diff --git a/.crow/archive-missed-packages.yaml b/.crow/archive-missed-packages.yaml index cb4de27..bb9ecb4 100644 --- a/.crow/archive-missed-packages.yaml +++ b/.crow/archive-missed-packages.yaml @@ -6,6 +6,7 @@ when: - event: cron cron: archive-missed-packages + matrix: include: - CODENAME: jammy @@ -62,7 +63,7 @@ steps: GIT_USER: pat-s R_VERSION: 4.5.3 commands: - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0", dependencies = TRUE)' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1", 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"), workers = 2L)' backend_options: diff --git a/.crow/build-all-versions-amd64.yaml b/.crow/build-all-versions-amd64.yaml index 0c74ef7..796c812 100644 --- a/.crow/build-all-versions-amd64.yaml +++ b/.crow/build-all-versions-amd64.yaml @@ -39,7 +39,7 @@ depends_on: steps: - name: 'Build binaries' - image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}' + image: "reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}" pull: true environment: RED_HAT_DEV_PW: @@ -57,7 +57,7 @@ steps: # normal env vars GIT_USER: pat-s # set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves - R_PKG_CACHE_DIR: '' + R_PKG_CACHE_DIR: "" R_LIBS_USER: /mnt/cache/R-pkgs CCACHE_DIR: /mnt/cache/ccache NCPUS: 2 @@ -70,15 +70,6 @@ steps: # pkgs = readRDS('/mnt/cache/pkgs_amd64.rds'); - 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 $NCPUS 2>&1 - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive pass under R $RV ===" - $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 = $NCPUS)" backend_options: @@ -106,47 +97,3 @@ steps: operator: 'Equal' value: 'true' effect: 'NoSchedule' - - name: 'Upload package indexes' - image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}' - pull: true - environment: - B2_S3_ACCESS_KEY: - from_secret: B2_S3_ACCESS_KEY - B2_S3_SECRET_KEY: - from_secret: B2_S3_SECRET_KEY - R_LIBS_USER: /mnt/cache/R-pkgs - volumes: - - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache - commands: - - | - CODENAME=$(/opt/R/$R_VERSION/bin/Rscript -e "cat(bincraft::set_codename(NULL))") - /opt/R/$R_VERSION/bin/R -q -e "bincraft::upload_package_index(codename = '$CODENAME', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))" - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - /opt/R/$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'))" || true - done - backend_options: - docker: - resources: - requests: - memory: 5Gi - cpu: 1000m - limits: - memory: 20Gi - cpu: 2000m - kubernetes: - resources: - requests: - memory: 5Gi - cpu: 1000m - limits: - memory: 20Gi - cpu: 2000m - nodeSelector: - kubernetes.io/arch: ${ARCH} - node.kubernetes.io/instance-type: ${K8S_INSTANCE_TYPE} - tolerations: - - key: 'CI' - operator: 'Equal' - value: 'true' - effect: 'NoSchedule' diff --git a/.crow/build-all-versions-arm64.yaml b/.crow/build-all-versions-arm64.yaml index aac08c3..37992df 100644 --- a/.crow/build-all-versions-arm64.yaml +++ b/.crow/build-all-versions-arm64.yaml @@ -54,7 +54,7 @@ depends_on: steps: - name: 'Build binaries' - image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}' + image: "reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}" pull: true environment: RED_HAT_DEV_PW: @@ -83,15 +83,6 @@ steps: - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - XVFB=$(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 $NCPUS 2>&1 - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive pass under R $RV ===" - $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 = $NCPUS)" backend_options: @@ -119,47 +110,3 @@ steps: operator: 'Equal' value: 'true' effect: 'NoSchedule' - - name: 'Upload package indexes' - image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}' - pull: true - environment: - B2_S3_ACCESS_KEY: - from_secret: B2_S3_ACCESS_KEY - B2_S3_SECRET_KEY: - from_secret: B2_S3_SECRET_KEY - R_LIBS_USER: /mnt/cache/R-pkgs - volumes: - - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache - commands: - - | - CODENAME=$(/opt/R/$R_VERSION/bin/Rscript -e "cat(bincraft::set_codename(NULL))") - /opt/R/$R_VERSION/bin/R -q -e "bincraft::upload_package_index(codename = '$CODENAME', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))" - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - /opt/R/$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'))" || true - done - backend_options: - docker: - resources: - requests: - memory: 5Gi - cpu: 1000m - limits: - memory: 20Gi - cpu: 2000m - kubernetes: - resources: - requests: - memory: 5Gi - cpu: 1000m - limits: - memory: 20Gi - cpu: 2000m - nodeSelector: - kubernetes.io/arch: ${ARCH} - node.kubernetes.io/instance-type: ${K8S_INSTANCE_TYPE} - tolerations: - - key: 'CI' - operator: 'Equal' - value: 'true' - effect: 'NoSchedule' diff --git a/.crow/build-all-versions-install-deps-amd64.yaml b/.crow/build-all-versions-install-deps-amd64.yaml index 285a4e2..4d50ddf 100644 --- a/.crow/build-all-versions-install-deps-amd64.yaml +++ b/.crow/build-all-versions-install-deps-amd64.yaml @@ -10,7 +10,7 @@ labels: steps: - name: 'Install deps and bincraft' - image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}' + image: "reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}" pull: true environment: REPO_RO_TOKEN: @@ -35,7 +35,7 @@ steps: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - git clone -q https://codefloe.com/rpkgs/bincraft.git /tmp/bincraft - /opt/R/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); pak::local_install("/tmp/bincraft"); pak::pak(c("RPostgres", "s3fs", "data.table", "future", "jsonlite")); packageVersion("bincraft")' - - /opt/R/$R_VERSION/bin/R -q -e "source('local/packages-to-build.R'); saveRDS(pkgs, '/mnt/cache/packages/pkgs_to_build.rds'); saveRDS(pkgs[r_minor_sensitive == TRUE], '/mnt/cache/packages/r_minor_sensitive_pkgs.rds'); sprintf('Precomputed %s package versions (%s r-minor-sensitive)', nrow(pkgs), nrow(pkgs[r_minor_sensitive == TRUE]))" + - /opt/R/$R_VERSION/bin/R -q -e "source('local/packages-to-build.R'); saveRDS(pkgs, '/mnt/cache/packages/pkgs_to_build.rds'); sprintf('Precomputed %s package versions to build', nrow(pkgs))" backend_options: docker: resources: diff --git a/.crow/build-all-versions-install-deps-arm64.yaml b/.crow/build-all-versions-install-deps-arm64.yaml index 98decea..2b3b881 100644 --- a/.crow/build-all-versions-install-deps-arm64.yaml +++ b/.crow/build-all-versions-install-deps-arm64.yaml @@ -9,7 +9,7 @@ labels: steps: - name: 'Install deps and bincraft' - image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}' + image: "reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}" pull: true environment: REPO_RO_TOKEN: @@ -34,7 +34,7 @@ steps: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - git clone -q https://codefloe.com/rpkgs/bincraft.git /tmp/bincraft - /opt/R/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); pak::local_install("/tmp/bincraft"); pak::pak(c("RPostgres", "s3fs", "data.table", "future", "jsonlite")); packageVersion("bincraft")' - - /opt/R/$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]))" + - /opt/R/$R_VERSION/bin/R -q -e "source('local/packages-to-build.R'); saveRDS(pkgs, '/mnt/cache/packages/pkgs_to_build.rds'); sprintf('Precomputed %s package versions to build', nrow(pkgs))" backend_options: docker: resources: diff --git a/.crow/build-r-minor-sensitive-packages.yaml b/.crow/build-r-minor-sensitive-packages.yaml new file mode 100644 index 0000000..a0c3c2d --- /dev/null +++ b/.crow/build-r-minor-sensitive-packages.yaml @@ -0,0 +1,80 @@ +when: + - event: manual + evaluate: 'build == "r-minor"' +# - event: manual +# evaluate: 'build == "alpine-322-arm64"' +# - event: manual +# evaluate: 'build == "alpine-322-arm64-1"' +# - event: manual +# evaluate: 'build == "all-arm64"' + +# skip_clone: true + +# depends_on: +# - alpine-322-arm64-install-deps + +matrix: + include: + - os: alpine + os_version: 3.21 + r_version: 4.5.3 + - os: alpine + os_version: 3.21 + r_version: 4.4.3 + # - os: alpine + # os_version: 3.21 + # r_version: 4.3 +steps: + - name: 'Build R-minor-sensitive binaries' + image: "docker.io/devxygmbh/rpkgs-build-env-${os}:${os_version}" + 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: /tmp/R-libs:/mnt/cache/R-pkgs + CCACHE_DIR: /mnt/cache/ccache + NCPUS: 2 + STRATEGY: sequential + commands: + - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + - rm -rf /mnt/cache/R-pkgs/00LOCK-* + - mkdir -p /tmp/R-libs + - git clone -q https://codefloe.com/rpkgs/bincraft.git /tmp/bincraft && /opt/R/$R_VERSION/bin/R CMD INSTALL --library=/tmp/R-libs /tmp/bincraft && /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' + - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages + - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run) + - $XVFB -- /opt/R/$R_VERSION/bin/R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); pkgs = bincraft::get_r_minor_sensitive_packages(r_minor_packages_issue_url = 'https://git.devxy.io/api/v1/repos/devxy/build-cran-binaries/issues/29'); foo = lapply(pkgs, function(x) bincraft::build_binary_package(x, is_debug = FALSE, is_r_minor_sensitive = TRUE, force = FALSE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE))" 2>&1 + backend_options: + kubernetes: + resources: + requests: + memory: 5Gi + cpu: 1000m + limits: + memory: 20Gi + cpu: 2000m + tolerations: + - key: 'CI' + operator: 'Equal' + value: 'true' + effect: 'NoSchedule' diff --git a/.crow/process-updates-alpine-322-amd64.yaml b/.crow/process-updates-alpine-322-amd64.yaml index 2e00d4c..1927d57 100644 --- a/.crow/process-updates-alpine-322-amd64.yaml +++ b/.crow/process-updates-alpine-322-amd64.yaml @@ -52,26 +52,12 @@ steps: commands: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - rm -rf /mnt/cache/R-pkgs/00LOCK-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run /opt/R/$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 = $INTERVAL, platform = 'alpine-322', process_updated = TRUE, process_new = FALSE, process_removed = TRUE, r_minor_detection = 'classifier', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'alpine-322', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, r_minor_detection = 'classifier', r_minor_sensitive_only = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true - done + - xvfb-run /opt/R/$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 = $INTERVAL, platform = 'alpine-322', process_updated = TRUE, process_new = FALSE, process_removed = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - /opt/R/$R_VERSION/bin/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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'alpine322', 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'))" || true - done backend_options: kubernetes: resources: diff --git a/.crow/process-updates-alpine-322-arm64.yaml b/.crow/process-updates-alpine-322-arm64.yaml index 0b56996..c89a22f 100644 --- a/.crow/process-updates-alpine-322-arm64.yaml +++ b/.crow/process-updates-alpine-322-arm64.yaml @@ -51,26 +51,12 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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 # 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 /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 = 'alpine-322', process_updated = TRUE, process_new = TRUE, 