Compare commits
| Author | SHA1 | Date | |
|---|---|---|---|
|
5acc52ea08 | ||
592c5e15f8
|
143 changed files with 5053 additions and 12323 deletions
59
.crow/alpine-322-amd64-install-deps.yaml
Normal file
59
.crow/alpine-322-amd64-install-deps.yaml
Normal file
|
|
@ -0,0 +1,59 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-amd64"'
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||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all-amd64"'
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Install common R deps'
|
||||||
|
image: docker.io/devxygmbh/rpkgs-build-env-alpine:3.22-4.5.0
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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
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||||||
|
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: alpine-322
|
||||||
|
volumes:
|
||||||
|
- amd64-binaries-r-dep-cache-alpine-322:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- mkdir -p /mnt/cache/R-pkgs
|
||||||
|
- rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraftR
|
||||||
|
- 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/bincraftr.git")'
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 1000Mi
|
||||||
|
cpu: 1000m
|
||||||
|
limits:
|
||||||
|
memory: 1500Mi
|
||||||
|
cpu: 2000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: amd64
|
||||||
|
node.kubernetes.io/instance-type: AX42
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||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
59
.crow/alpine-322-arm64-install-deps.yaml
Normal file
59
.crow/alpine-322-arm64-install-deps.yaml
Normal file
|
|
@ -0,0 +1,59 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-arm64"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all-arm64"'
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Install common R deps'
|
||||||
|
image: docker.io/devxygmbh/rpkgs-build-env-alpine:3.22-4.5.0
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: alpine-322
|
||||||
|
volumes:
|
||||||
|
- arm64-binaries-r-dep-cache-alpine-322:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- mkdir -p /mnt/cache/R-pkgs
|
||||||
|
- rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraftR
|
||||||
|
- 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/bincraftr.git")'
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 1000Mi
|
||||||
|
cpu: 1000m
|
||||||
|
limits:
|
||||||
|
memory: 1500Mi
|
||||||
|
cpu: 2000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: arm64
|
||||||
|
node.kubernetes.io/instance-type: cax41
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
|
|
@ -1,77 +0,0 @@
|
||||||
### Required extra vars
|
|
||||||
# woodpecker-cli pipeline create --var task=archive-missed-packages --branch=main --log-level=info 7
|
|
||||||
when:
|
|
||||||
- event: manual
|
|
||||||
evaluate: 'task == "archive-missed-packages"'
|
|
||||||
- event: cron
|
|
||||||
cron: archive-missed-packages
|
|
||||||
|
|
||||||
matrix:
|
|
||||||
include:
|
|
||||||
- CODENAME: jammy
|
|
||||||
ARCH: amd64
|
|
||||||
- CODENAME: jammy
|
|
||||||
ARCH: arm64
|
|
||||||
- CODENAME: noble
|
|
||||||
ARCH: amd64
|
|
||||||
- CODENAME: noble
|
|
||||||
ARCH: arm64
|
|
||||||
- CODENAME: redhat-8
|
|
||||||
ARCH: amd64
|
|
||||||
- CODENAME: redhat-8
|
|
||||||
ARCH: arm64
|
|
||||||
- CODENAME: redhat-9
|
|
||||||
ARCH: amd64
|
|
||||||
- CODENAME: redhat-9
|
|
||||||
ARCH: arm64
|
|
||||||
- CODENAME: redhat-10
|
|
||||||
ARCH: amd64
|
|
||||||
- CODENAME: redhat-10
|
|
||||||
ARCH: arm64
|
|
||||||
- CODENAME: alpine322
|
|
||||||
ARCH: amd64
|
|
||||||
- CODENAME: alpine322
|
|
||||||
ARCH: arm64
|
|
||||||
- CODENAME: alpine323
|
|
||||||
ARCH: amd64
|
|
||||||
- CODENAME: alpine323
|
|
||||||
ARCH: arm64
|
|
||||||
|
|
||||||
steps:
|
|
||||||
- name: 'Archive missed packages'
|
|
||||||
image: reg.devxy.io/rpkgs/build-env-alpine:3.24
|
|
||||||
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
|
|
||||||
R_VERSION: 4.5.3
|
|
||||||
commands:
|
|
||||||
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
|
|
||||||
- /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"), s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"), workers = 2L)'
|
|
||||||
backend_options:
|
|
||||||
kubernetes:
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
memory: 1Gi
|
|
||||||
cpu: 2000m
|
|
||||||
limits:
|
|
||||||
memory: 1200Mi
|
|
||||||
cpu: 2000m
|
|
||||||
tolerations:
|
|
||||||
- key: 'CI'
|
|
||||||
operator: 'Equal'
|
|
||||||
value: 'true'
|
|
||||||
effect: 'NoSchedule'
|
|
||||||
|
|
@ -1,76 +0,0 @@
|
||||||
# Auto-apply registry patches (issue #115, step 3 automation).
|
|
||||||
# Classifies `single_builds` failures and, for the top-N auto-proposable
|
|
||||||
# candidates by failure volume, writes the registry entries onto the reused
|
|
||||||
# `auto/registry-patch-proposals` branch and opens/updates a single PR.
|
|
||||||
# Nothing merges: the `trial-build-registry` pipeline is the merge gate, and a
|
|
||||||
# human reviews the PR. Novel source diffs / unknown signatures are never
|
|
||||||
# proposed. Global across platforms, so a single job -- no matrix.
|
|
||||||
#
|
|
||||||
# FORGEJO_TOKEN is used for both the branch push and opening the PR (no separate
|
|
||||||
# write-scoped secret needed). Register the `auto-apply-patches` cron in the crow
|
|
||||||
# UI, or run manually:
|
|
||||||
# crow pipeline create --branch main \
|
|
||||||
# --var auto_apply_patches=true devxy/build-cran-binaries
|
|
||||||
#
|
|
||||||
# The gate variable is `auto_apply_patches`, named after the pipeline: a manual
|
|
||||||
# run instantiates every pipeline in `.crow/`, so one without its own gate runs
|
|
||||||
# on *any* manual trigger in this repo. This one pushes a branch and opens a PR,
|
|
||||||
# so it must stay off unless it is what was asked for.
|
|
||||||
variables:
|
|
||||||
auto_apply_patches:
|
|
||||||
description: 'Run the auto-patch proposer. Also gates this pipeline.'
|
|
||||||
options:
|
|
||||||
- 'true'
|
|
||||||
- 'false'
|
|
||||||
default: 'false'
|
|
||||||
patch_limit:
|
|
||||||
description: 'Max candidates to propose per run (top by failure volume).'
|
|
||||||
default: '10'
|
|
||||||
|
|
||||||
when:
|
|
||||||
- event: manual
|
|
||||||
evaluate: 'auto_apply_patches == "true"'
|
|
||||||
- event: cron
|
|
||||||
cron: auto-apply-patches
|
|
||||||
|
|
||||||
skip_clone: true
|
|
||||||
|
|
||||||
labels:
|
|
||||||
group: rpkgs-amd64
|
|
||||||
|
|
||||||
steps:
|
|
||||||
- name: 'Auto-apply registry patches'
|
|
||||||
image: reg.devxy.io/rpkgs/build-env-alpine:3.24
|
|
||||||
pull: true
|
|
||||||
environment:
|
|
||||||
PGPASS:
|
|
||||||
from_secret: PGPASS
|
|
||||||
REPO_RO_TOKEN:
|
|
||||||
from_secret: REPO_RO_TOKEN
|
|
||||||
FORGEJO_TOKEN:
|
|
||||||
from_secret: FORGEJO_TOKEN
|
|
||||||
GIT_USER: devxy-bot
|
|
||||||
GIT_EMAIL: bot@devxy.io
|
|
||||||
PATCH_LIMIT: ${patch_limit}
|
|
||||||
R_VERSION: 4.5.3
|
|
||||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
|
||||||
commands:
|
|
||||||
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
|
|
||||||
- mkdir -p /mnt/cache/R-pkgs
|
|
||||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
|
|
||||||
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres httr2 jsonlite
|
|
||||||
- /opt/R/$R_VERSION/bin/Rscript local/propose-patches.R --open-pr --limit $PATCH_LIMIT
|
|
||||||
backend_options:
|
|
||||||
kubernetes:
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
memory: 1Gi
|
|
||||||
cpu: 2000m
|
|
||||||
limits:
|
|
||||||
memory: 2Gi
|
|
||||||
cpu: 2000m
|
|
||||||
tolerations:
|
|
||||||
- key: 'CI'
|
|
||||||
operator: 'Equal'
|
|
||||||
value: 'true'
|
|
||||||
effect: 'NoSchedule'
|
|
||||||
|
|
@ -1,97 +0,0 @@
|
||||||
# Consolidated install-deps for build-all (both arches in one file).
|
|
||||||
# Triggered together with build-all-versions; `target_arch` routes the matrix.
|
|
||||||
# Variables are declared so the manual-run form exposes them (crow #1165);
|
|
||||||
# they are merged with build-all-versions' identical declarations.
|
|
||||||
variables:
|
|
||||||
# Gates this pipeline. A manual pipeline creation instantiates every file in
|
|
||||||
# .crow/, and a declared default is applied even when the run never passed
|
|
||||||
# this variable, so the default must be a value that matches no matrix row.
|
|
||||||
target_arch:
|
|
||||||
description: 'Architecture to build, or "none" to run nothing.'
|
|
||||||
options:
|
|
||||||
- none
|
|
||||||
- amd64
|
|
||||||
- arm64
|
|
||||||
default: none
|
|
||||||
OS:
|
|
||||||
description: 'Base OS image name.'
|
|
||||||
options:
|
|
||||||
- alpine
|
|
||||||
- redhat
|
|
||||||
- ubuntu
|
|
||||||
default: alpine
|
|
||||||
OS_VERSION:
|
|
||||||
description: 'OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble).'
|
|
||||||
options:
|
|
||||||
- '3.24'
|
|
||||||
- '8'
|
|
||||||
- '9'
|
|
||||||
- '10'
|
|
||||||
- 'jammy'
|
|
||||||
- 'noble'
|
|
||||||
default: '3.24'
|
|
||||||
R_VERSION:
|
|
||||||
description: 'Primary R version under /opt/R.'
