Rcourse7 PDF

Debugging and Tuning R Functions
R.M. Ripley
Department of Statistics
University of Oxford
2012/13
R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 1 / 29

R Exception Handling Introduction
R Exception Handling
Exceptions are conditions which prevent R’s normal processing.

Some are so serious that processing cannot continue. Others are
less serious but R suspects they are unexpected, so will indicate
their occurrence.
The term exception handling refers to methods of dealing with
exceptions.
Two common types of exceptions are warnings and errors.
Various options control R’s exception handling.
The function try() can be wrapped around code which might fail,
to allow the writer of the code rather then R to deal with the
exception.

R Exception Handling Options
Use of R options
Options are used to control many different aspects of R. A list of

options and their current settings can be obtained by options().
Some examples of options:

digits suggested number of digits to use when printing
numbers. Default 7.
contrasts controls use of factor variables in model fitting. Default:
for unordered factors is "contr.treatment", for ordered
factors, "contr.poly".
help-type character string indicating the type of help preferred.
Possible values are "text", "html" and "pdf".

Use of R options
Options are used to control many different aspects of R. A list of

options and their current settings can be obtained by options().
Some examples of options:

digits suggested number of digits to use when printing
numbers. Default 7.
contrasts controls use of factor variables in model fitting. Default:
for unordered factors is "contr.treatment", for ordered
factors, "contr.poly".
help-type character string indicating the type of help preferred.
Possible values are "text", "html" and "pdf".

Use of R options, continued
Note that many available options are not set by default. Some are
set as packages are loaded.
The options available can be found by using the help system: the
page for options contains a detailed description.
Options used as default values for functions (e.g. na.action in

lm) will be mentioned on the help page for the function.
To set an option: options(digits=5)
To access a specific option:

getOption("digits")
or
options("digits")



getOption("digits")
or
options("digits")



getOption("digits")
or
options("digits")

R Exception Handling Errors
R exception handling: Errors
Serious exceptions but not catastrophic: R cannot continue, but is

still able to do something e.g. cannot find a variable.
Default behaviour: print a message and return to prompt.
Error messages can be suppressed by
options(show.error.messages=FALSE).
options(error) can be set to the name of a function which will
be called in the case of an error.
Default options(error) is NULL, in which case processing
stops.
Two useful alternatives are:
recover allows browsing on any currently active function
dump.frames dumps the currently active functions. Dump can be
examined using debugger, which is similar to
recover

stops.
recover

stops.
recover

stops.
recover

stops.
recover

stops.
recover
R Exception Handling Warnings
R exception handling: Warnings
Less serious exceptions, e.g. NA’s produced when converting

character data to numeric
Behaviour controlled by value of options(warn):

< 0 warnings are ignored
0 (default) warnings are stored till top level function returns.
Then, if there are no more than 10 warnings, they are
displayed. If there are more than 10, a message saying how
many (max 50) have been generated is displayed
1 prints warning immediately it is generated
>= 2 treats a warning as an error







Checking and Improving your functions Overview
Possible outcomes
You run your new function. It may

1 terminate successfully with no warnings
2 terminate successfully with anticipated warnings
e.g. NA’s produced when converting character data to numeric
3 terminate successfully with unexpected warnings
4 stop with a predictable error e.g. invalid arguments supplied
5 stop with an unpredictable error
In case 4, rerun the function with the correct input. In cases 1 and 2,
check the results and then consider profiling your function. Cases 3
and 5 are the problem: you need to find the error in your code.

Possible outcomes


Possible outcomes


Possible outcomes


Possible outcomes


Possible outcomes


Checking and Improving your functions Debugging functions
How to find the error

Debugging tools
One way to trace errors is to add cat or print statements where you
think they might be enlightening. But R provides several tools for more
powerful debugging. They are also useful for checking intermediate
results.
traceback() Prints the sequence of calls that led to the last error.
browser() Inserted into a function, interrupts it and allows access
to the R interpreter.
debug() Sets a debugging flag on a function: equivalent to
browser() at start of function. undebug() unsets
the flag
trace() Similar to debug but more powerful. untrace()
unsets the flag
recover() Allows browsing on any currently active function call.
Often used as an error option.