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)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'alpine-322', 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 - done + - xvfb-run /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 = '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)" - /opt/R/$R_VERSION/bin/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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'alpine322', 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'))" || true - done - name: Purge CDN cache image: reg.devxy.io/docker.io/library/alpine:3.24 diff --git a/.crow/process-updates-alpine-323-amd64.yaml b/.crow/process-updates-alpine-323-amd64.yaml index 4b19037..3a73df5 100644 --- a/.crow/process-updates-alpine-323-amd64.yaml +++ b/.crow/process-updates-alpine-323-amd64.yaml @@ -52,26 +52,12 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run /opt/R/$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 = $INTERVAL, platform = 'alpine-323', process_updated = TRUE, process_new = FALSE, process_removed = TRUE, r_minor_detection = 'classifier', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'alpine-323', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, r_minor_detection = 'classifier', r_minor_sensitive_only = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true - done + - xvfb-run /opt/R/$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 = $INTERVAL, platform = 'alpine-323', process_updated = TRUE, process_new = FALSE, process_removed = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "alpine323", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'alpine323', 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'))" || true - done backend_options: kubernetes: resources: diff --git a/.crow/process-updates-alpine-323-arm64.yaml b/.crow/process-updates-alpine-323-arm64.yaml index 3e20a90..2401859 100644 --- a/.crow/process-updates-alpine-323-arm64.yaml +++ b/.crow/process-updates-alpine-323-arm64.yaml @@ -51,26 +51,12 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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 # 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 /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 = 'alpine-323', process_updated = TRUE, process_new = TRUE, 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)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'alpine-323', 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 - done + - xvfb-run /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 = 'alpine-323', 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)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "alpine323", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'alpine323', 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'))" || true - done - name: Purge CDN cache image: reg.devxy.io/docker.io/library/alpine:3.24 diff --git a/.crow/process-updates-redhat-10-amd64.yaml b/.crow/process-updates-redhat-10-amd64.yaml index 81075d0..a4f0cd1 100644 --- a/.crow/process-updates-redhat-10-amd64.yaml +++ b/.crow/process-updates-redhat-10-amd64.yaml @@ -53,27 +53,13 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - XVFB=$(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 $XVFB_ARGS -- /opt/R/$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 = $INTERVAL, platform = 'redhat-10', process_updated = TRUE, process_new = TRUE, process_removed = TRUE, r_minor_detection = 'classifier', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'redhat-10', 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 - done + - $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 = $INTERVAL, platform = 'redhat-10', process_updated = TRUE, process_new = TRUE, process_removed = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "rhel10", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'rhel10', 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'))" || true - done backend_options: kubernetes: resources: diff --git a/.crow/process-updates-redhat-10-arm64.yaml b/.crow/process-updates-redhat-10-arm64.yaml index a2b7e06..a786070 100644 --- a/.crow/process-updates-redhat-10-arm64.yaml +++ b/.crow/process-updates-redhat-10-arm64.yaml @@ -51,27 +51,13 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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 # 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=$(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 -- /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 = 'redhat-10', process_updated = TRUE, process_new = TRUE, 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)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'redhat-10', 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 - done + - $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 = 'redhat-10', 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)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "rhel10", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'rhel10', 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'))" || true - done - name: Purge CDN cache image: reg.devxy.io/docker.io/library/alpine:3.24 diff --git a/.crow/process-updates-redhat-8-amd64.yaml b/.crow/process-updates-redhat-8-amd64.yaml index f148d44..09e5d47 100644 --- a/.crow/process-updates-redhat-8-amd64.yaml +++ b/.crow/process-updates-redhat-8-amd64.yaml @@ -52,26 +52,12 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run /opt/R/$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 = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = TRUE, process_removed = TRUE, r_minor_detection = 'classifier', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, r_minor_detection = 'classifier', r_minor_sensitive_only = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true - done + - xvfb-run /opt/R/$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 = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = TRUE, process_removed = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "rhel8", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'rhel8', 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'))" || true - done backend_options: kubernetes: resources: diff --git a/.crow/process-updates-redhat-8-arm64.yaml b/.crow/process-updates-redhat-8-arm64.yaml index ee3f79b..aa51437 100644 --- a/.crow/process-updates-redhat-8-arm64.yaml +++ b/.crow/process-updates-redhat-8-arm64.yaml @@ -51,26 +51,12 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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 # 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 /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 = 'redhat-8', process_updated = TRUE, process_new = TRUE, 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)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'redhat-8', 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 - done + - xvfb-run /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 = 'redhat-8', 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)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "rhel8", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'rhel8', 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'))" || true - done - name: Purge CDN cache image: reg.devxy.io/docker.io/library/alpine:3.24 diff --git a/.crow/process-updates-redhat-9-amd64.yaml b/.crow/process-updates-redhat-9-amd64.yaml index 063f978..bf2b54e 100644 --- a/.crow/process-updates-redhat-9-amd64.yaml +++ b/.crow/process-updates-redhat-9-amd64.yaml @@ -53,26 +53,12 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run /opt/R/$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 = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE, process_removed = TRUE, r_minor_detection = 'classifier', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, r_minor_detection = 'classifier', r_minor_sensitive_only = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true - done + - xvfb-run /opt/R/$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 = $INTERVAL, platform = 'redhat-9', process_updated = TRUE, process_new = TRUE, process_removed = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "rhel9", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'rhel9', 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'))" || true - done backend_options: kubernetes: resources: diff --git a/.crow/process-updates-redhat-9-arm64.yaml b/.crow/process-updates-redhat-9-arm64.yaml index 327a22a..0356998 100644 --- a/.crow/process-updates-redhat-9-arm64.yaml +++ b/.crow/process-updates-redhat-9-arm64.yaml @@ -51,26 +51,12 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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 # 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 /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 = 'redhat-9', process_updated = TRUE, process_new = TRUE, 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)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'redhat-9', 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 - done + - xvfb-run /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 = 'redhat-9', 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)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "rhel9", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'rhel9', 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'))" || true - done - name: Purge CDN cache image: reg.devxy.io/docker.io/library/alpine:3.24 diff --git a/.crow/process-updates-ubuntu-2204-amd64.yaml b/.crow/process-updates-ubuntu-2204-amd64.yaml index 7d00e9e..8940c70 100644 --- a/.crow/process-updates-ubuntu-2204-amd64.yaml +++ b/.crow/process-updates-ubuntu-2204-amd64.yaml @@ -53,26 +53,12 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run /opt/R/$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 = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = TRUE, process_removed = TRUE, r_minor_detection = 'classifier', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, r_minor_detection = 'classifier', r_minor_sensitive_only = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true - done + - xvfb-run /opt/R/$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 = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = TRUE, process_removed = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "jammy", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'jammy', 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'))" || true - done backend_options: kubernetes: resources: diff --git a/.crow/process-updates-ubuntu-2204-arm64.yaml b/.crow/process-updates-ubuntu-2204-arm64.yaml index 7728e63..2757c68 100644 --- a/.crow/process-updates-ubuntu-2204-arm64.yaml +++ b/.crow/process-updates-ubuntu-2204-arm64.yaml @@ -51,26 +51,12 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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 # 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 /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(global = TRUE); options(future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', process_updated = TRUE, process_new = TRUE, 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)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', 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 - done + - xvfb-run /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(global = TRUE); options(future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2204', 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)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "jammy", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'jammy', 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'))" || true - done - name: Purge CDN cache image: reg.devxy.io/docker.io/library/alpine:3.24 diff --git a/.crow/process-updates-ubuntu-2404-amd64.yaml b/.crow/process-updates-ubuntu-2404-amd64.yaml index 58f5be5..3dd25c9 100644 --- a/.crow/process-updates-ubuntu-2404-amd64.yaml +++ b/.crow/process-updates-ubuntu-2404-amd64.yaml @@ -52,26 +52,12 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise - - xvfb-run /opt/R/$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(global = TRUE); options(future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', process_updated = TRUE, process_new = TRUE, process_removed = TRUE, r_minor_detection = 'classifier', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, r_minor_detection = 'classifier', r_minor_sensitive_only = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true - done + - xvfb-run /opt/R/$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(global = TRUE); options(future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', process_updated = TRUE, process_new = TRUE, process_removed = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "noble", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'noble', 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'))" || true - done backend_options: kubernetes: resources: diff --git a/.crow/process-updates-ubuntu-2404-arm64.yaml b/.crow/process-updates-ubuntu-2404-arm64.yaml index 5da7620..69027ae 100644 --- a/.crow/process-updates-ubuntu-2404-arm64.yaml +++ b/.crow/process-updates-ubuntu-2404-arm64.yaml @@ -51,26 +51,12 @@ 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-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 - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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 # 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 /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 = 'ubuntu-2404', process_updated = TRUE, process_new = TRUE, 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)" - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'ubuntu-2404', 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 - done + - xvfb-run /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 = 'ubuntu-2404', 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)" - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "noble", 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"))' - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - "$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'noble', 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'))" || true - done - name: Purge CDN cache image: reg.devxy.io/docker.io/library/alpine:3.24 diff --git a/.crow/weekly-rebuild-missing-alpine-322-amd64.yaml b/.crow/weekly-rebuild-missing-alpine-322-amd64.yaml index e7b3904..ba7735c 100644 --- a/.crow/weekly-rebuild-missing-alpine-322-amd64.yaml +++ b/.crow/weekly-rebuild-missing-alpine-322-amd64.yaml @@ -39,7 +39,7 @@ 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/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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")' diff --git a/.crow/weekly-rebuild-missing-alpine-322-arm64.yaml b/.crow/weekly-rebuild-missing-alpine-322-arm64.yaml index 26624c4..076b267 100644 --- a/.crow/weekly-rebuild-missing-alpine-322-arm64.yaml +++ b/.crow/weekly-rebuild-missing-alpine-322-arm64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - rm -rf /mnt/cache/R-pkgs/00LOCK-* - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak("httr2")' diff --git a/.crow/weekly-rebuild-missing-alpine-323-amd64.yaml b/.crow/weekly-rebuild-missing-alpine-323-amd64.yaml index 2b05036..e6f95c2 100644 --- a/.crow/weekly-rebuild-missing-alpine-323-amd64.yaml +++ b/.crow/weekly-rebuild-missing-alpine-323-amd64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$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/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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")' diff --git a/.crow/weekly-rebuild-missing-alpine-323-arm64.yaml b/.crow/weekly-rebuild-missing-alpine-323-arm64.yaml index 8c87a02..5c1e732 100644 --- a/.crow/weekly-rebuild-missing-alpine-323-arm64.yaml +++ b/.crow/weekly-rebuild-missing-alpine-323-arm64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - rm -rf /mnt/cache/R-pkgs/00LOCK-* - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak("httr2")' diff --git a/.crow/weekly-rebuild-missing-redhat-10-amd64.yaml b/.crow/weekly-rebuild-missing-redhat-10-amd64.yaml index 87e21f0..6a70915 100644 --- a/.crow/weekly-rebuild-missing-redhat-10-amd64.yaml +++ b/.crow/weekly-rebuild-missing-redhat-10-amd64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$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/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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")' diff --git a/.crow/weekly-rebuild-missing-redhat-10-arm64.yaml b/.crow/weekly-rebuild-missing-redhat-10-arm64.yaml index 2b2cf88..dae5001 100644 --- a/.crow/weekly-rebuild-missing-redhat-10-arm64.yaml +++ b/.crow/weekly-rebuild-missing-redhat-10-arm64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - rm -rf /mnt/cache/R-pkgs/00LOCK-* - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak("httr2")' diff --git a/.crow/weekly-rebuild-missing-redhat-8-amd64.yaml b/.crow/weekly-rebuild-missing-redhat-8-amd64.yaml index 4ef638e..33326d2 100644 --- a/.crow/weekly-rebuild-missing-redhat-8-amd64.yaml +++ b/.crow/weekly-rebuild-missing-redhat-8-amd64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$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/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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")' diff --git a/.crow/weekly-rebuild-missing-redhat-8-arm64.yaml b/.crow/weekly-rebuild-missing-redhat-8-arm64.yaml index d02673b..fee0bb3 100644 --- a/.crow/weekly-rebuild-missing-redhat-8-arm64.yaml +++ b/.crow/weekly-rebuild-missing-redhat-8-arm64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - rm -rf /mnt/cache/R-pkgs/00LOCK-* - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak("httr2")' diff --git a/.crow/weekly-rebuild-missing-redhat-9-amd64.yaml b/.crow/weekly-rebuild-missing-redhat-9-amd64.yaml index c857116..b78dd37 100644 --- a/.crow/weekly-rebuild-missing-redhat-9-amd64.yaml +++ b/.crow/weekly-rebuild-missing-redhat-9-amd64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$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/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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")' diff --git a/.crow/weekly-rebuild-missing-redhat-9-arm64.yaml b/.crow/weekly-rebuild-missing-redhat-9-arm64.yaml index c7968ba..d339587 100644 --- a/.crow/weekly-rebuild-missing-redhat-9-arm64.yaml +++ b/.crow/weekly-rebuild-missing-redhat-9-arm64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - rm -rf /mnt/cache/R-pkgs/00LOCK-* - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak("httr2")' diff --git a/.crow/weekly-rebuild-missing-ubuntu-2204-amd64.yaml b/.crow/weekly-rebuild-missing-ubuntu-2204-amd64.yaml index 6a2d625..ee5c094 100644 --- a/.crow/weekly-rebuild-missing-ubuntu-2204-amd64.yaml +++ b/.crow/weekly-rebuild-missing-ubuntu-2204-amd64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$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/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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")' diff --git a/.crow/weekly-rebuild-missing-ubuntu-2204-arm64.yaml b/.crow/weekly-rebuild-missing-ubuntu-2204-arm64.yaml index d14c278..40b3b71 100644 --- a/.crow/weekly-rebuild-missing-ubuntu-2204-arm64.yaml +++ b/.crow/weekly-rebuild-missing-ubuntu-2204-arm64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - rm -rf /mnt/cache/R-pkgs/00LOCK-* - - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak("httr2")' diff --git a/.crow/weekly-rebuild-missing-ubuntu-2404-amd64.yaml b/.crow/weekly-rebuild-missing-ubuntu-2404-amd64.yaml index e9002f8..973b7c9 100644 --- a/.crow/weekly-rebuild-missing-ubuntu-2404-amd64.yaml +++ b/.crow/weekly-rebuild-missing-ubuntu-2404-amd64.yaml @@ -39,7 +39,7 @@ steps: - git clone -q https://pat-s:$$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/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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")' diff --git a/.crow/weekly-rebuild-missing-ubuntu-2404-arm64.yaml b/.crow/weekly-rebuild-missing-ubuntu-2404-arm64.yaml index 1f17c45..eaf0a94 100644 --- a/.crow/weekly-rebuild-missing-ubuntu-2404-arm64.yaml +++ b/.crow/weekly-rebuild-missing-ubuntu-2404-arm64.yaml @@ -39,7 +39,7 @@ 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/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")' + - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.1.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.1.1")' - /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/$R_VERSION/bin/R -q -e 'pak::pak("httr2")' diff --git a/.editorconfig b/.editorconfig index 82fac74..734c5ee 100644 --- a/.editorconfig +++ b/.editorconfig @@ -11,10 +11,6 @@ insert_final_newline = true [*.md] trim_trailing_whitespace = false -# Markdown code fences hold verbatim content (logs, snippets) whose -# indentation must not be forced to the source indent rules. -indent_style = unset -indent_size = unset # Ignore paths [/collections/ansible_collections/community/**] diff --git a/.editorconfig-checker.json b/.editorconfig-checker.json deleted file mode 100644 index f7abef3..0000000 --- a/.editorconfig-checker.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "Exclude": ["^LICENSE\\.md$", "^benchmark/", "^docker/reprex/"] -} diff --git a/.markdownlint-cli2.yaml b/.markdownlint-cli2.yaml deleted file mode 100644 index 66e7cc8..0000000 --- a/.markdownlint-cli2.yaml +++ /dev/null @@ -1,4 +0,0 @@ -# Rules live in .markdownlint.yaml; this file only sets cli2 options. -ignores: - - LICENSE.md - - docs/superpowers/** diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml deleted file mode 100644 index c7edc32..0000000 --- a/.pre-commit-config.yaml +++ /dev/null @@ -1,45 +0,0 @@ -# cSpell:ignore autofix autoupdate -# Excluded: verbatim GPL license and auxiliary shell scripts with intentional -# in-string formatting (reformatting would corrupt their output). -exclude: | - (?x)^( - LICENSE\.md| - benchmark/| - docker/reprex/ - ) -repos: - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v6.0.0 - hooks: - - id: end-of-file-fixer - - id: trailing-whitespace - args: - - --markdown-linebreak-ext=md - - repo: https://github.com/DavidAnson/markdownlint-cli2 - rev: v0.22.1 - hooks: - - id: markdownlint-cli2 - - repo: https://github.com/rbubley/mirrors-prettier - rev: v3.8.4 - hooks: - - id: prettier - - repo: https://github.com/posit-dev/air-pre-commit - rev: 0.8.2 - hooks: - - id: air-format - - repo: https://github.com/editorconfig-checker/editorconfig-checker - rev: v3.7.0 - hooks: - - id: editorconfig-checker - - repo: https://github.com/adrienverge/yamllint.git - rev: v1.38.0 - hooks: - - id: yamllint - args: [--strict, -c=.yamllint.yaml] - - repo: local - hooks: - - id: yaml-file-extension - name: Check if YAML files has *.yaml extension. - entry: YAML filenames must have .yaml extension. - language: fail - files: .yml$ diff --git a/.prettierignore b/.prettierignore deleted file mode 100644 index 0e4b780..0000000 --- a/.prettierignore +++ /dev/null @@ -1 +0,0 @@ -LICENSE.md diff --git a/.yamllint.yaml b/.yamllint.yaml deleted file mode 100644 index d0370a3..0000000 --- a/.yamllint.yaml +++ /dev/null @@ -1,19 +0,0 @@ -rules: - comments: - require-starting-space: false - ignore-shebangs: true - min-spaces-from-content: 1 - braces: - min-spaces-inside-empty: 0 - max-spaces-inside-empty: 0 - min-spaces-inside: 0 - max-spaces-inside: 1 - document-start: - present: false - indentation: - spaces: 2 - indent-sequences: true - # .crow/* workflows embed long single-line R commands (>1k chars) - line-length: disable - new-lines: - type: unix diff --git a/README.md b/README.md index 278a475..fd03609 100644 --- a/README.md +++ b/README.md @@ -186,19 +186,19 @@ Below is a collection of raw errors observed during the build process:
