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check package index warnings

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This commit is contained in:
Patrick Schratz 2024-11-21 21:38:58 +01:00
commit b69f33b6ce
Signed by: pat-s
GPG key ID: 3C6318841EF78925
5 changed files with 9 additions and 10 deletions
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2
.woodpecker/build-alpine-320-arm64.yaml
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2
.woodpecker/build-redhat-9-amd64.yaml
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@ -69,7 +69,7 @@ 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, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/rhel9/latest', CRAN = 'https://cloud.r-project.org'))); library(dplyr); library(bincraftR); cran_pkgs = tools::CRAN_package_db()[['Package']]; '%nin%' <- Negate('%in%'); foo = query_metadata_table() |> filter(platform == 'redhat-9', arch == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('adamethods', 'adaptIVPT', 'AFM', 'alphashape3d', 'Anthropometry', 'Apollonius', 'archeoViz', 'Arothron', 'atom4R', 'bigGP', 'BiplotGUI', 'blatr', 'BRugs', 'ConvertPar', 'crumble', 'D3mirt', 'DALSM', 'dataone', 'datapack', 'doMPI', 'dsmSearch', 'ETRep', 'excel.link', 'facmodTS', 'FeatureHashing', 'fect', 'fedmatch', 'fedstatAPIr', 'ff', 'fftw', 'fftwtools', 'fGarch', 'fgdr', 'fgeo', 'fgeo.analyze', 'fgeo.plot', 'FGLMtrunc', 'fgm', 'FHDI', 'fHMM', 'fido', 'fields', 'FieldSimR', 'fiery', 'FIESTA', 'FIESTAutils', 'filelock', 'FILEST', 'filling', 'finalsize', 'finbipartite', 'fingerPro', 'fingraph', 'finiteruinprob', 'finity', 'finreportr', 'fio', 'fipp', 'FiRE', 'first', 'fishMod', 'FishPhyloMaker', 'FisPro', 'FIT', 'fitbitViz', 'fitlandr', 'fixest', 'FKF', 'FKSUM', 'flam', 'flamingos', 'flan', 'flashClust', 'flashier', 'flashlight', 'flashr', 'flexclust', 'flexCWM', 'flexiblas', 'flexpolyline', 'FlexReg', 'flexrsurv', 'FlexScan', 'FlexVarJM', 'flifo', 'flintyR', 'float', 'flock', 'FLOPART', 'FLORAL', 'flowml', 'flowTraceR', 'flsa', 'FLSSS', 'fluidsynth', 'flying', 'FlyingR', 'FMC', 'FMCCSD', 'fmdu', 'FME', 'fmerPack', 'fmf', 'fmri', 'fmriqa', 'fMRIscrub', 'FMStable', 'fmx', 'FNN', 'fNonlinear', 'footprint', 'forecast', 'ForecastComb', 'forecastLSW', 'forecastSNSTS', 'ForecastTB', 'foreign', 'forensIT', 'forestControl', 'forestecology', 'forestly', 'forestRK', 'ForestTools', 'formods', 'FORTLS', 'FossilSimShiny', 'fourierin', 'fourPNO', 'fpeek', 'fplot', 'fpop', 'fpopw', 'fpow', 'fpp', 'fpp2', 'fqacalc', 'frab', 'fracdiff', 'fractional', 'fracture', 'frailtyEM', 'frailtyMMpen', 'frailtySurv', 'FRCC', 'frechet', 'free', 'freealg', 'freebird', 'FREEtree', 'frequentistSSDBinary', 'FRESHD', 'FRK', 'fRLR', 'frontier', 'frontiles', 'froth', 'fsbrain', 'FSelectorRcpp', 'FSInteract', 'fso', 'fssemR', 'FSSF', 'fst', 'fstcore', 'FuncDiv', 'fUnitRoots', 