Merge remote-tracking branch 'origin/main' into t3code/smarter-disk-pruning-macmini

# Conflicts:
#	.crow/build-all-versions-install-deps.yaml
#	.crow/build-all-versions.yaml
This commit is contained in:
Patrick Schratz 2026-07-13 09:30:21 +00:00
commit 6afa4e2405
No known key found for this signature in database
GPG key ID: 62050D5BC68AB6DC
5 changed files with 2119 additions and 69 deletions

View file

@ -62,9 +62,9 @@ steps:
GIT_USER: pat-s
R_VERSION: 4.5.3
commands:
- /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.2") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.2", dependencies = TRUE)'
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
- /opt/R/$R_VERSION/bin/R -q -e 'bincraft::process_unarchived_pkgs(Sys.getenv("CODENAME"), Sys.getenv("ARCH"), workers = 2L)'
- /opt/R/$R_VERSION/bin/R -q -e 'bincraft::process_unarchived_pkgs(Sys.getenv("CODENAME"), Sys.getenv("ARCH"), s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"), workers = 2L)'
backend_options:
kubernetes:
resources:

View file

@ -10,11 +10,22 @@ variables:
- arm64
default: amd64
OS:
description: 'Base OS image name (e.g. alpine, redhat, ubuntu).'
description: "Base OS image name."
options:
- alpine
- redhat
- ubuntu
default: alpine
OS_VERSION:
description: 'OS version / image tag (e.g. 3.24, 9, jammy, noble).'
default: '3.24'
description: "OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble)."
options:
- "3.24"
- "8"
- "9"
- "10"
- "jammy"
- "noble"
default: "3.24"
R_VERSION:
description: 'Primary R version under /opt/R.'
options:
@ -42,6 +53,9 @@ steps:
image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
pull: true
environment:
OTEL_R_TRACES_EXPORTER: none
OTEL_R_LOGS_EXPORTER: none
OTEL_R_METRICS_EXPORTER: none
REPO_RO_TOKEN:
from_secret: REPO_RO_TOKEN
GITHUB_PAT:
@ -66,8 +80,9 @@ steps:
- rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true
- 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://codefloe.com/rpkgs/bincraft.git /tmp/bincraft
- /opt/R/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); pak::local_install("/tmp/bincraft"); pak::pak(c("RPostgres", "s3fs", "data.table", "future", "jsonlite")); packageVersion("bincraft")'
# Pin the same bincraft version the build steps use, so the precomputed
# snapshot and the per-agent library stay consistent across the pipeline.
- /opt/R/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); source("local/install-bincraft.R"); 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]))"
backend_options:
docker:

