regionstat.R should be more verbose if it cannot find the BSGenome package used for calculating and plotting GC content

[donaldcampbelljr]

Currently, the pipeline may skip calculating GC content if it cannot find the associated BSGenoma package in the namespace. Unfortunately, it does not log this and silently skips attempting to calculate the GC content:

bedboss/bedboss/bedstat/tools/regionstat.R

Lines 95 to 98 in b23c0a7

	doItAall <- function(query, fileId, genome, cellMatrix) {
	plots = data.frame(stringsAsFactors=F)
	bsGenomeAvail = ifelse((requireNamespace(BSg, quietly=TRUE) | requireNamespace(BSgm, quietly=TRUE)), TRUE, FALSE)

bedboss/bedboss/bedstat/tools/regionstat.R

Lines 188 to 215 in b23c0a7

	if (run_plot){
	if (bsGenomeAvail) {
	tryCatch(
	expr = {
	if (requireNamespace(BSgm, quietly=TRUE)){
	library (BSgm, character.only = TRUE)
	bsg = eval(as.name(BSgm))
	gcvec = calcGCContent(query, bsg)
	} else {
	library (BSg, character.only = TRUE)
	bsg = eval(as.name(BSg))
	gcvec = calcGCContent(query, bsg)
	}
	plotBoth("gccontent", plotGCContent(gcvec))
	if (exists("bedmeta")){
	gc_content <- list(gc_content = signif(mean(gcvec), digits = 4))
	bedmeta = append(bedmeta, gc_content)
	}
	plots = rbind(plots, getPlotReportDF("gccontent", "GC content"))
	message("Successfully calculated and plot GC content.")
	},
	error = function(e){
	message('Caught an error in creating: GC content plot!')
	print(e, gcvec)
	}
	)
	}
	}

Simple solution would be to remove the quietly=TRUE from line 97, so that we capture this info:

Loading required namespace: BSgenome.Hsapiens.UCSC.hg38.masked
Failed with error:  'there is no package called 'BSgenome.Hsapiens.UCSC.hg38.masked''

[donaldcampbelljr]

Should we also add the common ones to our R dependency installation script?

# build BSgenome package ID to check whether it's installed
if ( startsWith(genome, "T2T")){
  BSg = "BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0"
} else {
  if (startsWith(genome, "hg") | startsWith(genome, "grch")) {
    orgName = "Hsapiens"
  } else if (startsWith(genome, "mm") | startsWith(genome, "grcm")){
    orgName = "Mmusculus"
  } else if (startsWith(genome, "dm")){
    orgName = "Dmelanogaster"
  } else if (startsWith(genome, "ce")){
    orgName = "Celegans"
  } else if (startsWith(genome, "danRer")){
    orgName = "Drerio"
  }  else if (startsWith(genome, "TAIR")){
    orgName = "Athaliana"
  } else {
    orgName = "Undefined"
  }
  BSg = paste0("BSgenome.", orgName , ".UCSC.", genome)
}

BSgm = paste0(BSg, ".masked")

In installRdeps.R ?