From 5969724eadee152866949ef316f8d0918740484e Mon Sep 17 00:00:00 2001 From: pat-s Date: Sun, 15 Sep 2024 15:53:17 +0200 Subject: [PATCH] rebuild missing pkgs --- .woodpecker/build.yaml | 134 ++++++++++++++++++++------------- .woodpecker/warm_up_build.yaml | 96 +++++++++++------------ 2 files changed, 131 insertions(+), 99 deletions(-) diff --git a/.woodpecker/build.yaml b/.woodpecker/build.yaml index 03f2cf1..e800439 100644 --- a/.woodpecker/build.yaml +++ b/.woodpecker/build.yaml @@ -8,30 +8,30 @@ depends_on: matrix: include: - # - PLATFORM: redhat-9 - # BLOCK: 20099:21169 - # ARCH: arm64 - # NCPUS: 2 - # MEMORY: 29Gi - # STRATEGY: multisession - # - PLATFORM: redhat-8 - # BLOCK: 20099:21169 - # ARCH: arm64 - # NCPUS: 2 - # MEMORY: 29Gi - # STRATEGY: multisession - # - PLATFORM: ubuntu-2404 - # BLOCK: 20099:21169 - # ARCH: arm64 - # NCPUS: 2 - # MEMORY: 29Gi - # STRATEGY: multisession - # - PLATFORM: ubuntu-2204 - # BLOCK: 20099:21169 - # ARCH: arm64 - # NCPUS: 2 - # MEMORY: 29Gi - # STRATEGY: multisession + - PLATFORM: redhat-9 + BLOCK: 20099:21169 + ARCH: arm64 + NCPUS: 2 + MEMORY: 29Gi + STRATEGY: multisession + - PLATFORM: redhat-8 + BLOCK: 20099:21169 + ARCH: arm64 + NCPUS: 2 + MEMORY: 29Gi + STRATEGY: multisession + - PLATFORM: ubuntu-2404 + BLOCK: 20099:21169 + ARCH: arm64 + NCPUS: 2 + MEMORY: 29Gi + STRATEGY: multisession + - PLATFORM: ubuntu-2204 + BLOCK: 20099:21169 + ARCH: arm64 + NCPUS: 2 + MEMORY: 29Gi + STRATEGY: multisession - PLATFORM: alpine-320 BLOCK: 7065:length(pkgs) ARCH: arm64 @@ -39,30 +39,30 @@ matrix: MEMORY: 29Gi STRATEGY: multisession ### AMD - - PLATFORM: redhat-9 - BLOCK: 1:length(pkgs) - ARCH: amd64 - NCPUS: 2 - MEMORY: 29Gi - STRATEGY: multisession - - PLATFORM: redhat-8 - BLOCK: 1:length(pkgs) - ARCH: amd64 - NCPUS: 2 - MEMORY: 29Gi - STRATEGY: multisession - - PLATFORM: ubuntu-2404 - BLOCK: 1:length(pkgs) - ARCH: amd64 - NCPUS: 2 - MEMORY: 29Gi - STRATEGY: multisession - - PLATFORM: ubuntu-2204 - BLOCK: 1:length(pkgs) - ARCH: amd64 - NCPUS: 2 - MEMORY: 29Gi - STRATEGY: multisession + # - PLATFORM: redhat-9 + # BLOCK: 1:length(pkgs) + # ARCH: amd64 + # NCPUS: 2 + # MEMORY: 29Gi + # STRATEGY: multisession + # - PLATFORM: redhat-8 + # BLOCK: 1:length(pkgs) + # ARCH: amd64 + # NCPUS: 2 + # MEMORY: 29Gi + # STRATEGY: multisession + # - PLATFORM: ubuntu-2404 + # BLOCK: 1:length(pkgs) + # ARCH: amd64 + # NCPUS: 2 + # MEMORY: 29Gi + # STRATEGY: multisession + # - PLATFORM: ubuntu-2204 + # BLOCK: 1:length(pkgs) + # ARCH: amd64 + # NCPUS: 2 + # MEMORY: 29Gi + # STRATEGY: multisession - PLATFORM: alpine-320 BLOCK: 1090:length(pkgs) ARCH: amd64 @@ -96,10 +96,42 @@ steps: # more complicated system dependencies which pak cannot resolve - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point - # - R -q -e 'options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs[${BLOCK}], c("biplotbootGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "TextMiningGUI", "later", "RclusTool", "Rcmdr", "RcmdrMisc", "RcmdrPlugin.aRnova", "RcmdrPlugin.BiclustGUI", "RcmdrPlugin.BWS1", "RcmdrPlugin.BWS2", "RcmdrPlugin.BWS3", "RcmdrPlugin.cpd", "RcmdrPlugin.DCCV", "RcmdrPlugin.DCE", "RcmdrPlugin.depthTools", "RcmdrPlugin.DoE", "RcmdrPlugin.EACSPIR", "RcmdrPlugin.EBM", "RcmdrPlugin.EcoVirtual", "RcmdrPlugin.Export", "RcmdrPlugin.EZR", "RcmdrPlugin.FactoMineR", "RcmdrPlugin.GWRM", "RcmdrPlugin.HH", "RcmdrPlugin.KMggplot2", "RcmdrPlugin.MA", "RcmdrPlugin.MPAStats", "RcmdrPlugin.NMBU", "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "StratigrapheR", "tcltk2", "TVMM", "uHMM", "RInno", "webshot2")); library(bincraftR); future::plan("${STRATEGY}", workers = ${NCPUS}, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); pkgs = foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "${PLATFORM}"))' + # - R -q -e 'options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs[${BLOCK}], c( "RInno", "skedastic", "ROI.plugin.qpoases", "RPushbullet", "SimNPH", "SimDesign","simCAT", "SIAmodules", "shinytest2", "shinyIRT", "ShinyItemAnalysis", "shiny.benchmark", "scDIFtest", "RSP", "ROracle", "ROI.plugin.qpoases", "ROI.plugin.highs", "ROI.plugin.cplex", "RmecabKo", "rmarchingcubes", "RcppMeCab", "Rcplex", "ravetools", "Rbeast", "Rblpapi", "RcppEnsmallen", "qtkit", "priorCON", "prior3D", "PerFit", "outlierensembles", "nomnoml", "mxfda", "MultBiplotR", "mstDIF", "minic", "Mega2R", "mdsr", "MCARtest", "makepipe", "lordif", "KSgeneral", "kequate", "jstager", "jrt", "irtreliability", "irtQ", "irtpwr", "irtGUI", "irtawsi", "highs", "GRShiny", "gpuR", "GPCMlasso", "googletraffic", "giacR", "gamstransfer", "flps", "flow", "filters", "faoutlier", "EthSEQ", "equateIRT", "EnrichIntersect", "EFA.dimensions", "DFIT", "designmatch", "dartR.spatial", "dartR.sexlinked", "dartR.sim", "dartR.popgen", "dartR.captive", "dartR.base","dartR", "D3mirt", "ctsem", "ctgdist", "CoTiMA", "ConvertPar", "cncaGUI", "clrng", "bscui", "BifactorIndicesCalculator", "autoFC", "airt")); library(bincraftR); future::plan("${STRATEGY}", workers = ${NCPUS}, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); pkgs = foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "${PLATFORM}"))' ### Manual pkg builds - # webshot2: wait for https://github.com/rstudio/r-system-requirements/pull/178 - - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL); pkgs = c("WH", "ymd"); pkgs = setdiff(pkgs, c("biplotbootGUI", "cncaGUI", "dynBiplotGUI", "ade4TkGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "TextMiningGUI", "later", "RclusTool", "Rcmdr", "RcmdrMisc", "RcmdrPlugin.aRnova", "RcmdrPlugin.BiclustGUI", "RcmdrPlugin.BWS1", "RcmdrPlugin.BWS2", "RcmdrPlugin.BWS3", "RcmdrPlugin.cpd", "RcmdrPlugin.DCCV", "RcmdrPlugin.DCE", "RcmdrPlugin.depthTools", "RcmdrPlugin.DoE", "RcmdrPlugin.EACSPIR", "RcmdrPlugin.EBM", "RcmdrPlugin.EcoVirtual", "RcmdrPlugin.Export", "RcmdrPlugin.EZR", "RcmdrPlugin.FactoMineR", "RcmdrPlugin.GWRM", "RcmdrPlugin.HH", "RcmdrPlugin.KMggplot2", "RcmdrPlugin.MA", "RcmdrPlugin.MPAStats", "RcmdrPlugin.NMBU", "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "sf", "StratigrapheR", "tcltk2", "TVMM", "uHMM", "RInno")); library(bincraftR); future::plan("${STRATEGY}", workers = ${NCPUS}, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers(global = TRUE); progressr::handlers("cli"); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "${PLATFORM}"))' + # 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 + # 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.highs: /usr/bin/ccache: invalid option -- 'E' + # ROI.plugin.cplex: checking for cplex... no -> needs rule + # 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 + # Rcplex: checking for cplex... no + # 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 + # priorCON, prior3D, MCARtest, designmatch -> highs + # minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed: + # Mega2R -> gdsfmt + # KSgeneral -> fftw3 + # multibiplotGUI: always hangs even when using xvfb-run + # gwid -> gdsfmt + # gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory + # GPCMlasso + # gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits::int_type' {aka 'int'} to 'char' [-Wnarrowing] + # filters: + # EthSEQ, dartR.spatial, dartR.sim -> gdsfmt + # ctsem: g++: fatal error: Killed signal terminated program cc1plus + # cncaGUI: always hangs even when using xvfb-run + # clrng -> gpuR + # BRugs: configure: error: OpenBUGS 3.2.2 or later not found. + # biplotbootGUI always hangs even when using xvfb-run + - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL); pkgs = c("WH", "ymd", "VPdtw", "voi", "rjags", "unmconf", "TVMM", "TTAinterfaceTrendAnalysis", "tfrmtbuilder", "uHMM", "TextMiningGUI", "cncaGUI", "dynBiplotGUI", "ade4TkGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "tensorBSS", "RclusTool", "Rcmdr", "RcmdrMisc", "RcmdrPlugin.aRnova", "RcmdrPlugin.BiclustGUI", "RcmdrPlugin.BWS1", "RcmdrPlugin.BWS2", "RcmdrPlugin.BWS3", "RcmdrPlugin.cpd", "RcmdrPlugin.DCCV", "RcmdrPlugin.DCE", "RcmdrPlugin.depthTools", "RcmdrPlugin.DoE", "RcmdrPlugin.EACSPIR", "RcmdrPlugin.EBM", "RcmdrPlugin.EcoVirtual", "RcmdrPlugin.Export", "RcmdrPlugin.EZR", "RcmdrPlugin.FactoMineR", "RcmdrPlugin.GWRM", "RcmdrPlugin.HH", "RcmdrPlugin.KMggplot2", "RcmdrPlugin.MA", "RcmdrPlugin.MPAStats", "RcmdrPlugin.NMBU", "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta"); library(bincraftR); future::plan("${STRATEGY}", workers = ${NCPUS}, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers(global = TRUE); progressr::handlers("cli"); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "${PLATFORM}"))' backend_options: kubernetes: ### PROD-parallel diff --git a/.woodpecker/warm_up_build.yaml b/.woodpecker/warm_up_build.yaml index 625a731..0f1938e 100644 --- a/.woodpecker/warm_up_build.yaml +++ b/.woodpecker/warm_up_build.yaml @@ -5,30 +5,30 @@ skip_clone: true matrix: include: - # - PLATFORM: redhat-9 - # BLOCK: 20099:21169 - # ARCH: arm64 - # NCPUS: 2 - # MEMORY: 29Gi - # STRATEGY: multisession - # - PLATFORM: redhat-8 - # BLOCK: 20099:21169 - # ARCH: arm64 - # NCPUS: 2 - # MEMORY: 29Gi - # STRATEGY: multisession - # - PLATFORM: ubuntu-2404 - # BLOCK: 20099:21169 - # ARCH: arm64 - # NCPUS: 2 - # MEMORY: 29Gi - # STRATEGY: multisession - # - PLATFORM: ubuntu-2204 - # BLOCK: 20099:21169 - # ARCH: arm64 - # NCPUS: 2 - # MEMORY: 29Gi - # STRATEGY: multisession + - PLATFORM: redhat-9 + BLOCK: 20099:21169 + ARCH: arm64 + NCPUS: 2 + MEMORY: 29Gi + STRATEGY: multisession + - PLATFORM: redhat-8 + BLOCK: 20099:21169 + ARCH: arm64 + NCPUS: 2 + MEMORY: 29Gi + STRATEGY: multisession + - PLATFORM: ubuntu-2404 + BLOCK: 20099:21169 + ARCH: arm64 + NCPUS: 2 + MEMORY: 29Gi + STRATEGY: multisession + - PLATFORM: ubuntu-2204 + BLOCK: 20099:21169 + ARCH: arm64 + NCPUS: 2 + MEMORY: 29Gi + STRATEGY: multisession - PLATFORM: alpine-320 BLOCK: 7065:length(pkgs) ARCH: arm64 @@ -36,30 +36,30 @@ matrix: MEMORY: 29Gi STRATEGY: multisession ### AMD - - PLATFORM: redhat-9 - BLOCK: 1:length(pkgs) - ARCH: amd64 - NCPUS: 2 - MEMORY: 29Gi - STRATEGY: multisession - - PLATFORM: redhat-8 - BLOCK: 1:length(pkgs) - ARCH: amd64 - NCPUS: 2 - MEMORY: 29Gi - STRATEGY: multisession - - PLATFORM: ubuntu-2404 - BLOCK: 1:length(pkgs) - ARCH: amd64 - NCPUS: 2 - MEMORY: 29Gi - STRATEGY: multisession - - PLATFORM: ubuntu-2204 - BLOCK: 1:length(pkgs) - ARCH: amd64 - NCPUS: 2 - MEMORY: 29Gi - STRATEGY: multisession + # - PLATFORM: redhat-9 + # BLOCK: 1:length(pkgs) + # ARCH: amd64 + # NCPUS: 2 + # MEMORY: 29Gi + # STRATEGY: multisession + # - PLATFORM: redhat-8 + # BLOCK: 1:length(pkgs) + # ARCH: amd64 + # NCPUS: 2 + # MEMORY: 29Gi + # STRATEGY: multisession + # - PLATFORM: ubuntu-2404 + # BLOCK: 1:length(pkgs) + # ARCH: amd64 + # NCPUS: 2 + # MEMORY: 29Gi + # STRATEGY: multisession + # - PLATFORM: ubuntu-2204 + # BLOCK: 1:length(pkgs) + # ARCH: amd64 + # NCPUS: 2 + # MEMORY: 29Gi + # STRATEGY: multisession - PLATFORM: alpine-320 BLOCK: 1090:length(pkgs) ARCH: amd64