code in this gist attempts to prepare R to identify causes of CHECK_SUGGESTS_ONLY errors

check_discrepant_pkgs.R

stopifnot(Sys.getenv("_R_CHECK_SUGGESTS_ONLY_") == "true")
# these error in check on nebbiolo2 but not lconway

suggposs = c("AffyRNADegradation", "alabaster.spatial", "ANF", "animalcules", 
"BDMMAcorrect", "bnbc", "CancerSubtypes", "ccrepe", "CDI", "cellscape", 
"ClassifyR", "CNVgears", "CoGAPS", "compartmap", "CoRegNet", 
"crisprseekplus", "DEWSeq", "DEXSeq", "DMCFB", "dpeak", "DSS", 
"EasyCellType", "eegc", "EGSEA", "EpiCompare", "exomePeak2", 
"farms", "FCBF", "flowMap", "FoldGO", "FScanR", "GCSscore", "GenomicFeatures", 
"GEOmetadb", "GEOquery", "gscreend", "HelloRanges", "ILoReg", 
"Informeasure", "IRISFGM", "Linnorm", "logitT", "maigesPack", 
"MEAL", "MetaVolcanoR", "methrix", "miRBaseConverter", "miRmine", 
"mixOmics", "MSstatsSampleSize", "multiOmicsViz", "NeighborNet", 
"netDx", "NeuCA", "oneSENSE", "ontoProc", "orthos", "pathVar", 
"PERFect", "proteasy", "pwrEWAS", "RCAS", "RcisTarget", "Rcollectl", 
"RCSL", "ReactomeGSA", "RefPlus", "RegEnrich", "rexposome", "RIPAT", 
"rtracklayer", "SCATE", "SEPIRA", "SISPA", "sparseDOSSA", "sscore", 
"STROMA4", "trena")

ii = rownames(installed.packages())

getsrc = function(x) {
 z = tryCatch(
        BiocManager::install(x, dependencies=TRUE, ask=FALSE, update=TRUE),
            warning = function(cond) cond)  # purpose is to get dependencies before check
 if (inherits(z, "simpleWarning")) {
      chk = grep("is not available", z$message)
      if (length(chk)==0) stop(sprintf("atypical condition for BiocManager::install for %s"))
      message("trying a download.packages from BiocManager::repositories")
      download.packages(x, dest=".", repos=BiocManager::repositories())
      if (!file.exists(x)) {  # didn't work, use git
      message("trying git")
      system(sprintf("git clone https://git.bioconductor.org/packages/%s", x))
    }
   }
 if (file.exists(x)) system(sprintf("R CMD build %s", x))
 else stop("could not get a source folder to build")
}

ind = 22

# prepare R
library(BiocPkgTools)
bb = buildPkgDependencyDataFrame()
library(dplyr)
ndf = bb |> filter(Package == suggposs[ind]) |> select(dependency) |> as.data.frame()
toget = setdiff(ndf$dependency, ii)
BiocManager::install(toget)


getsrc(suggposs[ind])

system(paste0("R CMD check ", dir(patt=paste0(suggposs[ind], "_"))))