rebuild missing pkgs
This commit is contained in:
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df583bcf37
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GPG key ID:
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2 changed files with 113 additions and 81 deletions
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@ -8,30 +8,30 @@ depends_on:
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matrix:
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include:
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# - PLATFORM: redhat-9
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# BLOCK: 20099:21169
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: redhat-8
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# BLOCK: 20099:21169
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: ubuntu-2404
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# BLOCK: 20099:21169
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: ubuntu-2204
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# BLOCK: 20099:21169
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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- PLATFORM: redhat-9
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BLOCK: 20099:21169
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ARCH: arm64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: redhat-8
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BLOCK: 20099:21169
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ARCH: arm64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: ubuntu-2404
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BLOCK: 20099:21169
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ARCH: arm64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: ubuntu-2204
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BLOCK: 20099:21169
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ARCH: arm64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: alpine-320
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BLOCK: 7065:length(pkgs)
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ARCH: arm64
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@ -39,30 +39,30 @@ matrix:
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MEMORY: 29Gi
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STRATEGY: multisession
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### AMD
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- PLATFORM: redhat-9
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BLOCK: 1:length(pkgs)
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ARCH: amd64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: redhat-8
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BLOCK: 1:length(pkgs)
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ARCH: amd64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: ubuntu-2404
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BLOCK: 1:length(pkgs)
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ARCH: amd64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: ubuntu-2204
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BLOCK: 1:length(pkgs)
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ARCH: amd64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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# - PLATFORM: redhat-9
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# BLOCK: 1:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: redhat-8
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# BLOCK: 1:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: ubuntu-2404
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# BLOCK: 1:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: ubuntu-2204
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# BLOCK: 1:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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- PLATFORM: alpine-320
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BLOCK: 1090:length(pkgs)
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ARCH: amd64
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@ -96,10 +96,42 @@ steps:
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# more complicated system dependencies which pak cannot resolve
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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# 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
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# - 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}"))'
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# - 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}"))'
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### Manual pkg builds
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# webshot2: wait for https://github.com/rstudio/r-system-requirements/pull/178
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- 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}"))'
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# 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
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# RInno: Windows-only
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# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
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# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3
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# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
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# ROracle: sysdep missing -> create rule
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# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
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# ROI.plugin.highs: /usr/bin/ccache: invalid option -- 'E'
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# ROI.plugin.cplex: checking for cplex... no -> needs rule
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# RmecabKo: fatal error: mecab.h: No such file or directory
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# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
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# RcppMeCab: /bin/bash: line 2: mecab-config: command not found
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# Rcplex: checking for cplex... no
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# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
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# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
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# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
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# Racmacs -> rmarchingcubes
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# priorCON, prior3D, MCARtest, designmatch -> highs
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# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
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# Mega2R -> gdsfmt
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# KSgeneral -> fftw3
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# multibiplotGUI: always hangs even when using xvfb-run
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# gwid -> gdsfmt
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# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory
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# GPCMlasso
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# 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]
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# filters: <simpleError: `target` must be a character vector containing no `NA` values.>
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# EthSEQ, dartR.spatial, dartR.sim -> gdsfmt
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# ctsem: g++: fatal error: Killed signal terminated program cc1plus
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# cncaGUI: always hangs even when using xvfb-run
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# clrng -> gpuR
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# BRugs: configure: error: OpenBUGS 3.2.2 or later not found.
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# biplotbootGUI always hangs even when using xvfb-run
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- 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}"))'
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backend_options:
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kubernetes:
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### PROD-parallel
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matrix:
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include:
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# - PLATFORM: redhat-9
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# BLOCK: 20099:21169
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: redhat-8
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# BLOCK: 20099:21169
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: ubuntu-2404
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# BLOCK: 20099:21169
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: ubuntu-2204
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# BLOCK: 20099:21169
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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- PLATFORM: redhat-9
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BLOCK: 20099:21169
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ARCH: arm64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: redhat-8
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BLOCK: 20099:21169
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ARCH: arm64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: ubuntu-2404
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BLOCK: 20099:21169
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ARCH: arm64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: ubuntu-2204
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BLOCK: 20099:21169
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ARCH: arm64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: alpine-320
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BLOCK: 7065:length(pkgs)
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ARCH: arm64
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MEMORY: 29Gi
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STRATEGY: multisession
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### AMD
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- PLATFORM: redhat-9
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BLOCK: 1:length(pkgs)
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ARCH: amd64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: redhat-8
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BLOCK: 1:length(pkgs)
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ARCH: amd64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: ubuntu-2404
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BLOCK: 1:length(pkgs)
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ARCH: amd64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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- PLATFORM: ubuntu-2204
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BLOCK: 1:length(pkgs)
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ARCH: amd64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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# - PLATFORM: redhat-9
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# BLOCK: 1:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: redhat-8
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# BLOCK: 1:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: ubuntu-2404
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# BLOCK: 1:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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# - PLATFORM: ubuntu-2204
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# BLOCK: 1:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: multisession
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- PLATFORM: alpine-320
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BLOCK: 1090:length(pkgs)
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ARCH: amd64
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