Debugging tools
results.
the flag
unsets the flag

Debugging tools
results.
the flag
unsets the flag

Debugging tools
results.
the flag
unsets the flag

Debugging tools
results.
the flag
unsets the flag
traceback
Use after the error: no forward planning required
Example of traceback()
library(MASS)
lda(Sex ~ FL + CL + CW + RW + BD, crabs)
Error in eval(expr,envir,enclos):object "Sex" not
found
traceback()
9: eval(expr, envir, enclos)
8: eval(predvars, data, env)
7: model.frame.default(formula = Sex ~ FL + CL + CW +
RW + BD, data = crabs)
6: model.frame(formula = Sex ~ FL + CL + CW + RW +
BD, data = crabs)
5: eval(expr, envir, enclos)
4: eval(expr, p)
3: eval.parent(m)
2: lda.formula(Sex ~ FL + CL + CW + RW + BD, crabs)
1: lda(Sex ~ FL + CL + CW + RW + BD, crabs)
browser()
Need to set up before the function is run. Change the function either by
usual route, or use fix(myfn) to leave your source file unchanged.
Add a call to browser() before the place you suspect the error
occurs. Rerun the job: R will stop with a prompt labelled "Browse":
Example of browser()
mymat<- cbind(1:4,c(1,4:6),4:7)
fn1(mymat)
Error in if (nmul > 1) nmul^3 else nmul^2 :
argument is of length zero
fix(fn1)
fn1(mymat)
Called from: fn1(mymat)
Browse[1]>

browser()
Need to set up before the function is run. Change the function either by
usual route, or use fix(myfn) to leave your source file unchanged.
Add a call to browser() before the place you suspect the error
occurs. Rerun the job: R will stop with a prompt labelled "Browse":
Example of browser()
mymat<- cbind(1:4,c(1,4:6),4:7)
fn1(mymat)
fix(fn1)
fn1(mymat)
Browse[1]>

Use of browser
Use the prompt like a normal one, and enter normal commands, but
there are a few special commands:
c or cont or just return: leave the browser and continue at the
next statement
n enter the step through debugger
where print a stack trace of all active function calls
Q exit the browser and the current function and return to the
toplevel prompt
Note than to examine a variable called c, cont, n, where, or Q, use
print()

Use of browser
next statement
toplevel prompt
print()

Use of browser
next statement
toplevel prompt
print()

Use of browser
next statement
toplevel prompt
print()

Use of browser
next statement
toplevel prompt
print()

Use of browser
next statement
toplevel prompt
print()

Example of use of browser(), continued

browser()
The function
fn1<- function(mat){
mults <- mat[mat[, 1]==mat[, 2], ]
nmul<- nrow(mults)
browser()
if (nmul > 1) nmul^3
else nmul^2 }
browser session
Browse[1]> ls()
[1] "mat" "mults" "nmul"
Browse[1]> mults
[1] 1 1 4
Browse[1]> nrow(mults)
NULL ## R has dropped a dimension

Example of use of browser(), continued

browser()
Fix the function
fn1<- function(mat){
mults <- mat[mat[,1]==mat[,2], , drop=FALSE]
nmul<- nrow(mults)
browser()
if (nmul > 1) nmul^3
else nmul^2 }
browser session
Browse[1]> mults
[,1] [,2] [,3]
[1,] 1 1 4
Browse[1]> nrow(mults)
[1] 1
Browse[1]> c
[1] 1

debug()
Alternative method for previous problem, using debug()
debug()
debug(fn1)
fn1(mymat)
debugging in: fn1(mymat)
debug: {
mults <- mat[mat[, 1] == mat[, 2], ]
nmul <- nrow(mults)
if (nmul > 1)
nmul^3
else nmul^2
}
Browse[2]>

Use of debug()
there are a few special commands, similar to those for browser()
(note c and n behave differently here)
c or cont : continue to the end of the current context (loop or
function)
n or just return: advance to the next step
toplevel prompt

Use of debug()
function)
toplevel prompt

Use of debug()
function)
toplevel prompt

Use of debug()
function)
toplevel prompt

Use of debug()
function)
toplevel prompt

Example of debug()
debug(), continued
Browse[2]> n
debug: mults <- mat[mat[, 1] == mat[, 2], ]
Browse[2]> n
debug: nmul <- nrow(mults)
Browse[2]> mults
[1] 1 1 4
Browse[2]> dim(mults)
NULL
Browse[2]> Q
undebug(fn1) ## remove the debugging flag from fn1
trace is similar, but with more facilities. Consult the help page for
more details.
recover()
recover()
##set up error function
options(error=recover)
##run our function
fn1(mymat)
Enter a frame number, or 0 to exit
1: fn1(mymat)
Selection:

recover()
recover(), continued
Selection: 1
Called from: eval(expr, envir, enclos)
Browse[1]> ls()
[1] "mat" "mults" "nmul"
Browse[1]> dim(mults)
NULL
Browse[1]> mults
[1] 1 1 4
Browse[1]> c
Enter a frame number, or 0 to exit
1: fn1(mymat)
Selection: 0
>
Then fix the function and rerun
Checking and Improving your functions Trapping expected errors
try()
A wrapper for your function, which returns the normal return value,
unless there is an error, when it returns an object of class
"try-error"
If there is an error, it prints an error message, unless you have
suppressed error messages using
options(show.error.messages=FALSE) or used the
argument silent=TRUE.
Surround your function by
if (!inherits(x <- try(myfn(y)), "try-error"))
do normal processing
else
do error processing

try() continued
try()
tmp <- try(solve(mymat[-3, ]))
inherits(tmp, "try-error")
[1] FALSE
tmp <- try(solve(mymat[-1, ]))
Error in solve.default(mymat[-1, ]) :
Lapack routine dgesv: system is exactly singular
[1] TRUE
tmp <- try(solve(mymat[-1, ]),silent=TRUE)
[1] TRUE

tryCatch
More powerful alternative to try().
tryCatch(expr, ..., finally)
expr Here you put the code which might cause an error or warning
... Here you define handlers for e.g. errors or warnings
finally Here you put code which should always be run (unless your
error handler stops things dead!).
The ... can include handlers for conditions you have defined.
The return value after a trapped condition will have the class of
the return value from the last handler invoked.

tryCatch

tryCatch

tryCatch, continued
tmp<- tryCatch(solve(mymat[-3,]),error=function(e){
cat("Matrix inversion failed\n"); e})
tmp
[,1] [,2] [,3]
[1,] 0.1666667 -1.4166667 0.9166667
[2,] -0.5000000 0.7500000 -0.2500000
[3,] 0.3333333 0.1666667 -0.1666667
tmp <- tryCatch(solve(mymat[-1,]),error=function(e){
cat("Matrix inversion failed\n"); e})
Matrix inversion failed
tmp
<simpleError in solve.default(mymat[-1, ]): Lapack
routine dgesv: system is exactly singular>
class(tmp)
[1] "simpleError" "error" "condition"
tmp <- tryCatch(solve(mymat[-1, ]), error=function(e) e,
finally=print("END"))
[1] "END"
Checking and Improving your functions Profiling
Profiling
Now your function works perfectly, but it might be a bit slow.

