new build image + index upload fixes
This commit is contained in:
parent
f888e4aa86
commit
6f1b8dfa8d
GPG key ID:
3C6318841EF78925
2 changed files with 51 additions and 51 deletions
|
|
@ -14,46 +14,45 @@ when:
|
|||
# - PLATFORM: opensuse-155
|
||||
# PLATFORM_ID: suse155
|
||||
steps:
|
||||
# - name: Build binaries
|
||||
# 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
|
||||
# # 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-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
|
||||
# - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/arm64-r-binaries.git && cd arm64-r-binaries
|
||||
# - 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 && 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/binaries /mnt/cache/ccache
|
||||
# - R -q -e 'options(crayon.enabled = TRUE, Ncpus = 6, future.globals.onReference = "error"); pkgs = tools::CRAN_package_db()[[1]][26:40]; 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))'
|
||||
# backend_options:
|
||||
# kubernetes:
|
||||
# resources:
|
||||
# requests:
|
||||
# memory: 25Gi
|
||||
# cpu: 12000m
|
||||
# limits:
|
||||
# memory: 28Gi
|
||||
# cpu: 16000m
|
||||
# nodeSelector:
|
||||
# kubernetes.io/arch: 'arm64'
|
||||
- name: Build binaries
|
||||
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
|
||||
# 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-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
|
||||
- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/arm64-r-binaries.git && cd arm64-r-binaries
|
||||
- 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 && 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/binaries /mnt/cache/ccache
|
||||
- R -q -e 'options(crayon.enabled = TRUE, Ncpus = 6, future.globals.onReference = "error"); pkgs = tools::CRAN_package_db()[[1]][26:40]; 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))'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
requests:
|
||||
memory: 25Gi
|
||||
cpu: 12000m
|
||||
limits:
|
||||
memory: 28Gi
|
||||
cpu: 16000m
|
||||
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
|
||||
|
|
@ -70,8 +69,9 @@ steps:
|
|||
# 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 && cd arm64-r-binaries
|
||||
- R -q -e 'pak::local_install(); packageVersion("rBinaries")'
|
||||
- R -q -e 'pak::pak("dyfanjones/s3fs")'
|
||||
- cd /mnt/cache/binaries/__linux__/rhel9/latest/src/contrib
|
||||
- R -q -e 'options(crayon.enabled = TRUE); library(rBinaries); upload_package_index()'
|
||||
- R -q -e 'files = list.files("/mnt/cache/binaries/", include.dirs = FALSE, full.names = TRUE, recursive = TRUE); foo = file.remove(files)'
|
||||
backend_options:
|
||||
kubernetes:
|
||||
resources:
|
||||
|
|
|
|||
|
|
@ -54,11 +54,11 @@ upload_package_index <- function(
|
|||
endpoint = "https://s3.eu-central-003.backblazeb2.com",
|
||||
region = "eu-central-003",
|
||||
bucket = "devxy-arm64-r-binaries",
|
||||
local_build_root = "/mnt/cache/binaries/",
|
||||
local_build_root = ".",
|
||||
codename = NULL, r_minor_version = NULL,
|
||||
build_for_minor = FALSE,
|
||||
debug = FALSE) {
|
||||
cli::cli_alert("{.fun create_package_index}: Uploading PACKAGES* files to S3.")
|
||||
cli::cli_alert("{.fun upload_package_index}: Uploading PACKAGES* files to S3.")
|
||||
|
||||
codename <- set_codename(codename)
|
||||
if (is.null(r_minor_version)) {
|
||||
|
|
@ -66,11 +66,11 @@ upload_package_index <- function(
|
|||
}
|
||||
|
||||
if (!build_for_minor) {
|
||||
local_bin_dir <- sprintf("%s/__linux__/%s/latest/src/contrib/", local_build_root, codename)
|
||||
remote_bin_dir <- sprintf("%s/__linux__/%s/latest/src/contrib/", bucket, codename)
|
||||
local_bin_dir <- sprintf("%s/__linux__/%s/latest/src/contrib", local_build_root, codename)
|
||||
remote_bin_dir <- sprintf("%s/__linux__/%s/latest/src/contrib", bucket, codename)
|
||||
} else {
|
||||
dir_out_bin <- sprintf("%s/__linux__/%s/%s/latest/src/contrib/", local_build_root, codename, r_minor_version)
|
||||
remote_bin_dir <- sprintf("%s/__linux__/%s/%s/latest/src/contrib/", bucket, codename, r_minor_version)
|
||||
dir_out_bin <- sprintf("%s/__linux__/%s/%s/latest/src/contrib", local_build_root, codename, r_minor_version)
|
||||
remote_bin_dir <- sprintf("%s/__linux__/%s/%s/latest/src/contrib", bucket, codename, r_minor_version)
|
||||
}
|
||||
|
||||
s3fs::s3_file_system(
|
||||
|
|
@ -82,18 +82,18 @@ upload_package_index <- function(
|
|||
|
||||
pkg_count = length(s3fs::s3_dir_ls(remote_bin_dir)) - 4
|
||||
t1 <- Sys.time()
|
||||
cranlike::update_PACKAGES(remote_bin_dir)
|
||||
cranlike::update_PACKAGES(sprintf("s3://%s", remote_bin_dir))
|
||||
total_build_time <- round(Sys.time() - t1, 2)
|
||||
cli::cli_alert("Time updating PACKAGES index for {.field {pkg_count}} packages: {.strong {total_build_time} {units(difftime(Sys.time(), t1))}}.")
|
||||
|
||||
purrr::walk2(
|
||||
sprintf("%s/%s", local_bin_dir, c("PACKAGES", "PACKAGES.db", "PACKAGES.rds", "PACKAGES.gz")),
|
||||
c("PACKAGES", "PACKAGES.db", "PACKAGES.rds", "PACKAGES.gz"),
|
||||
sprintf("%s/%s", remote_bin_dir, c("PACKAGES", "PACKAGES.db", "PACKAGES.rds", "PACKAGES.gz")),
|
||||
\(x, y) s3fs::s3_file_upload(x, y, overwrite = TRUE)
|
||||
)
|
||||
|
||||
pkgs_upload_local <- sprintf("%sPACKAGES", local_bin_dir)
|
||||
pkgs_upload_remote <- sprintf("%sPACKAGES", remote_bin_dir)
|
||||
# pkgs_upload_local <- sprintf("%sPACKAGES", local_bin_dir)
|
||||
# pkgs_upload_remote <- sprintf("%sPACKAGES", remote_bin_dir)
|
||||
|
||||
# if (debug) {
|
||||
# cli::cli_alert_warning("DEBUG: PACKAGES UPLOAD local dir: {pkgs_upload_local}")
|
||||
|
|
|
|||
Loading…
Reference in a new issue