87 lines
4.2 KiB
YAML
87 lines
4.2 KiB
YAML
when:
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event: [push, manual]
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skip_clone: true
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# matrix:
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# include:
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# - PLATFORM: rhel-9
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# PLATFORM_ID: el9
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# - PLATFORM: centos-8
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# PLATFORM_ID: el8
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# - PLATFORM: ubuntu-2204
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# PLATFORM_ID: 2204
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# - PLATFORM: ubuntu-2404
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# PLATFORM_ID: 2404
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# - PLATFORM: opensuse-155
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# PLATFORM_ID: suse155
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steps:
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- name: Build binaries
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secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token]
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image: docker.io/pats22/arm-binaries-r-ubi9
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pull: true
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# to ensure the PACKAGES upload step is being executed
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failure: ignore
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environment:
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GIT_USER: pat-s
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# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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R_LIBS_USER: /mnt/cache/R-pkgs
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CCACHE_DIR: /mnt/cache/ccache
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volumes:
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- arm-binaries-r-dep-cache-rhel9:/mnt/cache
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commands:
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# download latest package version (avoid having to rebuild image every time)
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# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
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- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/arm64-r-binaries.git .
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- rm -rf /mnt/cache/R-pkgs/00LOCK-arm64-r-binaries
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- R -q -e 'pak::pak("dyfanjones/s3fs")'
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- R -q -e 'pak::local_install(); packageVersion("rBinaries")'
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- mkdir -p /root/.R && echo -e "CXX_STD = CXX14\nCC=ccache gcc\nCPP=ccache gcc\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=ccache /usr/bin/gfortran\nFC=ccache /usr/bin/gfortran" > /root/.R/Makevars
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# manually install some packages into the cache so that some builds don't fail
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# Hmisc -> ABCanalysis
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- R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE, PKG_SYSREQS_PLATFORM = "redhat-9"); pak::pak(c("Hmisc", "pls", "abd", "doRNG", "devtools"))'
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# more complicated system dependencies which pak cannot resolve
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/binaries /mnt/cache/ccache /mnt/cache/packages
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# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA)
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- R -q -e 'options(crayon.enabled = TRUE, Ncpus = 6, future.globals.onReference = "error", repos = structure(c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"))); pkgs = tools::CRAN_package_db()[[1]][41:200]; library(rBinaries); future::plan("multisession", workers = 5, rscript_startup = quote(options(crayon.enabled = TRUE))); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE))'
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backend_options:
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kubernetes:
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resources:
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requests:
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memory: 25Gi
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cpu: 12000m
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limits:
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memory: 28Gi
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cpu: 16000m
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nodeSelector:
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kubernetes.io/arch: 'arm64'
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- name: Upload PACKAGES files
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secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token]
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image: docker.io/pats22/arm-binaries-r-ubi9
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pull: true
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environment:
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GIT_USER: pat-s
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# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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R_LIBS_USER: /mnt/cache/R-pkgs
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volumes:
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- arm-binaries-r-dep-cache-rhel9:/mnt/cache
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commands:
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# download latest package version (avoid having to rebuild image every time)
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# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
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- R -q -e 'pak::local_install(); packageVersion("rBinaries")'
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- R -q -e 'pak::pak(c("dyfanjones/s3fs", "pat-s/desc@description-from-remote", "pat-s/cranlike@s3"))'
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- cd /mnt/cache/packages
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- R -q -e 'options(crayon.enabled = TRUE); library(rBinaries); upload_package_index()'
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backend_options:
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kubernetes:
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resources:
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requests:
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memory: 1000Mi
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cpu: 0m
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limits:
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memory: 1300Mi
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cpu: 1000m
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nodeSelector:
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kubernetes.io/arch: 'arm64'
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