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use mountless update-packages steps

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This commit is contained in:
Patrick Schratz 2024-12-25 15:52:06 +01:00
commit 12deb4edd5
Signed by: pat-s
GPG key ID: 3C6318841EF78925
14 changed files with 23 additions and 37 deletions
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2
.woodpecker/build-alpine-321-amd64-single.yaml
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2
.woodpecker/build-alpine-321-arm64-single.yaml
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@ -46,7 +46,7 @@ steps:
- R -q -e 'packageVersion("bincraftR")'
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'rFUSION', 'MediaNews'
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c('adas.utils', 'BAREB', 'catalytic', 'datacutr', 'doBy', 'DoE.base', 'DoE.wrapper', 'eha', 'elrm', 'exhaustiveRasch', 'fasterRaster', 'FrF2', 'FrF2.catlg128', 'fuseMLR', 'gRain', 'gRbase', 'greta.gam', 'GrowthCurveME', 'IDPmisc', 'pacu', 'pbkrtest', 'PSGD', 'pwrFDR', 'qPRAentry', 'RVAideMemoire', 'seewave', 'shinychat', 'SNPassoc', 'spanishoddata', 'spdep', 'splineCox', 'stepSplitReg', 'surveillance', 'tatooheene'); pkgs = setdiff(pkgs, c('RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'rFUSION', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', 'compareGroups', 'pls', 'SNPassoc', 'spdep', 'surveillance')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'alpine-321'))"
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c('A3', 'abmR', 'abtest', 'AccelStab', 'Achilles', 'actel', 'actxps', 'AdhereRViz', 'aIc', 'ajv', 'AlleleShift', 'almanac', 'alphashape3d', 'amadeus', 'Anthropometry', 'AntMAN', 'APCalign', 'apcf', 'aPCoA', 'apisensr', 'Apollonius', 'appeears', 'AQEval', 'AquaBEHER', 'arakno', 'arcgisgeocode', 'arcgislayers', 'archeoViz', 'archive', 'arcpbf', 'areal', 'arealDB', 'aroma.affymetrix', 'aroma.cn', 'aroma.core', 'Arothron', 'ARPALData', 'arrangements', 'artfima', 'ARUtools', 'asciicast', 'atakrig', 'atom4R', 'atpolR', 'audubon', 'AurieLSHGaussian', 'autostats', 'av', 'AVGAS', 'aws', 'aws.wrfsmn', 'AZIAD', 'babelmixr2', 'badgen', 'baguette', 'bamm', 'bangladesh', 'base64', 'basemaps', 'basf', 'basifoR', 'bate', 'BAwiR', 'BayesfMRI', 'BayesOrdDesign', 'BayesVarSel', 'BayesXsrc', 'BBEST', 'bbl', 'bcROCsurface', 'bdl', 'BeeBDC', 'behaviorchange', 'bfboinet', 'bfsMaps', 'BIEN', 'bigDM', 'bigGP', 'bigrquerystorage', 'bioclim', 'biocompute', 'BIOMASS', 'biomod2', 'biopixR', 'biosensors.usc', 'BioTIMEr', 'biplotbootGUI', 'BiplotGUI', 'birdring', 'birdscanR', 'bispdep', 'bivgeom', 'bivpois', 'blackbox', 'blackmarbler', 'blatr', 'blockCV', 'bluebike', 'bmstdr', 'BNSP', 'BoolFilter', 'brickster', 'brsim', 'BRugs', 'C50', 'CAinterprTools', 'calmate', 'CaseBasedReasoning', 'cbl', 'ClickHouseHTTP', 'clrng', 'CTRing', 'dartR', 'dartR.base', 'dartR.captive', 'dartR.popgen', 'dartR.sexlinked', 'dartR.sim', 'dartR.spatial', 'DGP4LCF', 'diffdfs', 'diffeRenTES', 'disk.frame', 'DominoDataR', 'doMPI', 'DoubleML', 'dpkg', 'ebmc', 'ecdata', 'EFAfactors', 'enerscape', 'epidm', 'EthSEQ', 'excel.link', 'facmodTS', 'fangs', 'fingerPro', 'fmf', 'foundry'); pkgs = setdiff(pkgs, c('RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'rFUSION', 'MediaNews', 'DoE.base', 'DoE.wrapper', 'FrF2', 'FrF2.catlg128', 'eha', 'gRain', 'gRbase', 'doBy', 'IDPmisc', 'RVAideMemoire', 'pbkrtest', 'seewave', 'compareGroups', 'pls', 'SNPassoc', 'spdep', 'surveillance')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'alpine-321'))"
### 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

1
.woodpecker/process-updates-alpine-320-arm64.yaml
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@ -67,6 +67,7 @@ steps:
commands:
- git clone https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR /mnt/cache/R-pkgs/00LOCK-pak /mnt/cache/pkgcache/R/pkgcache /mnt/cache/pkgcache/R/pkgcache /mnt/cache/R-pkgs/pkgcache /mnt/cache/R-pkgs/00LOCK-pak/mnt/cache/R-pkgs/00LOCK-RPostgres
- R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
- R -q -e 'packageVersion("bincraftR")'
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages

6
.woodpecker/update-package-index-alpine-320-amd64.yaml
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@ -10,7 +10,7 @@ skip_clone: true
steps:
- name: Upload PACKAGES files
image: docker.io/devxygmbh/amd64-binaries-r-alpine-320
image: docker.io/devxygmbh/amd64-binaries-r-ubuntu-2404
pull: true
environment:
RED_HAT_DEV_PW:
@ -30,15 +30,13 @@ steps:
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
R_LIBS_USER: /mnt/cache/R-pkgs
volumes:
- amd64-binaries-r-dep-cache-alpine-320:/mnt/cache
commands:
- git clone https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
- rm -rf /mnt/cache/packages/*
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
- R -q -e 'packageVersion("bincraftR")'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession", workers = 4); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession", workers = 4); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(codename = "alpine320")'
backend_options:
kubernetes:
resources:

6
.woodpecker/update-package-index-alpine-320-arm64.yaml
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@ -10,7 +10,7 @@ skip_clone: true
steps:
- name: Upload PACKAGES files
image: docker.io/devxygmbh/arm64-binaries-r-alpine-320
image: docker.io/devxygmbh/arm64-binaries-r-ubuntu-2404
pull: true
environment:
RED_HAT_DEV_PW:
@ -30,8 +30,6 @@ steps:
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
R_LIBS_USER: /mnt/cache/R-pkgs
volumes:
- arm64-binaries-r-dep-cache-alpine-320:/mnt/cache
commands:
- git clone https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
- rm -rf /mnt/cache/packages/*
@ -39,7 +37,7 @@ steps:
- R -q -e 'pak::pak("pat-s/cranlike@s3")'
- R -q -e 'packageVersion("bincraftR")'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(codename = "alpine320")'
backend_options:
kubernetes:
resources:

6
.woodpecker/update-package-index-alpine-321-arm64.yaml
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@ -10,7 +10,7 @@ skip_clone: true
steps:
- name: Upload PACKAGES files
image: docker.io/devxygmbh/arm64-binaries-r-alpine-321
image: docker.io/devxygmbh/arm64-binaries-r-ubuntu-2404
pull: true
environment:
RED_HAT_DEV_PW:
@ -30,8 +30,6 @@ steps:
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
R_LIBS_USER: /mnt/cache/R-pkgs
volumes:
- arm64-binaries-r-dep-cache-alpine-321:/mnt/cache
commands:
- git clone https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
- rm -rf /mnt/cache/packages/*
@ -39,7 +37,7 @@ steps:
- R -q -e 'pak::pak("pat-s/cranlike@s3")'
- R -q -e 'packageVersion("bincraftR")'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(codename = "alpine321")'
backend_options:
kubernetes:
resources:

6
.woodpecker/update-package-index-redhat-8-amd64.yaml
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@ -10,7 +10,7 @@ skip_clone: true
steps:
- name: Upload PACKAGES files
image: docker.io/devxygmbh/amd64-binaries-r-redhat-8
image: docker.io/devxygmbh/amd64-binaries-r-ubuntu-2404
pull: true
environment:
RED_HAT_DEV_PW:
@ -30,15 +30,13 @@ steps:
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
R_LIBS_USER: /mnt/cache/R-pkgs
volumes:
- amd64-binaries-r-dep-cache-redhat-8:/mnt/cache
commands:
- git clone https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
- rm -rf /mnt/cache/packages/*
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
- R -q -e 'pak::pak("pat-s/cranlike@s3")'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(codename = "rhel8")'
backend_options:
kubernetes:
resources:

