94 lines
4.5 KiB
YAML
94 lines
4.5 KiB
YAML
when:
|
|
event: [manual]
|
|
|
|
skip_clone: true
|
|
|
|
matrix:
|
|
include:
|
|
# - PLATFORM: redhat-9
|
|
# BLOCK: 1:1000
|
|
# - PLATFORM: redhat-8
|
|
# BLOCK: 1:1000
|
|
- PLATFORM: ubuntu-2404
|
|
BLOCK: 1:1000
|
|
# - PLATFORM: ubuntu-2204
|
|
# BLOCK: 1:1000
|
|
steps:
|
|
- name: "Build binaries (${PLATFORM}: ${BLOCK})"
|
|
secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token]
|
|
image: docker.io/pats22/arm-binaries-r-${PLATFORM}
|
|
pull: true
|
|
# to ensure the PACKAGES upload step is being executed
|
|
failure: ignore
|
|
environment:
|
|
GIT_USER: pat-s
|
|
# 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
|
|
CCACHE_DIR: /mnt/cache/ccache
|
|
volumes:
|
|
- arm-binaries-r-dep-cache-${PLATFORM}:/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
|
|
- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/arm64-r-binaries.git .
|
|
- rm -rf /mnt/cache/R-pkgs/00LOCK-arm64-r-binaries
|
|
- R -q -e 'pak::pak("dyfanjones/s3fs")'
|
|
- R -q -e 'pak::local_install(); packageVersion("rBinaries")'
|
|
- mkdir -p /root/.R && /bin/bash -c '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'
|
|
# manually install some packages into the cache so that some builds don't fail
|
|
# Hmisc -> ABCanalysis
|
|
# - 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"))'
|
|
# more complicated system dependencies which pak cannot resolve
|
|
- 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
|
|
- 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]][${BLOCK}]; library(rBinaries); future::plan("multisession", workers = 6, rscript_startup = quote(options(crayon.enabled = TRUE))); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "${PLATFORM}"))'
|
|
backend_options:
|
|
kubernetes:
|
|
### PROD
|
|
resources:
|
|
requests:
|
|
memory: 25Gi
|
|
cpu: 12000m
|
|
limits:
|
|
memory: 28Gi
|
|
cpu: 16000m
|
|
# DEBUG
|
|
# resources:
|
|
# requests:
|
|
# memory: 4Gi
|
|
# cpu: 2000m
|
|
# limits:
|
|
# memory: 4Gi
|
|
# cpu: 2000m
|
|
nodeSelector:
|
|
kubernetes.io/arch: 'arm64'
|
|
# - name: Upload PACKAGES files
|
|
# secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token]
|
|
# image: docker.io/pats22/arm-binaries-r-ubi9
|
|
# pull: true
|
|
# environment:
|
|
# GIT_USER: pat-s
|
|
# # 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:
|
|
# - arm-binaries-r-dep-cache-rhel9:/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
|
|
# - R -q -e 'pak::local_install(); packageVersion("rBinaries")'
|
|
# - R -q -e 'pak::pak(c("dyfanjones/s3fs", "pat-s/desc@description-from-remote", "pat-s/cranlike@s3"))'
|
|
# - cd /mnt/cache/packages
|
|
# - R -q -e 'options(crayon.enabled = TRUE); library(rBinaries); upload_package_index()'
|
|
# backend_options:
|
|
# kubernetes:
|
|
# resources:
|
|
# requests:
|
|
# memory: 1000Mi
|
|
# cpu: 0m
|
|
# limits:
|
|
# memory: 1300Mi
|
|
# cpu: 1000m
|
|
# nodeSelector:
|
|
# kubernetes.io/arch: 'arm64'
|