Use Trycatch Skip to Next Value of Loop Upon Error

Skipping error in for-loop

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")})
}

R tryCatch skips error in for loop but error statement is not executed

This because the tryCatch should wrap the cor.test() function and not the append() one. Also, you may use sapply() instead of a for loop here.

Generate some data

x <- data.frame(A=sample(1:100, size = 20),
                B=sample(1:100, size = 20),
                C=sample(1:100, size = 20),
                D=sample(1:100, size = 20))
y <- data.frame(A=sample(1:100, size = 20),
                B=sample(1:100, size = 20),
                C=sample(1:100, size = 20),
                D=NA)

And now the code

result <- sapply(2:ncol(x), (function(i){
  tryCatch({cor.test(x[,i], y[,i], na.action = "na.omit", method = "spearman")$p.value},
         error = function(e) NA)
}))
result
[1] 0.7238886 0.2668126        NA

Now, the result vector includes a NA corresponding to the correlation test between a numeric vector and a series of NA.

R: For loop skip if error / tryCatch

While I don't think this is necessarily the best solution, it does answer your question directly (simplified for reproducibility):

for(i in 1:10) {
  res <- try(if(i %% 2) stop("argh"))
  if(inherits(res, "try-error")) next
  cat(i, "\n")
}

Just using try instead of tryCatch b/c it's a bit simpler and tryCatch functionality is not needed. Really for your purposes you could:

for(i in 1:10) try(my_val[i] <- my_fun(my_val[i]))

since you don't need to do anything else. If it fails, the loop will just keep going merrily.

All this said, I have to say I am a bit confused by your error and the inability to do this in a vectorized manner.

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