R devel - Apr 2009 - How can I catch errors thrown from c via the Rcpp error() function?

Hi

I am using the flowClust package from BioConductor, which is largely 
implemented in c. For some of my data, the package occasionally (and 
quite stochastically) encounters a particular condition which halts its 
operation. At this point, it calls the error() function defined by Rcpp, 
and halts.

What I would like to be able to do is to catch the error thrown, and 
retry the operation a few times before giving up.

However, when I wrap the call to flowClust in try() or tryCatch(), the 
error seems to completely bypass them:

Examples:

1. This is a trivial example just to test the try() function, and 
correctly assigns the error to the variable x:

 > x <- try(stop(simpleError('blah')))
Error : blah
 > x
[1] "Error : blah\n"
attr(,"class")
[1] "try-error"

2. This is an example using flowClust (using real data, set up to 
guarantee that the error is thrown):

 > x <- try(res30 = flowClust(tFrame, K=30, B=1000,
varNames=c('CD4',
'CD8','KI67', 'CD45RO', 'CD28', 'CD57',
'CCR5', 'CD19', 'CD27', 'CCR7',
'CD127')))
Error in flowClust(tFrame, K = 30, B = 1000, varNames = c("CD4",
"CD8",  :

The covariance matrix is near singular!
Try running the program with a different initial configuration or less 
clusters
 > x
Error: object "x" not found


The c code throwing the error is as follows (from flowClust.c):

if(status!=0)
   {
       error("\n The covariance matrix is near singular! \n Try running 
the program with a different initial configuration or less clusters 
\n");          }


I looked up the error() function in Writing R Extensions  and it states: 
"The basic error handling routines are the equivalents of stop and 
warning in R code, and use the same interface."

Yet, it seems that they are not caught by R's error handling code.

So:

1. Is this the general case (that Rcpp error()s are not handled by try() 
and related methods in R)? (I'm sure this could be tested with a trivial 
example, but I'm not yet familiar enough with wrapping c code in R to do 
so.)

2. If so, what is the correct way to handle them in R?

3. If not, do you have any suggestions as to what may have caused 
flowClust to behave in this way? (So that I can contact the package 
maintainers and report the bug.)

Kieran,

On 15 April 2009 at 18:03, Kieran O'Neill wrote:
| I am using the flowClust package from BioConductor, which is largely 
| implemented in c. For some of my data, the package occasionally (and 
| quite stochastically) encounters a particular condition which halts its 
| operation. At this point, it calls the error() function defined by Rcpp, 
| and halts.
| 
| What I would like to be able to do is to catch the error thrown, and 
| retry the operation a few times before giving up.
| 
| However, when I wrap the call to flowClust in try() or tryCatch(), the 
| error seems to completely bypass them:
| 
| Examples:
| 
| 1. This is a trivial example just to test the try() function, and 
| correctly assigns the error to the variable x:
| 
|  > x <- try(stop(simpleError('blah')))
| Error : blah
|  > x
| [1] "Error : blah\n"
| attr(,"class")
| [1] "try-error"
| 
| 2. This is an example using flowClust (using real data, set up to 
| guarantee that the error is thrown):
| 
|  > x <- try(res30 = flowClust(tFrame, K=30, B=1000,
varNames=c('CD4',
| 'CD8','KI67', 'CD45RO', 'CD28',
'CD57', 'CCR5', 'CD19', 'CD27', 'CCR7',
| 'CD127')))
| Error in flowClust(tFrame, K = 30, B = 1000, varNames = c("CD4",
"CD8",  :
| 
| The covariance matrix is near singular!
| Try running the program with a different initial configuration or less 
| clusters
|  > x
| Error: object "x" not found
| 
| 
| The c code throwing the error is as follows (from flowClust.c):
| 
| if(status!=0)
|    {
|        error("\n The covariance matrix is near singular! \n Try running 
| the program with a different initial configuration or less clusters 
| \n");          }
| 
| 
| I looked up the error() function in Writing R Extensions  and it states: 
| "The basic error handling routines are the equivalents of stop and 
| warning in R code, and use the same interface."
| 
| Yet, it seems that they are not caught by R's error handling code.
| 
| So:
| 
| 1. Is this the general case (that Rcpp error()s are not handled by try() 
| and related methods in R)? (I'm sure this could be tested with a trivial 
| example, but I'm not yet familiar enough with wrapping c code in R to do 
| so.)

Allow me to take the narrow view here as Rcpp maintainer.  What you can do
with Rcpp is to provide a C++ layer of try/catch around inner code which may
throw C++ exception.  This will usually be caught, and (as shown in the Rcpp
docs and examples) we can pass the exception message back up to R as a
regular error message.  This is very useful as it gives you control back at
the R prompt rather than just going belly-up.

Now, R's try() and tryCatch() are completely separate and not tied into the
exception mechanism Rcpp deals with, which is at a much lower level. 

Likewise, you may be out of luck with flowClust if it is C program.  You
could try to add a C++ layer that tried to catch error and allows you do
continue your loops.  I did something like that 15 years ago in my
dissertation research to ensure I survived the occassional numerical error
from Fortran during longer Monte Carlo runs,

| 2. If so, what is the correct way to handle them in R?

Tricky. See 1. :)

| 3. If not, do you have any suggestions as to what may have caused 
| flowClust to behave in this way? (So that I can contact the package 
| maintainers and report the bug.)

You could always contact them anyway and ask for advice.

Hth,  Dirk

-- 
Three out of two people have difficulties with fractions.