devxy/build-cran-binaries
Watch
1
0
Fork
You've already forked build-cran-binaries
 0
Code Issues 11 Pull requests Releases Activity

fix: audit workflows
Some checks failed
ci/crow/manual/weekly-rebuild-missing-alpine-322-arm64 Pipeline failed
Details

Browse source
This commit is contained in:
Patrick Schratz 2026-04-21 20:30:33 +02:00
commit d0a243a1dc
Signed by: pat-s
GPG key ID: 3C6318841EF78925
10 changed files with 49 additions and 295 deletions
Download patch file Download diff file Expand all files Collapse all files

76
.crow/process-updates-alpine-321-amd64.yaml
View file

@ -1,76 +0,0 @@
when:
- event: [cron]
cron: process-cran-updates-alpine-321-amd64
- event: manual
evaluate: 'process_cran_updates == "all"'
- event: manual
evaluate: 'process_cran_updates == "alpine-321-amd64"'
skip_clone: true
labels:
agent: artemis
steps:
- name: 'Processing Updates'
image: reg.devxy.io/rpkgs/build-env-alpine:3.23-4.4.3
pull: true
environment:
RED_HAT_DEV_PW:
from_secret: RED_HAT_DEV_PW
B2_S3_ACCESS_KEY:
from_secret: B2_S3_ACCESS_KEY
B2_S3_SECRET_KEY:
from_secret: B2_S3_SECRET_KEY
PGPASS:
from_secret: PGPASS
REPO_RO_TOKEN:
from_secret: REPO_RO_TOKEN
GITHUB_PAT:
from_secret: GITHUB_PAT
# normal env vars
GIT_USER: pat-s
NTFY_SERVER:
from_secret: NTFY_SERVER
NTFY_TOPIC:
from_secret: NTFY_TOPIC
NTFY_AUTH: TRUE
NTFY_PASSWORD:
from_secret: ntfy_token
# 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
PLATFORM: alpine-321
ARCH: amd64
NCPUS: 2
STRATEGY: sequential
INTERVAL: lubridate::interval(lubridate::today() - 6, lubridate::today() - 3)
# volumes:
# - amd64-binaries-r-dep-cache-alpine-321:/mnt/cache
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-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraft /mnt/cache/R-pkgs/00LOCK-pak /mnt/cache/pkgcache/R/pkgcache /mnt/cache/pkgcache/R/pkgcache /mnt/cache/R-pkgs/pkgcache /mnt/cache/R-pkgs/00LOCK-pak/mnt/cache/R-pkgs/00LOCK-RPostgres /mnt/cache/R-pkgs/bincraft
- R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraft.git")'
- R -q -e 'packageVersion("bincraft")'
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
# 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-run 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 = 'alpine-321', process_updated = TRUE, process_new = FALSE, process_removed = 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)"
- R -q -e 'library(bincraft); upload_package_index(codename = "alpine321", 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"))'
backend_options:
kubernetes:
resources:
requests:
memory: 5Gi
cpu: 3000m
limits:
memory: 18Gi
cpu: 3000m
nodeSelector:
kubernetes.io/arch: amd64
node.kubernetes.io/instance-type: AX42
tolerations:
- key: 'CI'
operator: 'Equal'
value: 'true'
effect: 'NoSchedule'