-```text +``` * installing to library '/tmp/Rtmp7WPw19/temp_libpath114b846b58'\n* installing *source* package 'ade4' ...\n** using staged installation\nERROR: a 'NAMESPACE' file is required\n* removing '/tmp/Rtmp7WPw19/temp_libpath114b846b58/ade4'\n" ``` Tag does not have a NAMESPACE file and hence cannot be built. -```text +``` "* installing to library '/tmp/RtmpLcCitS/temp_libpath1146aabbe92'\nERROR: dependency 'tripack' is not available for package 'alphahull'\n* removing '/tmp/RtmpLcCitS/temp_libpath1146aabbe92/alphahull'\n" ``` Dependency not available: Either because the dependency was not declared or errored itself during installation. -```text +``` In function '\033[01m\033[KRcpp::List solveRRBLUP(const mat&, const mat&, const mat&)\033[m\033[K':\n\033[01m\033[KMME.cpp:162:61:\033[m\033[K \033[01;31m\033[Kerror: \033[m\033[K'\033[01m\033[KPI\033[m\033[K' was not declared in this scope\n 162 | double ll = -0.5*(double(optRes[\"objective\"])+df+df*log(2*\033[01;31m\033[KPI\033[m\033[K/df));\n | \033[01;31m\033[K^~\033[m\033[K\n\033[01m\033[KMME.cpp:\033[m\033[K In function '\033[01m\033[KRcpp::List solveRRBLUPMV(const mat&, const mat&, const mat&, int, double)\033[m\033[K':\n\033[01m\033[KMME.cpp:277:31:\033[m\033[K \033[01;31m\033[Kerror: \033[m\033[K'\033[01m\033[KPI\033[m\033[K' was not declared in this scope; did you mean '\033[01m\033[KHI\033[m\033[K'?\n 277 | ll -= double(n*m)/2.0*log(2*\033[01;31m\033[KPI\033[m\033[K);\n | \033[01;31m\033[K^~\033[m\033[K\n | \033[32m\033[KHI\033[m\033[K\nmake: *** [/opt/R/4.4.1/lib/R/etc/Makeconf:204: MME.o] Error 1\nERROR: compilation failed for package 'AlphaSimR'\n* removing '/tmp/RtmpclI5CE/temp_libpath11135d215d5/AlphaSimR'\n ``` @@ -230,26 +230,26 @@ For others it might be due to exotic external dependencies which require manual Help in resolving these issues are highly welcome! -| Name | Platform | Arch | Reason | Date Created | Date Solved | -| ------------- | -------------- | ------- | -------------------------------- | ------------ | ----------- | -| Apollonius | redhat-8 | | gmp missing | 2024-11-15 | | -| doBy | alpine-320 | amd | hangs | 2024-11-23 | | -| later | ubuntu 22 & 24 | amd | hangs for early versions - xfvb? | 2024-11-23 | | -| CoTiMA | ubuntu 22 & 24 | amd | OOM? | 2024-11-23 | | -| FrF2 | alpine | arm | hangs | 2024-11-23 | | -| FrF2.catlg128 | alpine | arm | hangs | 2024-11-23 | | -| DoE.base | alpine | arm/amd | hangs | 2024-11-23 | | -| eha | alpine | amd | hangs | 2024-11-23 | | -| gRain | alpine | amd | hangs | 2024-11-23 | | -| gRbase | alpine | amd | hangs | 2024-11-24 | | -| IDPmisc | alpine | amd | hangs | 2024-11-24 | | -| RVAideMemoire | alpine | amd | hangs | 2024-11-25 | | -| pbkrtest | alpine | arm | hangs | 2024-11-25 | | -| seewave | alpine | arm | hangs | 2024-11-25 | | -| spdep | alpine | arm | hangs | 2024-12-03 | | -| compareGroups | alpine | arm | hangs | 2024-12-11 | | -| SNPassoc | alpine | arm | hangs | 2024-12-11 | | -| surveillance | alpine | arm | hangs | 2024-12-13 | | +| Name | Platform | Arch | Reason | Solved via | Date Created | Date Solved | +| ------------- | -------------- | ------- | -------------------------------- | ---------- | ------------ | ----------- | +| Apollonius | redhat-8 | | gmp missing | 2024-11-15 | | +| doBy | alpine-320 | amd | hangs | 2024-11-23 | | +| later | ubuntu 22 & 24 | amd | hangs for early versions - xfvb? | 2024-11-23 | | +| CoTiMA | ubuntu 22 & 24 | amd | OOM? | 2024-11-23 | | +| FrF2 | alpine | arm | hangs | 2024-11-23 | | +| FrF2.catlg128 | alpine | arm | hangs | 2024-11-23 | | +| DoE.base | alpine | arm/amd | hangs | 2024-11-23 | | +| eha | alpine | amd | hangs | 2024-11-23 | | +| gRain | alpine | amd | hangs | 2024-11-23 | | +| gRbase | alpine | amd | hangs | 2024-11-24 | | +| IDPmisc | alpine | amd | hangs | 2024-11-24 | | +| RVAideMemoire | alpine | amd | hangs | 2024-11-25 | | +| pbkrtest | alpine | arm | hangs | 2024-11-25 | | +| seewave | alpine | arm | hangs | 2024-11-25 | | +| spdep | alpine | arm | hangs | 2024-12-03 | | +| compareGroups | alpine | arm | hangs | 2024-12-11 | | +| SNPassoc | alpine | arm | hangs | 2024-12-11 | | +| surveillance | alpine | arm | hangs | 2024-12-13 | | ## CDN Settings diff --git a/local/archive-missed-pkgs.R b/local/archive-missed-pkgs.R index f817c3e..57e92d7 100644 --- a/local/archive-missed-pkgs.R +++ b/local/archive-missed-pkgs.R @@ -11,34 +11,16 @@ s3fs::s3_file_system( arch = "arm64" os = "alpine321" -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/%s/%s/latest/src/contrib", - arch, - os -)) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/%s/%s/latest/src/contrib", arch, os)) length(unique(sapply(strsplit(basename(files), "_"), function(x) x[1]))) -non_archived = unique(sapply(strsplit(basename(files), "_"), function(x) { - x[1] -})[duplicated(sapply(strsplit(basename(files), "_"), function(x) x[1]))]) +non_archived = unique(sapply(strsplit(basename(files), "_"), function(x) x[1])[duplicated(sapply(strsplit(basename(files), "_"), function(x) x[1]))]) # RInno is not built because it only exists for Windows non_archived = setdiff(non_archived, "RInno") # future::plan("sequential", workers = 8) future::plan("sequential", workers = 1) # future.apply::future_lapply(non_archived, function(x) archive_package(x, codename = os, arch = arch)) -lapply(non_archived, function(x) { - archive_package( - x, - codename = os, - arch = arch, - s3_region = "hel1", - s3_endpoint = "https://hel1.your-objectstorage.com", - s3_bucket = "devxy-r-package-binaries-hel1", - s3_access_key_id = Sys.getenv( - "HETZNER_S3_ACCESS_KEY_K3S", - s3_secret_access_key = Sys.getenv("HETZNER_S3_SECRET_KEY_K3S") - ) - ) -}) +lapply(non_archived, function(x) archive_package(x, codename = os, arch = arch, s3_region = "hel1", s3_endpoint = "https://hel1.your-objectstorage.com", s3_bucket = "devxy-r-package-binaries-hel1", s3_access_key_id = Sys.getenv("HETZNER_S3_ACCESS_KEY_K3S", s3_secret_access_key = Sys.getenv("HETZNER_S3_SECRET_KEY_K3S")))) # archive_package() + # grep("duckdb_", files, value = T) diff --git a/local/build-all.R b/local/build-all.R index 4e7b44e..102d18c 100644 --- a/local/build-all.R +++ b/local/build-all.R @@ -1,13 +1,10 @@ sink(stdout(), type = "message") options(crayon.enabled = TRUE, future.globals.onReference = NULL) -source(file.path("local", "r-minor-helpers.R")) args <- commandArgs(trailingOnly = TRUE) -parsed <- parse_build_args(args) -split_into <- parsed$split_into -split_index <- parsed$split_index -ncpus <- parsed$ncpus -sensitive_only <- parsed$sensitive_only +split_into <- as.integer(args[1]) +split_index <- as.integer(args[2]) +ncpus <- as.integer(args[3]) options(Ncpus = ncpus) # Load bincraft eagerly to avoid lazy-load memory spike during first build call @@ -15,20 +12,9 @@ library(bincraft, quietly = TRUE) library(future) plan("sequential") -pkgs <- if (sensitive_only) { - readRDS("/mnt/cache/packages/r_minor_sensitive_pkgs.rds") -} else { - readRDS("/mnt/cache/packages/pkgs_to_build.rds") -} -# Back-compat: tolerate an older RDS without the column (treat all as non-sensitive) -if (is.null(pkgs$r_minor_sensitive)) { - pkgs$r_minor_sensitive <- FALSE -} -sprintf( - "Total# of remaining package versions: %s (sensitive_only=%s)", - nrow(pkgs), - sensitive_only -) +# Read precomputed package+version pairs +pkgs <- readRDS("/mnt/cache/packages/pkgs_to_build.rds") +sprintf("Total# of remaining package versions: %s", nrow(pkgs)) # Split into chunks for this worker chunks <- split(pkgs, cut(seq_len(nrow(pkgs)), split_into, labels = FALSE)) @@ -46,33 +32,26 @@ s3_cache <- readRDS("/mnt/cache/packages/s3_cache.rds") sprintf("S3 cache: %s files", length(s3_cache)) n <- nrow(chunk) -mapply( - function(pkg, ver, sens, i) { - cat(sprintf("[%d/%d] %s_%s (r_minor_sensitive=%s)\n", i, n, pkg, ver, sens)) - bincraft::build_binary_package( - pkg, - tag = ver, - is_r_minor_sensitive = isTRUE(sens), - 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"), - s3_package_cache = s3_cache, - 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 - ) - }, - chunk$Package, - chunk$Version, - chunk$r_minor_sensitive, - seq_len(n) -) +mapply(function(pkg, ver, i) { + cat(sprintf("[%d/%d] %s_%s\n", i, n, pkg, ver)) + bincraft::build_binary_package( + pkg, + tag = ver, + s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", + s3_region = "eu-central-003", + s3_bucket = "devxy-rpkgs-binaries", + s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), + s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"), + s3_package_cache = s3_cache, + metadata_db_host = "r-binaries.devxy.io", + metadata_db_name = "build_metadata", + metadata_db_table = "single_builds", + metadata_db_user = "rpkgs", + metadata_db_password = Sys.getenv("PGPASS"), + metadata_db_sslmode = "require", + metadata_db_port = 15432, + archive = TRUE, + upload = TRUE, + store_build_metadata = TRUE + ) +}, chunk$Package, chunk$Version, seq_len(n)) diff --git a/local/check-NA.R b/local/check-NA.R index 95c158e..7405db4 100644 --- a/local/check-NA.R +++ b/local/check-NA.R @@ -1,3 +1,4 @@ + ### Scope: Check whether there are any incomplete entries in PACKAGES.rds. These will result in NA when calling available.packages() foo = available.packages("https://cran.devxy.io/amd64/jammy/latest/src/contrib") sum((is.na(foo[, "Version"]))) @@ -16,9 +17,7 @@ foo = available.packages("https://cran.devxy.io/amd64/rhel9/latest/src/contrib") sum((is.na(foo[, "Version"]))) which((is.na(foo[, "Version"]))) -foo = available.packages( - "https://cran.devxy.io/amd64/alpine320/latest/src/contrib" -) +foo = available.packages("https://cran.devxy.io/amd64/alpine320/latest/src/contrib") sum((is.na(foo[, "Version"]))) which((is.na(foo[, "Version"]))) @@ -41,8 +40,6 @@ foo = available.packages("https://cran.devxy.io/arm64/rhel9/latest/src/contrib") sum((is.na(foo[, "Version"]))) which((is.na(foo[, "Version"]))) -foo = available.packages( - "https://cran.devxy.io/arm64/alpine320/latest/src/contrib" -) +foo = available.packages("https://cran.devxy.io/arm64/alpine320/latest/src/contrib") sum((is.na(foo[, "Version"]))) which((is.na(foo[, "Version"]))) diff --git a/local/debug-packages-writing.R b/local/debug-packages-writing.R index 533ae2b..5a0fd24 100644 --- a/local/debug-packages-writing.R +++ b/local/debug-packages-writing.R @@ -2,58 +2,42 @@ library(future) future::plan(multisession) future::plan(sequential) time = Sys.time() -files <- s3fs::s3_dir_ls( - sprintf( - "devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib/Archive" - ), - recurse = T -) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib/Archive"), recurse = T) Sys.time() - time + archive <- llply(dirs, function(dir) { - files <- list.files( - dir, - recursive = FALSE, - full.names = TRUE, - pattern = "*.tar.gz" - ) + files <- list.files(dir, recursive = FALSE, full.names = TRUE, pattern = "*.tar.gz") if (length(files) == 0) { print(paste0("Error: Empty directory: ", dir)) return(NULL) } info <- file.info(files) - tryCatch( - { - rownames(info) <- paste0(basename(dirname(files)), "/", basename(files)) - }, - error = function(e) { - print(paste0("Error: Exception catched for Archived directory: ", dir)) - print(e) - return(NULL) - } - ) + tryCatch({ + rownames(info) <- paste0(basename(dirname(files)), "/", basename(files)) + }, error = function(e) { + print(paste0("Error: Exception catched for Archived directory: ", dir)) + print(e) + return(NULL) + }) info }) -tryCatch( - { - rownames(info) <- paste0(basename(dirname(files)), "/", basename(files)) - }, - error = function(e) { - print(paste0("Error: Exception catched for Archived directory: ", dir)) - print(e) - return(NULL) - } -) +tryCatch({ + rownames(info) <- paste0(basename(dirname(files)), "/", basename(files)) +}, error = function(e) { + print(paste0("Error: Exception catched for Archived directory: ", dir)) + print(e) + return(NULL) +}) -curl::curl_download( - "https://cran.devxy.io/amd64/rhel9/latest/src/contrib/PACKAGES.db", - "PACKAGES.db" -) + + +curl::curl_download("https://cran.devxy.io/amd64/rhel9/latest/src/contrib/PACKAGES.db", "PACKAGES.db") con = DBI::dbConnect(RSQLite::SQLite(), "PACKAGES.db") df = DBI::dbReadTable(con, "packages") @@ -66,14 +50,6 @@ which(grepl("digest", df$Package)) system("cat /tmp/PACKAGES | grep '^Package: digest' | wc -l") -curl::curl_fetch_memory( - "https://cloud.r-project.org/src/contrib/Meta/archive.rds" -) -remotes = readRDS(url( - "https://cloud.r-project.org/src/contrib/Meta/archive.rds", - "rb" -)) -packages = readRDS(url( - "https://cran.devxy.io/arm64/noble/latest/src/contrib/PACKAGES.rds", - "rb" -)) +curl::curl_fetch_memory("https://cloud.r-project.org/src/contrib/Meta/archive.rds") +remotes = readRDS(url("https://cloud.r-project.org/src/contrib/Meta/archive.rds", "rb")) +packages = readRDS(url("https://cran.devxy.io/arm64/noble/latest/src/contrib/PACKAGES.rds", "rb")) diff --git a/local/detect-duplicates.R b/local/detect-duplicates.R index f7e2c18..076499d 100644 --- a/local/detect-duplicates.R +++ b/local/detect-duplicates.R @@ -37,13 +37,10 @@ future.apply::future_lapply( files <- s3fs::s3_dir_ls( sprintf( "devxy-r-package-binaries-hel1/%s/%s/latest/src/contrib", - arch, - codename + arch, codename ) ) - if (length(files) == 0) { - return(NULL) - } + if (length(files) == 0) return(NULL) files_b <- basename(files) pkg_names <- sapply(strsplit(files_b, "_"), `[`, 1) dupes <- unique(pkg_names[duplicated(pkg_names)]) diff --git a/local/excluded-packages.json b/local/excluded-packages.json index 6489998..dccfc0b 100644 --- a/local/excluded-packages.json +++ b/local/excluded-packages.json @@ -1,77 +1,77 @@ [ - { "package": "RInno", "reason": "windows-only" }, - { "package": "KeyboardSimulator", "reason": "windows-only" }, - { "package": "R2PPT", "reason": "windows-only" }, - { "package": "RWinEdt", "reason": "windows-only" }, - { "package": "blatr", "reason": "windows-only" }, - { "package": "excel.link", "reason": "windows-only" }, - { "package": "spectrino", "reason": "windows-only" }, - { "package": "taskscheduleR", "reason": "windows-only" }, - { "package": "MDSGUI", "reason": "windows-only" }, - { "package": "BiplotGUI", "reason": "windows-only" }, - { "package": "R2wd", "reason": "windows-only" }, - { "package": "rFUSION", "reason": "windows-only" }, - { "package": "MediaNews", "reason": "windows-only" }, - { "package": "doBy", "reason": "hang" }, - { "package": "IDPmisc", "reason": "hang" }, - { "package": "frailtypack", "reason": "hang" }, - { "package": "afex", "reason": "hang" }, - { "package": "FrF2", "reason": "hang" }, - { "package": "DoE.base", "reason": "hang" }, - { "package": "agricolae", "reason": "hang" }, - { "package": "doFuture", "reason": "hang" }, - { "package": "fscaret", "reason": "hang" }, - { "package": "PHYLOGR", "reason": "hang" }, - { "package": "seewave", "reason": "hang" }, - { "package": "pls", "reason": "hang" }, - { "package": "relaimpo", "reason": "hang" }, - { "package": "geepack", "reason": "hang" }, - { "package": "gggenes", "reason": "hang" }, - { "package": "NPCirc", "reason": "hang" }, - { "package": "repmis", "reason": "hang" }, - { "package": "PNDSIBGE", "reason": "hang" }, - { "package": "lidR", "reason": "hang" }, - { "package": "poismf", "reason": "hang" }, - { "package": "neonstore", "reason": "hang" }, - { "package": "MachineShop", "reason": "hang" }, - { "package": "mvst", "reason": "hang" }, - { "package": "MacBehaviour", "reason": "hang" }, - { "package": "mcmcderive", "reason": "hang" }, - { "package": "RGIFT", "reason": "hang" }, - { "package": "KnowBR", "reason": "hang" }, - { "package": "netmeta", "reason": "hang" }, - { "package": "spdep", "reason": "hang" }, - { "package": "Rfast", "reason": "hang" }, - { "package": "compareGroups", "reason": "hang" }, - { "package": "ff", "reason": "hang" }, - { "package": "GsymPoint", "reason": "hang" }, - { "package": "RcppDynProg", "reason": "hang" }, - { "package": "comtradr", "reason": "hang" }, - { "package": "FD", "reason": "hang" }, - { "package": "PearsonDS", "reason": "hang" }, - { "package": "DCluster", "reason": "hang" }, - { "package": "gRc", "reason": "hang" }, - { "package": "mixlm", "reason": "hang" }, - { "package": "geospt", "reason": "hang" }, - { "package": "fdth", "reason": "hang" }, - { "package": "ffmanova", "reason": "hang" }, - { "package": "fiery", "reason": "hang" }, - { "package": "ffscrapr", "reason": "hang" }, - { "package": "cold", "reason": "hang" }, - { "package": "RcmdrPlugin.DoE", "reason": "hang" }, - { "package": "RcmdrPlugin.NMBU", "reason": "hang" }, - { "package": "RcmdrPlugin.RiskDemo", "reason": "hang" }, - { "package": "RcmdrPlugin.ROC", "reason": "hang" }, - { "package": "RcmdrPlugin.TeachStat", "reason": "hang" }, - { "package": "RcmdrPlugin.TeachingDemos", "reason": "hang" }, - { "package": "RcmdrPlugin.UCA", "reason": "hang" }, - { "package": "RcmdrPlugin.WorldFlora", "reason": "hang" }, - { "package": "RcmdrPlugin.aRnova", "reason": "hang" }, - { "package": "RcmdrPlugin.depthTools", "reason": "hang" }, - { "package": "RcmdrPlugin.orloca", "reason": "hang" }, - { "package": "RcmdrPlugin.sos", "reason": "hang" }, - { "package": "RcmdrPlugin.survival", "reason": "hang" }, - { "package": "RcmdrPlugin.temis", "reason": "hang" }, - { "package": "GWlasso", "reason": "hang" }, - { "package": "GWmodelVis", "reason": "hang" } + {"package": "RInno", "reason": "windows-only"}, + {"package": "KeyboardSimulator", "reason": "windows-only"}, + {"package": "R2PPT", "reason": "windows-only"}, + {"package": "RWinEdt", "reason": "windows-only"}, + {"package": "blatr", "reason": "windows-only"}, + {"package": "excel.link", "reason": "windows-only"}, + {"package": "spectrino", "reason": "windows-only"}, + {"package": "taskscheduleR", "reason": "windows-only"}, + {"package": "MDSGUI", "reason": "windows-only"}, + {"package": "BiplotGUI", "reason": "windows-only"}, + {"package": "R2wd", "reason": "windows-only"}, + {"package": "rFUSION", "reason": "windows-only"}, + {"package": "MediaNews", "reason": "windows-only"}, + {"package": "doBy", "reason": "hang"}, + {"package": "IDPmisc", "reason": "hang"}, + {"package": "frailtypack", "reason": "hang"}, + {"package": "afex", "reason": "hang"}, + {"package": "FrF2", "reason": "hang"}, + {"package": "DoE.base", "reason": "hang"}, + {"package": "agricolae", "reason": "hang"}, + {"package": "doFuture", "reason": "hang"}, + {"package": "fscaret", "reason": "hang"}, + {"package": "PHYLOGR", "reason": "hang"}, + {"package": "seewave", "reason": "hang"}, + {"package": "pls", "reason": "hang"}, + {"package": "relaimpo", "reason": "hang"}, + {"package": "geepack", "reason": "hang"}, + {"package": "gggenes", "reason": "hang"}, + {"package": "NPCirc", "reason": "hang"}, + {"package": "repmis", "reason": "hang"}, + {"package": "PNDSIBGE", "reason": "hang"}, + {"package": "lidR", "reason": "hang"}, + {"package": "poismf", "reason": "hang"}, + {"package": "neonstore", "reason": "hang"}, + {"package": "MachineShop", "reason": "hang"}, + {"package": "mvst", "reason": "hang"}, + {"package": "MacBehaviour", "reason": "hang"}, + {"package": "mcmcderive", "reason": "hang"}, + {"package": "RGIFT", "reason": "hang"}, + {"package": "KnowBR", "reason": "hang"}, + {"package": "netmeta", "reason": "hang"}, + {"package": "spdep", "reason": "hang"}, + {"package": "Rfast", "reason": "hang"}, + {"package": "compareGroups", "reason": "hang"}, + {"package": "ff", "reason": "hang"}, + {"package": "GsymPoint", "reason": "hang"}, + {"package": "RcppDynProg", "reason": "hang"}, + {"package": "comtradr", "reason": "hang"}, + {"package": "FD", "reason": "hang"}, + {"package": "PearsonDS", "reason": "hang"}, + {"package": "DCluster", "reason": "hang"}, + {"package": "gRc", "reason": "hang"}, + {"package": "mixlm", "reason": "hang"}, + {"package": "geospt", "reason": "hang"}, + {"package": "fdth", "reason": "hang"}, + {"package": "ffmanova", "reason": "hang"}, + {"package": "fiery", "reason": "hang"}, + {"package": "ffscrapr", "reason": "hang"}, + {"package": "cold", "reason": "hang"}, + {"package": "RcmdrPlugin.DoE", "reason": "hang"}, + {"package": "RcmdrPlugin.NMBU", "reason": "hang"}, + {"package": "RcmdrPlugin.RiskDemo", "reason": "hang"}, + {"package": "RcmdrPlugin.ROC", "reason": "hang"}, + {"package": "RcmdrPlugin.TeachStat", "reason": "hang"}, + {"package": "RcmdrPlugin.TeachingDemos", "reason": "hang"}, + {"package": "RcmdrPlugin.UCA", "reason": "hang"}, + {"package": "RcmdrPlugin.WorldFlora", "reason": "hang"}, + {"package": "RcmdrPlugin.aRnova", "reason": "hang"}, + {"package": "RcmdrPlugin.depthTools", "reason": "hang"}, + {"package": "RcmdrPlugin.orloca", "reason": "hang"}, + {"package": "RcmdrPlugin.sos", "reason": "hang"}, + {"package": "RcmdrPlugin.survival", "reason": "hang"}, + {"package": "RcmdrPlugin.temis", "reason": "hang"}, + {"package": "GWlasso", "reason": "hang"}, + {"package": "GWmodelVis", "reason": "hang"} ] diff --git a/local/fetch-rebuild-packages-from-issue.R b/local/fetch-rebuild-packages-from-issue.R index 26e544d..d944dd0 100644 --- a/local/fetch-rebuild-packages-from-issue.R +++ b/local/fetch-rebuild-packages-from-issue.R @@ -1,21 +1,15 @@ library(httr2, quietly = TRUE) forgejo_base <- "https://git.devxy.io/api/v1" -repo <- "devxy/build-cran-binaries" -platform <- Sys.getenv("PLATFORM") -arch <- Sys.getenv("ARCH") -token <- Sys.getenv("FORGEJO_TOKEN") -output_file <- Sys.getenv("REBUILD_PKG_LIST", "/tmp/rebuild_pkgs.txt") +repo <- "devxy/build-cran-binaries" +platform <- Sys.getenv("PLATFORM") +arch <- Sys.getenv("ARCH") +token <- Sys.getenv("FORGEJO_TOKEN") +output_file <- Sys.getenv("REBUILD_PKG_LIST", "/tmp/rebuild_pkgs.txt") -if (nchar(platform) == 0) { - stop("PLATFORM env var is not set") -} -if (nchar(arch) == 0) { - stop("ARCH env var is not set") -} -if (nchar(token) == 0) { - stop("FORGEJO_TOKEN env var is not set") -} +if (nchar(platform) == 0) stop("PLATFORM env var is not set") +if (nchar(arch) == 0) stop("ARCH env var is not set") +if (nchar(token) == 0) stop("FORGEJO_TOKEN env var is not set") os_family <- if (grepl("^ubuntu", platform)) { "Ubuntu" @@ -27,16 +21,12 @@ os_family <- if (grepl("^ubuntu", platform)) { platform } -issue_title <- sprintf( - "Missing package binaries for latest version (%s)", - os_family -) +issue_title <- sprintf("Missing package binaries for latest version (%s)", os_family) cat(sprintf("Searching for issue: %s\n", issue_title)) search_url <- sprintf( "%s/repos/%s/issues?type=issues&state=open&q=%s&limit=50", - forgejo_base, - repo, + forgejo_base, repo, utils::URLencode(issue_title, reserved = TRUE) ) search_resp <- request(search_url) |> @@ -44,9 +34,7 @@ search_resp <- request(search_url) |> req_perform() issues <- resp_body_json(search_resp, simplifyVector = FALSE) -match_idx <- which( - vapply(issues, function(x) x$title, character(1)) == issue_title -) +match_idx <- which(vapply(issues, function(x) x$title, character(1)) == issue_title) if (length(match_idx) == 0) { cat("No matching issue found - nothing to rebuild\n") @@ -67,10 +55,7 @@ lines <- strsplit(body, "\n", fixed = TRUE)[[1]] plat_header <- sprintf("## %s", platform) plat_idx <- which(lines == plat_header) if (length(plat_idx) == 0) { - cat(sprintf( - "No section found for platform %s - nothing to rebuild\n", - platform - )) + cat(sprintf("No section found for platform %s - nothing to rebuild\n", platform)) writeLines(character(0), output_file) q("no") } @@ -79,11 +64,7 @@ if (length(plat_idx) == 0) { arch_pattern <- sprintf("^### %s ", arch) arch_idx <- which(grepl(arch_pattern, lines) & seq_along(lines) > plat_idx[1]) if (length(arch_idx) == 0) { - cat(sprintf( - "No section found for arch %s under %s - nothing to rebuild\n", - arch, - platform - )) + cat(sprintf("No section found for arch %s under %s - nothing to rebuild\n", arch, platform)) writeLines(character(0), output_file) q("no") } @@ -101,11 +82,6 @@ pkg_lines <- section_lines[grepl("^- ", section_lines)] pkgs <- sub("^- ([^ ]+) \\(.*\\)$", "\\1", pkg_lines) pkgs <- pkgs[nchar(pkgs) > 0 & pkgs != "_None_"] -cat(sprintf( - "Found %d rebuildable packages for %s/%s\n", - length(pkgs), - platform, - arch -)) +cat(sprintf("Found %d rebuildable packages for %s/%s\n", length(pkgs), platform, arch)) writeLines(pkgs, output_file) cat(sprintf("Wrote package list to %s\n", output_file)) diff --git a/local/label-removed-cran-packages.R b/local/label-removed-cran-packages.R index 12dff9d..92cd940 100644 --- a/local/label-removed-cran-packages.R +++ b/local/label-removed-cran-packages.R @@ -6,13 +6,9 @@ archived <- quickcode::archivedPkg() |> pull(name) # Query all distinct pkgs in the DB -con <- DBI::dbConnect( - RPostgres::Postgres(), - dbname = "build_metadata", - host = "r-binaries.devxy.io", - port = 15432, - user = "r_binaries", - password = Sys.getenv("PGPASS"), +con <- DBI::dbConnect(RPostgres::Postgres(), + dbname = "build_metadata", host = "r-binaries.devxy.io", + port = 15432, user = "r_binaries", password = Sys.getenv("PGPASS"), sslmode = "require" ) @@ -26,9 +22,7 @@ to_process <- pkgs_db[pkgs_db %in% archived] # for all matches, set 'removed = TRUE' sapply(to_process, function(.x) { - DBI::dbExecute( - con, - "UPDATE single_builds SET removed = 'TRUE' where name = $1", + DBI::dbExecute(con, "UPDATE single_builds SET removed = 'TRUE' where name = $1", params = list(.x) ) }) diff --git a/local/last-processed-by-platform.R b/local/last-processed-by-platform.R index 398b6c1..f913610 100644 --- a/local/last-processed-by-platform.R +++ b/local/last-processed-by-platform.R @@ -7,4 +7,4 @@ query_metadata_table() |> group_by(platform, arch) |> arrange(desc(timestamp)) |> select(name, timestamp) |> - filter(row_number() == 1) + filter(row_number()==1) diff --git a/local/missing-cran-packages-db.R b/local/missing-cran-packages-db.R index 882bca4..56b3d94 100644 --- a/local/missing-cran-packages-db.R +++ b/local/missing-cran-packages-db.R @@ -3,34 +3,22 @@ library(bincraft) library(dplyr) library(DBI) -con <- DBI::dbConnect( - RPostgres::Postgres(), - dbname = "build_metadata", - host = "r-binaries.devxy.io", - port = 15432, - user = "r_binaries", - password = Sys.getenv("PGPASS"), +con <- DBI::dbConnect(RPostgres::Postgres(), + dbname = "build_metadata", host = "r-binaries.devxy.io", + port = 15432, user = "r_binaries", password = Sys.getenv("PGPASS"), sslmode = "require" ) `%nin%` <- Negate(`%in%`) -new_packages <- get_new_cran_packages(lubridate::interval( - lubridate::today(), - lubridate::today() - 2 -))$name -removed_pkgs <- get_removed_cran_packages(lubridate::interval( - lubridate::today(), - lubridate::today() - 2 -))$name +new_packages <- get_new_cran_packages(lubridate::interval(lubridate::today(), lubridate::today() - 2))$name +removed_pkgs <- get_removed_cran_packages(lubridate::interval(lubridate::today(), lubridate::today() - 2))$name # filter windows packages # filter new packages from the last X days -cran_pkgs <- unique( - tools::CRAN_package_db() |> - filter(`OS_type` != "windows" | is.na(`OS_type`)) |> - filter(`Package` %nin% new_packages) |> - pull(Package) -) +cran_pkgs <- unique(tools::CRAN_package_db() |> + filter(`OS_type` != "windows" | is.na(`OS_type`)) |> + filter(`Package` %nin% new_packages) |> + pull(Package)) arch <- "arm64" platform <- "redhat-8" @@ -40,24 +28,13 @@ platform <- "alpine-321" platform <- "ubuntu-2204" platform <- "ubuntu-2404" -data <- dbGetQuery( - con, - "SELECT name FROM single_builds WHERE platform = $1 AND arch = $2 and removed = FALSE;", - params = list(platform, arch) -) -removed_pkgs = get_removed_cran_packages(lubridate::interval( - lubridate::today(), - lubridate::today() - 2 -))$name +data <- dbGetQuery(con, "SELECT name FROM single_builds WHERE platform = $1 AND arch = $2 and removed = FALSE;", params = list(platform, arch)) +removed_pkgs = get_removed_cran_packages(lubridate::interval(lubridate::today(), lubridate::today() - 2))$name pkgs_db <- unique(data$name) pkgs_db = setdiff(pkgs_db, removed_pkgs) pkgs <- setdiff(cran_pkgs, pkgs_db) -formatted_pkgs <- gsub( - '"', - "'", - capture.output(dput(as.character(na.omit(pkgs[1:length(pkgs)])))) -) +formatted_pkgs <- gsub('"', "'", capture.output(dput(as.character(na.omit(pkgs[1:length(pkgs)]))))) formatted_pkgs_one_line <- paste(formatted_pkgs, collapse = " ") cat(formatted_pkgs_one_line, "\n", sep = "") @@ -67,6 +44,7 @@ clipr::write_clip(formatted_pkgs_one_line) # sapply(pkgs, function(x) which(grepl(sprintf("^%s$", x), cran_pkgs))) + s3fs::s3_file_system( aws_access_key_id = Sys.getenv("HETZNER_S3_ACCESS_KEY_K3S"), aws_secret_access_key = Sys.getenv("HETZNER_S3_SECRET_KEY_K3S"), diff --git a/local/missing-cran-packages.R b/local/missing-cran-packages.R index ca5cad8..ab71b5b 100644 --- a/local/missing-cran-packages.R +++ b/local/missing-cran-packages.R @@ -10,39 +10,19 @@ s3fs::s3_file_system( ) s3fs::s3_dir_ls("s3://devxy-r-package-binaries") -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/jammy/latest/src/contrib" -)) # done -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib" -)) # done -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib" -)) # done -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib" -)) # done -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib" -)) # done +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/jammy/latest/src/contrib")) # done +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib")) # done +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib")) # done +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib")) # done +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib")) # done -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib" -)) # done -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib" -)) # done -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib" -)) # done -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib" -)) # done -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib" -)) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib")) # done +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib")) # done +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib")) # done +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib")) # done +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib")) -files_b = basename(files) +files_b=basename(files) files_b_split = sapply(strsplit(basename(files_b), "_"), function(x) x[1]) cran_pkgs <- tools::CRAN_package_db() |> @@ -50,11 +30,7 @@ cran_pkgs <- tools::CRAN_package_db() |> pull(Package) pkgs = setdiff(cran_pkgs, files_b_split) -formatted_pkgs <- gsub( - '"', - "'", - capture.output(dput(as.character(na.omit(pkgs[1:900])))) -) +formatted_pkgs <- gsub('"', "'", capture.output(dput(as.character(na.omit(pkgs[1:900]))))) formatted_pkgs_one_line <- paste(formatted_pkgs, collapse = " ") cat(formatted_pkgs_one_line, "\n", sep = "") diff --git a/local/missing-packages-in-index.R b/local/missing-packages-in-index.R index 6453888..810c89d 100644 --- a/local/missing-packages-in-index.R +++ b/local/missing-packages-in-index.R @@ -7,109 +7,42 @@ s3fs::s3_file_system( region_name = "hel1", ) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/jammy/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib" -)) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/jammy/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib")) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib" -)) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib")) -files_b = basename(files) +files_b=basename(files) files_b_split = sapply(strsplit(basename(files_b), "_"), function(x) x[1]) -files_b_split = setdiff( - files_b_split, - c("PACKAGES", "PACKAGES.gz", "PACKAGES.rds", "PACKAGES.db", "Archive") -) +files_b_split = setdiff(files_b_split, c("PACKAGES", "PACKAGES.gz", "PACKAGES.rds", "PACKAGES.db", "Archive")) # windows-only -files_b_split = setdiff( - files_b_split, - c( - "PACKAGES", - "PACKAGES.gz", - "PACKAGES.rds", - "PACKAGES.db", - "Archive", - "RInno", - "KeyboardSimulator", - "R2PPT", - "RWinEdt", - "blatr", - "excel.link", - "spectrino", - "taskscheduleR", - "MDSGUI", - "BiplotGUI", - "R2wd" - ) -) -pkgs_index = available.packages( - "https://cran.devxy.io/amd64/jammy/latest/src/contrib" -)[, "Package"] -pkgs_index_b = basename(pkgs_index) +files_b_split = setdiff(files_b_split, c("PACKAGES", "PACKAGES.gz", "PACKAGES.rds", "PACKAGES.db", "Archive", "RInno", "KeyboardSimulator", "R2PPT", "RWinEdt", "blatr", "excel.link", "spectrino", "taskscheduleR", "MDSGUI", "BiplotGUI", "R2wd")) +pkgs_index = available.packages("https://cran.devxy.io/amd64/jammy/latest/src/contrib")[, "Package"] +pkgs_index_b=basename(pkgs_index) if (length(files_b_split) != length(pkgs_index_b)) { pkgs_missing = setdiff(files_b_split, pkgs_index_b) message("Packages missing in index but present in S3:") pkgs_missing - formatted_pkgs <- gsub( - '"', - "'", - capture.output(dput(as.character(na.omit(pkgs_missing[1:900])))) - ) + formatted_pkgs <- gsub('"', "'", capture.output(dput(as.character(na.omit(pkgs_missing[1:900]))))) formatted_pkgs_one_line <- paste(formatted_pkgs, collapse = " ") cat(formatted_pkgs_one_line, "\n", sep = "") } -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib" -)) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib")) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib" -)) -files <- s3fs::s3_dir_ls(sprintf( - "devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib" -)) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib")) +files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib")) diff --git a/local/packages-to-build.R b/local/packages-to-build.R index 7a3652d..91ee96e 100644 --- a/local/packages-to-build.R +++ b/local/packages-to-build.R @@ -17,11 +17,7 @@ suppressPackageStartupMessages(library(data.table)) arch = Sys.getenv("ARCH") # target: alpine-322, ubuntu-2404, redhat-9, etc. -platform = paste( - Sys.getenv("OS"), - gsub("[.]", "", Sys.getenv("OS_VERSION")), - sep = "-" -) +platform = paste(Sys.getenv("OS"), gsub("[.]", "", Sys.getenv("OS_VERSION")), sep = "-") # Use bincraft's codename detection for S3 paths (e.g. "rhel10" not "redhat10") codename = bincraft::set_codename(NULL) @@ -38,9 +34,7 @@ con <- DBI::dbConnect( cran_archive = tools::CRAN_archive_db() cran_release = tools::CRAN_package_db() # Subset cran_archive to only those packages -cran_archive_in_release <- cran_archive[ - names(cran_archive) %in% cran_release$Package -] +cran_archive_in_release <- cran_archive[names(cran_archive) %in% cran_release$Package] archive_versions <- rbindlist( lapply(names(cran_archive), function(pkg) { @@ -132,15 +126,11 @@ query_error <- function(pkg, ver) { # Fetch all relevant columns from the database errored_pkgs <- DBI::dbGetQuery( con, - sprintf( - "SELECT name, tag FROM single_builds WHERE error_occurred = TRUE and platform='%s' and arch='%s'", - platform, - arch - ) + sprintf("SELECT name, tag FROM single_builds WHERE error_occurred = TRUE and platform='%s' and arch='%s'", platform, arch) ) errored_pkgs <- as.data.table(errored_pkgs) setkey(pkgs_to_build, Package, Version) -setnames(errored_pkgs, c("Package", "Version")) +setnames(errored_pkgs, c("Package","Version")) setkey(errored_pkgs, Package, Version) ### Final subsetting @@ -150,62 +140,3 @@ pkgs <- pkgs_no_error[!s3_dt] # Deduplicate pkgs <- unique(pkgs) setorder(pkgs, Package, Version) - -### R-minor sensitivity (classify once per package, applied to all versions) -source(file.path("local", "r-minor-helpers.R")) -risky_deps <- bincraft::abi_risky_linking_deps() - -release_meta <- data.table( - Package = cran_release$Package, - NeedsCompilation = cran_release$NeedsCompilation, - LinkingTo = cran_release$LinkingTo -) - -meta <- release_meta[Package %in% unique(pkgs$Package)] -meta[, - triage := mapply( - classify_from_metadata, - NeedsCompilation, - LinkingTo, - MoreArgs = list(risky_deps = risky_deps) - ) -] - -# Only the "ambiguous" compiled packages need a source grep. -ambiguous <- meta[triage == "ambiguous", Package] -sensitive_ambiguous <- character() -if (length(ambiguous) > 0L) { - tmp_src <- file.path(tempdir(), "abi_src") - dir.create(tmp_src, showWarnings = FALSE, recursive = TRUE) - sens <- vapply( - ambiguous, - function(pkg) { - out <- tryCatch( - { - dl <- utils::download.packages( - pkg, - destdir = tmp_src, - repos = "https://cloud.r-project.org", - quiet = TRUE - ) - isTRUE(as.logical(bincraft::needs_per_minor_recompile(dl[1L, 2L]))) - }, - error = function(e) TRUE - ) # fail safe: treat as sensitive - out - }, - logical(1L) - ) - sensitive_ambiguous <- ambiguous[sens] -} - -sensitive_pkgs <- unique(c( - meta[triage == "sensitive", Package], - sensitive_ambiguous -)) -pkgs[, r_minor_sensitive := Package %in% sensitive_pkgs] -sprintf( - "R-minor-sensitive packages: %s of %s", - length(sensitive_pkgs), - uniqueN(pkgs$Package) -) diff --git a/local/packages-without-any-binary.R b/local/packages-without-any-binary.R index f42196f..a6994ad 100644 --- a/local/packages-without-any-binary.R +++ b/local/packages-without-any-binary.R @@ -1,24 +1,17 @@ ### Lists packages without any successful binaries, i.e. pkgs for which all builds errored (per platform & arch) library(DBI) library(dplyr) -con <- DBI::dbConnect( - RPostgres::Postgres(), - dbname = "build_metadata", - host = "r-binaries.devxy.io", - port = 15432, - user = "r_binaries", - password = Sys.getenv("PGPASS"), +con <- DBI::dbConnect(RPostgres::Postgres(), + dbname = "build_metadata", host = "r-binaries.devxy.io", + port = 15432, user = "r_binaries", password = Sys.getenv("PGPASS"), sslmode = "require" ) -cran_pkgs <- tools::CRAN_package_db() |> - filter(`Date/Publication` <= "2024-12-02") |> +cran_pkgs <- tools::CRAN_package_db() |> + filter(`Date/Publication` <= "2024-12-02") |> pull(Package) -data <- dbGetQuery( - con, - "SELECT name,platform,arch,removed,error_occurred FROM single_builds;" -) +data <- dbGetQuery(con, "SELECT name,platform,arch,removed,error_occurred FROM single_builds;") pkgs <- data |> filter(platform == "alpine-320", arch == "arm64") |> @@ -29,11 +22,7 @@ pkgs <- data |> pkgs = setdiff(cran_pkgs, pkgs) # Format, remove line breaks, and print as a single line -formatted_pkgs <- gsub( - '"', - "'", - capture.output(dput(as.character(na.omit(pkgs[1:900])))) -) +formatted_pkgs <- gsub('"', "'", capture.output(dput(as.character(na.omit(pkgs[1:900]))))) formatted_pkgs_one_line <- paste(formatted_pkgs, collapse = " ") diff --git a/local/r-minor-helpers.R b/local/r-minor-helpers.R index 65aafdf..ffe56fb 100644 --- a/local/r-minor-helpers.R +++ b/local/r-minor-helpers.R @@ -20,14 +20,3 @@ classify_from_metadata <- function(needs_compilation, linking_to, risky_deps) { } "ambiguous" } - -parse_build_args <- function(args) { - sensitive_only <- "--sensitive-only" %in% args - pos <- args[!startsWith(args, "--")] - list( - sensitive_only = sensitive_only, - split_into = as.integer(pos[1L]), - split_index = as.integer(pos[2L]), - ncpus = as.integer(pos[3L]) - ) -} diff --git a/local/tests/test-build-all-args.R b/local/tests/test-build-all-args.R deleted file mode 100644 index 3308fc3..0000000 --- a/local/tests/test-build-all-args.R +++ /dev/null @@ -1,13 +0,0 @@ -source(file.path("..", "r-minor-helpers.R")) - -test_that("parse_build_args splits flags from positionals", { - a <- parse_build_args(c("--sensitive-only", "4", "2", "8")) - expect_true(a$sensitive_only) - expect_identical(a$split_into, 4L) - expect_identical(a$split_index, 2L) - expect_identical(a$ncpus, 8L) - - b <- parse_build_args(c("4", "2", "8")) - expect_false(b$sensitive_only) - expect_identical(b$split_into, 4L) -}) diff --git a/local/tests/test-r-minor-helpers.R b/local/tests/test-r-minor-helpers.R index ac7b0a6..d68e99b 100644 --- a/local/tests/test-r-minor-helpers.R +++ b/local/tests/test-r-minor-helpers.R @@ -2,27 +2,15 @@ source(file.path("..", "r-minor-helpers.R")) test_that("pure-r (NeedsCompilation != yes) is not sensitive", { expect_identical(classify_from_metadata("no", NA, c("Rcpp")), "not-sensitive") - expect_identical( - classify_from_metadata("", "Rcpp", c("Rcpp")), - "not-sensitive" - ) + expect_identical(classify_from_metadata("", "Rcpp", c("Rcpp")), "not-sensitive") }) test_that("LinkingTo a risky dep is sensitive (version constraints stripped)", { - expect_identical( - classify_from_metadata("yes", "Rcpp (>= 1.0)", c("Rcpp")), - "sensitive" - ) - expect_identical( - classify_from_metadata("yes", "R6,\n cpp11", c("Rcpp", "cpp11")), - "sensitive" - ) + expect_identical(classify_from_metadata("yes", "Rcpp (>= 1.0)", c("Rcpp")), "sensitive") + expect_identical(classify_from_metadata("yes", "R6,\n cpp11", c("Rcpp", "cpp11")), "sensitive") }) test_that("compiled but no risky LinkingTo is ambiguous (needs source)", { - expect_identical( - classify_from_metadata("yes", "R6", c("Rcpp", "cpp11")), - "ambiguous" - ) + expect_identical(classify_from_metadata("yes", "R6", c("Rcpp", "cpp11")), "ambiguous") expect_identical(classify_from_metadata("yes", NA, c("Rcpp")), "ambiguous") }) diff --git a/local/weekly-missing-binaries-audit.R b/local/weekly-missing-binaries-audit.R index 6b32037..c6b67e5 100644 --- a/local/weekly-missing-binaries-audit.R +++ b/local/weekly-missing-binaries-audit.R @@ -15,14 +15,10 @@ library(httr2, quietly = TRUE) # Environment / config # --------------------------------------------------------------------------- platform <- Sys.getenv("PLATFORM") -arch <- Sys.getenv("ARCH") +arch <- Sys.getenv("ARCH") -if (nchar(platform) == 0) { - stop("PLATFORM env var is not set") -} -if (nchar(arch) == 0) { - stop("ARCH env var is not set") -} +if (nchar(platform) == 0) stop("PLATFORM env var is not set") +if (nchar(arch) == 0) stop("ARCH env var is not set") # Map platform names to S3 codenames s3_codename <- gsub("-", "", platform) @@ -41,13 +37,8 @@ os_family <- if (grepl("^ubuntu", platform)) { platform } -cat(sprintf( - "Platform: %s | Arch: %s | S3 codename: %s | OS family: %s\n", - platform, - arch, - s3_codename, - os_family -)) +cat(sprintf("Platform: %s | Arch: %s | S3 codename: %s | OS family: %s\n", + platform, arch, s3_codename, os_family)) # --------------------------------------------------------------------------- # 1. Query PostgreSQL for known build failures (before s3fs init to avoid @@ -56,20 +47,19 @@ cat(sprintf( cat("Connecting to PostgreSQL...\n") con <- DBI::dbConnect( RPostgres::Postgres(), - dbname = "build_metadata", - host = "r-binaries.devxy.io", - port = 15432, - user = "rpkgs", + dbname = "build_metadata", + host = "r-binaries.devxy.io", + port = 15432, + user = "rpkgs", password = Sys.getenv("PGPASS"), - sslmode = "require" + 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 + platform, arch ) ) DBI::dbDisconnect(con) @@ -79,12 +69,7 @@ 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 -)) +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) @@ -101,36 +86,28 @@ cran_dt <- data.table( # --------------------------------------------------------------------------- cat("Connecting to S3...\n") s3fs::s3_file_system( - aws_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), + aws_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), aws_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"), - endpoint = "https://s3.eu-central-003.backblazeb2.com", - region_name = "eu-central-003", - refresh = TRUE + endpoint = "https://s3.eu-central-003.backblazeb2.com", + region_name = "eu-central-003", + refresh = TRUE ) -s3_path <- sprintf( - "devxy-rpkgs-binaries/%s/%s/latest/src/contrib", - arch, - s3_codename -) +s3_path <- sprintf("devxy-rpkgs-binaries/%s/%s/latest/src/contrib", arch, s3_codename) cat(sprintf("Listing S3 path: %s\n", s3_path)) s3_pkgs <- tryCatch( s3fs::s3_dir_ls(s3_path, recurse = FALSE), error = function(e) { - cat(sprintf( - "WARNING: Could not list S3 path %s: %s\n", - s3_path, - conditionMessage(e) - )) + cat(sprintf("WARNING: Could not list S3 path %s: %s\n", s3_path, conditionMessage(e))) character(0) } ) file_names <- basename(s3_pkgs) -matches <- regexec("^([A-Za-z0-9.]