-
+
- Built in conditions +
- Controlling the output of warnings +
- Checking for errors and stopping +
- Capturing errors and handling them +
July 30, 2019
+ +Outline
Built in conditions
-
+
- message:
+
+
-
+
- ‘simple’ diagnostic messages +
+ - warning:
+
+
-
+
- A warning message but execution continues +
+ - stop:
+
+
-
+
- An error message that can cause execution is stop +
+
Using message instead of print
-
+
- Instead of using ‘print’ for debugging, use message(). +
- It goes to stderr(). Better control with using sinks +
add <- function (...) {
+ message(paste("add:Parameters:", paste(..., collapse = ", ")))
+ result <- sum(...)
+ message(paste("add:returned:", result))
+ result
+ invisible()
+}
+add(1:10)
+
+## add:Parameters: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10+ +
## add:returned: 55+ +
You can suppress the messages
-
+
- Suppress messages instead of adding/removing print statements +
add <- function (...) {
+ message(paste("add:Parameters:", paste(..., collapse = ", ")))
+ result <- sum(...)
+ message(paste("add:returned:", result))
+ result
+ invisible()
+}
+suppressMessages(add(1:10))
+
+Now you do not have to comment them out!
+ +Warning messages
-
+
- Used to advise when business logic is handling a strange situation, such as:
+
+
-
+
- using default parameters, +
- type casting weirdness i.e. as.numeric(“a”) +
+ - Works similar to message() but has output controls +
test <- function() {
+ warning("The British are coming",
+ call. = TRUE, # make 'call' part of the message
+ immediate. = TRUE) # override getOption('warn'))
+}
+test()
+
+## Warning in test(): The British are coming+ +
Controlling Output: When to print
-
+
- Output is controlled with global options
+
+
-
+
- accessor: getOption(‘<OPTION>’) +
- mutator: options(<OPTION> = <VALUE>) +
+ - <Option>: warn
+
+
-
+
- Controls when the warnings are printed +
- Allowed values:
+
+
-
+
- -1: suppress output (technically warn < 0) +
- 0: printed after the top-level function has complete +
- 1: printed as they occur +
- 2: convert into errors (technically warn > 1) +
+
+
Controlling Output: Message length
-
+
- <Option>: warning.length
+
+
-
+
- Truncates the length of each message (error and warning) +
- values: 100…8170 default:1000 (long) +
+
options(warning.length = 100) +warning(msg)+ +
## Warning: +## SAISXBBULMPFRAMTTEKROXCPWHOSCINBGGHPGQKAUFGYQQAFQMCAIGUOVEWGMDMMQRMUIGVUJIXSENUSHXJOSWKYCVYNNENPNCWOWMMCICWWNDWBSPDBOHFXUFLHQHMJBEWVJWWCINUGVWKMXQTYCFRPOIKDQYGNEGJLGYWHESEJRSMFKGAFHGPBDJDOPUFOSOMGYIMVDKZKUPDMWKUJADVJUPOVHCGVYAWREZSWAUYPCEVRFXULQMBBVKADCEGEVMZLDYQJGDEMERUCMGYONWUOYOEVNLQZELURLQVESQJEXJMIMPIOPHDNTRUBVOWDVMQPOFRBXSKRJXQRVLJUVOTCXMFWFNWUVNOTSFHHMVEBEFJRXCJYDRGUKTRWKEUNFEEIHMAHRDTPRGMQYEUMNAWXHHJSHDHQHNPNMIHIRCGKVGPTJBLOJZSDHXTCSACPTBXMXUJZSCJMETLPXWYNNANSLUIFJPMPDEPCPQHMHQDYNTRVGEUMMRFIKEMTBBTQPQWUKBKBBOYGWSBXAJJRAXBOYAMFNMJGSIBELTRGGIMEFXKGXROUSWUCHBCMCNYDUJAQOTAJYHBEKCCXTJNCMZXWSPDMIWHNTFEPJPYOPTFFYAJKYLHLWQJAAAGYHKMAPWKVUSVIFTJHXVHRTZQQMYQIWYEBTWEAXFKKBZPWIHFVRLFHUHTUCQTUHIDPMPEYDHLPQJSOWJODFOJLYNRERZWBHPLUZSHVKRGPTCQDPHKBFQQNKVIIQSUBFMIZKZDCJYGSBSZOJQOCVUCEMAFCREGJKFWKLMYPSHJRZOGUHBGWIEKWKORUNOPJVYEKPLEVPIMFKTEMDXNBUANQICSRUNKDRSFQKDVQFLORKTHEGSFHSCTSAFEABBQTTGFJWDBJNUEODCDVRSFLDKOVWQUCPBAUQAOKBKOHSAYRMNQFXBRIYGGNJSSUUWPVAIHKIRGLRMRVFVRSNKKGSREVESTQPYVPPQHGVEBKLVSIZZEP+ +
Controlling Output: Number of messages printed
-
+
- <Option>: nwarning
+
+
-
+
- When warn = 0, the error and warn messages are buffered +
- sets the size of the buffer. Default: 50 +
+
Accessing the warnings
-
+
- If getOption(‘warn’) == 0 then there is a buffer of warning messages +
- warnings(…) prints this buffer +
- Parameters “…” are passed to cat() to control output +
- The buffer is a variable called last.warning +
- last.warning is:
+
+
-
+
- a named list +
- undocumented (subject to change) +
- use it in the console but not in your scripts +
- does not always exist +
+
Controlling Output: Modifying the message
-
+
- <Option>: warning.expression
+
+
-
+
- custom code is run with each call to warning() +
+
options(warning.expression = quote(getwd()))
+warning("Test")
+
+## Warning: Test+ +
BUG in ioslides (?) because this code outputs the following in the console:
+ +## [1] "/Users/jpeach/git/ocrug/presentations/2019-07-30_error_and_condition_handling_in_R"+ +
Warning messages suppression
-
+
- Just like messages, we can suppress the warnings +
test <- function() {
+ warning("The British are coming",
+ call. = TRUE, # make 'call' part of the message
+ immediate. = TRUE) # override getOption('warn'))
+}
+suppressWarnings(test())
+
+-
+
- The warning is not printed +
warnings()+ +
and it is not stored in the buffer
+ +Error Messages
-
+
- Used when there is an unrecoverable error +
- By default, program execution is halted +
test <- function() {
+ stop("In the name of love",
+ call. = TRUE) # call is part of the message
+}
+test()
+
+## Error in test() : In the name of love
+ +What was the last error?
