[R] How to catch an error using try

ONKELINX, Thierry Thierry.ONKELINX at inbo.be
Tue Aug 4 10:31:14 CEST 2009

Put your function in try() and the test it's class

gene.seq <- try(getSequence (id=gene.map[,"ensembl_transcript_id"],
type="ensembl_transcript_id", seqType="3utr", mart=hmart))
if(class(gene.seq) == "try-error"){
	#code to run when an error occurs
} else {
	#code to run when no error occurs


ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens mauede at alice.it
Verzonden: maandag 3 augustus 2009 17:54
Aan: r-help at stat.math.ethz.ch
Onderwerp: [R] How to catch an error using try

Sometimes the following function call causes a database exception:

>  gene.seq <- getSequence (id=gene.map[,"ensembl_transcript_id"], 
> type="ensembl_transcript_id",
+                              seqType="3utr", mart=hmart)

I understand the above function must be called by try to capture the
eventual error.
WHat is not clear to me is how to realize that an error has occurred.
The on-line documentation mentions an invisible object of class
How shall I test whetehr such object has been created or not ?
I assume it is created whenever an error does occur ....?

Thank you for your help.

tutti i telefonini TIM!

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