limits: memory: 14Gi - cpu: 4000m - # DEBUG - # resources: - # requests: - # memory: 4Gi - # cpu: 2000m - # limits: - # memory: 4Gi - # cpu: 2000m + cpu: 3000m nodeSelector: kubernetes.io/arch: amd64 - node.kubernetes.io/instance-type: cpx41 + node.kubernetes.io/instance-type: AX42 tolerations: - key: 'CI' operator: 'Equal' diff --git a/.woodpecker/process-updates-redhat-9-arm64.yaml b/.woodpecker/process-updates-redhat-9-arm64.yaml index 3d2a849..6637138 100644 --- a/.woodpecker/process-updates-redhat-9-arm64.yaml +++ b/.woodpecker/process-updates-redhat-9-arm64.yaml @@ -63,7 +63,7 @@ steps: - 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 - - xvfb-run 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', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE)" + - xvfb-run 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', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: ### PROD diff --git a/.woodpecker/process-updates-ubuntu-2204-amd64.yaml b/.woodpecker/process-updates-ubuntu-2204-amd64.yaml index 3c7fc8b..fcd761e 100644 --- a/.woodpecker/process-updates-ubuntu-2204-amd64.yaml +++ b/.woodpecker/process-updates-ubuntu-2204-amd64.yaml @@ -9,29 +9,29 @@ 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: 4000m - limits: - memory: 14Gi - cpu: 4000m - nodeSelector: - kubernetes.io/arch: amd64 - node.kubernetes.io/instance-type: cpx41 - tolerations: - - key: 'CI' - operator: 'Equal' - value: 'true' - effect: 'NoSchedule' + # - name: 'Warming up' + # image: busybox:latest + # failure: ignore + # commands: + # - sleep 300 + # - echo "Warmed Up" + # backend_options: + # kubernetes: + # resources: + # requests: + # memory: 14Gi + # cpu: 3000m + # limits: + # memory: 14Gi + # cpu: 3000m + # nodeSelector: + # kubernetes.io/arch: amd64 + # node.kubernetes.io/instance-type: ccx23 + # tolerations: + # - key: 'CI' + # operator: 'Equal' + # value: 'true' + # effect: 'NoSchedule' - name: 'Processing Updates' secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] @@ -48,10 +48,10 @@ steps: NCPUS: 2 MEMORY: 14Gi STRATEGY: sequential - INSTANCE_TYPE: cpx41 + # INSTANCE_TYPE: ccx23 INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3) - 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) - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git . @@ -63,17 +63,17 @@ steps: - 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 - - xvfb-run 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', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: ### PROD resources: requests: memory: 14Gi - cpu: 4000m + cpu: 3000m limits: memory: 14Gi - cpu: 4000m + cpu: 3000m # DEBUG # resources: # requests: @@ -84,7 +84,7 @@ steps: # cpu: 2000m nodeSelector: kubernetes.io/arch: amd64 - node.kubernetes.io/instance-type: cpx41 + node.kubernetes.io/instance-type: AX42 tolerations: - key: 'CI' operator: 'Equal' diff --git a/.woodpecker/process-updates-ubuntu-2204-arm64.yaml b/.woodpecker/process-updates-ubuntu-2204-arm64.yaml index f6b81b7..0bb038a 100644 --- a/.woodpecker/process-updates-ubuntu-2204-arm64.yaml +++ b/.woodpecker/process-updates-ubuntu-2204-arm64.yaml @@ -63,7 +63,7 @@ steps: - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: ### PROD diff --git a/.woodpecker/process-updates-ubuntu-2404-amd64.yaml b/.woodpecker/process-updates-ubuntu-2404-amd64.yaml index 67d8e92..c0f9455 100644 --- a/.woodpecker/process-updates-ubuntu-2404-amd64.yaml +++ b/.woodpecker/process-updates-ubuntu-2404-amd64.yaml @@ -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: 1000m - limits: - memory: 14Gi - cpu: 4000m - nodeSelector: - kubernetes.io/arch: amd64 - node.kubernetes.io/instance-type: cpx41 - tolerations: - - key: 'CI' - operator: 'Equal' - value: 'true' - effect: 'NoSchedule' - - name: 'Processing Updates' 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-2404 @@ -46,9 +22,7 @@ steps: PLATFORM: ubuntu-2404 ARCH: amd64 NCPUS: 1 - MEMORY: 14Gi STRATEGY: sequential - INSTANCE_TYPE: cpx41 INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 3) volumes: - amd64-binaries-r-dep-cache-ubuntu-2404:/mnt/cache @@ -63,28 +37,20 @@ steps: - 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 - - xvfb-run 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', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: ### PROD resources: requests: memory: 14Gi - cpu: 4000m + cpu: 3000m limits: memory: 14Gi - cpu: 4000m - # DEBUG - # resources: - # requests: - # memory: 4Gi - # cpu: 2000m - # limits: - # memory: 4Gi - # cpu: 2000m + cpu: 3000m nodeSelector: kubernetes.io/arch: amd64 - node.kubernetes.io/instance-type: cpx41 + node.kubernetes.io/instance-type: AX42 tolerations: - key: 'CI' operator: 'Equal' diff --git a/.woodpecker/process-updates-ubuntu-2404-arm64.yaml b/.woodpecker/process-updates-ubuntu-2404-arm64.yaml index edaebc0..bd93fa3 100644 --- a/.woodpecker/process-updates-ubuntu-2404-arm64.yaml +++ b/.woodpecker/process-updates-ubuntu-2404-arm64.yaml @@ -68,7 +68,7 @@ steps: - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', process_updated = TRUE, process_new = TRUE)" + - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', '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('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', process_updated = TRUE, process_new = TRUE)" backend_options: kubernetes: ### PROD