Skipping error in for-loop

96
votes

I am doing a for loop for generating 180 graphs for my 6000 X 180 matrix (1 graph per column), some of the data don't fit my criteria and i get the error: 

"Error in cut.default(x, breaks = bigbreak, include.lowest = T) 
'breaks' are not unique".

I am fine with the error, I want the program to continue running the for loop, and give me a list of what columns made this error (as a variable containing column names maybe?).

Here's my command:

for (v in 2:180){
    mypath=file.path("C:", "file1", (paste("graph",names(mydata[columnname]), ".pdf", sep="-")))
    pdf(file=mypath)
    mytitle = paste("anything")
    myplotfunction(mydata[,columnnumber]) ## this function is defined previously in the program
    dev.off()
}

Note: I have found numerous posts about tryCatch and none of them worked for me (or at least i couldn't apply the function correctly). The help file wasn't very helpful as well.

Help would be appreciated. Thanks.

3
rfor-loop
Take a minute to think about your question. Do we need to know about the vector mypath or the fact you are saving pdfs? - csgillespie
OK, so you need to "practice" using tryCatch. It's really not that hard. Make up some simple loop function and feed it bad data. Then apply to your current loop, which after all contains a very simple set of commands. - Carl Witthoft
I definitley need to, now that i know how it works, I can play around with it. :) - Error404

3 Answers

170
votes

One (dirty) way to do it is to use tryCatch with an empty function for error handling. For example, the following code raises an error and breaks the loop :

for (i in 1:10) {
    print(i)
    if (i==7) stop("Urgh, the iphone is in the blender !")
}

[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
Erreur : Urgh, the iphone is in the blender !

But you can wrap your instructions into a tryCatch with an error handling function that does nothing, for example :

for (i in 1:10) {
  tryCatch({
    print(i)
    if (i==7) stop("Urgh, the iphone is in the blender !")
  }, error=function(e){})
}

[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10

But I think you should at least print the error message to know if something bad happened while letting your code continue to run :

for (i in 1:10) {
  tryCatch({
    print(i)
    if (i==7) stop("Urgh, the iphone is in the blender !")
  }, error=function(e){cat("ERROR :",conditionMessage(e), "\n")})
}

[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
ERROR : Urgh, the iphone is in the blender ! 
[1] 8
[1] 9
[1] 10

EDIT : So to apply tryCatch in your case would be something like :

for (v in 2:180){
    tryCatch({
        mypath=file.path("C:", "file1", (paste("graph",names(mydata[columnname]), ".pdf", sep="-")))
        pdf(file=mypath)
        mytitle = paste("anything")
        myplotfunction(mydata[,columnnumber]) ## this function is defined previously in the program
        dev.off()
    }, error=function(e){cat("ERROR :",conditionMessage(e), "\n")})
}
10
votes

Here's a simple way

for (i in 1:10) {
  
  skip_to_next <- FALSE
  
  # Note that print(b) fails since b doesn't exist
  
  tryCatch(print(b), error = function(e) { skip_to_next <<- TRUE})
  
  if(skip_to_next) { next }     
}

Note that the loop completes all 10 iterations, despite errors. You can obviously replace print(b) with any code you want. You can also wrap many lines of code in { and } if you have more than one line of code inside the tryCatch

3
votes

Instead of catching the error, wouldn't it be possible to test in or before the myplotfunction() function first if the error will occur (i.e. if the breaks are unique) and only plot it for those cases where it won't appear?!