|
|
||||||
options:
|
|
||||||
- 4.5.3
|
|
||||||
- 4.4.3
|
|
||||||
default: 4.5.3
|
|
||||||
|
|
||||||
when:
|
|
||||||
- event: manual
|
|
||||||
evaluate: 'target_arch == "${ARCH}"'
|
|
||||||
|
|
||||||
skip_clone: true
|
|
||||||
|
|
||||||
labels:
|
|
||||||
platform: linux/${ARCH}
|
|
||||||
group: rpkgs-${ARCH}
|
|
||||||
|
|
||||||
matrix:
|
|
||||||
include:
|
|
||||||
- ARCH: amd64
|
|
||||||
- ARCH: arm64
|
|
||||||
|
|
||||||
steps:
|
|
||||||
- name: 'Install deps and bincraft'
|
|
||||||
image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
|
|
||||||
pull: true
|
|
||||||
environment:
|
|
||||||
OTEL_R_TRACES_EXPORTER: none
|
|
||||||
OTEL_R_LOGS_EXPORTER: none
|
|
||||||
OTEL_R_METRICS_EXPORTER: none
|
|
||||||
REPO_RO_TOKEN:
|
|
||||||
from_secret: REPO_RO_TOKEN
|
|
||||||
GITHUB_PAT:
|
|
||||||
from_secret: GITHUB_PAT
|
|
||||||
B2_S3_ACCESS_KEY:
|
|
||||||
from_secret: B2_S3_ACCESS_KEY
|
|
||||||
B2_S3_SECRET_KEY:
|
|
||||||
from_secret: B2_S3_SECRET_KEY
|
|
||||||
PGPASS:
|
|
||||||
from_secret: PGPASS
|
|
||||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
|
||||||
# Keep uvr's downloads and extracted-package entries on the persistent
|
|
||||||
# volume instead of the container-local ~/.uvr default.
|
|
||||||
UVR_CACHE_DIR: /mnt/cache/uvr/cache
|
|
||||||
UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
|
|
||||||
CCACHE_DIR: /mnt/cache/ccache
|
|
||||||
volumes:
|
|
||||||
- ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
|
|
||||||
commands:
|
|
||||||
# one-time full wipe to fix corrupted .so files from previous failed builds
|
|
||||||
# - rm -rf /mnt/cache/R-pkgs
|
|
||||||
- mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
|
||||||
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
|
|
||||||
# Pin the same bincraft version the build steps use, so the precomputed
|
|
||||||
# snapshot and the per-agent library stay consistent across the pipeline.
|
|
||||||
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
|
|
||||||
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite
|
|
||||||
- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
|
|
||||||
- /opt/R/$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]))"
|
|
||||||
backend_options:
|
|
||||||
docker:
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
memory: 5Gi
|
|
||||||
cpu: 1000m
|
|
||||||
|
|
@ -1,209 +0,0 @@
|
||||||
### Manual full rebuild of all CRAN binaries for one OS/arch.
|
|
||||||
# Set the variables below in the manual-run form (or via --var on the CLI).
|
|
||||||
# `target_arch` routes the matrix; OS/OS_VERSION/R_VERSION select the platform
|
|
||||||
# image and cache volume. Placement is via the group label (rpkgs-amd64/rpkgs-arm64).
|
|
||||||
# Skip list lives in local/excluded-packages.json (read by local/build-all.R).
|
|
||||||
variables:
|
|
||||||
# Gates this pipeline. A manual pipeline creation instantiates every file in
|
|
||||||
# .crow/, and a declared default is applied even when the run never passed
|
|
||||||
# this variable, so the default must be a value that matches no matrix row.
|
|
||||||
target_arch:
|
|
||||||
description: 'Architecture to build, or "none" to run nothing.'
|
|
||||||
options:
|
|
||||||
- none
|
|
||||||
- amd64
|
|
||||||
- arm64
|
|
||||||
default: none
|
|
||||||
OS:
|
|
||||||
description: 'Base OS image name.'
|
|
||||||
options:
|
|
||||||
- alpine
|
|
||||||
- redhat
|
|
||||||
- ubuntu
|
|
||||||
default: alpine
|
|
||||||
OS_VERSION:
|
|
||||||
description: 'OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble).'
|
|
||||||
options:
|
|
||||||
- '3.22'
|
|
||||||
- '3.23'
|
|
||||||
- '3.24'
|
|
||||||
- '8'
|
|
||||||
- '9'
|
|
||||||
- '10'
|
|
||||||
- 'jammy'
|
|
||||||
- 'noble'
|
|
||||||
- 'resolute'
|
|
||||||
default: '3.24'
|
|
||||||
R_VERSION:
|
|
||||||
# The slot's *primary* R minor: what `local/build-all.R` builds into the
|
|
||||||
# generic slot. The loop below already runs `--sensitive-only` for every
|
|
||||||
# other installed minor, so filling a non-primary minor's gap needs this
|
|
||||||
# left alone, not changed.
|
|
||||||
#
|
|
||||||
# 4.6.0 was briefly offered here (#183) and removed: selecting it for a
|
|
||||||
# slot whose generic binaries are 4.5-built would publish 4.6 binaries
|
|
||||||
# into the generic slot and break every 4.5 client.
|
|
||||||
description: 'Primary R version under /opt/R.'
|
|
||||||
options:
|
|
||||||
- 4.5.3
|
|
||||||
- 4.4.3
|
|
||||||
default: 4.5.3
|
|
||||||
|
|
||||||
when:
|
|
||||||
- event: manual
|
|
||||||
evaluate: 'target_arch == "${ARCH}"'
|
|
||||||
|
|
||||||
skip_clone: true
|
|
||||||
|
|
||||||
labels:
|
|
||||||
platform: linux/${ARCH}
|
|
||||||
group: rpkgs-${ARCH}
|
|
||||||
|
|
||||||
# Empty UVR_CACHE_DIR/UVR_PACKAGES_DIR fall back to uvr's container-local
|
|
||||||
# ~/.uvr defaults; amd64 deliberately does not persist them (as with the
|
|
||||||
# pkgcache dir it replaces), arm64 does.
|
|
||||||
matrix:
|
|
||||||
include:
|
|
||||||
- ARCH: amd64
|
|
||||||
UVR_CACHE_DIR: ''
|
|
||||||
UVR_PACKAGES_DIR: ''
|
|
||||||
SPLIT_INTO: 4
|
|
||||||
SPLIT_INDEX: 1
|
|
||||||
- ARCH: amd64
|
|
||||||
UVR_CACHE_DIR: ''
|
|
||||||
UVR_PACKAGES_DIR: ''
|
|
||||||
SPLIT_INTO: 4
|
|
||||||
SPLIT_INDEX: 2
|
|
||||||
- ARCH: amd64
|
|
||||||
UVR_CACHE_DIR: ''
|
|
||||||
UVR_PACKAGES_DIR: ''
|
|
||||||
SPLIT_INTO: 4
|
|
||||||
SPLIT_INDEX: 3
|
|
||||||
- ARCH: amd64
|
|
||||||
UVR_CACHE_DIR: ''
|
|
||||||
UVR_PACKAGES_DIR: ''
|
|
||||||
SPLIT_INTO: 4
|
|
||||||
SPLIT_INDEX: 4
|
|
||||||
- ARCH: arm64
|
|
||||||
UVR_CACHE_DIR: /mnt/cache/uvr/cache
|
|
||||||
UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
|
|
||||||
SPLIT_INTO: 4
|
|
||||||
SPLIT_INDEX: 1
|
|
||||||
- ARCH: arm64
|
|
||||||
UVR_CACHE_DIR: /mnt/cache/uvr/cache
|
|
||||||
UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
|
|
||||||
SPLIT_INTO: 4
|
|
||||||
SPLIT_INDEX: 2
|
|
||||||
- ARCH: arm64
|
|
||||||
UVR_CACHE_DIR: /mnt/cache/uvr/cache
|
|
||||||
UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
|
|
||||||
SPLIT_INTO: 4
|
|
||||||
SPLIT_INDEX: 3
|
|
||||||
- ARCH: arm64
|
|
||||||
UVR_CACHE_DIR: /mnt/cache/uvr/cache
|
|
||||||
UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
|
|
||||||
SPLIT_INTO: 4
|
|
||||||
SPLIT_INDEX: 4
|
|
||||||
|
|
||||||
depends_on:
|
|
||||||
- build-all-versions-install-deps
|
|
||||||
|
|
||||||
steps:
|
|
||||||
- name: 'Build binaries'
|
|
||||||
image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
|
|
||||||
pull: true
|
|
||||||
environment:
|
|
||||||
OTEL_R_TRACES_EXPORTER: none
|
|
||||||
OTEL_R_LOGS_EXPORTER: none
|
|
||||||
OTEL_R_METRICS_EXPORTER: none
|
|
||||||
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
|
|
||||||
# set the location of uvr's caches, which persist the R package
|
|
||||||
# dependencies needed to install the packages themselves
|
|
||||||
UVR_CACHE_DIR: ${UVR_CACHE_DIR}
|
|
||||||
UVR_PACKAGES_DIR: ${UVR_PACKAGES_DIR}
|
|
||||||
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 .
|
|
||||||
- mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
|
||||||
# The primary pass must not rely on build-all-versions-install-deps having
|
|
||||||
# run on *this* agent: depends_on only orders the steps, but the cache
|
|
||||||
# volume is per-agent, so a job landing on an agent where install-deps did
|
|
||||||
# not run would otherwise use a stale bincraft (which resolves `platform`
|
|
||||||
# to a zero-length value and breaks every metadata query and the sysdeps
|
|
||||||
# install). Pin bincraft here, exactly like the R-minor pass below.
|
|
||||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
|
|
||||||
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
|
|
||||||
- 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/[0-9]*/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 ==="
|
|
||||||
LIB="/mnt/cache/R-pkgs-$RMINOR"
|
|
||||||
mkdir -p "$LIB"
|
|
||||||
R_LIBS_USER="$LIB" "$(dirname "$RBIN")/Rscript" local/install-bincraft.R || true
|
|
||||||
R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- "$(dirname "$RBIN")/Rscript" local/build-all.R --sensitive-only $SPLIT_INTO $SPLIT_INDEX $NCPUS 2>&1 || true
|
|
||||||
done
|
|
||||||
# archive missed packages; first arg is the codename (e.g. "alpine324"),
|
|
||||||
# derived via bincraft like the upload step, not paste(OS, OS_VERSION).
|
|
||||||
- /opt/R/$R_VERSION/bin/R -q -e "bincraft::process_unarchived_pkgs(bincraft::set_codename(NULL), Sys.getenv('ARCH'), s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), workers = $NCPUS)"
|
|
||||||
backend_options:
|
|
||||||
docker:
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
memory: 5Gi
|
|
||||||
cpu: 1000m
|
|
||||||
limits:
|
|
||||||
memory: 20Gi
|
|
||||||
cpu: 2000m
|
|
||||||
- name: 'Upload package indexes'
|
|
||||||
image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
|
|
||||||
pull: true
|
|
||||||
environment:
|
|
||||||
OTEL_R_TRACES_EXPORTER: none
|
|
||||||
OTEL_R_LOGS_EXPORTER: none
|
|
||||||
OTEL_R_METRICS_EXPORTER: none
|
|
||||||
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/[0-9]*/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
|
|
||||||
77
.crow/build-alpine-322-amd64-1.yaml
Normal file
77
.crow/build-alpine-322-amd64-1.yaml
Normal file
|
|
@ -0,0 +1,77 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-amd64"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-amd64-1"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all-amd64"'
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
depends_on:
|
||||||
|
- alpine-322-amd64-install-deps
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/rpkgs-build-env-alpine:3.22-4.5.0
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: alpine-322
|
||||||
|
BLOCK_START: 10001
|
||||||
|
BLOCK_END: 12000
|
||||||
|
ARCH: amd64
|
||||||
|
NCPUS: 2
|
||||||
|
STRATEGY: sequential
|
||||||
|
volumes:
|
||||||
|
- amd64-binaries-r-dep-cache-alpine-322:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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 = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[$BLOCK_START:$BLOCK_END]; 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')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = FALSE, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'alpine-322'))"
|
||||||
|
# hanging: 'doBy', 'IDPmisc', 'frailtypack', 'afex'
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 1000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 2000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: amd64
|
||||||
|
node.kubernetes.io/instance-type: AX42
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
77
.crow/build-alpine-322-amd64-2.yaml
Normal file
77
.crow/build-alpine-322-amd64-2.yaml
Normal file
|
|
@ -0,0 +1,77 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-amd64"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-amd64-1"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all-amd64"'
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
depends_on:
|
||||||
|
- alpine-322-amd64-install-deps
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/rpkgs-build-env-alpine:3.22-4.5.0
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: alpine-322
|
||||||
|
BLOCK_START: 12001
|
||||||
|
BLOCK_END: 14000
|
||||||
|
ARCH: amd64
|
||||||
|
NCPUS: 2
|
||||||
|
STRATEGY: sequential
|
||||||
|
volumes:
|
||||||
|
- amd64-binaries-r-dep-cache-alpine-322:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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(); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[$BLOCK_START:$BLOCK_END]; 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')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = FALSE, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'alpine-322'))"
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 1000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 2000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: amd64
|
||||||
|
node.kubernetes.io/instance-type: AX42
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
|
|
||||||
76
.crow/build-alpine-322-amd64-3.yaml
Normal file
76
.crow/build-alpine-322-amd64-3.yaml
Normal file
|
|
@ -0,0 +1,76 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-amd64"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-amd64-1"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all-amd64"'
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
depends_on:
|
||||||
|
- alpine-322-amd64-install-deps
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/rpkgs-build-env-ubuntu:noble-4.4.3
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: alpine-322
|
||||||
|
BLOCK_START: 14001
|
||||||
|
BLOCK_END: 16000
|
||||||
|
ARCH: amd64
|
||||||
|
NCPUS: 2
|
||||||
|
STRATEGY: sequential
|
||||||
|
volumes:
|
||||||
|
- amd64-binaries-r-dep-cache-alpine-322:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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 = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[$BLOCK_START:$BLOCK_END]; 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')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = FALSE, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'alpine-322'))"
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 1000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 2000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: amd64
|
||||||
|
node.kubernetes.io/instance-type: AX42
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
76
.crow/build-alpine-322-amd64-4.yaml
Normal file
76
.crow/build-alpine-322-amd64-4.yaml
Normal file
|
|
@ -0,0 +1,76 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-amd64"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-amd64-1"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all-amd64"'
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
depends_on:
|
||||||
|
- alpine-322-amd64-install-deps
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/rpkgs-build-env-ubuntu:noble-4.4.3
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: alpine-322
|
||||||
|
BLOCK_START: 16001
|
||||||
|
BLOCK_END: 18000
|
||||||
|
ARCH: amd64
|
||||||
|
NCPUS: 2
|
||||||
|
STRATEGY: sequential
|
||||||
|
volumes:
|
||||||
|
- amd64-binaries-r-dep-cache-alpine-322:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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(); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[$BLOCK_START:$BLOCK_END]; 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')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = FALSE, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'alpine-322'))"
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 1000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 2000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: amd64
|
||||||
|
node.kubernetes.io/instance-type: AX42
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
76
.crow/build-alpine-322-amd64-5.yaml
Normal file
76
.crow/build-alpine-322-amd64-5.yaml
Normal file
|
|
@ -0,0 +1,76 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-amd64"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "alpine-322-amd64-1"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all-amd64"'
