reprocess packages without history

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

@@ -80,7 +80,7 @@ steps:
       - 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'
-      - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); source('local/packages-to-build.R'); pkgs = bincraft::get_missing_pkgs_db('alpine-322', 'amd64'); 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', 'sf', 'Rfast', 'compareGroups', 'ff', 'GsymPoint', 'RcppDynProg', 'comtradr', 'RcppDynProg', 'FD', 'PearsonDS', 'DCluster', 'gRc', 'mixlm', 'geospt', 'fdth', 'ffmanova', 'fiery', 'ffscrapr', 'cold', 'fiery', 'RcmdrPlugin.DoE', 'RcmdrPlugin.NMBU')); library(future); plan('multisession'); foo = lapply(pkgs, function(x) bincraft::build_binary_package(x, is_debug = FALSE, force = TRUE, s3_endpoint = 'https://hel1.your-objectstorage.com', s3_region = 'hel1', 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'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE))"
+      - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); source('local/packages-to-build.R'); pkgs = readRDS('/mnt/cache/pkgs_amd64.rds'); 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', 'sf', 'Rfast', 'compareGroups', 'ff', 'GsymPoint', 'RcppDynProg', 'comtradr', 'RcppDynProg', 'FD', 'PearsonDS', 'DCluster', 'gRc', 'mixlm', 'geospt', 'fdth', 'ffmanova', 'fiery', 'ffscrapr', 'cold', 'fiery', 'RcmdrPlugin.DoE', 'RcmdrPlugin.NMBU')); library(future); plan('multisession'); foo = lapply(pkgs, function(x) bincraft::build_binary_package(x, is_debug = FALSE, force = TRUE, s3_endpoint = 'https://hel1.your-objectstorage.com', s3_region = 'hel1', 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'), 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))"
     backend_options:
       docker:
         resources:

.crow/build-all-versions-arm64.yaml

@@ -3,8 +3,10 @@
 # OS (alpine)
 # OS_VERSION (3.22)
 # R_VERSION (4.5)
-# woodpecker-cli pipeline create --var ARCH=arm64 --var OS=alpine --var OS_VERSION=3.22 --var R_VERSION=4.5 --var task=build-all-arm64 --var K8S_INSTANCE_TYPE=cax41 --branch=main --var SKIP_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', 'sf', 'Rfast', 'compareGroups', 'ff', 'GsymPoint', 'RcppDynProg', 'comtradr', 'RcppDynProg', 'FD', 'PearsonDS', 'DCluster', 'gRc', 'mixlm', 'geospt', 'fdth', 'ffmanova', 'fiery', 'ffscrapr', 'cold', 'fiery', 'RcmdrPlugin.DoE', 'RcmdrPlugin.NMBU') --log-level=info 7
+# echo "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','sf','Rfast','compareGroups','ff','GsymPoint','RcppDynProg','comtradr','RcppDynProg','FD','PearsonDS','DCluster','gRc','mixlm','geospt','fdth','ffmanova','fiery','ffscrapr','cold','fiery','RcmdrPlugin.DoE','RcmdrPlugin.NMBU')" | base64
-# woodpecker-cli pipeline create --var ARCH=arm64 --var OS=redhat --var OS_VERSION=10 --var R_VERSION=4.5 --var task=build-all-arm64 --var K8S_INSTANCE_TYPE=cax41 --var SKIP_PKGS=c(RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'rFUSION', 'MediaNews', 'rFUSION') --branch=main --log-level=info 7
+# woodpecker-cli pipeline create --var ARCH=arm64 --var OS=alpine --var OS_VERSION=3.22 --var R_VERSION=4.5 --var task=build-all-arm64 --var K8S_INSTANCE_TYPE=cax41 --branch=main --var SKIP_PKGS=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 --log-level=info 7
+# woodpecker-cli pipeline create --var ARCH=arm64 --var OS=redhat --var OS_VERSION=10 --var R_VERSION=4.5 --var task=build-all-arm64 --var K8S_INSTANCE_TYPE=cax41 --var SKIP_PKGS="c('RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'rFUSION', 'MediaNews', 'rFUSION')" --branch=main --log-level=info 7
+# woodpecker-cli pipeline create --var ARCH=arm64 --var OS=alpine --var OS_VERSION=3.22 --var R_VERSION=4.5 --var task=build-all-arm64 --var K8S_INSTANCE_TYPE=cax41 --branch=main --log-level=info 7
 when:
   - event: manual
     evaluate: 'task == "build-all-arm64"'
@@ -34,18 +36,18 @@ matrix:
     - SPLIT_INTO: 5
       SPLIT_INDEX: 1
       BACKEND: docker
-    # - SPLIT_INTO: 5
+    - SPLIT_INTO: 5
-    #   SPLIT_INDEX: 2
+      SPLIT_INDEX: 2
-    #   BACKEND: docker
+      BACKEND: docker
-    # - SPLIT_INTO: 5
+    - SPLIT_INTO: 5
-    #   SPLIT_INDEX: 3
+      SPLIT_INDEX: 3
-    #   BACKEND: docker
+      BACKEND: docker
-    # - SPLIT_INTO: 5
+    - SPLIT_INTO: 5
-    #   SPLIT_INDEX: 4
+      SPLIT_INDEX: 4
-    #   BACKEND: docker
+      BACKEND: docker
-    # - SPLIT_INTO: 5
+    - SPLIT_INTO: 5
-    #   SPLIT_INDEX: 5
+      SPLIT_INDEX: 5
-    #   BACKEND: docker
+      BACKEND: docker
 
 # depends_on:
 #   - build-all-versions-install-deps
@@ -82,7 +84,7 @@ steps:
       - R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraft.git", dependencies = TRUE)'
       - R -q -e 'packageVersion("bincraft")'
       - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
-      - xvfb-run 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, $SKIP_PKGS); library(future); plan('multisession'); foo = lapply(pkgs, function(x) bincraft::build_binary_package(x, is_debug = FALSE, force = TRUE, s3_endpoint = 'https://hel1.your-objectstorage.com', s3_region = 'hel1', 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'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE));"
+      - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); source('local/packages-to-build.R'); pkgs = readRDS('/mnt/cache/pkgs_arm64.rds'); 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','sf','Rfast','compareGroups','ff','GsymPoint','RcppDynProg','comtradr','RcppDynProg','FD','PearsonDS','DCluster','gRc','mixlm','geospt','fdth','ffmanova','fiery','ffscrapr','cold','fiery','RcmdrPlugin.DoE','RcmdrPlugin.NMBU')); library(future); plan('multisession'); foo = lapply(pkgs, function(x) bincraft::build_binary_package(x, is_debug = FALSE, force = TRUE, s3_endpoint = 'https://hel1.your-objectstorage.com', s3_region = 'hel1', 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'), 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));"
       # archive missed packages
       - R -q -e '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

@@ -20,6 +20,10 @@ steps:
         from_secret: GIT_RO_TOKEN
       GITHUB_PAT:
         from_secret: GITHUB_PAT
+      HETZNER_S3_ACCESS_KEY_K3S:
+        from_secret: HETZNER_S3_ACCESS_KEY_K3S
+      HETZNER_S3_SECRET_KEY_K3S:
+        from_secret: HETZNER_S3_SECRET_KEY_K3S
       # 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
@@ -35,6 +39,8 @@ steps:
       - R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
       - R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraft.git", dependencies = TRUE)'
       - R -q -e 'packageVersion("bincraft")'
+      # - R -q -e "future::plan('multisession', workers = 6L); pkgs = bincraft::query_packages_without_historic_versions('alpine322', 'amd64'); saveRDS(pkgs, '/mnt/cache/pkgs_amd64.rds')"
+      - R -q -e "future::plan('multisession', workers = 6L); pkgs = bincraft::query_packages_without_historic_versions('alpine322', 'arm64'); saveRDS(pkgs, '/mnt/cache/pkgs_arm64.rds')"
     backend_options:
       kubernetes:
         resources:
@@ -42,8 +48,8 @@ steps:
             memory: 1000Mi
             cpu: 1000m
           limits:
-            memory: 1500Mi
+            memory: 4500Mi
-            cpu: 2000m
+            cpu: 8000m
         nodeSelector:
           kubernetes.io/arch: ${ARCH}
         tolerations: