From 1fd8d811e7c65ba7fcfeb3b9dd2da37bbb5f6c53 Mon Sep 17 00:00:00 2001 From: pat-s Date: Tue, 30 Jun 2026 10:46:18 +0200 Subject: [PATCH] ci(patches): wire patches into all build workflows; pin bincraft v4.3.1 Pass patches = 'local/patches' to the daily process_cran_updates() calls (requires bincraft v4.3.1) and the weekly-rebuild build_binary_package() call, so every CI build path applies the patch registry like build-all/build-one already do. Bump the bincraft pin v4.3.0 -> v4.3.1 across all .crow workflows. --- .crow/archive-missed-packages.yaml | 2 +- .crow/build-all-versions-install-deps.yaml | 2 +- .crow/build-all-versions.yaml | 4 ++-- .crow/process-updates.yaml | 8 ++++---- .crow/weekly-rebuild-missing.yaml | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.crow/archive-missed-packages.yaml b/.crow/archive-missed-packages.yaml index 97793f6..3feb157 100644 --- a/.crow/archive-missed-packages.yaml +++ b/.crow/archive-missed-packages.yaml @@ -62,7 +62,7 @@ steps: GIT_USER: pat-s R_VERSION: 4.5.3 commands: - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.3.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.0", dependencies = TRUE)' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.3.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.1", dependencies = TRUE)' - /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"), 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: diff --git a/.crow/build-all-versions-install-deps.yaml b/.crow/build-all-versions-install-deps.yaml index ea73fbe..3a7d92c 100644 --- a/.crow/build-all-versions-install-deps.yaml +++ b/.crow/build-all-versions-install-deps.yaml @@ -75,7 +75,7 @@ steps: - 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 # snapshot and the per-agent library stay consistent across the pipeline. - - /opt/R/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.0"); 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@v4.3.1"); 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: diff --git a/.crow/build-all-versions.yaml b/.crow/build-all-versions.yaml index 9bcb0a4..076e482 100644 --- a/.crow/build-all-versions.yaml +++ b/.crow/build-all-versions.yaml @@ -121,7 +121,7 @@ steps: # 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") != "4.3.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.3.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.1")' - 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 - | @@ -133,7 +133,7 @@ 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") != "4.3.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.0")' || true + R_LIBS_USER="$LIB" "$(dirname "$RBIN")/R" -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.3.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.1")' || 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 # archive missed packages; first arg is the codename (e.g. "alpine324"), diff --git a/.crow/process-updates.yaml b/.crow/process-updates.yaml index 6657c7c..b943b2d 100644 --- a/.crow/process-updates.yaml +++ b/.crow/process-updates.yaml @@ -192,13 +192,13 @@ 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/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.3.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.3.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.1")' - /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 @@ -208,8 +208,8 @@ 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") != "4.3.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.0")' || 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 "$RBIN")/R" -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.3.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.1")' || true + R_LIBS_USER="$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"))' - | diff --git a/.crow/weekly-rebuild-missing.yaml b/.crow/weekly-rebuild-missing.yaml index faacb19..5d88dec 100644 --- a/.crow/weekly-rebuild-missing.yaml +++ b/.crow/weekly-rebuild-missing.yaml @@ -129,12 +129,12 @@ 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/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.3.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.3.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.1")' - /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: