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I am trying to set the working directory to a different subfolder in a function. I expected the print command to print 

C:/Users/Blah/Desktop/dir2/SUBFOLDER

instead it prints 

C:/Users/Blah/Desktop/dir2

Yet when I run dirs in console I get: 

C:/Users/Blah/Desktop/dir2/SUBFOLDER 
...(Much longer list)

like I expected. Here is my code:

temp<-function(path)
{
  print(path) #output is C:/Users/Blah/Desktop/dir2
  setwd(path)
  print(getwd())
  xml=xmlParse("filename.xml")
  ...
}

dirs<-list.dirs("C:/Users/Blah/Desktop/dir2")
lapply(dirs,temp)#apply function tempt to every item in dirs
Rilcon42
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    I guess the first directory is the root directory you specified. What about `lapply(dirs[-1],temp)`? – lukeA Feb 16 '15 at 21:48
  • I don't know exactly what you see as output, but the first element of the vector (after running `dirs<-list.dirs("C:/Users/Blah/Desktop/dir2"`) is the current directory i.e. in your case `"C:/Users/Blah/Desktop/dir2"`. So, this is the one that would be printed first by your function (and then all the subfolders). At least this is the normal behaviour. – LyzandeR Feb 16 '15 at 21:49

2 Answers2

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Your question is rather difficult to follow.

list.dirs will return (by default) the paths relative to the current working directory.

If you change the working directory, then the relative paths will not be valid.

You could try using full.names = TRUE within list.dirs having your temp function return the working directory to it's original state

temp <- function(path) {
           owd <- getwd()
           on.exit(setwd(owd))
           print(path) 
           setwd(path)
         print(getwd())
    }

An even better idea might be to, instead of messing with the working directory, simply pass the appropriate file name to xmlParse (or whatever your function is doing)

files <- list.files(pattern = '\\.xml$', recurvise = TRUE)
XML <-   lapply(files, xmlParse)
mnel
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  • In my final code I did as you suggested (rather then changing setwd()) but @davidrd's solution was what I needed. Thanks! – Rilcon42 Feb 16 '15 at 22:16
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Have you checked the optional arguments of list.dirs() ? (https://stat.ethz.ch/R-manual/R-devel/library/base/html/list.files.html)

The documentation says that by default, the answer includes "path" itself, so your function temp will first be applied with the directory you give to list.dirs(), "C:/Users/Blah/Desktop/dir2". You may want to try with list.dirs("C:/Users/Blah/Desktop/dir2", recursive = FALSE) (if it's ok with what you want)

davidrd
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