'funLBM', 'funmediation', 'funspace', 'funtimes', 'fusen', 'fuser', 'fuzzyRankTests', 'FuzzySimRes', 'FVDDPpkg', 'fwsim', 'fy', 'GADAG', 'gadget2', 'gafit', 'GAGAs', 'galamm', 'galigor', 'GALLO', 'gam', 'gamesGA', 'gamlr', 'gamlss.dist', 'gamlss.ggplots', 'gamlssx', 'gamma', 'gammSlice', 'gamreg', 'gamsel', 'gamselBayes', 'ganDataModel', 'ganGenerativeData', 'GANPA', 'gap', 'gapfill', 'GAS', 'gaselect', 'GaSP', 'gasper', 'gastempt', 'gaston', 'gateR', 'GauPro', 'gausscov', 'GaussSuppression', 'gb', 'GB2group', 'gbeta', 'GBJ', 'gbm', 'gbm.auto', 'gbp', 'gCat', 'gcdnet', 'gcKrig', 'gclm', 'gcmr', 'GCPBayes', 'GCPM', 'GCSM', 'gcTensor', 'gcxgclab', 'gdalcubes', 'gdalraster', 'GDELTtools', 'GDILM.ME', 'GDINA', 'gdpc', 'GE', 'GeDS', 'gee', 'GEEaSPU', 'geepack', 'geigen', 'gelnet', 'glpkAPI', 'imbalanceDatRel', 'IMIFA', 'KeyboardSimulator', 'leafR', 'lgpr', 'lidaRtRee', 'lidR', 'mcrPioda', 'MDSGUI', 'MediaNews', 'metajam', 'minired', 'moc.gapbk', 'mregions2', 'MVA', 'mvabund', 'mvctm', 'mvDFA', 'mvgam', 'mvLSW', 'mvLSWimpute', 'mvMAPIT', 'mvMORPH', 'mvna', 'mvnfast', 'mvnimpute', 'mvnmle', 'mvord', 'mvp', 'MVR', 'mvrsquared', 'mvSLOUCH', 'mvst', 'MVT', 'mwa', 'mwcsr', 'mwTensor', 'mxsem', 'n1qn1', 'N2R', 'nabor', 'NADA2', 'nadiv', 'NAIR', 'NAM', 'nametagger', 'nandb', 'nanoarrow', 'nanoparquet', 'nanostringr', 'naryn', 'natcpp', 'nat.nblast', 'natstrat', 'nat.templatebrains', 'natural', 'navigation', 'NBDesign', 'nbfar'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, 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'))); library(dplyr); library(bincraftR); cran_pkgs = tools::CRAN_package_db()[['Package']]; '%nin%' <- Negate('%in%'); foo = query_metadata_table() |> filter(platform == 'redhat-9', arch == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('BiplotGUI', 'blatr', 'BRugs', 'ConvertPar', 'crumble', 'D3mirt', 'DALSM', 'dataone', 'datapack', 'doMPI', 'dsmSearch', 'ETRep', 'excel.link', 'facmodTS', 'FeatureHashing', 'fect', 'fedmatch', 'fedstatAPIr', 'ff', 'fftw', 'fftwtools', 'fGarch', 'fgdr', 'fgeo', 'fgeo.analyze', 'fgeo.plot', 'FGLMtrunc', 'fgm', 'FHDI', 'fHMM', 'fido', 'fields', 'FieldSimR', 'fiery', 'FIESTA', 'FIESTAutils', 'filelock', 'FILEST', 'filling', 'finalsize', 'finbipartite', 'fingerPro', 'fingraph', 'finiteruinprob', 'finity', 'finreportr', 'fio', 'fipp', 'FiRE', 'first', 'fishMod', 'FishPhyloMaker', 'FisPro', 'FIT', 'fitbitViz', 'fitlandr', 'fixest', 'FKF', 'FKSUM', 'flam', 'flamingos', 'flan', 'flashClust', 'flashier', 'flashlight', 'flashr', 'flexclust', 'flexCWM', 'flexiblas', 'flexpolyline', 'FlexReg', 'flexrsurv', 'FlexScan', 'FlexVarJM', 'flifo', 'flintyR', 'float', 'flock', 'FLOPART', 'FLORAL', 'flowml', 'flowTraceR', 'flsa', 'FLSSS', 'fluidsynth', 'flying', 'FlyingR', 'FMC', 'FMCCSD', 'fmdu', 'FME', 'fmerPack', 'fmf', 'fmri', 'fmriqa', 'fMRIscrub', 