123 lines
11 KiB
YAML
123 lines
11 KiB
YAML
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
|
|
AWS_ACCESS_KEY_ID:
|
|
from_secret: aws_access_key_id
|
|
AWS_SECRET_ACCESS_KEY:
|
|
from_secret: aws_secret_access_key
|
|
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
|
|
# 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 https://pat-s:$$GIT_RO_TOKEN@git.devxy.io/devxy/r-pkg-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://gitlab.com/devxy/r-package-binaries/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'
|
|
- xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs = c('sirus', 'sisireg', 'SIT', 'SITH', 'sitmo', 'sits', 'sjdbc', 'SK4FGA', 'SKAT', 'sketching', 'SKFCPD', 'sklarsomega', 'skm', 'skpr', 'slasso', 'SLBDD', 'slcm', 'sld', 'sleev', 'slfm', 'SLHD', 'slider', 'SLOPE', 'slp', 'smaa', 'smacof', 'smam', 'smfishHmrf', 'smfsb', 'smile', 'SMITIDvisu', 'SMMA', 'SMME', 'smmR', 'smoof', 'smooth', 'smoothAPC', 'SmoothHazard', 'smoothSurv', 'SMUT', 'smvgraph', 'sna', 'SnowballC', 'SNPknock', 'snplist', 'snpsettest', 'SNSeg', 'SobolSequence', 'socceR', 'social', 'sodium', 'SoftBart', 'softImpute', 'som', 'sorcering', 'SoundexBR', 'sourcetools', 'sp', 'spAbundance', 'spacefillr', 'SpaceTimeBSS', 'SpaCOAP', 'SpaDES.tools', 'spam', 'spam64', 'spaMM', 'sparcl', 'SparseChol', 'sparseDFM', 'sparsegl', 'sparseHessianFD', 'sparseinv', 'SparseLPM', 'sparseLTSEigen', 'SparseM', 'SPARSEMODr', 'sparsereg', 'sparseSEM', 'sparsesvd', 'sparseSVM', 'SparseTSCGM', 'sparsevb', 'sparsevctrs', 'sparsio', 'sparta', 'sparvaride', 'spass', 'spate', 'spatgraphs', 'spaths', 'spatial', 'SpatialBSS', 'SpatialEpi', 'SpatialExtremes', 'SpatialfdaR', 'SpatialGEV', 'spatialising', 'SpatialKDE', 'SpatialKWD', 'SpatialPack', 'spatialrisk', 'SpatialTools', 'spatialwarnings', 'spatialwidget', 'SpatMCA', 'SpaTopic', 'SpatPCA', 'spatstat.explore', 'spatstat.Knet', 'spatstat.random', 'spatstat.sparse', 'spbal', 'spBayes', 'spBayesSurv', 'spBFA', 'Spbsampling', 'spc', 'spcosa', 'spCP', 'spcr', 'spduration', 'speakeasyR', 'SPECIES', 'specklestar', 'specs', 'SpecsVerification', 'spectralGraphTopology', 'spectralR', 'spectre', 'spectrino', 'sped', 'speedytax', 'spfa', 'spFW', 'spGARCH', 'spgs', 'spgwr', 'sphereplot', 'sphunif', 'spiderbar', 'spikeslab', 'spikeSlabGAM', 'spinBayes', 'splancs', 'SPlit', 'SplitGLM', 'SplitReg', 'splmm', 'splusTimeDate', 'spMC', 'spNNGP', 'spOccupancy', 'sport', 'spray', 'spreadr', 'springer', 'sprintr', 'SPSP', 'spsurv', 'spTDyn', 'SpTe2M', 'spTimer', 'squat', 'srm', 'SRTsim', 'ssh', 'Sshaped', 'SSLR', 'ssMousetrack', 'SSN2', 'SSOSVM', 'sspse', 'stable', 'staggered', 'stan4bart', 'StanMoMo', 'STAREG', 'starma', 'starsExtra', 'STARTdesign', 'starvz', 'statcomp', 'StatDA', 'statgenIBD', 'statgenQTLxT', 'statip', 'STB', 'stcos', 'stcpR6', 'stdvectors', 'steepness', 'stelfi', 'stepPlr', 'stepR', 'steps', 'StepSignalMargiLike', 'stepSplitReg', 'StepwiseTest', 'stfit', 'stima', 'stlplus', 'StochBlock', 'stochQN', 'stockR', 'stocks', 'stopp', 'stops', 'stosim', 'stpm', 'stpp', 'stpphawkes', 'surveyvoi', 'symbolicDA', 'symbolicQspray', 'T4cluster', 'taskscheduleR', 'TDAkit', 'tessellation', 'TestGardener', 'thames', 'TML', 'Toothnroll', 'TPMplt', 'traineR', 'treats', 'trinROC', 'triptych', 'TSclust', 'TSCS', 'tsmarch', 'TUFLOWR', 'TukeyRegion', 'uavRmp', 'UBayFS', 'ucie', 'UCSCXenaShiny', 'UnalR', 'valhallr', 'valueSetCompare', 'vegan3d', 'vennplot', 'VICatMix', 'viewpoly', 'VIRF', 'vivid', 'voiceR', 'VOSONDash', 'vvdoctor', 'wallace', 'WaveletLSTM', 'WaverideR', 'WCluster', 'webglobe', 'x3ptools'); 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, 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, platform = "arm64"))'
|
|
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'
|