[Bioc-devel] Error handling in AnnotatedDataFrames
anders at embl.de
Thu Dec 16 18:47:49 CET 2010
These AnnotatedDataFrames are driving me nuts. Somehow, I always stumble
over unexpected behaviour.
Here is a test case, resulting in an error mesage, that just managed to
severely confuse me:
Let's make an AnnotatedDataFrame with two columns, called 'a' and 'b'.
> adf <- new("AnnotatedDataFrame",
+ data=data.frame( a = 1:10, b = 11:20 ) )
Document the first column:
> varMetadata( adf )[ "a", "labelDescription" ] <- "a column named 'a'"
Now, I try to document the second column, but misspell its name as 'c'
instead of 'b'. Let's see how this error is reported:
> varMetadata( adf )[ "c", "labelDescription" ] <-
+ "a column that does not exist"
Error in `row.names<-.data.frame`(`*tmp*`, value = c("a", "b")) :
invalid 'row.names' length
From this error message, it is quite hard to guess the cause of the
error. Could somebody who is more familiar with the internals of Biobase
maybe have a look whether this error condition could be caught earlier
to give a more helpful error?
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)
 LC_CTYPE=en_US.utf8 LC_NUMERIC=C
 LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
 LC_MONETARY=C LC_MESSAGES=en_US.utf8
 LC_PAPER=en_US.utf8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 ExonSeq_0.1.0 MASS_7.3-8 Biobase_2.10.0
loaded via a namespace (and not attached):
 hwriter_1.3 tools_2.12.0
| Dr. Simon Anders, Dipl.-Phys.
| European Molecular Biology Laboratory (EMBL), Heidelberg
| office phone +49-6221-387-8632
| preferred (permanent) e-mail: sanders at fs.tum.de
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