+)_([0-9][^/]*)\\.tar\\.gz$", file_names) -parts <- regmatches(file_names, matches) -parts <- parts[sapply(parts, length) == 3] +matches <- regexec("^([A-Za-z0-9.]+)_([0-9][^/]*)\\.tar\\.gz$", file_names) +parts <- regmatches(file_names, matches) +parts <- parts[sapply(parts, length) == 3] if (length(parts) == 0) { s3_dt <- data.table(Package = character(0), Version = character(0)) } else { @@ -140,18 +117,13 @@ if (length(parts) == 0) { ) } -cat(sprintf( - "S3 contains %d tarballs for %s/%s\n", - nrow(s3_dt), - arch, - s3_codename -)) +cat(sprintf("S3 contains %d tarballs for %s/%s\n", nrow(s3_dt), arch, s3_codename)) # --------------------------------------------------------------------------- # 4. Find missing packages (CRAN release version not in S3) # --------------------------------------------------------------------------- setkey(cran_dt, Package, Version) -setkey(s3_dt, Package, Version) +setkey(s3_dt, Package, Version) missing_dt <- cran_dt[!s3_dt] cat(sprintf("%d CRAN release packages missing from S3\n", nrow(missing_dt))) @@ -160,15 +132,9 @@ cat(sprintf("%d CRAN release packages missing from S3\n", nrow(missing_dt))) # --------------------------------------------------------------------------- script_dir <- tryCatch( dirname(normalizePath( - if (exists("ofile", envir = sys.frame(1), inherits = FALSE)) { - sys.frame(1)$ofile - } else { - commandArgs(trailingOnly = FALSE)[grepl( - "--file=", - commandArgs(trailingOnly = FALSE) - )] |> - sub("--file=", "", x = _) - }, + if (exists("ofile", envir = sys.frame(1), inherits = FALSE)) sys.frame(1)$ofile + else commandArgs(trailingOnly = FALSE)[grepl("--file=", commandArgs(trailingOnly = FALSE))] |> + sub("--file=", "", x = _), mustWork = FALSE )), error = function(e) "local" @@ -177,23 +143,13 @@ excluded_path <- file.path(script_dir, "excluded-packages.json") excluded_pkgs <- data.table(package = character(0), reason = character(0)) if (file.exists(excluded_path)) { - excluded_raw <- jsonlite::fromJSON(excluded_path) + excluded_raw <- jsonlite::fromJSON(excluded_path) excluded_pkgs <- as.data.table(excluded_raw) - cat(sprintf( - "Loaded %d excluded packages from %s\n", - nrow(excluded_pkgs), - excluded_path - )) + cat(sprintf("Loaded %d excluded packages from %s\n", nrow(excluded_pkgs), excluded_path)) missing_dt <- missing_dt[!Package %in% excluded_pkgs$package] - cat(sprintf( - "%d packages remain after removing exclusions\n", - nrow(missing_dt) - )) + cat(sprintf("%d packages remain after removing exclusions\n", nrow(missing_dt))) } else { - cat(sprintf( - "No excluded-packages.json found at %s -- skipping exclusion step\n", - excluded_path - )) + cat(sprintf("No excluded-packages.json found at %s -- skipping exclusion step\n", excluded_path)) } # --------------------------------------------------------------------------- @@ -201,34 +157,24 @@ if (file.exists(excluded_path)) { # --------------------------------------------------------------------------- if (nrow(errored_dt) > 0) { known_failures_dt <- missing_dt[errored_dt, nomatch = 0] - rebuildable_dt <- missing_dt[!errored_dt] + rebuildable_dt <- missing_dt[!errored_dt] } else { known_failures_dt <- missing_dt[0] - rebuildable_dt <- missing_dt + rebuildable_dt <- missing_dt } -cat(sprintf( - "Rebuildable: %d | Known failures: %d\n", - nrow(rebuildable_dt), - nrow(known_failures_dt) -)) +cat(sprintf("Rebuildable: %d | Known failures: %d\n", + nrow(rebuildable_dt), nrow(known_failures_dt))) # --------------------------------------------------------------------------- # 7. Write rebuildable package names to cache RDS # --------------------------------------------------------------------------- -cache_dir <- "/mnt/cache/packages" -cache_file <- file.path( - cache_dir, - sprintf("weekly_rebuild_%s_%s.rds", platform, arch) -) +cache_dir <- "/mnt/cache/packages" +cache_file <- file.path(cache_dir, sprintf("weekly_rebuild_%s_%s.rds", platform, arch)) if (dir.exists(cache_dir)) { saveRDS(rebuildable_dt$Package, cache_file) - cat(sprintf( - "Wrote %d rebuildable packages to %s\n", - nrow(rebuildable_dt), - cache_file - )) + cat(sprintf("Wrote %d rebuildable packages to %s\n", nrow(rebuildable_dt), cache_file)) } else { cat(sprintf("Cache dir %s does not exist -- skipping RDS write\n", cache_dir)) } @@ -240,47 +186,29 @@ forgejo_token <- Sys.getenv("FORGEJO_TOKEN") if (nchar(forgejo_token) == 0) { cat("FORGEJO_TOKEN not set -- skipping issue update\n") } else { - issue_title <- sprintf( - "Missing package binaries for latest version (%s)", - os_family - ) + issue_title <- sprintf("Missing package binaries for latest version (%s)", os_family) - n_missing <- nrow(missing_dt) - n_rebuild <- nrow(rebuildable_dt) + n_missing <- nrow(missing_dt) + n_rebuild <- nrow(rebuildable_dt) - arch_lines <- sprintf( - "### %s (%d missing, %d to rebuild)", - arch, - n_missing, - n_rebuild - ) + arch_lines <- sprintf("### %s (%d missing, %d to rebuild)", arch, n_missing, n_rebuild) if (nrow(rebuildable_dt) > 0) { - arch_lines <- c( - arch_lines, + arch_lines <- c(arch_lines, paste0("- ", rebuildable_dt$Package, " (", rebuildable_dt$Version, ")") ) } else { arch_lines <- c(arch_lines, "_None_") } if (nrow(known_failures_dt) > 0) { - arch_lines <- c( - arch_lines, + arch_lines <- c(arch_lines, "", "#### Known build failures", - paste0( - "- ", - known_failures_dt$Package, - " (", - known_failures_dt$Version, - ")" - ) + paste0("- ", known_failures_dt$Package, " (", known_failures_dt$Version, ")") ) } build_excluded_footer <- function() { - if (nrow(excluded_pkgs) == 0) { - return(character(0)) - } + if (nrow(excluded_pkgs) == 0) return(character(0)) entries <- paste( paste0(excluded_pkgs$package, " (", excluded_pkgs$reason, ")"), collapse = ", " @@ -289,12 +217,11 @@ if (nchar(forgejo_token) == 0) { } forgejo_base <- "https://git.devxy.io/api/v1" - repo <- "devxy/build-cran-binaries" + repo <- "devxy/build-cran-binaries" search_url <- sprintf( "%s/repos/%s/issues?type=issues&state=open&q=%s&limit=50", - forgejo_base, - repo, + forgejo_base, repo, utils::URLencode(issue_title, reserved = TRUE) ) search_resp <- httr2::request(search_url) |> @@ -303,19 +230,15 @@ if (nchar(forgejo_token) == 0) { existing_issues <- httr2::resp_body_json(search_resp, simplifyVector = FALSE) - match_idx <- which( - sapply(existing_issues, function(x) x$title) == issue_title - ) + match_idx <- which(sapply(existing_issues, function(x) x$title) == issue_title) today_str <- format(Sys.Date(), "%Y-%m-%d") if (length(match_idx) > 0) { # ---- Update existing issue ---- issue_number <- existing_issues[[match_idx[1]]]$number - old_body <- existing_issues[[match_idx[1]]]$body - if (is.null(old_body)) { - old_body <- "" - } + old_body <- existing_issues[[match_idx[1]]]$body + if (is.null(old_body)) old_body <- "" lines <- strsplit(old_body, "\n", fixed = TRUE)[[1]] @@ -335,11 +258,7 @@ if (nchar(forgejo_token) == 0) { if (length(plat_idx) == 0) { # Platform section missing -- insert before --- footer footer_idx <- which(lines == "---") - insert_at <- if (length(footer_idx) > 0) { - footer_idx[length(footer_idx)] - } else { - length(lines) + 1 - } + insert_at <- if (length(footer_idx) > 0) footer_idx[length(footer_idx)] else length(lines) + 1 new_plat_block <- c(sprintf("## %s", platform), "", arch_lines, "") lines <- c( @@ -352,14 +271,10 @@ if (nchar(forgejo_token) == 0) { # End of platform section: next ## or --- at a higher level, or EOF next_section <- which(grepl("^## |^---", lines) & seq_along(lines) > pi) - plat_end <- if (length(next_section) > 0) { - next_section[1] - 1 - } else { - length(lines) - } + plat_end <- if (length(next_section) > 0) next_section[1] - 1 else length(lines) - plat_lines <- lines[seq(pi, plat_end)] - arch_local_idx <- which(plat_lines == arch_header) + plat_lines <- lines[seq(pi, plat_end)] + arch_local_idx <- which(plat_lines == arch_header) if (length(arch_local_idx) == 0) { # Append arch subsection at end of platform block @@ -370,13 +285,11 @@ if (nchar(forgejo_token) == 0) { lines[seq(plat_end + 1, length(lines))] ) } else { - ai <- pi + arch_local_idx[1] - 1 # absolute line index + ai <- pi + arch_local_idx[1] - 1 # absolute line index # End of arch subsection - next_arch <- which( - grepl("^### |^## |^---", lines) & seq_along(lines) > ai - ) - arch_end <- if (length(next_arch) > 0) next_arch[1] - 1 else plat_end + next_arch <- which(grepl("^### |^## |^---", lines) & seq_along(lines) > ai) + arch_end <- if (length(next_arch) > 0) next_arch[1] - 1 else plat_end lines <- c( lines[seq_len(ai - 1)], @@ -389,12 +302,8 @@ if (nchar(forgejo_token) == 0) { # Rebuild excluded footer excl_hdr_idx <- which(lines == "## Excluded packages") if (length(excl_hdr_idx) > 0) { - pre_dash <- which(lines == "---" & seq_along(lines) < excl_hdr_idx[1]) - remove_from <- if (length(pre_dash) > 0) { - pre_dash[length(pre_dash)] - } else { - excl_hdr_idx[1] - } + pre_dash <- which(lines == "---" & seq_along(lines) < excl_hdr_idx[1]) + remove_from <- if (length(pre_dash) > 0) pre_dash[length(pre_dash)] else excl_hdr_idx[1] lines <- lines[seq_len(remove_from - 1)] } footer <- build_excluded_footer() @@ -404,15 +313,10 @@ if (nchar(forgejo_token) == 0) { new_body <- paste(lines, collapse = "\n") - patch_url <- sprintf( - "%s/repos/%s/issues/%d", - forgejo_base, - repo, - issue_number - ) + patch_url <- sprintf("%s/repos/%s/issues/%d", forgejo_base, repo, issue_number) httr2::request(patch_url) |> httr2::req_headers( - Authorization = paste("token", forgejo_token), + Authorization = paste("token", forgejo_token), `Content-Type` = "application/json" ) |> httr2::req_body_json(list(body = new_body)) |> @@ -420,6 +324,7 @@ if (nchar(forgejo_token) == 0) { httr2::req_perform() cat(sprintf("Updated Forgejo issue #%d: %s\n", issue_number, issue_title)) + } else { # ---- Create new issue ---- body_lines <- c( @@ -437,21 +342,17 @@ if (nchar(forgejo_token) == 0) { post_url <- sprintf("%s/repos/%s/issues", forgejo_base, repo) create_resp <- httr2::request(post_url) |> httr2::req_headers( - Authorization = paste("token", forgejo_token), + Authorization = paste("token", forgejo_token), `Content-Type` = "application/json" ) |> httr2::req_body_json(list( title = issue_title, - body = paste(body_lines, collapse = "\n") + body = paste(body_lines, collapse = "\n") )) |> httr2::req_perform() new_issue <- httr2::resp_body_json(create_resp) - cat(sprintf( - "Created Forgejo issue #%d: %s\n", - new_issue$number, - issue_title - )) + cat(sprintf("Created Forgejo issue #%d: %s\n", new_issue$number, issue_title)) } } diff --git a/renovate.json b/renovate.json index 53c7306..97ca6ad 100644 --- a/renovate.json +++ b/renovate.json @@ -1,7 +1,11 @@ { "$schema": "https://docs.renovatebot.com/renovate-schema.json", - "extends": ["local>devxy/renovate-config"], - "ignorePaths": ["docker/**"], + "extends": [ + "local>devxy/renovate-config" + ], + "ignorePaths": [ + "docker/**" + ], "customManagers": [ { "customType": "regex",