58
.crow/process-updates-alpine-321-arm64.yaml
View file

@ -1,58 +0,0 @@
when:
- event: [cron]
cron: process-cran-updates-alpine-321-arm64
- event: manual
evaluate: 'process_cran_updates == "all"'
- event: manual
evaluate: 'process_cran_updates == "alpine-321-arm64"'
skip_clone: true
labels:
agent: gaia
steps:
- name: 'Processing Updates'
image: reg.devxy.io/rpkgs/build-env-alpine:3.23-4.4.3
pull: true
environment:
RED_HAT_DEV_PW:
from_secret: RED_HAT_DEV_PW
B2_S3_ACCESS_KEY:
from_secret: B2_S3_ACCESS_KEY
B2_S3_SECRET_KEY:
from_secret: B2_S3_SECRET_KEY
PGPASS:
from_secret: PGPASS
REPO_RO_TOKEN:
from_secret: REPO_RO_TOKEN
GITHUB_PAT:
from_secret: GITHUB_PAT
# normal env vars
GIT_USER: pat-s
NTFY_SERVER:
from_secret: NTFY_SERVER
NTFY_TOPIC:
from_secret: NTFY_TOPIC
NTFY_AUTH: TRUE
NTFY_PASSWORD:
from_secret: ntfy_token
# 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
PLATFORM: alpine-321
ARCH: arm64
NCPUS: 2
INTERVAL: lubridate::interval(lubridate::today() - 6, lubridate::today() - 3)
# volumes:
# - arm64-binaries-r-dep-cache-alpine-321:/mnt/cache
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-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraft /mnt/cache/R-pkgs/00LOCK-pak /mnt/cache/pkgcache/R/pkgcache /mnt/cache/pkgcache/R/pkgcache /mnt/cache/R-pkgs/pkgcache /mnt/cache/R-pkgs/00LOCK-pak/mnt/cache/R-pkgs/00LOCK-RPostgres /mnt/cache/R-pkgs/bincraft
- R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraft.git")'
- R -q -e 'packageVersion("bincraft")'
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
# 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-run 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 = 'alpine-321', process_updated = TRUE, process_new = TRUE, process_removed = 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)"
- R -q -e 'library(bincraft); upload_package_index(codename = "alpine321", 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"))'

2
.crow/process-updates-alpine-322-amd64.yaml
View file

@ -13,7 +13,7 @@ labels:
steps:
- name: 'Processing Updates'
image: reg.devxy.io/rpkgs/build-env-alpine:3.23-4.5
image: reg.devxy.io/rpkgs/build-env-alpine:3.22-4.5
pull: true
environment:
RED_HAT_DEV_PW:

4
.crow/process-updates-alpine-322-arm64.yaml
View file

@ -13,7 +13,7 @@ labels:
steps:
- name: 'Processing Updates'
image: reg.devxy.io/rpkgs/build-env-alpine:3.23-4.5
image: reg.devxy.io/rpkgs/build-env-alpine:3.22-4.5
pull: true
environment:
RED_HAT_DEV_PW:
@ -56,5 +56,3 @@ steps:
# 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-run 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 = 'alpine-322', process_updated = TRUE, process_new = TRUE, process_removed = 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)"
- R -q -e 'library(bincraft); upload_package_index(codename = "alpine322", 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"))'

2
.crow/weekly-audit-missing-alpine-322-arm64.yaml
View file

@ -20,6 +20,8 @@ steps:
from_secret: REPO_RO_TOKEN
GITHUB_PAT:
from_secret: GITHUB_PAT
FORGEJO_TOKEN:
from_secret: FORGEJO_TOKEN
PLATFORM: alpine-322
ARCH: arm64
R_LIBS_USER: /mnt/cache/R-pkgs

59
.crow/weekly-rebuild-missing-alpine-321-amd64.yaml
View file

@ -1,59 +0,0 @@
when:
- event: cron
cron: weekly-rebuild-missing-alpine-321-amd64
- event: manual
evaluate: 'task == "weekly-rebuild-missing-alpine-321-amd64"'
skip_clone: true
steps:
- name: 'Rebuild missing binaries'
image: reg.devxy.io/rpkgs/build-env-alpine:3.23-4.5
pull: true
environment:
RED_HAT_DEV_PW:
from_secret: RED_HAT_DEV_PW
B2_S3_ACCESS_KEY:
from_secret: B2_S3_ACCESS_KEY
B2_S3_SECRET_KEY:
from_secret: B2_S3_SECRET_KEY
PGPASS:
from_secret: PGPASS
REPO_RO_TOKEN:
from_secret: REPO_RO_TOKEN
GITHUB_PAT:
from_secret: GITHUB_PAT
GIT_USER: pat-s
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
R_LIBS_USER: /mnt/cache/R-pkgs
CCACHE_DIR: /mnt/cache/ccache
PLATFORM: alpine-321
ARCH: amd64
NCPUS: 2
volumes:
- amd64-binaries-r-dep-cache-alpine321:/mnt/cache
commands:
- 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-*
- R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraft.git")'
- 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
- $XVFB $XVFB_ARGS -- R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); rds_path <- '/mnt/cache/packages/weekly_rebuild_alpine-321_amd64.rds'; if (!file.exists(rds_path)) { cat('No RDS file found at', rds_path, '- nothing to rebuild\n'); q('no') }; pkgs <- readRDS(rds_path); if (length(pkgs) == 0) { cat('RDS is empty - 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
backend_options:
kubernetes:
resources:
requests:
memory: 5Gi
cpu: 3000m
limits:
memory: 18Gi
cpu: 3000m
nodeSelector:
kubernetes.io/arch: amd64
node.kubernetes.io/instance-type: AX42
tolerations:
- key: 'CI'
operator: 'Equal'
value: 'true'
effect: 'NoSchedule'

58
.crow/weekly-rebuild-missing-alpine-321-arm64.yaml
View file

@ -1,58 +0,0 @@
when:
- event: cron
cron: weekly-rebuild-missing-alpine-321-arm64
- event: manual
evaluate: 'task == "weekly-rebuild-missing-alpine-321-arm64"'
skip_clone: true
steps:
- name: 'Rebuild missing binaries'
image: reg.devxy.io/rpkgs/build-env-alpine:3.23-4.5
pull: true
environment:
RED_HAT_DEV_PW:
from_secret: RED_HAT_DEV_PW
B2_S3_ACCESS_KEY:
from_secret: B2_S3_ACCESS_KEY
B2_S3_SECRET_KEY:
from_secret: B2_S3_SECRET_KEY
PGPASS:
from_secret: PGPASS
REPO_RO_TOKEN:
from_secret: REPO_RO_TOKEN
GITHUB_PAT:
from_secret: GITHUB_PAT
GIT_USER: pat-s
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
R_LIBS_USER: /mnt/cache/R-pkgs
CCACHE_DIR: /mnt/cache/ccache
PLATFORM: alpine-321
ARCH: arm64
NCPUS: 2
volumes:
- arm64-binaries-r-dep-cache-alpine321:/mnt/cache
commands:
- 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-*
- R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraft.git")'
- 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
- $XVFB $XVFB_ARGS -- R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); rds_path <- '/mnt/cache/packages/weekly_rebuild_alpine-321_arm64.rds'; if (!file.exists(rds_path)) { cat('No RDS file found at', rds_path, '- nothing to rebuild\n'); q('no') }; pkgs <- readRDS(rds_path); if (length(pkgs) == 0) { cat('RDS is empty - 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
backend_options:
kubernetes:
resources:
requests:
memory: 5Gi
cpu: 3000m
limits:
memory: 18Gi
cpu: 3000m
nodeSelector:
kubernetes.io/arch: arm64
tolerations:
- key: 'CI'
operator: 'Equal'
value: 'true'
effect: 'NoSchedule'

2
.crow/weekly-rebuild-missing-alpine-322-amd64.yaml
View file

@ -8,7 +8,7 @@ skip_clone: true
steps:
- name: 'Rebuild missing binaries'
image: reg.devxy.io/rpkgs/build-env-alpine:3.23-4.5
image: reg.devxy.io/rpkgs/build-env-alpine:3.22-4.5
pull: true
environment:
RED_HAT_DEV_PW:

14
.crow/weekly-rebuild-missing-alpine-322-arm64.yaml
View file

@ -2,13 +2,15 @@ when:
- event: cron
cron: weekly-rebuild-missing-alpine-322-arm64
- event: manual
evaluate: 'task == "weekly-rebuild-missing-alpine-322-arm64"'
skip_clone: true
labels:
agent: gaia
steps:
- name: 'Rebuild missing binaries'
image: reg.devxy.io/rpkgs/build-env-alpine:3.23-4.5
image: reg.devxy.io/rpkgs/build-env-alpine:3.22-4.5
pull: true
environment:
RED_HAT_DEV_PW:
@ -23,6 +25,8 @@ steps:
from_secret: REPO_RO_TOKEN
GITHUB_PAT:
from_secret: GITHUB_PAT
FORGEJO_TOKEN:
from_secret: FORGEJO_TOKEN
GIT_USER: pat-s
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
R_LIBS_USER: /mnt/cache/R-pkgs
@ -30,8 +34,6 @@ steps:
PLATFORM: alpine-322
ARCH: arm64
NCPUS: 2
volumes:
- arm64-binaries-r-dep-cache-alpine322:/mnt/cache
commands:
- 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
@ -39,7 +41,9 @@ steps:
- R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraft.git")'
- 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
- $XVFB $XVFB_ARGS -- R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); rds_path <- '/mnt/cache/packages/weekly_rebuild_alpine-322_arm64.rds'; if (!file.exists(rds_path)) { cat('No RDS file found at', rds_path, '- nothing to rebuild\n'); q('no') }; pkgs <- readRDS(rds_path); if (length(pkgs) == 0) { cat('RDS is empty - 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
- R -q -e 'pak::pak("httr2")'
- R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")'
- $XVFB $XVFB_ARGS -- 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
backend_options:
kubernetes:
resources:

