build alpine 3.23

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

@@ -3,7 +3,7 @@
 # OS (alpine)
 # OS_VERSION (3.22)
 # R_VERSION (4.5)
-# woodpecker-cli pipeline create --var ARCH=amd64 --var OS=alpine --var OS_VERSION=3.22 --var R_VERSION=4.5 --var task=build-all-amd64 --var K8S_INSTANCE_TYPE=AX42 --branch=main --log-level=info 7
+# woodpecker-cli pipeline create --var ARCH=amd64 --var OS=alpine --var OS_VERSION=3.23 --var R_VERSION=4.5 --var task=build-all-amd64 --var K8S_INSTANCE_TYPE=AX42 --branch=main --log-level=info 5
 when:
   - event: manual
     evaluate: 'task == "build-all-amd64"'
@@ -11,47 +11,48 @@ when:
 skip_clone: true
 
 labels:
-  backend: ${BACKEND}
+  platform: linux/amd64
+  backend: kubernetes
 
 matrix:
   include:
-    - SPLIT_INTO: 10
+    - SPLIT_INTO: 5
       SPLIT_INDEX: 1
       BACKEND: kubernetes
-    - SPLIT_INTO: 10
+    - SPLIT_INTO: 5
       SPLIT_INDEX: 2
       BACKEND: kubernetes
-    - SPLIT_INTO: 10
+    - SPLIT_INTO: 5
       SPLIT_INDEX: 3
       BACKEND: kubernetes
-    - SPLIT_INTO: 10
+    - SPLIT_INTO: 5
       SPLIT_INDEX: 4
       BACKEND: kubernetes
-    - SPLIT_INTO: 10
+    - SPLIT_INTO: 5
       SPLIT_INDEX: 5
       BACKEND: kubernetes
-    - SPLIT_INTO: 10
-      SPLIT_INDEX: 6
-      BACKEND: kubernetes
-    - SPLIT_INTO: 10
-      SPLIT_INDEX: 7
-      BACKEND: kubernetes
-    - SPLIT_INTO: 10
-      SPLIT_INDEX: 8
-      BACKEND: kubernetes
-    - SPLIT_INTO: 10
-      SPLIT_INDEX: 9
-      BACKEND: kubernetes
-    - SPLIT_INTO: 10
-      SPLIT_INDEX: 10
-      BACKEND: kubernetes
+    # - SPLIT_INTO: 10
+    #   SPLIT_INDEX: 6
+    #   BACKEND: kubernetes
+    # - SPLIT_INTO: 10
+    #   SPLIT_INDEX: 7
+    #   BACKEND: kubernetes
+    # - SPLIT_INTO: 10
+    #   SPLIT_INDEX: 8
+    #   BACKEND: kubernetes
+    # - SPLIT_INTO: 10
+    #   SPLIT_INDEX: 9
+    #   BACKEND: kubernetes
+    # - SPLIT_INTO: 10
+    #   SPLIT_INDEX: 10
+    #   BACKEND: kubernetes
 
 depends_on:
   - build-all-versions-install-deps
 
 steps:
   - name: 'Build binaries'
-    image: docker.io/devxygmbh/rpkgs-build-env-${OS}:${OS_VERSION}-${R_VERSION}
+    image: reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}-${R_VERSION}
     pull: true
     environment:
       RED_HAT_DEV_PW:
@@ -69,7 +70,7 @@ 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: /mnt/cache/pkgcache
+      R_PKG_CACHE_DIR: ""
       R_LIBS_USER: /mnt/cache/R-pkgs
       CCACHE_DIR: /mnt/cache/ccache
       NCPUS: 2
@@ -80,7 +81,8 @@ 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 = 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))"
+      # pkgs = readRDS('/mnt/cache/pkgs_amd64.rds');
+      - 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, 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')); library(future); plan('multisession'); foo = lapply(pkgs, function(x) bincraft::build_binary_package(x, 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

@@ -4,9 +4,9 @@
 # OS_VERSION (3.22)
 # R_VERSION (4.5)
 # 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=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
+# crow 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
+# crow 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=3.23 --var R_VERSION=4.5 --var task=build-all-arm64 --var K8S_INSTANCE_TYPE=cax41 --branch=main --log-level=info 5
 when:
   - event: manual
     evaluate: 'task == "build-all-arm64"'
@@ -14,7 +14,7 @@ when:
 skip_clone: true
 
 labels:
-  backend: ${BACKEND}
+  agent: gaia
 
 matrix:
   include:
@@ -33,28 +33,28 @@ matrix:
     # - SPLIT_INTO: 5
     #   SPLIT_INDEX: 5
     #   BACKEND: kubernetes
-    - SPLIT_INTO: 5
+    - SPLIT_INTO: 4
       SPLIT_INDEX: 1
       BACKEND: docker
-    - SPLIT_INTO: 5
+    - SPLIT_INTO: 4
       SPLIT_INDEX: 2
       BACKEND: docker
-    - SPLIT_INTO: 5
+    - SPLIT_INTO: 4
       SPLIT_INDEX: 3
       BACKEND: docker
-    - SPLIT_INTO: 5
+    - SPLIT_INTO: 4
       SPLIT_INDEX: 4
       BACKEND: docker
-    - SPLIT_INTO: 5
-      SPLIT_INDEX: 5
-      BACKEND: docker
+    # - SPLIT_INTO: 5
+    #   SPLIT_INDEX: 5
+    #   BACKEND: docker
 
 # depends_on:
 #   - build-all-versions-install-deps
 
 steps:
   - name: 'Build binaries'
-    image: docker.io/devxygmbh/rpkgs-build-env-${OS}:${OS_VERSION}-${R_VERSION}
+    image: reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}-${R_VERSION}
     pull: true
     environment:
       RED_HAT_DEV_PW:
@@ -84,7 +84,8 @@ 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'); 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));"
+      # pkgs = readRDS('/mnt/cache/pkgs_arm64.rds');
+      - 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)); foo = lapply(pkgs, function(x) bincraft::build_binary_package(x, 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

@@ -11,9 +11,13 @@ when:
 
 skip_clone: true
 
+labels:
+  platform: linux/amd64
+  backend: kubernetes
+
 steps:
   - name: 'Install common R deps'
-    image: reg.devxy.io/rpkgs/rpkgs-build-env-alpine:${OS_VERSION}-${R_VERSION}
+    image: reg.devxy.io/rpkgs/build-env-alpine:${OS_VERSION}-${R_VERSION}
     pull: true
     environment:
       REPO_RO_TOKEN:
@@ -27,7 +31,7 @@ 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: /mnt/cache/pkgcache
+      # R_PKG_CACHE_DIR: /mnt/cache/pkgcache
       R_LIBS_USER: /mnt/cache/R-pkgs
       CCACHE_DIR: /mnt/cache/ccache
     volumes:
@@ -40,7 +44,7 @@ steps:
       - 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')"
+      - R -q -e "future::plan('multisession', workers = 6L); pkgs = bincraft::query_packages_without_historic_versions('alpine323', 'arm64'); saveRDS(pkgs, '/mnt/cache/pkgs_arm64.rds')"
     backend_options:
       kubernetes:
         resources: