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Code Issues 12 Pull requests Releases Activity

fix(ci): install the R packages pipelines use instead of relying on the image #238

Merged
pat-s merged 1 commit from fix/pipeline-r-deps into main 2026-10-20 08:51:07 +00:00
Conversation 0 Commits 1 Files changed 13 +18 -8
13 changed files with 18 additions and 8 deletions
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1
.crow/backfill-abi-classification.yaml
View file

@ -74,6 +74,7 @@ steps:
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
- mkdir -p /tmp/R-pkgs
- /opt/R/4.5.3/bin/Rscript local/install-bincraft.R
- UVR_R_BIN=/opt/R/4.5.3/bin/R local/uvr-install.sh RPostgres
- |
set -eu
LIMIT=""

1
.crow/backfill-flat-safety.yaml
View file

@ -155,6 +155,7 @@ steps:
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
- mkdir -p /tmp/R-pkgs
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
- |
set -eu
LIMIT=""

2
.crow/build-all-versions-install-deps.yaml
View file

@ -86,7 +86,7 @@ steps:
# 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/$R_VERSION/bin/Rscript local/install-bincraft.R
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite purrr
- /opt/R/$R_VERSION/bin/R -q -e '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:

2
.crow/build-all-versions.yaml
View file

@ -152,7 +152,7 @@ steps:
# The dependency-prep job may run on another agent whose cache volume is
# not visible here. Install the packages needed to recompute the snapshot
# and query build metadata in every build job.
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite purrr
- XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS="-a"; 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
- |

4
.crow/process-updates.yaml
View file

@ -189,7 +189,7 @@ steps:
- rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft
- mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres progressr lubridate
- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
# rhel-10 ships xwfb-run (Xwayland) instead of xvfb-run; prefer it and start weston, else fall back to xvfb-run
- XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS="-a"; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
@ -205,7 +205,7 @@ steps:
LIB="/mnt/cache/R-pkgs-$RMINOR"
mkdir -p "$LIB"
R_LIBS_USER="$LIB" "$(dirname "$RBIN")/Rscript" local/install-bincraft.R || true
R_LIBS_USER="$LIB" UVR_R_BIN="$RBIN" local/uvr-install.sh RPostgres || true
R_LIBS_USER="$LIB" UVR_R_BIN="$RBIN" local/uvr-install.sh RPostgres lubridate || 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 = 'verify-full', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true
# Also build current packages whose required dependency tree needs a newer R.
R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -- "$(dirname "$RBIN")/Rscript" local/build-newer-r.R "$R_VERSION"

5
.crow/prune-stale-flat-binaries.yaml
View file

@ -167,6 +167,7 @@ steps:
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
- mkdir -p /tmp/R-pkgs
- /opt/R/4.5.3/bin/Rscript local/install-bincraft.R
- UVR_R_BIN=/opt/R/4.5.3/bin/R local/uvr-install.sh RPostgres
- |
set -eu
APPLY=""
@ -208,6 +209,10 @@ steps:
echo "Dry run: nothing was deleted, so there is nothing to re-index."
exit 0
fi
# /tmp is container-local, so the library installed by the prune step is gone here.
mkdir -p /tmp/R-pkgs
/opt/R/4.5.3/bin/Rscript local/install-bincraft.R
UVR_R_BIN=/opt/R/4.5.3/bin/R local/uvr-install.sh RPostgres
/opt/R/4.5.3/bin/R -q -e 'library(bincraft); upload_package_index(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"))'
FAILED_MINORS=""
for RBIN in /opt/R/[0-9]*/bin/R; do

1
.crow/rebuild-abi-gap.yaml
View file

@ -193,6 +193,7 @@ steps:
export R_LIBS_USER="$$LIB"
rm -rf "$$LIB"/00LOCK-*
"$$RBIN/Rscript" local/install-bincraft.R
UVR_R_BIN="$$RBIN/R" local/uvr-install.sh RPostgres
rc=0
for spec in $$ABI_PACKAGES; do
pkg=$${spec%@*}

1
.crow/reindex.yaml
View file

@ -158,6 +158,7 @@ steps:
- mkdir -p /mnt/cache/R-pkgs
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
# The codename is detected from the image's /etc/os-release.
- /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(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/repair-unsafe-flat-objects.yaml
View file

@ -144,6 +144,7 @@ steps:
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
- mkdir -p /tmp/R-pkgs
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
- |
set -eu
CODENAME=$(/opt/R/$R_VERSION/bin/Rscript -e 'cat(bincraft::set_codename(NULL))')
@ -158,6 +159,7 @@ steps:
LIB="/tmp/R-pkgs-$$RMINOR"
mkdir -p "$$LIB"
R_LIBS_USER="$$LIB" "$(dirname "$$RBIN")/Rscript" local/install-bincraft.R || true
R_LIBS_USER="$$LIB" UVR_R_BIN="$$RBIN" local/uvr-install.sh RPostgres || true
while read -r pkg ver; do
[ -z "$$pkg" ] && continue
R_LIBS_USER="$$LIB" "$(dirname "$$RBIN")/Rscript" \

2
.crow/weekly-audit-missing.yaml
View file

@ -137,7 +137,7 @@ steps:
- mkdir -p /mnt/cache/packages /mnt/cache/R-pkgs
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres httr2 jsonlite
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres httr2 jsonlite data.table
- /opt/R/$R_VERSION/bin/R -q -e 'source("local/weekly-missing-binaries-audit.R")'
backend_options:
docker:

2
.crow/weekly-rebuild-missing.yaml
View file

@ -389,7 +389,7 @@ steps:
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
- XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS="-a"; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres httr2
- /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")'
- $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/rebuild-missing.R $SPLIT_INTO $SPLIT_INDEX $REBUILD_BUDGET_HOURS 2>&1
backend_options:

1
.crow/weekly-rebuild-reindex.yaml
View file

@ -161,6 +161,7 @@ steps:
- mkdir -p /mnt/cache/R-pkgs
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
# The codename is detected from the image's /etc/os-release.
- /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(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
local/packages-to-build.R
View file

@ -5,10 +5,8 @@ options(error = function() {
})
library(bincraft, quietly = TRUE)
suppressPackageStartupMessages(library(dplyr))
library(DBI, quietly = TRUE)
library(purrr, quietly = TRUE)
library(progressr, quietly = TRUE)
suppressPackageStartupMessages(library(data.table))
# Sys.setenv("OS" = "alpine")