ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [cbind, rbind]

HenrikBengtsson / illuminaio

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http://bioconductor.org/packages/devel/bioc/html/illuminaio.html

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ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [cbind, rbind] #14

Closed HenrikBengtsson closed 4 years ago

HenrikBengtsson commented 4 years ago

$ for pkg in $pkgs; do echo "$pkg:"; (cd "$pkg"; grep -E "^[ \t]*[^#].*[cr]bind" -- */*.R | grep -vF stringsAsFactors;); echo; read -r -p "Press ENTER to continue ..."; done

illuminaio:
R/readIDAT_enc.R:    idx <- cbind(grep("<ProcessEntry>", lines), grep("</ProcessEntry>", lines))
R/readIDAT_nonenc.R:    Quants <- cbind(res$Mean, res$SD, res$NBeads)

HenrikBengtsson commented 4 years ago

Nothing to do here; there're no stringsAsFactors for any of the cbind() methods;

Functions that use stringsAsFactors = default.stringsAsFactors():

base::data.frame(x) for character columns in x
base::as.data.frame.character(x)
base::as.data.frame.matrix(x) if mode(x) == "character"
base::as.data.frame.list(x)
base::rbind.data.frame() for arguments that are (character) matrices
base::rbind.data.frame()
utils::read.DIF()
utils::read.table()