Using provenance to debug errors and warnings

June 11, 2020

Errors and warnings are a clear sign that a script is not working correctly. While sometimes just seeing the error message is enough to know how to fix the problem, that is not always the case.
debug.error, debug.warning, and debug.type.changes are three functions to help a user understand an error and what portions of the script led to the error.

debug.error and debug.warning

debug.error and debug.warning both provide information on the backwards lineage of an error or warning message produced by R. The backward lineage contains the lines of code that led either directly or indirectly to computing a value that is used on the line that produced the error.


Let myScript.R be the following:

x <- 1
y <- 2
x <- a + x

Running this script will result in the following error since no value has been assigned to a:

Error in eval(annot, environ, NULL) : object 'a' not found

The result of debug.error() is:

Your Error: Error in eval(annot, environ, NULL): object 'a' not found

Code that led to error message:

  scriptNum scriptName startLine       code
1         1 myScript.R         1     x <- 1
2         1 myScript.R         3 x <- a + x

This shows that lines 1 and 3 may have contributed to the error. Notice that line 2 is not shown. It is not part of the lineage of the statement that resulted in the error, since statement 3 neither uses y nor any other variable that itself depends on y.

The data frame returned by debug.error contains the following columns:

debug.warning similarly displays the lineage of a warning message, although it does not currently support the connection with Stack Overflow, which is discussed below.


The function signature for debug.error is:

debug.error(stack.overflow = FALSE)

The parameter for this function is:

This function may be called only after initialising the debugger using either prov.debug,, or prov.debug.file. For example:"myScript.R")
debug.error(stack.overflow = TRUE)

Stack Overflow

When TRUE is passed in for the stack.overflow parameter, in addition to returning the backwards lineage of the error, the error will also be searched on Stack Overflow. The user will be presented with the titles of the top 6 matching search results. The user can then select one or more of these and a browser window will open displaying the corresponding Stack Overflow page.

The result of debug.error(stack.overflow = TRUE) is:

Your Error: Error in eval(annot, environ, NULL): object 'a' not found

Code that led to error message:

  scriptNum scriptName startLine       code
1         1 myScript.R         1     x <- 1
2         1 myScript.R         3 x <- a + x

Results from StackOverflow:
1. "Object not found error with ddply inside a function"                  
2. "ggplot object not found error when adding layer with different data"  
3. "Error in eval(expr, envir, enclos) : object not found"                
4. "data.table throws \"object not found\" error"                         
5. "Object not found error when passing model formula to another function"
6. "Object not found error with ggplot2"                                  

Choose a numeric value that matches your error the best or q to quit: 


debug.type.changes is also intended to help users resolve errors.
In this case, it is intended to help with a specific error in which a variable is bound to a new value and that new value has a different type. Since R is not a type-checked language, these errors can easily creep into a program and can be hard to debug. For example, this can occur if a variable name gets reused for a different purpose, or if a vectorizing operation changes a variable from a single scalar value to a long vector unexpectedly.

Consider this simple example:

a <- 1
<code omitted>
a <- a + b

If the programmer thought that b was an integer and instead it was a longer vector, they might have expected that they were simply adding two integers together. However, now the type of a has changed from a vector of length 1 to a vector as long as the vector referenced by b.

Calling debug.type.changes() will show all variables whose type has changed, what those values were, and where the changes occurred, as shown here:

                          value container dimension    type       code  scriptNum    scriptName startLine
1                             1    vector         1 numeric     a <- 1  1         1 typechanges.R         1
2  2  3  4  5  6  7  8  9 10 11    vector        10 numeric a <- a + b  2         1 typechanges.R         3