refactor: move bincraft install to separate pre-matrix pipeline step

Adds build-all-versions-install-deps pipeline that runs once before the matrix builds, cleaning stale locks and installing bincraft to the shared cache without contention.

.crow/build-all-versions-amd64.yaml

@@ -33,8 +33,8 @@ matrix:
       SPLIT_INDEX: 5
       BACKEND: kubernetes
 
-# depends_on:
-#   - build-all-versions-install-deps
+depends_on:
+  - build-all-versions-install-deps
 
 steps:
   - name: 'Build binaries'
@@ -57,21 +57,18 @@ steps:
       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_LIBS_USER: /tmp/R-libs:/mnt/cache/R-pkgs
+      R_LIBS_USER: /mnt/cache/R-pkgs
       CCACHE_DIR: /mnt/cache/ccache
       NCPUS: 2
     volumes:
       - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
     commands:
       - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
-      - rm -rf /mnt/cache/R-pkgs/00LOCK-*
-      - mkdir -p /tmp/R-libs
-      - git clone -q https://codefloe.com/rpkgs/bincraft.git /tmp/bincraft && R CMD INSTALL --library=/tmp/R-libs /tmp/bincraft && R -q -e 'packageVersion("bincraft")'
       - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       # Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'rFUSION', 'MediaNews', 'rFUSION', 'MediaNews'
       # pkgs = readRDS('/mnt/cache/pkgs_amd64.rds');
       - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run)
-      - $XVFB -- R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); source('local/packages-to-build.R'); sprintf('Total# of remaining packages:%s', length(pkgs)); pkgs <- split(pkgs, cut(seq_along(pkgs), $SPLIT_INTO, labels = F))[[$SPLIT_INDEX]]; sprintf('# of packages for this job:%s', length(pkgs)); pkgs = setdiff(pkgs, c('RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'rFUSION', 'MediaNews', 'doBy', 'IDPmisc', 'frailtypack', 'afex', 'FrF2', 'DoE.base', 'agricolae', 'doFuture', 'fscaret', 'PHYLOGR', 'seewave', 'pls', 'relaimpo', 'geepack', 'gggenes', 'NPCirc', 'repmis', 'PNDSIBGE', 'lidR', 'poismf', 'neonstore', 'MachineShop', 'mvst', 'MacBehaviour', 'mcmcderive', 'RGIFT', 'KnowBR', 'netmeta', 'spdep', 'Rfast', 'compareGroups', 'ff', 'GsymPoint', 'RcppDynProg', 'comtradr', 'RcppDynProg', 'FD', 'PearsonDS', 'DCluster', 'gRc', 'mixlm', 'geospt', 'fdth', 'ffmanova', 'fiery', 'ffscrapr', 'cold', 'fiery', 'RcmdrPlugin.DoE', 'RcmdrPlugin.NMBU', 'RcmdrPlugin.RiskDemo', 'RcmdrPlugin.TeachStat', 'RcmdrPlugin.TeachingDemos', 'RcmdrPlugin.UCA', 'RcmdrPlugin.WorldFlora', 'RcmdrPlugin.aRnova', 'RcmdrPlugin.depthTools', 'RcmdrPlugin.orloca', 'RcmdrPlugin.sos', 'RcmdrPlugin.survival', 'RcmdrPlugin.temis', 'GWlasso', 'GWmodelVis')); foo = lapply(pkgs, function(x) bincraft::build_binary_package(x, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', tag_limit = 5L, 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
+      - $XVFB -- R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); source('local/packages-to-build.R'); sprintf('Total# of remaining packages:%s', length(pkgs)); pkgs <- split(pkgs, cut(seq_along(pkgs), $SPLIT_INTO, labels = F))[[$SPLIT_INDEX]]; sprintf('# of packages for this job:%s', length(pkgs)); pkgs = setdiff(pkgs, c('RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'rFUSION', 'MediaNews', 'doBy', 'IDPmisc', 'frailtypack', 'afex', 'FrF2', 'DoE.base', 'agricolae', 'doFuture', 'fscaret', 'PHYLOGR', 'seewave', 'pls', 'relaimpo', 'geepack', 'gggenes', 'NPCirc', 'repmis', 'PNDSIBGE', 'lidR', 'poismf', 'neonstore', 'MachineShop', 'mvst', 'MacBehaviour', 'mcmcderive', 'RGIFT', 'KnowBR', 'netmeta', 'spdep', 'Rfast', 'compareGroups', 'ff', 'GsymPoint', 'RcppDynProg', 'comtradr', 'RcppDynProg', 'FD', 'PearsonDS', 'DCluster', 'gRc', 'mixlm', 'geospt', 'fdth', 'ffmanova', 'fiery', 'ffscrapr', 'cold', 'fiery', 'RcmdrPlugin.DoE', 'RcmdrPlugin.NMBU', 'RcmdrPlugin.RiskDemo', 'RcmdrPlugin.TeachStat', 'RcmdrPlugin.TeachingDemos', 'RcmdrPlugin.UCA', 'RcmdrPlugin.WorldFlora', 'RcmdrPlugin.aRnova', 'RcmdrPlugin.depthTools', 'RcmdrPlugin.orloca', 'RcmdrPlugin.sos', 'RcmdrPlugin.survival', 'RcmdrPlugin.temis', 'GWlasso', 'GWmodelVis')); library(future); plan('multisession'); foo = lapply(pkgs, function(x) bincraft::build_binary_package(x, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', tag_limit = 5L, 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
       # archive missed packages
       - R -q -e "bincraft::process_unarchived_pkgs(paste(Sys.getenv('OS'), Sys.getenv('OS_VERSION')), Sys.getenv('ARCH'), workers = $NCPUS)"
     backend_options:

.crow/build-all-versions-install-deps.yaml

@@ -0,0 +1,48 @@
+when:
+  - event: manual
+    evaluate: 'task == "build-all-amd64" || task == "build-all-arm64"'
+
+skip_clone: true
+
+labels:
+  platform: linux/${ARCH}
+  agent: artemis
+
+steps:
+  - name: 'Install deps and bincraft'
+    image: reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}-${R_VERSION}
+    pull: true
+    environment:
+      REPO_RO_TOKEN:
+        from_secret: REPO_RO_TOKEN
+      GITHUB_PAT:
+        from_secret: GITHUB_PAT
+      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      R_LIBS_USER: /mnt/cache/R-pkgs
+      CCACHE_DIR: /mnt/cache/ccache
+    volumes:
+      - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
+    commands:
+      - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft
+      - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
+      - git clone -q https://codefloe.com/rpkgs/bincraft.git /tmp/bincraft
+      - R -q -e 'pak::local_install("/tmp/bincraft"); packageVersion("bincraft")'
+    backend_options:
+      docker:
+        resources:
+          requests:
+            memory: 5Gi
+            cpu: 1000m
+      kubernetes:
+        resources:
+          requests:
+            memory: 5Gi
+            cpu: 1000m
+        nodeSelector:
+          kubernetes.io/arch: ${ARCH}
+          node.kubernetes.io/instance-type: ${K8S_INSTANCE_TYPE}
+        tolerations:
+          - key: 'CI'
+            operator: 'Equal'
+            value: 'true'
+            effect: 'NoSchedule'