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
depends_on:
|
||||||
|
- alpine-322-amd64-install-deps
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/rpkgs-build-env-ubuntu:noble-4.4.3
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: alpine-322
|
||||||
|
BLOCK_START: 18001
|
||||||
|
BLOCK_END: 20000
|
||||||
|
ARCH: amd64
|
||||||
|
NCPUS: 2
|
||||||
|
STRATEGY: sequential
|
||||||
|
volumes:
|
||||||
|
- amd64-binaries-r-dep-cache-alpine-322:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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 = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[$BLOCK_START:$BLOCK_END]; 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')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = FALSE, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'alpine-322'))"
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 1000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 2000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: amd64
|
||||||
|
node.kubernetes.io/instance-type: AX42
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
76
.crow/build-alpine-322-arm64-1.yaml
Normal file
76
.crow/build-alpine-322-arm64-1.yaml
Normal file
|
|
@ -0,0 +1,76 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- 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
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/rpkgs-build-env-alpine:3.22-4.5.0
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: alpine-322
|
||||||
|
BLOCK_START: 6601
|
||||||
|
BLOCK_END: 9000
|
||||||
|
ARCH: arm64
|
||||||
|
NCPUS: 2
|
||||||
|
STRATEGY: sequential
|
||||||
|
volumes:
|
||||||
|
- arm64-binaries-r-dep-cache-alpine-322:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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(); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[$BLOCK_START:$BLOCK_END]; 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')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = FALSE, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'alpine-322'))"
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 1000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 2000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: arm64
|
||||||
|
node.kubernetes.io/instance-type: cax41
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
76
.crow/build-alpine-322-arm64-2.yaml
Normal file
76
.crow/build-alpine-322-arm64-2.yaml
Normal file
|
|
@ -0,0 +1,76 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- 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
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/rpkgs-build-env-alpine:3.22-4.5.0
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: alpine-322
|
||||||
|
BLOCK_START: 9001
|
||||||
|
BLOCK_END: 12000
|
||||||
|
ARCH: arm64
|
||||||
|
NCPUS: 2
|
||||||
|
STRATEGY: sequential
|
||||||
|
volumes:
|
||||||
|
- arm64-binaries-r-dep-cache-alpine-322:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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 = $NCPUS, future.globals.onReference = NULL); pak::sysreqs_db_update(); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[$BLOCK_START:$BLOCK_END]; 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')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = FALSE, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'alpine-322'))"
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 1000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 2000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: arm64
|
||||||
|
node.kubernetes.io/instance-type: cax41
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
76
.crow/build-alpine-322-arm64-3.yaml
Normal file
76
.crow/build-alpine-322-arm64-3.yaml
Normal file
|
|
@ -0,0 +1,76 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- 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
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/rpkgs-build-env-alpine:3.22-4.5.0
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: alpine-322
|
||||||
|
BLOCK_START: 12001
|
||||||
|
BLOCK_END: 15000
|
||||||
|
ARCH: arm64
|
||||||
|
NCPUS: 2
|
||||||
|
STRATEGY: sequential
|
||||||
|
volumes:
|
||||||
|
- arm64-binaries-r-dep-cache-alpine-322:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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(); pkgs = as.character(available.packages('cloud.r-project.org/src/contrib')[, 'Package'])[$BLOCK_START:$BLOCK_END]; 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')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = FALSE, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'alpine-322'))"
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 1000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 2000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: arm64
|
||||||
|
node.kubernetes.io/instance-type: cax41
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
68
.crow/build-redhat-8-amd64-single.yaml
Normal file
68
.crow/build-redhat-8-amd64-single.yaml
Normal file
|
|
@ -0,0 +1,68 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'task == "build-single-rhel8-amd64"'
|
||||||
|
# PACKAGE:
|
||||||
|
# TAG: # set NULL to build all versions
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/amd64-binaries-r-redhat-8
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: redhat-8
|
||||||
|
ARCH: amd64
|
||||||
|
NCPUS: 4
|
||||||
|
STRATEGY: sequential
|
||||||
|
# volumes:
|
||||||
|
# - amd64-binaries-r-dep-cache-redhat-8:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR /mnt/cache/R-pkgs/00LOCK-pak /mnt/cache/pkgcache/R/pkgcache /mnt/cache/pkgcache/R/pkgcache /mnt/cache/R-pkgs/pkgcache
|
||||||
|
- R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraftr.git")'
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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 = $NCPUS, future.globals.onReference = NULL, repos = structure(c(CRAN = 'https://cran.devxy.io/$ARCH/rhel8/latest'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); bincraftR::build_binary_package(\"$$package\", tag = \"$$tag\", 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'redhat-8')"
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 2000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 3000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: amd64
|
||||||
|
node.kubernetes.io/instance-type: AX42
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
107
.crow/build-redhat-8-amd64.yaml
Normal file
107
.crow/build-redhat-8-amd64.yaml
Normal file
|
|
@ -0,0 +1,107 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "redhat-8-amd64"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all-amd64"'
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/amd64-binaries-r-redhat-8
|
||||||
|
pull: true
|
||||||
|
# to ensure the PACKAGES upload step is being executed
|
||||||
|
failure: ignore
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: redhat-8
|
||||||
|
BLOCK: 1833:1833
|
||||||
|
ARCH: amd64
|
||||||
|
NCPUS: 4
|
||||||
|
# MEMORY: 14Gi
|
||||||
|
# INSTANCE_TYPE: ccx23
|
||||||
|
