On Feb 13, 2013, at 12:07 PM, Scott Robinson <scott.robin...@glasgow.ac.uk>
wrote:
> Dear All,
>
> I am using WriteXLS to write tables with multiple sheets with the command:
>
> WriteXLS("tables", ExcelFileName = fileName, SheetNames = tableList, perl =
> "perl",
> verbose = FALSE, Encoding = c("UTF-8", "latin1"),
> row.names = TRUE, col.names = TRUE,
> AdjWidth = TRUE, AutoFilter = FALSE, BoldHeaderRow = FALSE,
> FreezeRow = 0, FreezeCol = 0,
> envir = parent.frame())
>
>
> ...where "tables" is the name of a list of data.frames which are the tables
> to go into my sheets. I am having no problem running my code unless it is
> within a function in which case I get the error:
>
> "Error in get(as.character(x), envir = envir) : object 'tables' not found"
>
> I have checked that there is not an issue with scope using these two lines
> within my function immediately before calling the WriteXLS function:
>
> print(class(tables))
> flush.console()
> [1] "list"
>
>
> At least I would have thought this would have ruled out any scope-related
> issues. Has anyone else had this problem or have any ideas why it might be
> happening?
>
> Thanks,
>
> Scott
>
>
> PS here is the function in full:
>
> makeTables <- function(design, designInfo, oldMatrix, matrix, annot,
> tableList)
> {
> rownames(design) <- designInfo[,1]
>
> fit <- lmFit(matrix, design)
> fit <- eBayes(fit)
>
> tables<-list()
>
> for (i in 1:length(tableList))
> {
> table <- makeTable(oldMatrix, matrix, annot, fit, tableList[i])
> print(paste(tableList[i], "=", sep=""))
> print(table)
> tables[[i]] <- table
> }
>
> #Saving bit (set to FALSE if not using)
> saveIt <- TRUE
>
> if(saveIt)
> {
> fileName <-
> paste0("~",paste(colnames(design)[2:length(colnames(design))], collapse =
> "+"),".xls")
>
> print(paste("sheetnames=",length(tableList),
>
> print(class(tables))
> flush.console()
>
> WriteXLS("tables", ExcelFileName = fileName, SheetNames = tableList,
> perl = "perl",
> verbose = FALSE, Encoding = c("UTF-8", "latin1"),
> row.names = TRUE, col.names = TRUE,
> AdjWidth = TRUE, AutoFilter = FALSE, BoldHeaderRow = FALSE,
> FreezeRow = 0, FreezeCol = 0,
> envir = parent.frame())
> }
> }
Hi Scott,
In the call to WriteXLS() within your function, leave out the final argument
line 'envir = parent.frame()'. That is causing WriteXLS() to look for "tables"
in the environment in which your function makeTables() is being called and of
course, "tables" does not exist there, but only within the scope of
makeTables(). Leaving the argument out allows WriteXLS() to look for "tables"
within the environment in which it is called.
This is a nuance when using environments within functions. The same thing
commonly happens when folks use the 'subset' argument with modeling functions
that are themselves called within a function body.
As an example with WriteXLS():
test <- function() {
localData <- split(iris, iris$Species)
WriteXLS("localData", "LocalData.xls", envir = parent.frame())
}
> test()
Error in get(as.character(x), envir = envir) :
object 'localData' not found
localData <- split(iris, iris$Species)
test() # Works fine
rm(localData)
> test()
Error in get(as.character(x), envir = envir) :
object 'localData' not found
test <- function() {
localData <- split(iris, iris$Species)
WriteXLS("localData", "LocalData.xls")
}
test() # Works fine
Hope that clarifies.
Regards,
Marc Schwartz
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