'FMStable', 'fmx', 'FNN', 'fNonlinear', 'footprint', 'forecast', 'ForecastComb', 'forecastLSW', 'forecastSNSTS', 'ForecastTB', 'foreign', 'forensIT', 'forestControl', 'forestecology', 'forestly', 'forestRK', 'ForestTools', 'formods', 'FORTLS', 'FossilSimShiny', 'fourierin', 'fourPNO', 'fpeek', 'fplot', 'fpop', 'fpopw', 'fpow', 'fpp', 'fpp2', 'fqacalc', 'frab', 'fracdiff', 'fractional', 'fracture', 'frailtyEM', 'frailtyMMpen', 'frailtySurv', 'FRCC', 'frechet', 'free', 'freealg', 'freebird', 'FREEtree', 'frequentistSSDBinary', 'FRESHD', 'FRK', 'fRLR', 'frontier', 'frontiles', 'froth', 'fsbrain', 'FSelectorRcpp', 'FSInteract', 'fso', 'fssemR', 'FSSF', 'fst', 'fstcore', 'FuncDiv', 'fUnitRoots', 'funLBM', 'funmediation', 'funspace', 'funtimes', 'fusen', 'fuser', 'fuzzyRankTests', 'FuzzySimRes', 'FVDDPpkg', 'fwsim', 'fy', 'GADAG', 'gadget2', 'gafit', 'GAGAs', 'galamm', 'galigor', 'GALLO', 'gam', 'gamesGA', 'gamlr', 'gamlss.dist', 'gamlss.ggplots', 'gamlssx', 'gamma', 'gammSlice', 'gamreg', 'gamsel', 'gamselBayes', 'ganDataModel', 'ganGenerativeData', 'GANPA', 'gap', 'gapfill', 'GAS', 'gaselect', 'GaSP', 'gasper', 'gastempt', 'gaston', 'gateR', 'GauPro', 'gausscov', 'GaussSuppression', 'gb', 'GB2group', 'gbeta', 'GBJ', 'gbm', 'gbm.auto', 'gbp', 'gCat', 'gcdnet', 'gcKrig', 'gclm', 'gcmr', 'GCPBayes', 'GCPM', 'GCSM', 'gcTensor', 'gcxgclab', 'gdalcubes', 'gdalraster', 'GDELTtools', 'GDILM.ME', 'GDINA', 'gdpc', 'GE', 'GeDS', 'gee', 'GEEaSPU', 'geepack', 'geigen', 'gelnet', 'glpkAPI', 'imbalanceDatRel', 'IMIFA', 'KeyboardSimulator', 'leafR', 'lgpr', 'lidaRtRee', 'lidR', 'mcrPioda', 'MDSGUI', 'MediaNews', 'metajam', 'minired', 'moc.gapbk', 'mregions2', 'MVA', 'mvabund', 'mvctm', 'mvDFA', 'mvgam', 'mvLSW', 'mvLSWimpute', 'mvMAPIT', 'mvMORPH', 'mvna', 'mvnfast', 'mvnimpute', 'mvnmle', 'mvord', 'mvp', 'MVR', 'mvrsquared', 'mvSLOUCH', 'mvst', 'MVT', 'mwa', 'mwcsr', 'mwTensor', 'mxsem', 'n1qn1', 'N2R', 'nabor', 'NADA2', 'nadiv', 'NAIR', 'NAM', 'nametagger', 'nandb', 'nanoarrow', 'nanoparquet', 'nanostringr', 'naryn', 'natcpp', 'nat.nblast', 'natstrat', 'nat.templatebrains', 'natural', 'navigation', 'NBDesign', 'nbfar'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, 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

2
.woodpecker/build-ubuntu-2404-amd64.yaml
View file

@ -46,7 +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, repos = structure(c(devxy = 'https://cran.devxy.io/amd64/noble/latest', CRAN = 'https://cloud.r-project.org'))); library(dplyr); library(bincraftR); cran_pkgs = tools::CRAN_package_db()[['Package']]; '%nin%' <- Negate('%in%'); foo = query_metadata_table() |> filter(platform == 'ubuntu-2404', arch == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('abmR', 'adw', 'AgroTech', 'agua', 'AQEval', 'arakno', 'arcgisgeocode', 'arcgisutils', 'archeofrag', 'archeoViz', 'archetyper', 'arcpbf', 