Error saving in resultDir

[kimleed]

Analysis DONE, saving the results...
Error in if (!dir.exists(rawFCSdir)) { : the condition has length > 1

I keep getting the above error message.

Any tips on troubleshooting?

Using R 4.3.1 on Mac and Bioconductor 3.17

[Diffeyb]

Hi,

I came across this a while back and found the problem/solution. It's due to this section in the main function:

cytofkit2/R/cytofkit.R

Lines 136 to 148 in 173744d

	if (is.null(fcsFiles) || is.na(fcsFiles) || is.nan(fcsFiles)){
	stop("Wrong input fcsFiles!")
	}else if (length(fcsFiles) == 1 && file.info(fcsFiles)$isdir) {
	fcsFiles <- list.files(path = fcsFiles, pattern = ".fcs$",
	full.names = TRUE)
	rawFCSdir <- dirname(fcsFiles)
	}else{
	if(dirname(fcsFiles[1]) == "."){
	rawFCSdir <- getwd()
	}else{
	rawFCSdir <- dirname(fcsFiles[1])
	}
	}

Specifically lines 138:141. You're supplying a path to your FCS files, so it updates 'fcsFiles' to a path list of fcs files in that folder, but then doesn't take that into account when setting the rawFCSdir and assigns it the dir of every FCS file. That's what causes the condition has length>1 error, rawFCSdir is as long as the number of files you have.

There are two solutions, either move the definition of rawFCSdir above the file discovery and drop the dirname() as it's already the directory :
rawFCSdir <- fcsFiles
fcsFiles <- list.files(path = fcsFiles, pattern = ".fcs$",
full.names = TRUE)
Or my preference (as it's simpler), only take the first directory from the list:
fcsFiles <- list.files(path = fcsFiles, pattern = ".fcs$",
full.names = TRUE)
rawFCSdir <- dirname(fcsFiles)[1]
That way you only have the one raw directory and nothing breaks.

As for how to update it. I've no idea if this is a common practice or not, but something I stumbled across is trace(). Put your function in and set edit=TRUE and it'll pop a window to edit the function in your session, so for this you'd have:
'trace(cytofkit2::cytofkit,edit=TRUE)'
Then save it and it'll update the function when it until you end the session.