Compare commits

..
3 changed files with 7 additions and 65 deletions

View file

@ -62,9 +62,8 @@ steps:
# - rm -rf /mnt/cache/R-pkgs # - rm -rf /mnt/cache/R-pkgs
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
# Pin the same bincraft version the build steps use, so the precomputed - git clone -q https://codefloe.com/rpkgs/bincraft.git /tmp/bincraft
# snapshot and the per-agent library stay consistent across the pipeline. - /opt/R/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); pak::local_install("/tmp/bincraft"); pak::pak(c("RPostgres", "s3fs", "data.table", "future", "jsonlite")); packageVersion("bincraft")'
- /opt/R/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.3"); pak::pak(c("RPostgres", "s3fs", "data.table", "future", "jsonlite")); packageVersion("bincraft")'
- /opt/R/$R_VERSION/bin/R -q -e "source('local/packages-to-build.R'); saveRDS(pkgs, '/mnt/cache/packages/pkgs_to_build.rds'); saveRDS(pkgs[r_minor_sensitive == TRUE], '/mnt/cache/packages/r_minor_sensitive_pkgs.rds'); sprintf('Precomputed %s package versions (%s r-minor-sensitive)', nrow(pkgs), nrow(pkgs[r_minor_sensitive == TRUE]))" - /opt/R/$R_VERSION/bin/R -q -e "source('local/packages-to-build.R'); saveRDS(pkgs, '/mnt/cache/packages/pkgs_to_build.rds'); saveRDS(pkgs[r_minor_sensitive == TRUE], '/mnt/cache/packages/r_minor_sensitive_pkgs.rds'); sprintf('Precomputed %s package versions (%s r-minor-sensitive)', nrow(pkgs), nrow(pkgs[r_minor_sensitive == TRUE]))"
backend_options: backend_options:
docker: docker:

View file

@ -100,14 +100,6 @@ steps:
commands: commands:
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
# The primary pass must not rely on build-all-versions-install-deps having
# run on *this* agent: depends_on only orders the steps, but the cache
# volume is per-agent, so a job landing on an agent where install-deps did
# not run would otherwise use a stale bincraft (which resolves `platform`
# to a zero-length value and breaks every metadata query and the sysdeps
# install). Pin bincraft here, exactly like the R-minor pass below.
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
- /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.3") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.3")'
- XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
- $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/build-all.R $SPLIT_INTO $SPLIT_INDEX $NCPUS 2>&1 - $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/build-all.R $SPLIT_INTO $SPLIT_INDEX $NCPUS 2>&1
- | - |
@ -119,12 +111,11 @@ steps:
echo "=== R-minor-sensitive pass under R $RV ===" echo "=== R-minor-sensitive pass under R $RV ==="
LIB="/mnt/cache/R-pkgs-$RMINOR" LIB="/mnt/cache/R-pkgs-$RMINOR"
mkdir -p "$LIB" mkdir -p "$LIB"
R_LIBS_USER="$LIB" "$(dirname "$RBIN")/R" -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.3") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.3")' || true R_LIBS_USER="$LIB" "$(dirname "$RBIN")/R" -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.2") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.2")' || true
R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- "$(dirname "$RBIN")/Rscript" local/build-all.R --sensitive-only $SPLIT_INTO $SPLIT_INDEX $NCPUS 2>&1 || true R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- "$(dirname "$RBIN")/Rscript" local/build-all.R --sensitive-only $SPLIT_INTO $SPLIT_INDEX $NCPUS 2>&1 || true
done done
# archive missed packages; first arg is the codename (e.g. "alpine324"), # archive missed packages
# derived via bincraft like the upload step, not paste(OS, OS_VERSION). - /opt/R/$R_VERSION/bin/R -q -e "bincraft::process_unarchived_pkgs(paste(Sys.getenv('OS'), Sys.getenv('OS_VERSION')), Sys.getenv('ARCH'), workers = $NCPUS)"
- /opt/R/$R_VERSION/bin/R -q -e "bincraft::process_unarchived_pkgs(bincraft::set_codename(NULL), Sys.getenv('ARCH'), workers = $NCPUS)"
backend_options: backend_options:
docker: docker:
resources: resources:

View file

@ -15,31 +15,6 @@ library(bincraft, quietly = TRUE)
library(future) library(future)
plan("sequential") plan("sequential")
# The install-deps step precomputes the package snapshot into /mnt/cache, but
# that volume is per-agent: a job landing on a fresh agent (or racing
# install-deps) finds it empty. Recompute the snapshot here when any part is
# missing, so the first job on an agent repopulates the cache for the jobs that
# follow; concurrent jobs that also miss simply redo the work. Write via a
# temp file + atomic rename so a concurrent reader never sees a half-written rds.
package_cache_files <- c(
"/mnt/cache/packages/pkgs_to_build.rds",
"/mnt/cache/packages/r_minor_sensitive_pkgs.rds",
"/mnt/cache/packages/s3_cache.rds"
)
if (!all(file.exists(package_cache_files))) {
message("Package snapshot missing from cache; recomputing via packages-to-build.R")
dir.create("/mnt/cache/packages", showWarnings = FALSE, recursive = TRUE)
save_rds_atomic <- function(obj, path) {
tmp <- paste0(path, ".tmp.", Sys.getpid())
saveRDS(obj, tmp)
file.rename(tmp, path)
}
source(file.path("local", "packages-to-build.R"))
save_rds_atomic(pkgs, "/mnt/cache/packages/pkgs_to_build.rds")
save_rds_atomic(pkgs[r_minor_sensitive == TRUE], "/mnt/cache/packages/r_minor_sensitive_pkgs.rds")
message("Package snapshot recomputed.")
}
pkgs <- if (sensitive_only) { pkgs <- if (sensitive_only) {
readRDS("/mnt/cache/packages/r_minor_sensitive_pkgs.rds") readRDS("/mnt/cache/packages/r_minor_sensitive_pkgs.rds")
} else { } else {
@ -68,31 +43,8 @@ chunk <- chunk[!chunk$Package %in% exclude, ]
# pkgs_to_build.rds is a static snapshot from the install-deps step, so on a # pkgs_to_build.rds is a static snapshot from the install-deps step, so on a
# restart it still lists everything an interrupted run already produced. The # restart it still lists everything an interrupted run already produced. The
# metadata DB reflects that progress, so we re-derive the remaining set here. # metadata DB reflects that progress, so we re-derive the remaining set here.
# Derive platform + arch from the running container, mirroring the codename -> platform <- paste(Sys.getenv("OS"), gsub("[.]", "", Sys.getenv("OS_VERSION")), sep = "-")
# platform mapping bincraft uses internally. The OS/OS_VERSION selectors are arch <- Sys.getenv("ARCH")
# workflow-level CI variables that are not injected into the container
# environment, so Sys.getenv() would return "" and this pre-filter would query
# platform "-" and skip nothing.
codename <- bincraft::set_codename(NULL)
platform <- switch(
codename,
jammy = "ubuntu-2204",
noble = "ubuntu-2404",
resolute = "ubuntu-2604",
rhel10 = "redhat-10",
rhel9 = "redhat-9",
rhel8 = "redhat-8",
alpine320 = "alpine-320",
alpine321 = "alpine-321",
alpine322 = "alpine-322",
alpine323 = "alpine-323",
alpine324 = "alpine-324",
alpine325 = "alpine-325",
alpine326 = "alpine-326",
NA_character_
)
local_machine <- Sys.info()[["machine"]]
arch <- if (grepl("arm64|aarch64", local_machine)) "arm64" else "amd64"
con <- DBI::dbConnect( con <- DBI::dbConnect(
RPostgres::Postgres(), RPostgres::Postgres(),
dbname = "build_metadata", dbname = "build_metadata",