-
+
- Forgot the details of the last error message, you can use +
geterrmessage()+ +
## Error: In the name of love
+ +-
+
- A string with the last error message is returned +
- A \n is appended to the error message +
stopifnot()
-
+
- Throw an error if any condition is FALSE +
- No message is returned +
stopifnot(...)+ +
… is any number of logical R expressions which should be TRUE
+ +stopifnot(A, B) +# Is short hand for +if ( any(is.na(A)) || !all(A) || any(is.na(B)) || !all(B)) stop(...)+ +
NULL is treated as TRUE
+ +Example: stopifnot()
-
+
- Generally used to check function parameters +
- Wrapper function for sum that checks:
+
+
-
+
- all parameters are integer +
- there must be a non-zero length vector +
- there are no NULLs or NANs +
+
Sum <- function(...){
+ stopifnot(is.integer(...), length(...) > 0,
+ !is.null(...), !is.nan(...))
+ as.integer(sum(...))
+}
+Sum(1L:10L)
+
+## [1] 55+ +
Condition System
-
+
- message(), warning(), stop() are built on the Condition System +
- It is used for error handling but is more flexible than that +
- Consists of three parts
+
+
-
+
- Signalling Condition +
- Handling Condition +
- Restarting (Advanced topic) +
+ - The task of handling the error is split between the Handler and the Restart +
Components
-
+
- Signaller
+
+
-
+
- A method that raises / throws and exception object +
- Creates an object derived from the S3 class ‘condition’ +
- Language framework handles its execution path +
- message(), warning() and stop() are signallers +
+ - Handler
+
+
-
+
- Agrees to catch / process exception of specific classes +
- Handles exception only from the call stack below it +
- Handlers lower on the stack may capture exception +
+
Exceptions - Sequence of execution
## Exceptions
-
+
- Errors are handled by:
+
+
-
+
- Exiting the failing function +
- Calling function can recover or fail itself +
+ - Primary issue is that the stack unwinds
+
+
-
+
- Recovery code must do so without the context of the failing function +
+
tryCatch
-
+
- Unwinds the call stack +
tryCatch(expression, + condition_class_1 = function(var) ..., + condition_class_2 = function(var) ..., + finally = ... +)+ +
-
+
- expression: must be a single expression, use { } +
- var: is the condition object +
- tryCatch returns the value of expression or one of the condition_class +
- If the condition is not handled by one of the condition_class it moves up the call stack +
tryCatch: Handler not invoked
`%+%` <- function(lhs, rhs) {
+ if (!is.integer(lhs) || !is.integer(rhs)){
+ stop("parameters must be numeric")
+ }
+ lhs + rhs
+}
+tryCatch( { 5L %+% 4L },
+ error = function(e) 0
+)
+
+## [1] 9+ +
-
+
- There was no error so the handler ‘error’ was not invoked +
- tryCatch returned the value of the expression +
tryCatch: Handler invoked
`%+%` <- function(lhs, rhs) {
+ if (!is.integer(lhs) || !is.integer(rhs)){
+ stop("parameters must be numeric")
+ }
+ lhs + rhs
+}
+tryCatch( { 5L %+% 4 },
+ error = function(e) 0
+)
+
+## [1] 0+ +
-
+
- stop() was called because 4 is double not integer +
- tryCatch returned the value of the ‘error’ handler +
tryCatch: No warning handler
`%+%` <- function(lhs, rhs) {
+ if (is.double(rhs)) {
+ rhs = as.integer(rhs); warning("casting rhs to integer")
+ }
+ if (!is.integer(lhs) || !is.integer(rhs)){
+ stop("parameters must be numeric")
+ }
+ lhs + rhs
+}
+tryCatch( { 5L %+% 4 },
+ error = function(e) 0
+)
+
+## Warning in 5L %+% 4: casting rhs to integer+ +
## [1] 9+ +
-
+
- Sum is computed and a warning is displayed +
tryCatch: finally
tryCatch( {
+ text <- 'foo'
+ message(text)
+ },
+ message = function(e) {
+ text <- paste(conditionMessage(e), 'bar')
+ text # This is the value returned by tryCatch. Different environment
+ },
+ finally = {
+ # This block is run iff a handler is called
+ print(text) # handler does not alter value
+ }
+)
+
+## [1] "foo"+ +
## [1] "foo\n bar"+ +
Comment on Condition System
-
+
- I showed you how to use R like you use error systems in Java/python +
- R has a much more powerful system that is based on lisp +
- Code is not “rolled-up” the call stack, it can be restarted +
- We can build custom conditions and handle them +
- The Condition System can be used for much more than errors +