6
.woodpecker/update-package-index-redhat-8-arm64.yaml
View file

@ -10,7 +10,7 @@ skip_clone: true
steps:
- name: Upload PACKAGES files
image: docker.io/devxygmbh/arm64-binaries-r-redhat-8
image: docker.io/devxygmbh/arm64-binaries-r-ubuntu-2404
pull: true
environment:
RED_HAT_DEV_PW:
@ -30,8 +30,6 @@ steps:
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
R_LIBS_USER: /mnt/cache/R-pkgs
volumes:
- arm64-binaries-r-dep-cache-redhat-8:/mnt/cache
commands:
- git clone https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
- rm -rf /mnt/cache/packages/*
@ -39,7 +37,7 @@ steps:
- R -q -e 'pak::pak("pat-s/cranlike@s3")'
- R -q -e 'packageVersion("bincraftR")'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(codename = "rhel8")'
backend_options:
kubernetes:
resources:

4
.woodpecker/update-package-index-redhat-9-amd64.yaml
View file

@ -10,7 +10,7 @@ skip_clone: true
steps:
- name: Upload PACKAGES files
image: docker.io/devxygmbh/amd64-binaries-r-redhat-9
image: docker.io/devxygmbh/amd64-binaries-r-ubuntu-2404
pull: true
environment:
RED_HAT_DEV_PW:
@ -39,7 +39,7 @@ steps:
- R -q -e 'pak::pak("pat-s/cranlike@s3")'
- R -q -e 'packageVersion("bincraftR")'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(codename = "rhel9")'
backend_options:
kubernetes:
resources:

7
.woodpecker/update-package-index-redhat-9-arm64.yaml
View file

@ -10,7 +10,7 @@ skip_clone: true
steps:
- name: Upload PACKAGES files
image: docker.io/devxygmbh/arm64-binaries-r-redhat-9
image: docker.io/devxygmbh/arm64-binaries-r-ubuntu-2404
pull: true
environment:
RED_HAT_DEV_PW:
@ -30,16 +30,15 @@ steps:
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
R_LIBS_USER: /mnt/cache/R-pkgs
volumes:
- arm64-binaries-r-dep-cache-redhat-9:/mnt/cache
commands:
- git clone https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
- rm -rf /mnt/cache/packages/*
- R -q -e 'pak::pak("stringi")'
- R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
- R -q -e 'pak::pak("pat-s/cranlike@s3")'
- R -q -e 'packageVersion("bincraftR")'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(codename = "rhel9")'
backend_options:
kubernetes:
resources:

6
.woodpecker/update-package-index-ubuntu-2204-amd64.yaml
View file

@ -10,7 +10,7 @@ skip_clone: true
steps:
- name: Upload PACKAGES files
image: docker.io/devxygmbh/amd64-binaries-r-ubuntu-2204
image: docker.io/devxygmbh/amd64-binaries-r-ubuntu-2404
pull: true
environment:
RED_HAT_DEV_PW:
@ -30,8 +30,6 @@ steps:
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
R_LIBS_USER: /mnt/cache/R-pkgs
volumes:
- amd64-binaries-r-dep-cache-ubuntu-2204:/mnt/cache
commands:
- git clone https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
- rm -rf /mnt/cache/packages/*
@ -39,7 +37,7 @@ steps:
- R -q -e 'pak::pak("pat-s/cranlike@s3")'
- R -q -e 'packageVersion("bincraftR")'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(); warnings()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(codename = "jammy"); warnings()'
backend_options:
kubernetes:
resources:

4
.woodpecker/update-package-index-ubuntu-2204-arm64.yaml
View file

@ -30,8 +30,6 @@ steps:
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
R_LIBS_USER: /mnt/cache/R-pkgs
volumes:
- arm64-binaries-r-dep-cache-ubuntu-2204:/mnt/cache
commands:
- git clone https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
- rm -rf /mnt/cache/packages/*
@ -39,7 +37,7 @@ steps:
- R -q -e 'pak::pak("pat-s/cranlike@s3")'
- R -q -e 'packageVersion("bincraftR")'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(codename = "jammy")'
backend_options:
kubernetes:
resources:

2
.woodpecker/update-package-index-ubuntu-2404-amd64.yaml
View file

@ -39,7 +39,7 @@ steps:
- R -q -e 'pak::pak("pat-s/cranlike@s3")'
- R -q -e 'packageVersion("bincraftR")'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(codename = "noble")'
backend_options:
kubernetes:
resources:

2
.woodpecker/update-package-index-ubuntu-2404-arm64.yaml
View file

@ -39,7 +39,7 @@ steps:
- R -q -e 'pak::pak("pat-s/cranlike@s3")'
- R -q -e 'packageVersion("bincraftR")'
- cd /mnt/cache/packages
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index()'
- R -q -e 'options(crayon.enabled = TRUE); library(bincraftR); future::plan("multisession"); library(progressr); handlers(global = TRUE); handlers("progress"); upload_package_index(codename = "noble")'
backend_options:
kubernetes:
resources: