/usr/lib/R/site-library/Biobase/UnitTests/utilities.R is in r-bioc-biobase 2.14.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ## these assume we're in Biobase/inst/UnitTests
createCurrentInstances <- function(instanceDir = "VersionedClass_data") {
require("Biobase")
classes <- getClasses("package:Biobase")
isVirtual <- sapply(classes, function(nm) getClass(nm)@virtual)
nonvirtualClasses <- classes[!isVirtual]
instances <- sub(".Rda", "",
list.files(path=file.path(instanceDir, "devel"), pattern=".*.Rda"))
need <- nonvirtualClasses[!nonvirtualClasses %in% instances]
if (length(need)!=0) {
cat("need:", need, "\n")
lapply(need, function(cls) {
cat("creating", cls, "\n")
assign(cls, new(cls))
save(list=cls,
file=file.path(instanceDir, "devel", paste(cls, ".Rda", sep="")))
})
} else cat("no instances need creating\n")
}
createComponentClasses <- function(ExpressionSet, vers="devel", instanceDir = "VersionedClass_data") {
MIAME <- experimentData(ExpressionSet)
AnnotatedDataFrame <- phenoData(ExpressionSet)
cat("creating MIAME\n")
save(MIAME, file=file.path(instanceDir, vers, "MIAME.Rda"))
cat("creating AnnotatedDataFrame\n")
save(AnnotatedDataFrame, file=file.path(instanceDir, vers, "AnnotatedDataFrame.Rda"))
}
|