From 442b9bfaa4179023c203bbe422ed641ee31a8715 Mon Sep 17 00:00:00 2001 From: pat-s Date: Sat, 21 Sep 2024 12:10:41 +0200 Subject: [PATCH] fix rhel8 deps --- .woodpecker/build.yaml | 7 +++++-- R/install-deps.R | 2 +- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.woodpecker/build.yaml b/.woodpecker/build.yaml index 1fa82c4..edd0d09 100644 --- a/.woodpecker/build.yaml +++ b/.woodpecker/build.yaml @@ -15,7 +15,7 @@ matrix: MEMORY: 29Gi STRATEGY: multisession - PLATFORM: redhat-8 - BLOCK: 105:length(pkgs) + BLOCK: 1:length(pkgs) ARCH: arm64 NCPUS: 2 MEMORY: 29Gi @@ -46,7 +46,7 @@ matrix: MEMORY: 29Gi STRATEGY: multisession - PLATFORM: redhat-8 - BLOCK: 156:length(pkgs) + BLOCK: 1:length(pkgs) ARCH: amd64 NCPUS: 2 MEMORY: 29Gi @@ -96,6 +96,9 @@ 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 + ### Check + # - Rsymphony + # - Rglpk - 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", "RPushbullet", "SimNPH", "SimDesign","simCAT", "SIAmodules", "shinytest2", "shinyIRT", "ShinyItemAnalysis", "shiny.benchmark", "scDIFtest", "RSP", "ROracle", "ROI.plugin.qpoases", "ROI.plugin.cplex", "RmecabKo", "rmarchingcubes", "RcppMeCab", "Rcplex", "ravetools", "Rbeast", "Rblpapi", "RcppEnsmallen", "qtkit", "priorCON", "prior3D", "PerFit", "outlierensembles", "nomnoml", "mxfda", "MultBiplotR", "mstDIF", "mdsr", "makepipe", "lordif", "KSgeneral", "kequate", "jstager", "jrt", "irtreliability", "irtQ", "irtpwr", "irtawsi", "GRShiny", "gpuR", "googletraffic", "giacR", "gamstransfer", "flps", "flow", "filters", "faoutlier", "equateIRT", "EnrichIntersect", "EFA.dimensions", "DFIT", "D3mirt", "ctgdist", "CoTiMA", "ConvertPar", "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, 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 diff --git a/R/install-deps.R b/R/install-deps.R index ccfb916..9545b73 100644 --- a/R/install-deps.R +++ b/R/install-deps.R @@ -28,7 +28,7 @@ install_package_system_dependencies <- function(package_name, # FIXME: https://github.com/r-lib/pak/issues/610 if (grepl("rhel-9", pak::system_r_platform())) { Sys.setenv(PKG_SYSREQS_PLATFORM = "redhat-9") - } else if (grepl("rhel-9", pak::system_r_platform())) { + } else if (grepl("rhel-8", pak::system_r_platform())) { Sys.setenv(PKG_SYSREQS_PLATFORM = "redhat-8") } if (deps_verbose) {