STRATEGY: sequential
|
||||||
|
# volumes:
|
||||||
|
# - amd64-binaries-r-dep-cache-redhat-8:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR /mnt/cache/R-pkgs/00LOCK-pak /mnt/cache/pkgcache/R/pkgcache /mnt/cache/pkgcache/R/pkgcache /mnt/cache/R-pkgs/pkgcache
|
||||||
|
- R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraftr.git")'
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||||
|
# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
|
||||||
|
# Windows-only: 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd', 'rFUSION', 'MediaNews'
|
||||||
|
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(CRAN = 'https://cran.devxy.io/amd64/rhel8/latest'))); pkgs = c('aphylo', 'atime'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'later', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'redhat-8'))"
|
||||||
|
### Manual pkg builds
|
||||||
|
# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
|
||||||
|
# RInno: Windows-only
|
||||||
|
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||||
|
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||||
|
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||||
|
# ROracle: sysdep missing -> create rule
|
||||||
|
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||||
|
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||||
|
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||||
|
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||||
|
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||||
|
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||||
|
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||||
|
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||||
|
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||||
|
# Racmacs -> rmarchingcubes
|
||||||
|
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||||
|
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||||
|
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||||
|
# clrng -> gpuR
|
||||||
|
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||||
|
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
|
||||||
|
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||||
|
# magickGUI, biplotbootGUI
|
||||||
|
# ymd (alpine, voi)
|
||||||
|
# tfrmtbuilder -> V8 (alpine)
|
||||||
|
# Rcmdr (alpine)
|
||||||
|
# readstata13 (alpine)
|
||||||
|
# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = "amd64"))'
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 2000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 3000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: amd64
|
||||||
|
node.kubernetes.io/instance-type: AX42
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
68
.crow/build-redhat-8-arm64-single.yaml
Normal file
68
.crow/build-redhat-8-arm64-single.yaml
Normal file
|
|
@ -0,0 +1,68 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'task == "build-single-rhel8-arm64"'
|
||||||
|
# PACKAGE:
|
||||||
|
# TAG: # set NULL to build all versions
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/arm64-binaries-r-redhat-8
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: redhat-8
|
||||||
|
ARCH: arm64
|
||||||
|
NCPUS: 4
|
||||||
|
STRATEGY: sequential
|
||||||
|
# volumes:
|
||||||
|
# - arm64-binaries-r-dep-cache-redhat-8:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR /mnt/cache/R-pkgs/00LOCK-pak /mnt/cache/pkgcache/R/pkgcache /mnt/cache/pkgcache/R/pkgcache /mnt/cache/R-pkgs/pkgcache
|
||||||
|
- R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraftr.git")'
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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 = $NCPUS, future.globals.onReference = NULL, repos = structure(c(CRAN = 'https://cran.devxy.io/$ARCH/rhel8/latest'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); bincraftR::build_binary_package(\"$$package\", tag = \"$$tag\", 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'redhat-8')"
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 2000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 3000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: arm64
|
||||||
|
node.kubernetes.io/instance-type: AX42
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
130
.crow/build-redhat-8-arm64.yaml
Normal file
130
.crow/build-redhat-8-arm64.yaml
Normal file
|
|
@ -0,0 +1,130 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "redhat-8-arm64"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all-arm64"'
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
steps:
|
||||||
|
# - name: 'Warming up'
|
||||||
|
# image: busybox:latest
|
||||||
|
# failure: ignore
|
||||||
|
# commands:
|
||||||
|
# - sleep 300
|
||||||
|
# - echo "Warmed Up"
|
||||||
|
# backend_options:
|
||||||
|
# kubernetes:
|
||||||
|
# resources:
|
||||||
|
# requests:
|
||||||
|
# memory: 14Gi
|
||||||
|
# cpu: 3000m
|
||||||
|
# limits:
|
||||||
|
# memory: 14Gi
|
||||||
|
# cpu: 3000m
|
||||||
|
# nodeSelector:
|
||||||
|
# kubernetes.io/arch: arm64
|
||||||
|
# node.kubernetes.io/instance-type: cax31
|
||||||
|
# tolerations:
|
||||||
|
# - key: 'CI'
|
||||||
|
# operator: 'Equal'
|
||||||
|
# value: 'true'
|
||||||
|
# effect: 'NoSchedule'
|
||||||
|
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/arm64-binaries-r-redhat-8
|
||||||
|
pull: true
|
||||||
|
# to ensure the PACKAGES upload step is being executed
|
||||||
|
failure: ignore
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: redhat-8
|
||||||
|
BLOCK: 20500:length(pkgs)
|
||||||
|
ARCH: arm64
|
||||||
|
NCPUS: 2
|
||||||
|
MEMORY: 14Gi
|
||||||
|
INSTANCE_TYPE: cax31
|
||||||
|
STRATEGY: multisession
|
||||||
|
# volumes:
|
||||||
|
# - arm64-binaries-r-dep-cache-redhat-8:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR /mnt/cache/R-pkgs/00LOCK-pak /mnt/cache/pkgcache/R/pkgcache /mnt/cache/pkgcache/R/pkgcache /mnt/cache/R-pkgs/pkgcache
|
||||||
|
- R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraftr.git")'
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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'
|
||||||
|
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c('aphylo', 'atime'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'redhat-8'))"
|
||||||
|
### Manual pkg builds
|
||||||
|
# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
|
||||||
|
# RInno: Windows-only
|
||||||
|
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||||
|
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||||
|
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||||
|
# ROracle: sysdep missing -> create rule
|
||||||
|
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||||
|
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||||
|
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||||
|
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||||
|
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||||
|
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||||
|
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||||
|
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||||
|
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||||
|
# Racmacs -> rmarchingcubes
|
||||||
|
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||||
|
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||||
|
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||||
|
# clrng -> gpuR
|
||||||
|
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||||
|
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
|
||||||
|
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||||
|
# magickGUI, biplotbootGUI
|
||||||
|
# ymd (alpine, voi)
|
||||||
|
# tfrmtbuilder -> V8 (alpine)
|
||||||
|
# Rcmdr (alpine)
|
||||||
|
# readstata13 (alpine)
|
||||||
|
# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = "arm64"))'
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 3000m
|
||||||
|
limits:
|
||||||
|
memory: 14Gi
|
||||||
|
cpu: 3000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: arm64
|
||||||
|
node.kubernetes.io/instance-type: cax41
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
69
.crow/build-redhat-9-amd64-single.yaml
Normal file
69
.crow/build-redhat-9-amd64-single.yaml
Normal file
|
|
@ -0,0 +1,69 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'task == "build-single-rhel9-amd64"'
|
||||||
|
# PACKAGE:
|
||||||
|
# TAG: # set NULL to build all versions
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/amd64-binaries-r-redhat-9
|
||||||
|
pull: true
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: redhat-9
|
||||||
|
ARCH: amd64
|
||||||
|
NCPUS: 4
|
||||||
|
STRATEGY: sequential
|
||||||
|
# volumes:
|
||||||
|
# - amd64-binaries-r-dep-cache-redhat-9:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR /mnt/cache/R-pkgs/00LOCK-pak /mnt/cache/pkgcache/R/pkgcache /mnt/cache/pkgcache/R/pkgcache /mnt/cache/R-pkgs/pkgcache
|
||||||
|
- R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraftr.git")'
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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'
|
||||||
|
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(CRAN = 'https://cran.devxy.io/$ARCH/rhel9/latest'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); bincraftR::build_binary_package(\"$$package\", tag = \"$$tag\", 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'redhat-9')"
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 2000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 3000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: amd64
|
||||||
|
node.kubernetes.io/instance-type: AX42
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
105
.crow/build-redhat-9-amd64.yaml
Normal file
105
.crow/build-redhat-9-amd64.yaml
Normal file
|
|
@ -0,0 +1,105 @@
|
||||||
|
when:
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "redhat-9-amd64"'
|
||||||
|
- event: manual
|
||||||
|
evaluate: 'build == "all-amd64"'
|
||||||
|
|
||||||
|
skip_clone: true
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: 'Build binaries'
|
||||||
|
image: docker.io/devxygmbh/amd64-binaries-r-redhat-9
|
||||||
|
pull: true
|
||||||
|
# to ensure the PACKAGES upload step is being executed
|
||||||
|
failure: ignore
|
||||||
|
environment:
|
||||||
|
RED_HAT_DEV_PW:
|
||||||
|
from_secret: RED_HAT_DEV_PW
|
||||||
|
HETZNER_S3_ACCESS_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_ACCESS_KEY_K3S
|
||||||
|
HETZNER_S3_SECRET_KEY_K3S:
|
||||||
|
from_secret: HETZNER_S3_SECRET_KEY_K3S
|
||||||
|
PGPASS:
|
||||||
|
from_secret: PGPASS
|
||||||
|
GIT_RO_TOKEN:
|
||||||
|
from_secret: GIT_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: /mnt/cache/R-pkgs
|
||||||
|
CCACHE_DIR: /mnt/cache/ccache
|
||||||
|
PLATFORM: redhat-9
|
||||||
|
BLOCK: 2394:2428
|
||||||
|
ARCH: amd64
|
||||||
|
NCPUS: 4
|
||||||
|
INSTANCE_TYPE: AX42
|
||||||
|
STRATEGY: sequential
|
||||||
|
# volumes:
|
||||||
|
# - amd64-binaries-r-dep-cache-redhat-9:/mnt/cache
|
||||||
|
commands:
|
||||||
|
- git clone -q https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/build-binaries.git .
|
||||||
|
- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR /mnt/cache/R-pkgs/00LOCK-pak /mnt/cache/pkgcache/R/pkgcache /mnt/cache/pkgcache/R/pkgcache /mnt/cache/R-pkgs/pkgcache
|
||||||
|
- R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraftr.git")'
|
||||||
|
- R -q -e 'packageVersion("bincraftR")'
|
||||||
|
- 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'
|
||||||
|
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL, repos = structure(c(CRAN = 'https://cran.devxy.io/$ARCH/rhel9/latest'))); pkgs = c('aphylo', 'atime'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews', 'RInno', 'KeyboardSimulator', 'R2PPT', 'RWinEdt', 'blatr', 'excel.link', 'spectrino', 'taskscheduleR', 'MDSGUI', 'BiplotGUI', 'R2wd')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = 'redhat-9'))"
|
||||||
|
### Manual pkg builds
|
||||||
|
# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
|
||||||
|
# RInno: Windows-only
|
||||||
|
# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
|
||||||
|
# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
|
||||||
|
# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
|
||||||
|
# ROracle: sysdep missing -> create rule
|
||||||
|
# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
|
||||||
|
# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||||
|
# RmecabKo: fatal error: mecab.h: No such file or directory
|
||||||
|
# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
|
||||||
|
# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
|
||||||
|
# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
|
||||||
|
# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
|
||||||
|
# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
|
||||||
|
# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
|
||||||
|
# Racmacs -> rmarchingcubes
|
||||||
|
# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
|
||||||
|
# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
|
||||||
|
# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
|
||||||
|
# clrng -> gpuR
|
||||||
|
# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
|
||||||
|
# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
|
||||||
|
# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
|
||||||
|
# magickGUI, biplotbootGUI
|
||||||
|
# ymd (alpine, voi)
|
||||||
|
# tfrmtbuilder -> V8 (alpine)
|
||||||
|
# Rcmdr (alpine)
|
||||||
|
# readstata13 (alpine)
|
||||||
|
# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, 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 = 'r_binaries', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE, platform = "amd64"))'
|
||||||
|
backend_options:
|
||||||
|
kubernetes:
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
memory: 5Gi
|
||||||
|
cpu: 2000m
|
||||||
|
limits:
|
||||||
|
memory: 20Gi
|
||||||
|
cpu: 3000m
|
||||||
|
nodeSelector:
|
||||||
|
kubernetes.io/arch: amd64
|
||||||
|
node.kubernetes.io/instance-type: AX42
|
||||||
|
tolerations:
|
||||||
|
- key: 'CI'
|
||||||
|
operator: 'Equal'
|
||||||
|
value: 'true'
|
||||||
|
effect: 'NoSchedule'
|
||||||
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