# Installs every CRAN package one by one and checks that it loads. Dependencies
# go through uvr via local/uvr-install.sh, which bootstraps the uvr binary on
# first use and installs into .libPaths()[1].
uvr_install <- function(pkg) {
  Sys.setenv(
    UVR_R_BIN = file.path(R.home("bin"), "R"),
    UVR_TARGET_LIB = .libPaths()[1L]
  )
  status <- system2("local/uvr-install.sh", shQuote(pkg))
  if (!identical(status, 0L)) {
    stop(
      sprintf("uvr failed to install %s (exit %s)", pkg, status),
      call. = FALSE
    )
  }
}

all_pkgs <- rownames(available.packages())

to_skip <- c("ABRSQOL", "ACA", "ACE.CoCo")
all_pkgs <- setdiff(all_pkgs, to_skip)

for (i in all_pkgs) {
  message(sprintf("\nInstalling %s", i))
  uvr_install(i)
  library(i, character.only = TRUE)
}


# Example data
all_pkgs <- rownames(available.packages())
to_skip <- c(
  "ABRSQOL",
  "ACA",
  "ACE.CoCo",
  "ACEsimFit",
  "ACNE",
  "absorber",
  "adapt4pv",
  "adaptMCMC",
  "addhaz",
  "ADDT",
  "ahaz",
  "arm",
  "arules",
  "arulesCBA",
  "aster2",
  "BayesFactor",
  "bc3net",
  "bgsmtr",
  "biglasso",
  "BinNonNor",
  "BinNor",
  "bioassayR",
  "birankr",
  "BiRewire",
  "bolasso",
  "Boptbd",
  "Brobdingnag",
  "BSW",
  "BTLLasso",
  "bvartools",
  "cAIC4",
  "Category",
  "celda",
  "centiserve",
  "cjoint",
  "clinical",
  "clipper",
  "CodataGS",
  "conos",
  "CopulaInference",
  "covEB",
  "cplm",
  "CRTgeeDR",
  "cthreshER",
  "ctmcmove",
  "curephEM",
  "CVST",
  "dcGSA",
  "dclone",
  "dcsvm",
  "DelayedArray",
  "dglars",
  "dhglm",
  "disordR",
  "distrom",
  "dmm",
  "DNABarcodes",
  "DoubleCone",
  "DRR",
  "DTRlearn2",
  "DWDLargeR",
  "eds",
  "EMCluster",
  "EMMREML",
  "evalITR",
  "EventPointer",
  "evola",
  "excursions",
  "expm",
  "fanc",
  "FAS",
  "fastadi",
  "fastPLS",
  "fastRG",
  "fdaPDE",
  "flare",
  "FoReco",
  "frailtyHL",
  "freebird",
  "FSTpackage",
  "gamlr",
  "gamlss.lasso",
  "gamm4",
  "gbmt",
  "gdim",
  "gdistance",
  "GeDS",
  "geeM",
  "genlasso",
  "GenOrd",
  "GenoScan",
  "geomorph",
  "geostatsp",
  "GhostKnockoff",
  "GIGSEA",
  "GlarmaVarSel",
  "glmm",
  "glmmrBase",
  "glmmrOptim",
  "glmnet",
  "glober",
  "GPvam",
  "graphpcor",
  "gremlin",
  "growthrate",
  "grpCox",
  "GSD",
  "HelpersMG",
  "hglm",
  "hglm.data",
  "hibayes",
  "hierSDR",
  "HMTL",
  "hsem",
  "ibmdbR",
  "inca",
  "INLAspacetime",
  "INLAtools",
  "invertiforms",
  "irlba",
  "islasso",
  "ISLET",
  "isotonic.pen",
  "jordan",
  "kinship2",
  "KnockoffScreen",
  "lcpm",
  "leidenAlg",
  "lfe",
  "lingmatch",
  "LKT",
  "lme4",
  "lme4breeding",
  "lme4GS",
  "logcondiscr",
  "LPmerge",
  "LRMF3",
  "MAP",
  "marcox",
  "markovchain",
  "MatrixExtra",
  "matter",
  "MBC",
  "mcen",
  "mclogit",
  "MCMCglmm",
  "mdhglm",
  "MDPtoolbox",
  "mediation",
  "mefa4",
  "metafor",
  "mgwrsar",
  "mi",
  "midasml",
  "mind",
  "monocle",
  "msda",
  "MuData",
  "MultiGlarmaVarSel",
  "MultiOrd",
  "MultiVarSel",
  "mvglmmRank",
  "N2R",
  "nadiv",
  "NBtsVarSel",
  "NegBinBetaBinreg",
  "NetworkRiskMeasures",
  "neuroim2",
  "NOISeq",
  "numbat",
  "optbdmaeAT",
  "optimbase",
  "OptimModel",
  "optrcdmaeAT",
  "OrdNor",
  "pagoda2",
  "PCovR",
  "pedgene",
  "pedigree",
  "pedigreemm",
  "pense",
  "PERMANOVA",
  "phateR",
  "PhylogeneticEM",
  "pleio",
  "POINT",
  "PoisBinNonNor",
  "PoisBinOrd",
  "PoisBinOrdNonNor",
  "PoisBinOrdNor",
  "PoisNonNor",
  "PoisNor",
  "PRISMA",
  "ProbitSpatial",
  "prodest",
  "psqn",
  "qlcMatrix",
  "qpcR",
  "QRM",
  "quadrupen",
  "QZ",
  "ramps",
  "randnet",
  "randPedPCA",
  "rBMF",
  "RCBR",
  "RealVAMS",
  "REBayes",
  "recommenderlab",
  "Rediscover",
  "reglogit",
  "RESET",
  "RGE",
  "RGENERATEPREC",
  "riemtan",
  "RNewsflow",
  "robustlmm",
  "rsparse",
  "rSPDE",
  "rwc",
  "S4Arrays",
  "saeMSPE",
  "sbw",
  "scITD",
  "scoup",
  "sdwd",
  "SEAGLE",
  "sensory",
  "serrsBayes",
  "sglasso",
  "sharpPen",
  "SiPSiC",
  "SKAT",
  "snpReady",
  "snpStats",
  "softImpute",
  "sommer",
  "soptdmaeA",
  "SOR",
  "SparseArray",
  "SparseChol",
  "sparseLRMatrix",
  "sparsenet",
  "sparsenetgls",
  "sparsestep",
  "spatialprobit",
  "spatialreg",
  "spatstat.sparse",
  "speedglm",
  "sRDA",
  "sSDR",
  "ssfa",
  "stcos",
  "StratifiedSampling",
  "sureLDA",
  "survey",
  "surveyvoi",
  "svydiags",
  "systemfit",
  "TargetScore",
  "text2map",
  "textir",
  "textmineR",
  "textTinyR",
  "tmvtnorm",
  "TPEA",
  "triversity",
  "tsapp",
  "tvReg",
  "uwot",
  "vagam",
  "VAM",
  "WaveSampling",
  "WGScan",
  "wordspace",
  "workflowsets",
  "ACSSpack",
  "ADDT",
  "AER"
)

# Find the position of the last package in to_skip within all_pkgs
last_skip <- tail(to_skip, 1)

# Find its position in all_pkgs (returns NA if not found)
start_pos <- match(last_skip, all_pkgs)

# If not found, start from the beginning; else, start after last_skip
if (is.na(start_pos)) {
  to_process <- all_pkgs
} else {
  to_process <- all_pkgs[(start_pos + 1):length(all_pkgs)]
}

if (length(to_process) == 0) {
  message("All packages have been processed.")
} else {
  for (i in to_process) {
    message(sprintf("\nInstalling %s", i))
    uvr_install(i)
    library(i, character.only = TRUE)
  }
  # Update to_skip to include all up to the last processed
  to_skip <- all_pkgs[1:(last_skip_pos + length(to_process))]
}