Error Trapping In R
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R -- Basic error Handing with tryCatch() Posted on December 7, 2011 by Jonathan Callahan This entry is part 4 of 20 in the series Using RThe R language definition section on Exception Handling describes
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a very few basics about exceptions in R but is of little use to
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anyone trying to write robust code that can recover gracefully in the face of errors. In fact, if you do a little r error handling searching you will find that quite a few people have read through the ?tryCatch documentation but come away just as confused as when they started. In this post we'll try to clarify a few things and http://www.win-vector.com/blog/2012/10/error-handling-in-r/ describe how R's error handling functions can be used to write code that functions similarly to Java's try-catch-finally construct. List of error handling functions Without any simple documentation on the subject, the first thing we need is a list of the functions involved in error handling. With this list in hand we can then start up R and type ?function_of_interest to read associated documentation or function_of_interest [without the ‘()'] to see how http://mazamascience.com/WorkingWithData/?p=912 the function is implemented. Here is a minimal list of functions that anyone writing error handling code should read up on: warning(…) -- generates warnings stop(…) -- generates errors suppressWarnings(expr) -- evaluates expression and ignores any warnings tryCatch(…) -- evaluates code and assigns exception handlers Other functions exist that relate to error handling but the above are enough to get started. (The documentation for these functions will lead to all the other error-related functions for any RTFM enthusiasts.) R does try-catch-finally differently In case you hadn't noticed, R does a lot of things differently from most other programming languages. Java and Python and C and all other languages covered in Wikipedia's excellent page on Exception handling syntax use language statements to enable try-catch-finally. R, needing to be different, uses a function. But the tryCatch() function actually looks a lot like other languages' try-catch syntax if you format it properly: result = tryCatch({ expr }, warning = function(w) { warning-handler-code }, error = function(e) { error-handler-code }, finally = { cleanup-code } 123456789 result = tryCatch({ expr}, warning = function(w) { warning-handler-code}, error = function(e) { error-handler-code}, finally = { cleanup-code} In tryCatch() there are two ‘conditions' that can be handled: ‘warnings' and ‘errors'. The important thing to understand when writin
here for a quick overview of the site Help Center Detailed answers to any questions you might have http://stackoverflow.com/questions/12193779/how-to-write-trycatch-in-r Meta Discuss the workings and policies of this site About Us https://stat.ethz.ch/R-manual/R-devel/library/base/html/try.html Learn more about Stack Overflow the company Business Learn more about hiring developers or posting ads with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x Dismiss Join the Stack Overflow Community Stack Overflow is a community of 4.7 million programmers, just error trapping like you, helping each other. Join them; it only takes a minute: Sign up How to write trycatch in R up vote 121 down vote favorite 86 I want to write trycatch code to deal with error in downloading from web. url <- c( "http://stat.ethz.ch/R-manual/R-devel/library/base/html/connections.html", "http://en.wikipedia.org/wiki/Xz") y <- mapply(readLines, con=url) These two statements run successfully. Below, I error trapping java create a non-exist web address: url <- c("xxxxx", "http://en.wikipedia.org/wiki/Xz") url[1] does not exist. How does one write a trycatch loop (function) so that: When the url is wrong, the output will be: "web url is wrong, can't get". When the url is wrong, the code does not stop, but continues to download until the end of list of urls? r r-faq share|improve this question edited Sep 10 '14 at 19:56 Andrie 102k19255332 asked Aug 30 '12 at 9:27 Dd Pp 8622714 add a comment| 3 Answers 3 active oldest votes up vote 252 down vote accepted +50 Well then: welcome to the R world ;-) Here you go Setting up the code urls <- c( "http://stat.ethz.ch/R-manual/R-devel/library/base/html/connections.html", "http://en.wikipedia.org/wiki/Xz", "xxxxx" ) readUrl <- function(url) { out <- tryCatch( { # Just to highlight: if you want to use more than one # R expression in the "try" part then you'll have to # use curly brackets. # 'tryCatch()' will return the last evaluated expression # in case the "
= stderr())) Arguments expr an R expression to try. silent logical: should the report of error messages be suppressed? outFile a connection, or a character string naming the file to print to (via cat(*, file = outFile)); used only if silent is false, as by default. Details try evaluates an expression and traps any errors that occur during the evaluation. If an error occurs then the error message is printed to the stderr connection unless options("show.error.messages") is false or the call includes silent = TRUE. The error message is also stored in a buffer where it can be retrieved by geterrmessage. (This should not be needed as the value returned in case of an error contains the error message.) try is implemented using tryCatch; for programming, instead of try(expr, silent = TRUE), something like tryCatch(expr, error = function(e) e) (or other simple error handler functions) may be more efficient and flexible. It may be useful to set the default for outFile to stdout(), i.e., options(try.outFile = stdout()) instead of the default stderr(), notably when try() is used inside a Sweave code chunk and the error message should appear in the resulting document. Value The value of the expression if expr is evaluated without error, but an invisible object of class "try-error" containing the error message, and the error condition as the "condition" attribute, if it fails. See Also options for setting error handlers and suppressing the printing of error messages; geterrmessage for retrieving the last error message. The underlying tryCatch<