If it is not slow, don’t change it!
Don’t waste your time thinking of clever ways to perform the
processing until you know what is taking the time.
Use the function Rprof() to tell you what is worth tweaking.
Rprof()
mymat <- matrix(runif(1000000),nrow=1000)
Rprof()
inefficientFn(mymat)
Rprof(NULL)
summaryRprof()

Profiling: example function
inefficientFn
inefficientFn<- function(x)
{
tmp <- 0
for (i in 1:nrow(x))
{
b <- exp(1/1:ncol(x))
tmp <- tmp + x[i,] * b
}
sum(tmp)
}

Profiling: sample output

summaryRprof output
$by.self
self.time self.pct total.time total.pct
inefficientFn 0.06 42.9 0.14 100.0
exp 0.06 42.9 0.06 42.9
* 0.02 14.3 0.02 14.3
$by.total
total.time total.pct self.time self.pct
inefficientFn 0.14 100.0 0.06 42.9
exp 0.06 42.9 0.06 42.9
* 0.02 14.3 0.02 14.3
$sampling.time
[1] 0.14
Profiling: improved function
moreEfficientFn
moreEfficientFn<- function(x)
{
tmp <- 0
b <- exp(1/1:ncol(x))
for (i in 1:nrow(x))
{
tmp <- tmp + x[i,] * b
}
sum(tmp)
}

Profiling: new output
Now the call to exp() does not use up significant time.
summaryRprof output
$by.self
self.time self.pct total.time total.pct
moreEfficientFn 0.04 100 0.04 100
$by.total
total.time total.pct self.time self.pct
moreEfficientFn 0.04 100 0.00 100
$sampling.time
[1] 0.04

Profiling: timings
Timing the functions, using system.time shows the improvement

achieved.
system timings
system.time(inefficientFn(mymat))
user system elapsed
0.19 0.00 0.19
system.time(moreEfficientFn(mymat))
user system elapsed
0.06 0.00 0.07

Exercises
Exercises
Use the techniques while writing the project.

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Debugging and Tuning R Functions

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 1 / 29

Exceptions are conditions which prevent R’s normal processing.

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 2 / 29

Options are used to control many different aspects of R. A list of

Some examples of options:

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 3 / 29

Options are used to control many different aspects of R. A list of

Some examples of options:

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 3 / 29

Use of R options, continued

Options used as default values for functions (e.g. na.action in

To set an option: options(digits=5)

To access a specific option:

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 4 / 29

Use of R options, continued

Options used as default values for functions (e.g. na.action in

To set an option: options(digits=5)

To access a specific option:

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 4 / 29

Use of R options, continued

Options used as default values for functions (e.g. na.action in

To set an option: options(digits=5)

To access a specific option:

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 4 / 29

R exception handling: Errors

Serious exceptions but not catastrophic: R cannot continue, but is

R exception handling: Errors

Serious exceptions but not catastrophic: R cannot continue, but is

R exception handling: Errors

Serious exceptions but not catastrophic: R cannot continue, but is

R exception handling: Errors

Serious exceptions but not catastrophic: R cannot continue, but is

R exception handling: Errors

Serious exceptions but not catastrophic: R cannot continue, but is

R exception handling: Errors

Serious exceptions but not catastrophic: R cannot continue, but is

R exception handling: Warnings

Less serious exceptions, e.g. NA’s produced when converting

Behaviour controlled by value of options(warn):

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 6 / 29

R exception handling: Warnings

Less serious exceptions, e.g. NA’s produced when converting

Behaviour controlled by value of options(warn):

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 6 / 29

R exception handling: Warnings

Less serious exceptions, e.g. NA’s produced when converting

Behaviour controlled by value of options(warn):

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 6 / 29

You run your new function. It may

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 7 / 29

You run your new function. It may

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 7 / 29

You run your new function. It may

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 7 / 29

You run your new function. It may

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 7 / 29

You run your new function. It may

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 7 / 29

You run your new function. It may

R.M. Ripley (University of Oxford) Debugging R Functions 2012/13 7 / 29

How to find the error

How to find the error