pat-s
f3c18b6805bincraft dropped pak in favour of uvr, so the pipelines, helper scripts and images in this repo move with it. - add local/uvr-install.sh as the single replacement for pak::pak(); it bootstraps a pinned uvr, mints a throwaway project under TMPDIR and runs `uvr add --no-install` + `uvr sync --library`, because `uvr add` refuses to run outside a project and only `sync` honours --library - install bincraft via its Forgejo spec (forgejo::codefloe.com/rpkgs/ bincraft@<tag>) instead of a git:: URL, keeping the git ls-remote tag resolution - pass UVR_R_BIN/UVR_TARGET_LIB from install-bincraft.R so the per-R-minor passes target their own R and library - replace R_PKG_CACHE_DIR with UVR_CACHE_DIR/UVR_PACKAGES_DIR on the persistent volume, preserving the amd64-off/arm64-on split - drop trim_pkgcache_metadata() and its test; uvr's cache does not grow the way pkgcache's _metadata dir did - let uvr install system requirements from its vendored r-system-requirements rules, replacing pak::sysreqs_db_update() - migrate the shiny app image, the alpine reprex and the CRAN loading test; ship uvr-install.sh in the build-one image - track the uvr pin with renovate
337 lines
5.2 KiB
R
337 lines
5.2 KiB
R
# Installs every CRAN package one by one and checks that it loads. Dependencies
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# go through uvr via local/uvr-install.sh, which bootstraps the uvr binary on
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# first use and installs into .libPaths()[1].
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uvr_install <- function(pkg) {
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Sys.setenv(
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UVR_R_BIN = file.path(R.home("bin"), "R"),
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UVR_TARGET_LIB = .libPaths()[1L]
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)
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status <- system2("local/uvr-install.sh", shQuote(pkg))
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if (!identical(status, 0L)) {
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stop(
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sprintf("uvr failed to install %s (exit %s)", pkg, status),
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call. = FALSE
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)
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}
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}
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all_pkgs <- rownames(available.packages())
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to_skip <- c("ABRSQOL", "ACA", "ACE.CoCo")
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all_pkgs <- setdiff(all_pkgs, to_skip)
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for (i in all_pkgs) {
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message(sprintf("\nInstalling %s", i))
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uvr_install(i)
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library(i, character.only = TRUE)
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}
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# Example data
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all_pkgs <- rownames(available.packages())
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to_skip <- c(
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"ABRSQOL",
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"ACA",
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"ACE.CoCo",
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"ACEsimFit",
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"ACNE",
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"absorber",
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"adapt4pv",
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"adaptMCMC",
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"addhaz",
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"ADDT",
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"ahaz",
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"arm",
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"arules",
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"arulesCBA",
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"aster2",
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"BayesFactor",
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"bc3net",
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"bgsmtr",
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"biglasso",
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"BinNonNor",
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"BinNor",
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"bioassayR",
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"birankr",
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"BiRewire",
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"bolasso",
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"Boptbd",
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"Brobdingnag",
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"BSW",
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"BTLLasso",
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"bvartools",
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"cAIC4",
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"Category",
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"celda",
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"centiserve",
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"cjoint",
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"clinical",
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"clipper",
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"CodataGS",
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"conos",
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"CopulaInference",
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"covEB",
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"cplm",
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"CRTgeeDR",
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"cthreshER",
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"ctmcmove",
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"curephEM",
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"CVST",
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"dcGSA",
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"dclone",
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"dcsvm",
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"DelayedArray",
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"dglars",
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"dhglm",
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"disordR",
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"distrom",
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"dmm",
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"DNABarcodes",
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"DoubleCone",
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"DRR",
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"DTRlearn2",
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"DWDLargeR",
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"eds",
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"EMCluster",
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"EMMREML",
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"evalITR",
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"EventPointer",
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"evola",
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"excursions",
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"expm",
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"fanc",
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"FAS",
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"fastadi",
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"fastPLS",
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"fastRG",
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"fdaPDE",
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"flare",
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"FoReco",
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"frailtyHL",
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"freebird",
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"FSTpackage",
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"gamlr",
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"gamlss.lasso",
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"gamm4",
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"gbmt",
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"gdim",
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"gdistance",
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"GeDS",
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"geeM",
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"genlasso",
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"GenOrd",
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"GenoScan",
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"geomorph",
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"geostatsp",
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"GhostKnockoff",
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"GIGSEA",
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"GlarmaVarSel",
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"glmm",
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"glmmrBase",
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"glmmrOptim",
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"glmnet",
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"glober",
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"GPvam",
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"graphpcor",
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"gremlin",
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"growthrate",
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"grpCox",
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"GSD",
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"HelpersMG",
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"hglm",
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"hglm.data",
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"hibayes",
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"hierSDR",
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"HMTL",
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"hsem",
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"ibmdbR",
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"inca",
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"INLAspacetime",
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"INLAtools",
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"invertiforms",
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"irlba",
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"islasso",
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"ISLET",
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"isotonic.pen",
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"jordan",
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"kinship2",
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"KnockoffScreen",
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"lcpm",
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"leidenAlg",
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"lfe",