69
local/weekly-missing-binaries-audit.R
View file

@ -38,7 +38,38 @@ cat(sprintf("Platform: %s | Arch: %s | S3 codename: %s | OS family: %s\n",
platform, arch, s3_codename, os_family))
# ---------------------------------------------------------------------------
# 1. CRAN release packages
# 1. Query PostgreSQL for known build failures (before s3fs init to avoid
# C++ pointer conflicts between s3fs/curl and RPostgres/libpq)
# ---------------------------------------------------------------------------
cat("Connecting to PostgreSQL...\n")
con <- DBI::dbConnect(
RPostgres::Postgres(),
dbname = "build_metadata",
host = "r-binaries.devxy.io",
port = 15432,
user = "rpkgs",
password = Sys.getenv("PGPASS"),
sslmode = "require"
)
errored_pkgs <- DBI::dbGetQuery(
con,
sprintf(
"SELECT name, tag FROM single_builds WHERE error_occurred = TRUE AND platform = '%s' AND arch = '%s'",
platform, arch
)
)
DBI::dbDisconnect(con)
errored_dt <- as.data.table(errored_pkgs)
if (nrow(errored_dt) > 0) {
setnames(errored_dt, c("Package", "Version"))
setkey(errored_dt, Package, Version)
}
cat(sprintf("Found %d known build failures for %s/%s\n", nrow(errored_dt), platform, arch))
# ---------------------------------------------------------------------------
# 2. CRAN release packages (uses curl internally - must come after PG)
# ---------------------------------------------------------------------------
cat("Fetching CRAN package database...\n")
cran_release <- tools::CRAN_package_db()
@ -48,7 +79,7 @@ cran_dt <- data.table(
)
# ---------------------------------------------------------------------------
# 2. S3 tarballs
# 3. S3 tarballs
# ---------------------------------------------------------------------------
cat("Connecting to S3...\n")
s3fs::s3_file_system(
@ -82,7 +113,7 @@ s3_dt <- data.table(
cat(sprintf("S3 contains %d tarballs for %s/%s\n", nrow(s3_dt), arch, s3_codename))
# ---------------------------------------------------------------------------
# 3. Find missing packages (CRAN release version not in S3)
# 4. Find missing packages (CRAN release version not in S3)
# ---------------------------------------------------------------------------
setkey(cran_dt, Package, Version)
setkey(s3_dt, Package, Version)
@ -90,7 +121,7 @@ missing_dt <- cran_dt[!s3_dt]
cat(sprintf("%d CRAN release packages missing from S3\n", nrow(missing_dt)))
# ---------------------------------------------------------------------------
# 4. Remove excluded packages
# 5. Remove excluded packages
# ---------------------------------------------------------------------------
script_dir <- tryCatch(
dirname(normalizePath(
@ -114,36 +145,6 @@ if (file.exists(excluded_path)) {
cat(sprintf("No excluded-packages.json found at %s -- skipping exclusion step\n", excluded_path))
}
# ---------------------------------------------------------------------------
# 5. Query PostgreSQL for known build failures
# ---------------------------------------------------------------------------
cat("Connecting to PostgreSQL...\n")
con <- DBI::dbConnect(
RPostgres::Postgres(),
dbname = "build_metadata",
host = "r-binaries.devxy.io",
port = 15432,
user = "rpkgs",
password = Sys.getenv("PGPASS"),
sslmode = "require"
)
on.exit(DBI::dbDisconnect(con), add = TRUE)
errored_pkgs <- DBI::dbGetQuery(
con,
sprintf(
"SELECT name, tag FROM single_builds WHERE error_occurred = TRUE AND platform = '%s' AND arch = '%s'",
platform, arch
)
)
errored_dt <- as.data.table(errored_pkgs)
if (nrow(errored_dt) > 0) {
setnames(errored_dt, c("Package", "Version"))
setkey(errored_dt, Package, Version)
}
cat(sprintf("Found %d known build failures for %s/%s\n", nrow(errored_dt), platform, arch))
# ---------------------------------------------------------------------------
# 6. Split into rebuildable vs known failures
# ---------------------------------------------------------------------------