tryCatch - namespace? - r

Question

I am quite new to R and I am confused by the correct usage of tryCatch. My goal is to make a prediction for a large data set. If the predictions cannot fit into memory, I want to circumvent the problem by splitting my data.
Right now, my code looks roughly as follows:
tryCatch({
large_vector = predict(model, large_data_frame)
}, error = function(e) { # I ran out of memory
for (i in seq(from = 1, to = dim(large_data_frame)[1], by = 1000)) {
small_vector = predict(model, large_data_frame[i:(i+step-1), ])
save(small_vector, tmpfile)
}
rm(large_data_frame) # free memory
large_vector = NULL
for (i in seq(from = 1, to = dim(large_data_frame)[1], by = 1000)) {
load(tmpfile)
unlink(tmpfile)
large_vector = c(large_vector, small_vector)
}
})
The point is that if no error occurs, large_vector is filled with my predictions as expected. If an error occurs, large_vector seems to exist only in the namespace of the error code - which makes sense because I declared it as a function. For the same reason, I get a warning saying that large_data_frame cannot be removed.
Unfortunately, this behavior is not what I want. I would want to assign the variable large_vector from within my error function. I figured that one possibility is to specify the environment and use assign. Thus, I would use the following statements in my error code:
rm(large_data_frame, envir = parent.env(environment()))
[...]
assign('large_vector', large_vector, parent.env(environment()))
However, this solution seems rather dirty to me. I wonder whether there is any possibility to achieve my goal with "clean" code?
[EDIT]
There seems to be some confusion because I put the code above mainly to illustrate the problem, not to give a working example. Here's a minimal example that shows the namespace issue:
# Example 1 : large_vector fits into memory
rm(large_vector)
tryCatch({
large_vector = rep(5, 1000)
}, error = function(e) {
# do stuff to build the vector
large_vector = rep(3, 1000)
})
print(large_vector) # all 5
# Example 2 : pretend large_vector does not fit into memory; solution using parent environment
rm(large_vector)
tryCatch({
stop(); # simulate error
}, error = function(e) {
# do stuff to build the vector
large_vector = rep(3, 1000)
assign('large_vector', large_vector, parent.env(environment()))
})
print(large_vector) # all 3
# Example 3 : pretend large_vector does not fit into memory; namespace issue
rm(large_vector)
tryCatch({
stop(); # simulate error
}, error = function(e) {
# do stuff to build the vector
large_vector = rep(3, 1000)
})
print(large_vector) # does not exist

Answer 1

I would do something like this :
res <- tryCatch({
large_vector = predict(model, large_data_frame)
}, error = function(e) { # I ran out of memory
ll <- lapply(split(data,seq(1,nrow(large_data_frame),1000)),
function(x)
small_vector = predict(model, x))
return(ll)
})
rm(large_data_frame)
if(is.list(ll))
res <- do.call(rbind,res)
The idea is to return a list of predictions results if you run out of the memory.
NOTE, i am not sure of the result here, because we don't have a reproducible example.

Answer 2

EDIT: Let's try again:
You can use finally argument of tryCatch:
step<-1000
n<-dim(large_data_frame)[1]
large_vector <- NULL
tryCatch({
large_vector <- predict(model, large_data_frame)
}, error = function(e) { # ran out of memory
for (i in seq(from = 1, to = n, by = step)) {
small_vector <- predict(model, large_data_frame[i:(i+step-1),]) #predict in pieces
save(small_vector,file=paste0("tmpfile",i)) #same pieces
}
rm(large_data_frame) #free memory
},finally={if(is.null(large_vector)){ #if we run out of memory
large_vector<-numeric(n) #make vector
for (i in seq(from = 1, to = n, by = step)){
#collect pieces
load(paste0("tmpfile",i))
large_vector[i:(i+step-1)] <- small_vector
}
}})
Here's a simplified version to see what is going on:
large_vector<-NULL
rm(y)
tryCatch({
large_vector <- y
}, error = function(e) {# y is not found
print("error")
},finally={if(is.null(large_vector)){
large_vector<-1
}})
> large_vector
[1] 1
EDIT2: Another tip regarding the scope which could be useful for you (although maybe not in this situation as you didn't want to declare large_vector beforehand): The <<- operator, from R-help:
The operators <<- and ->> are normally only used in functions, and
cause a search to made through parent environments for an existing
definition of the variable being assigned...
Therefore you could use above example code like this:
large_vector<-NULL
rm(y)
tryCatch({
large_vector <- y
}, error = function(e) {# y is not found
large_vector <<- 1
print("error")
})
> large_vector
[1] 1

Answer 3

The code below is quite self explanatory. Indeed the problem is that anything inside the error function is not by default applied to the parent environment.
b=0
as explained, this doesn't work:
tryCatch(expr = {stop("error1")}, error=function(e) {b=1})
b
SOLUTION 1: assign to the parent environment
tryCatch(expr = {stop("error2")}, error=function(e) {assign(x = "b", value =
2, envir = parent.env(env = environment()))})
b
SOLUTION 2: the most simple (only works if you are assigning to b in both expr and error)
b = tryCatch(expr = {stop("error3")}, error=function(e) {b=3;return(b)})
b