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"lingmatch",
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"LKT",
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"lme4",
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"lme4breeding",
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"lme4GS",
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"logcondiscr",
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"LPmerge",
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"LRMF3",
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"MAP",
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"marcox",
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"markovchain",
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"MatrixExtra",
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"matter",
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"MBC",
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"mcen",
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"mclogit",
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"MCMCglmm",
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"mdhglm",
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"MDPtoolbox",
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"mediation",
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"mefa4",
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"metafor",
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"mgwrsar",
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"mi",
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"midasml",
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"mind",
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"monocle",
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"msda",
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"MuData",
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"MultiGlarmaVarSel",
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"MultiOrd",
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"MultiVarSel",
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"mvglmmRank",
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"N2R",
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"nadiv",
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"NBtsVarSel",
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"NegBinBetaBinreg",
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"NetworkRiskMeasures",
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"neuroim2",
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"NOISeq",
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"numbat",
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"optbdmaeAT",
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"optimbase",
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"OptimModel",
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"optrcdmaeAT",
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"OrdNor",
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"pagoda2",
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"PCovR",
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"pedgene",
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"pedigree",
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"pedigreemm",
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"pense",
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"PERMANOVA",
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"phateR",
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"PhylogeneticEM",
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"pleio",
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"POINT",
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"PoisBinNonNor",
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"PoisBinOrd",
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"PoisBinOrdNonNor",
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"PoisBinOrdNor",
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"PoisNonNor",
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"PoisNor",
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"PRISMA",
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"ProbitSpatial",
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"prodest",
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"psqn",
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"qlcMatrix",
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"qpcR",
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"QRM",
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"quadrupen",
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"QZ",
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"ramps",
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"randnet",
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"randPedPCA",
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"rBMF",
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"RCBR",
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"RealVAMS",
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"REBayes",
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"recommenderlab",
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"Rediscover",
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"reglogit",
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"RESET",
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"RGE",
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"RGENERATEPREC",
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"riemtan",
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"RNewsflow",
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"robustlmm",
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"rsparse",
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"rSPDE",
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"rwc",
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"S4Arrays",
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"saeMSPE",
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"sbw",
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"scITD",
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"scoup",
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"sdwd",
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"SEAGLE",
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"sensory",
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"serrsBayes",
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"sglasso",
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"sharpPen",
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"SiPSiC",
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"SKAT",
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"snpReady",
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"snpStats",
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"softImpute",
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"sommer",
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"soptdmaeA",
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"SOR",
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"SparseArray",
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"SparseChol",
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"sparseLRMatrix",
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"sparsenet",
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"sparsenetgls",
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"sparsestep",
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"spatialprobit",
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"spatialreg",
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"spatstat.sparse",
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"speedglm",
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"sRDA",
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"sSDR",
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"ssfa",
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"stcos",
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"StratifiedSampling",
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"sureLDA",
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"survey",
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"surveyvoi",
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"svydiags",
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"systemfit",
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"TargetScore",
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"text2map",
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"textir",
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"textmineR",
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"textTinyR",
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"tmvtnorm",
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"TPEA",
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"triversity",
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"tsapp",
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"tvReg",
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"uwot",
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"vagam",
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"VAM",
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"WaveSampling",
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"WGScan",
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"wordspace",
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"workflowsets",
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"ACSSpack",
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"ADDT",
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"AER"
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)
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# Find the position of the last package in to_skip within all_pkgs
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last_skip <- tail(to_skip, 1)
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# Find its position in all_pkgs (returns NA if not found)
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start_pos <- match(last_skip, all_pkgs)
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# If not found, start from the beginning; else, start after last_skip
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if (is.na(start_pos)) {
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to_process <- all_pkgs
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} else {
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to_process <- all_pkgs[(start_pos + 1):length(all_pkgs)]
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}
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if (length(to_process) == 0) {
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message("All packages have been processed.")
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} else {
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for (i in to_process) {
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message(sprintf("\nInstalling %s", i))
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uvr_install(i)
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library(i, character.only = TRUE)
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}
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# Update to_skip to include all up to the last processed
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to_skip <- all_pkgs[1:(last_skip_pos + length(to_process))]
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}
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