'arcpullr', 'ardl.nardl', 'areal', 'arealDB', 'arenar', 'ARGOS', 'ari', 'arlclustering', 'Arothron', 'ARPALData', 'arrangements', 'artfima', 'aslib', 'asremlPlus', 'Ball', 'Benchmarking', 'BiplotGUI', 'blatr', 'BRugs', 'clrng', 'CoTiMA', 'deeptrafo', 'disclosuR', 'doconv', 'ecoCopula', 'Eunomia', 'excel.link', 'filters', 'gpuR', 'KeyboardSimulator', 'lgpr', 'MDSGUI', 'MediaNews', 'MPCR', 'ondisc', 'R2PPT', 'R2wd', 'ravetools', 'Rcplex', 'RcppCWB', 'rFUSION', 'RWinEdt', 'spectrino', 'taskscheduleR', 'TaxaNorm', 'verbaliseR'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, 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'))); library(dplyr); library(bincraftR); cran_pkgs = tools::CRAN_package_db()[['Package']]; '%nin%' <- Negate('%in%'); foo = query_metadata_table() |> filter(platform == 'ubuntu-2404', arch == 'amd64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('BiplotGUI', 'blatr', 'BRugs', 'clrng', 'CoTiMA', 'deeptrafo', 'disclosuR', 'doconv', 'ecoCopula', 'Eunomia', 'excel.link', 'filters', 'gpuR', 'KeyboardSimulator', 'lgpr', 'MDSGUI', 'MediaNews', 'MPCR', 'ondisc', 'R2PPT', 'R2wd', 'ravetools', 'Rcplex', 'RcppCWB', 'rFUSION', 'RWinEdt', 'spectrino', 'taskscheduleR', 'TaxaNorm', 'verbaliseR'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, 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

4
.woodpecker/update-package-index-ubuntu-2204-amd64.yaml
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@ -26,10 +26,10 @@ steps:
- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git .
- rm -rf /mnt/cache/packages/*
- rm -rf /mnt/cache/R-pkgs/stringr
- R CMD INSTALL .
- R -q -e 'packageVersion("bincraftR")'
- R -q -e 'pak::pak(c("pat-s/desc@description-from-remote", "pat-s/cranlike@s3"))'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession", workers = 2); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession", workers = 2); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(); warnings()'
backend_options:
kubernetes:
resources:

9
.woodpecker/update-package-index-ubuntu-2404-amd64.yaml
View file

@ -24,12 +24,11 @@ steps:
# 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
- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git .
- rm -rf /mnt/cache/packages/*
- rm -rf /mnt/cache/R-pkgs/stringr
- R CMD INSTALL .
# # - rm -rf /mnt/cache/packages/*
- R -q -e 'packageVersion("bincraftR")'
- R -q -e 'pak::pak(c("pat-s/desc@description-from-remote", "pat-s/cranlike@s3"))'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession", workers = 2); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession", workers = future::availableCores()); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
backend_options:
kubernetes:
resources:
@ -38,7 +37,7 @@ steps:
cpu: 2000m
limits:
memory: 2000Mi
cpu: 2000m
cpu: 8000m
nodeSelector:
kubernetes.io/arch: 'amd64'