pat-s
930a4acd12bincraft v5.5.1 dropped lubridate, dplyr, purrr, data.table and others from its imports, so the pipelines' own calls now depend on whatever the build-env image's site library or the shared R_LIBS_USER cache happens to hold. The arm64 redhat:9 image has no progressr under R 4.4.3, which fails every process-cran-updates-redhat-9-arm64 run since v5.5.1. - Install progressr and lubridate for process-updates, which call them inline. - Install purrr for packages-to-build.R and data.table for the weekly audit. - Drop the unused dplyr and progressr library() calls from packages-to-build.R. - Install RPostgres in every pipeline that talks to the metadata DB, since bincraft silently skips the DB (and the per-minor index aborts) without it. - Reinstall bincraft in the prune re-index step, whose /tmp library does not survive from the prune step.
224 lines
9.4 KiB
YAML
224 lines
9.4 KiB
YAML
### Manual full rebuild of all CRAN binaries for one OS/arch.
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# Set the variables below in the manual-run form (or via --var on the CLI).
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# `target_arch` routes the matrix; OS/OS_VERSION/R_VERSION select the platform
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# image and cache volume. Placement is via the group label (rpkgs-amd64/rpkgs-arm64).
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# Skip list lives in local/excluded-packages.json (read by local/build-all.R).
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variables:
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# Gates this pipeline. A manual pipeline creation instantiates every file in
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# .crow/, and a declared default is applied even when the run never passed
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# this variable, so the default must be a value that matches no matrix row.
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target_arch:
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description: 'Architecture to build, or "none" to run nothing.'
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options:
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- none
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- amd64
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- arm64
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default: none
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OS:
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description: 'Base OS image name.'
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options:
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- alpine
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- redhat
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- ubuntu
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default: alpine
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OS_VERSION:
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description: 'OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble).'
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options:
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- '3.23'
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- '3.24'
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- '8'
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- '9'
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- '10'
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- 'jammy'
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- 'noble'
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- 'resolute'
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default: '3.24'
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R_VERSION:
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# The slot's *primary* R minor: what `local/build-all.R` builds into the
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# generic slot. The loop below already runs `--sensitive-only` for every
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# other installed minor, so filling a non-primary minor's gap needs this
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# left alone, not changed.
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#
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# 4.6.0 was briefly offered here (#183) and removed: selecting it for a
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# slot whose generic binaries are 4.5-built would publish 4.6 binaries
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# into the generic slot and break every 4.5 client.
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description: 'Primary R version under /opt/R.'
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options:
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- 4.5.3
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- 4.4.3
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default: 4.5.3
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when:
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- event: manual
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evaluate: 'target_arch == "${ARCH}"'
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skip_clone: true
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labels:
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platform: linux/${ARCH}
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group: rpkgs-${ARCH}
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# Empty UVR_CACHE_DIR/UVR_PACKAGES_DIR fall back to uvr's container-local
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# ~/.uvr defaults; amd64 deliberately does not persist them (as with the
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# pkgcache dir it replaces), arm64 does.
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matrix:
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include:
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- ARCH: amd64
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UVR_CACHE_DIR: ''
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UVR_PACKAGES_DIR: ''
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SPLIT_INTO: 4
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SPLIT_INDEX: 1
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- ARCH: amd64
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UVR_CACHE_DIR: ''
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UVR_PACKAGES_DIR: ''
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SPLIT_INTO: 4
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SPLIT_INDEX: 2
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- ARCH: amd64
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UVR_CACHE_DIR: ''
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UVR_PACKAGES_DIR: ''
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SPLIT_INTO: 4
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SPLIT_INDEX: 3
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- ARCH: amd64
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UVR_CACHE_DIR: ''
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UVR_PACKAGES_DIR: ''
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SPLIT_INTO: 4
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SPLIT_INDEX: 4
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- ARCH: arm64
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UVR_CACHE_DIR: /mnt/cache/uvr/cache
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UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
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SPLIT_INTO: 4
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SPLIT_INDEX: 1
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- ARCH: arm64
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UVR_CACHE_DIR: /mnt/cache/uvr/cache
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UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
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SPLIT_INTO: 4
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SPLIT_INDEX: 2
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- ARCH: arm64
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UVR_CACHE_DIR: /mnt/cache/uvr/cache
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UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
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SPLIT_INTO: 4
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SPLIT_INDEX: 3
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- ARCH: arm64
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UVR_CACHE_DIR: /mnt/cache/uvr/cache
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UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
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SPLIT_INTO: 4
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SPLIT_INDEX: 4
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depends_on:
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- build-all-versions-install-deps
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steps:
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- name: 'Build binaries'
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image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
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pull: true
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environment:
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OTEL_R_TRACES_EXPORTER: none
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OTEL_R_LOGS_EXPORTER: none
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OTEL_R_METRICS_EXPORTER: none
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RED_HAT_DEV_PW:
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from_secret: RED_HAT_DEV_PW
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B2_S3_ACCESS_KEY:
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from_secret: B2_S3_ACCESS_KEY
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B2_S3_SECRET_KEY:
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from_secret: B2_S3_SECRET_KEY
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PGPASS:
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from_secret: PGPASS
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REPO_RO_TOKEN:
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from_secret: REPO_RO_TOKEN
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GITHUB_PAT:
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from_secret: GITHUB_PAT
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# normal env vars
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GIT_USER: pat-s
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# set the location of uvr's caches, which persist the R package
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# dependencies needed to install the packages themselves
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UVR_CACHE_DIR: ${UVR_CACHE_DIR}
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UVR_PACKAGES_DIR: ${UVR_PACKAGES_DIR}
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R_LIBS_USER: /mnt/cache/R-pkgs
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CCACHE_DIR: /mnt/cache/ccache
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NCPUS: 2
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volumes:
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- ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
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commands:
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- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
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- mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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# The primary pass must not rely on build-all-versions-install-deps having
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# run on *this* agent: depends_on only orders the steps, but the cache
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# volume is per-agent, so a job landing on an agent where install-deps did
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# not run would otherwise use a stale bincraft (which resolves `platform`
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# to a zero-length value and breaks every metadata query and the sysdeps
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# install). Pin bincraft here, exactly like the R-minor pass below.
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- rm -rf /mnt/cache/R-pkgs/00LOCK-*
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- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
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# The dependency-prep job may run on another agent whose cache volume is
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# not visible here. Install the packages needed to recompute the snapshot
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# and query build metadata in every build job.
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- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite purrr
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- 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
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- $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/build-all.R $SPLIT_INTO $SPLIT_INDEX $NCPUS 2>&1
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- |
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PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2)
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for RBIN in /opt/R/[0-9]*/bin/R; do
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RV=$(basename "$(dirname "$(dirname "$RBIN")")")
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RMINOR=$(echo "$RV" | cut -d. -f1-2)
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[ "$RMINOR" = "$PRIMARY_MINOR" ] && continue
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echo "=== R-minor-sensitive pass under R $RV ==="
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LIB="/mnt/cache/R-pkgs-$RMINOR"
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mkdir -p "$LIB"
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R_LIBS_USER="$LIB" "$(dirname "$RBIN")/Rscript" local/install-bincraft.R || true
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R_LIBS_USER="$LIB" UVR_R_BIN="$RBIN" local/uvr-install.sh RPostgres || true
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R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- "$(dirname "$RBIN")/Rscript" local/build-all.R --sensitive-only $SPLIT_INTO $SPLIT_INDEX $NCPUS 2>&1 || true
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# Also build current packages whose required dependency tree needs a newer R.
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R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- "$(dirname "$RBIN")/Rscript" local/build-newer-r.R "$R_VERSION" $SPLIT_INTO $SPLIT_INDEX
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done
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# archive missed packages; first arg is the codename (e.g. "alpine324"),
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# derived via bincraft like the upload step, not paste(OS, OS_VERSION).
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- /opt/R/$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 = $NCPUS)"
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backend_options:
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docker:
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resources:
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requests:
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memory: 5Gi
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cpu: 1000m
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limits:
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memory: 20Gi
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cpu: 2000m
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- name: 'Upload package indexes'
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image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
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pull: true
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environment:
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OTEL_R_TRACES_EXPORTER: none
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OTEL_R_LOGS_EXPORTER: none
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OTEL_R_METRICS_EXPORTER: none
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B2_S3_ACCESS_KEY:
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from_secret: B2_S3_ACCESS_KEY
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B2_S3_SECRET_KEY:
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from_secret: B2_S3_SECRET_KEY
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# A per-minor index reads the ABI classifier cache and the flat-object
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# safety table from the build database, and is not republished without it.
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PGPASS:
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from_secret: PGPASS
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R_LIBS_USER: /mnt/cache/R-pkgs
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volumes:
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- ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
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commands:
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- |
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CODENAME=$(/opt/R/$R_VERSION/bin/Rscript -e "cat(bincraft::set_codename(NULL))")
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/opt/R/$R_VERSION/bin/R -q -e "bincraft::upload_package_index(codename = '$CODENAME', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))"
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FAILED_MINORS=""
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for RBIN in /opt/R/[0-9]*/bin/R; do
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RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2)
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/opt/R/$R_VERSION/bin/R -q -e "bincraft::upload_package_index(codename = '$CODENAME', r_minor = '$RMINOR', 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_port = 15432L, metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'verify-full')" || FAILED_MINORS="$FAILED_MINORS $RMINOR"
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done
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if [ -n "$FAILED_MINORS" ]; then
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echo "Could not republish the per-minor index for:$FAILED_MINORS" >&2
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exit 1
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fi
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backend_options:
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docker:
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resources:
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requests:
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memory: 5Gi
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cpu: 1000m
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limits:
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memory: 20Gi
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cpu: 2000m
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