[R] question about TryCatch and lapply

[Martin Morgan]

On 5/25/2012 12:48 PM, John Kerpel wrote:
> Jim:
>
> That's the ticket!  I'm actually using parLapply with a long, ugly function
> - so I was loath to post that mess.
>
> Many thanks - you saved my weekend.

In the context of tryCatch in your question

   lst <- list(1, 2, -3, 4)
   sapply(lst, function(x) tryCatch({
       stopifnot(x > 0)
       x
   }, error=function(err) {
       NA
   }))

which separates out the implementation of the function from the error 
handling instead of intermingling the two as with try(). Or a little 
more elaboration, reporting the error to stderr as might be appropriate 
for a parallel job

   sapply(lst, function(x) {
       tryCatch({
           stopifnot(x>0)
           sqrt(x)
       }, error=function(err) {
           ## demote to message on stderr; in context of tryCatch so
           ## 'x' visible
           message(conditionMessage(err), "; x = ", x)
           NaN
       })
   })

or for warnings, showing use of restarts

   withCallingHandlers({
       sapply(lst, sqrt)
   }, warning=function(warn) {
       message(conditionMessage(warn))
       ## restart where the warning occurs; see ?warning and source for
       ## warning()
       invokeRestart("muffleWarning")
   })

Martin

>
> On Fri, May 25, 2012 at 2:23 PM, jim holtman<jholtman at gmail.com>  wrote:
>
>> Please show us the 'lapply' statement you are using.  Here is a simple
>> case of catching an error in an lapply and continuing:
>>
>>> lapply(c(1,2,-3, 4), function(x){
>> +     a<- try(stopifnot(x>  0))  # force an error
>> +     if (inherits(a, 'try-error')) return(NULL)
>> +     x
>> + })
>> Error : x>  0 is not TRUE
>> [[1]]
>> [1] 1
>>
>> [[2]]
>> [1] 2
>>
>> [[3]]
>> NULL
>>
>> [[4]]
>> [1] 4
>>
>>
>> On Fri, May 25, 2012 at 2:51 PM, John Kerpel<john.kerpel at gmail.com>
>> wrote:
>>> Folks:
>>>
>>> I've replaced an outer for-loop with lapply and it works great.  But, I
>>> can't seem to do the following type of exception handling:
>>>
>>> tryCatch(dlmMLE(x)$value==Inf,error = function(e) NULL)
>>>
>>> which basically says if the likelihood is Inf, throw an error.  But what
>> I
>>> want it to do is just go to the next index in the list.  When I was
>> using a
>>> for-loop I used:
>>>
>>> if(tryCatch(dlmMLE(x)$value==Inf,error = function(e) 1)==1) {next} else
>>> .... which worked fine.
>>>
>>> Is there a way to do the same thing in lapply?
>>>
>>> Thanks for your time. (I've checked Gmane for this type of problem and I
>>> wasn't sure if this problem was answered or not...)
>>>
>>> John
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>> --
>> Jim Holtman
>> Data Munger Guru
>>
>> What is the problem that you are trying to solve?
>> Tell me what you want to do, not how you want to do it.
>>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109