r - Skipping error in for-loop

Question

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.

Answer 1

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), "
")})
}

[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), "
")})
}