View file

@ -11,11 +11,25 @@ variables:
- arm64
default: amd64
OS:
description: 'Base OS image name (e.g. alpine, redhat, ubuntu).'
description: "Base OS image name."
options:
- alpine
- redhat
- ubuntu
default: alpine
OS_VERSION:
description: 'OS version / image tag (e.g. 3.24, 9, jammy, noble).'
default: '3.24'
description: "OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble)."
options:
- "3.22"
- "3.23"
- "3.24"
- "8"
- "9"
- "10"
- "jammy"
- "noble"
- "resolute"
default: "3.24"
R_VERSION:
description: 'Primary R version under /opt/R.'
options:
@ -76,6 +90,9 @@ steps:
image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
pull: true
environment:
OTEL_R_TRACES_EXPORTER: none
OTEL_R_LOGS_EXPORTER: none
OTEL_R_METRICS_EXPORTER: none
RED_HAT_DEV_PW:
from_secret: RED_HAT_DEV_PW
B2_S3_ACCESS_KEY:
@ -105,6 +122,14 @@ steps:
# growth is bounded separately by trim_pkgcache_metadata() in build-all.R.
- rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true
- 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/$R_VERSION/bin/Rscript local/install-bincraft.R
- XVFB=$(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
- |
@ -116,11 +141,12 @@ steps:
echo "=== R-minor-sensitive pass under R $RV ==="
LIB="/mnt/cache/R-pkgs-$RMINOR"
mkdir -p "$LIB"
R_LIBS_USER="$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="$LIB" "$(dirname "$RBIN")/Rscript" local/install-bincraft.R || true
R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- "$(dirname "$RBIN")/Rscript" local/build-all.R --sensitive-only $SPLIT_INTO $SPLIT_INDEX $NCPUS 2>&1 || true
done
# archive missed packages
- /opt/R/$R_VERSION/bin/R -q -e "bincraft::process_unarchived_pkgs(paste(Sys.getenv('OS'), Sys.getenv('OS_VERSION')), Sys.getenv('ARCH'), workers = $NCPUS)"
# archive missed packages; first arg is the codename (e.g. "alpine324"),
# derived via bincraft like the upload step, not paste(OS, OS_VERSION).
- /opt/R/$R_VERSION/bin/R -q -e "bincraft::process_unarchived_pkgs(bincraft::set_codename(NULL), Sys.getenv('ARCH'), s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), workers = $NCPUS)"
backend_options:
docker:
resources:
@ -134,6 +160,9 @@ steps:
image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
pull: true
environment:
OTEL_R_TRACES_EXPORTER: none
OTEL_R_LOGS_EXPORTER: none
OTEL_R_METRICS_EXPORTER: none
B2_S3_ACCESS_KEY:
from_secret: B2_S3_ACCESS_KEY
B2_S3_SECRET_KEY:

View file

@ -15,6 +15,8 @@ variables:
- alpine-322-arm64
- alpine-323-amd64
- alpine-323-arm64
- alpine-324-amd64
- alpine-324-arm64
- redhat-8-amd64
- redhat-8-arm64
- redhat-9-amd64
@ -25,6 +27,8 @@ variables:
- ubuntu-2204-arm64
- ubuntu-2404-amd64
- ubuntu-2404-arm64
- ubuntu-2604-amd64
- ubuntu-2604-arm64
default: all
when:
@ -64,6 +68,18 @@ matrix:
IMG: alpine:3.24
OS_ID: alpine323
PROCESS_NEW: "FALSE"
- OS: alpine-324
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.24
OS_ID: alpine324
PROCESS_NEW: "FALSE"
- OS: alpine-324
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.24
OS_ID: alpine324
PROCESS_NEW: "FALSE"
- OS: redhat-8
ARCH: amd64
R_VERSION: 4.4.3
@ -124,12 +140,27 @@ matrix:
IMG: ubuntu:noble
OS_ID: noble
PROCESS_NEW: "TRUE"
- OS: ubuntu-2604
ARCH: amd64
R_VERSION: 4.5.3
IMG: ubuntu:resolute
OS_ID: resolute
PROCESS_NEW: "TRUE"
- OS: ubuntu-2604
ARCH: arm64
R_VERSION: 4.5.3
IMG: ubuntu:resolute
OS_ID: resolute
PROCESS_NEW: "TRUE"
steps:
- name: 'Processing Updates'
image: reg.devxy.io/rpkgs/build-env-${IMG}
pull: true
environment:
OTEL_R_TRACES_EXPORTER: none
OTEL_R_LOGS_EXPORTER: none
OTEL_R_METRICS_EXPORTER: none
RED_HAT_DEV_PW:
from_secret: RED_HAT_DEV_PW
B2_S3_ACCESS_KEY:
@ -164,13 +195,13 @@ steps:
commands:
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
- rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft /mnt/cache/R-pkgs/pkgcache /mnt/cache/pkgcache/R/pkgcache
- /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.2") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.2")'
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
# rhel-10 ships xwfb-run (Xwayland) instead of xvfb-run; prefer it and start weston, else fall back to xvfb-run
- XVFB=$(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
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
- $XVFB $XVFB_ARGS -- /opt/R/$R_VERSION/bin/R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = '${OS}', process_updated = TRUE, process_new = ${PROCESS_NEW}, process_removed = TRUE, r_minor_detection = 'classifier', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)"
- $XVFB $XVFB_ARGS -- /opt/R/$R_VERSION/bin/R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = '${OS}', process_updated = TRUE, process_new = ${PROCESS_NEW}, process_removed = TRUE, patches = 'local/patches', r_minor_detection = 'classifier',s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)"
- |
PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2)
for RBIN in /opt/R/[0-9]*/bin/R; do
@ -180,8 +211,8 @@ steps:
echo "=== R-minor-sensitive update pass under R $RV ==="
LIB="/mnt/cache/R-pkgs-$RMINOR"
mkdir -p "$LIB"
R_LIBS_USER="$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 $XVFB_ARGS -- "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = '${OS}', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, r_minor_detection = 'classifier', r_minor_sensitive_only = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true
R_LIBS_USER="$LIB" "$(dirname "$RBIN")/Rscript" local/install-bincraft.R || true
R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -- "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = '${OS}', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, patches = 'local/patches', r_minor_detection = 'classifier',r_minor_sensitive_only = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true
done
- /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "${OS_ID}", s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"))'
- |
@ -202,6 +233,9 @@ steps:
- name: Purge CDN cache
image: reg.devxy.io/docker.io/library/alpine:3.24
environment:
OTEL_R_TRACES_EXPORTER: none
OTEL_R_LOGS_EXPORTER: none
OTEL_R_METRICS_EXPORTER: none
BUNNYNET_API_KEY:
from_secret: BUNNYNET_API_KEY
SUBDOMAIN1: 'cran.devxy.io'

View file

@ -103,6 +103,9 @@ steps:
image: reg.devxy.io/rpkgs/build-env-${IMG}
pull: true
environment:
OTEL_R_TRACES_EXPORTER: none
OTEL_R_LOGS_EXPORTER: none
OTEL_R_METRICS_EXPORTER: none
RED_HAT_DEV_PW:
from_secret: RED_HAT_DEV_PW
B2_S3_ACCESS_KEY:
@ -129,12 +132,12 @@ steps:
- 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
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
- /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.2") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.2")'
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
- XVFB=$(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
- /opt/R/$R_VERSION/bin/R -q -e 'pak::pak("httr2")'
- /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")'
- $XVFB $XVFB_ARGS -- /opt/R/$R_VERSION/bin/R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs <- readLines('/tmp/rebuild_pkgs.txt'); if (length(pkgs) == 0) { cat('Nothing to rebuild\n'); q('no') }; excluded <- jsonlite::fromJSON('local/excluded-packages.json')[['package']]; pkgs <- setdiff(pkgs, excluded); cat(sprintf('Rebuilding %d packages\n', length(pkgs))); n <- length(pkgs); for (i in seq_along(pkgs)) { x <- pkgs[i]; cat(sprintf('[%d/%d] %s\n', i, n, x)); tryCatch(bincraft::build_binary_package(x, tag_limit = 1L, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE), error = function(e) cat(sprintf('ERROR building %s - %s\n', x, conditionMessage(e)))) }" 2>&1
- $XVFB $XVFB_ARGS -- /opt/R/$R_VERSION/bin/R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs <- readLines('/tmp/rebuild_pkgs.txt'); if (length(pkgs) == 0) { cat('Nothing to rebuild\n'); q('no') }; excluded <- jsonlite::fromJSON('local/excluded-packages.json')[['package']]; pkgs <- setdiff(pkgs, excluded); cat(sprintf('Rebuilding %d packages\n', length(pkgs))); n <- length(pkgs); for (i in seq_along(pkgs)) { x <- pkgs[i]; cat(sprintf('[%d/%d] %s\n', i, n, x)); tryCatch(bincraft::build_binary_package(x, tag_limit = 1L, patches = 'local/patches', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE), error = function(e) cat(sprintf('ERROR building %s - %s\n', x, conditionMessage(e)))) }" 2>&1
backend_options:
docker:
resources: