Related
I would like to generate dynamic text without the need to create webhooks whenever possible. I understand that the only way to create dynamic text is by either creating different routes depending on parameters or by using inline system functions like $sys.func.ADD(1, 2) within text fulfillments.
But inline system functions like $sys.func.ADD(1, 2) do not work for me if used in text fulfillments. System functions just don't get executed for me. I.e. instead of uttering "3" my bot just utters "$sys.func.ADD(1, 2)" as a result of a test fulfillemnt. What am I doing wrong here? Does anybody have an example for using inline system functions in text fulfillment?
Thanks!
To resolve this issue, you need to check the result of system functions in order to identify the error that occurred.
For the system function $sys.func.ADD, when using it as a text response in your fulfillment, you need to convert it to type STRING to be embedded in text since the output of this system function returns a type DOUBLE.
You can convert the output of the $sys.func.ADD function to STRING by creating a nested function in your text response and utilizing the $sys.func.TO_TEXT which converts a value of other types to string.
Here’s an example for reference:
I made a program that is similar to clearing RAM. However, it always leaves a "Done" message followed by a dotted line after being executed. In addition, if you scroll up, you can see that the program was executed. Is there a way to remove both of these things? If you can't hide the fact that a program was executed, could you suppress the 'Done' message?
I have tried adding ClearHome" and " as the last line of my program, and neither stops the Done message from displaying.
Bonus points if your solution can be contained within the original program.
In a separate program, type the following line of code:
AsmPrgmFDCB00AEC9
Then at the end of the original program, type the following line of code:
Asm(prgmPROGRAMNAME
It is recommended that you test this out first with all programs archived, just running the above line of code alone, in case it fails. Hex codes like that one have been known to fail, and sometimes clears the RAM.
You can also try these other hex codes, but always keep in mind the warning above. My RAM has been cleared by this before, so use caution:
http://tibasicdev.wikidot.com/hexcodes
This works on TI 83 and 84, may be different with other calculator types.
EDIT:
I found a way to do this without an external program, and is much simpler.
Just add the following line of code to the end of your program:
Output(1,1," //no space, just a quote
You may or may not have to add ClrHome before that line of code.
This should prevent the Done message from appearing at the end.
Hope this helps!
Put an empty string at the end of your program, so your last line looks like this:
""
Or this
"
The empty string is stored to ans and will be displayed as a blank line rather than the Done message.
There is also an assembly hexcode to do this without leaving the blank line at the top:
FDCB00AEC9
When run at the end of the program using one of the various methods of running assembly, it will leave you with a blank, fully operational homescreen.
Outputting an empty string will prevent the Done message and also preserve Ans, in case a calling program is expecting to use it.
Output(Y,X,"")
See http://tibasicdev.wikidot.com/output for more details on Output(.
In your situation, run Clear Entries (found under Mem), then scroll up so that the Done message is selected and press Clear to get rid of it.
i am new to matlab. While working through the Matlab GUI, i faced a problem which is as follows..i want to have 2 figure files, with one figure file calling the other. i know that just by calling the name of the 2nd fig file from the first fig file, we can call the 2nd figure. however, i also wish to send some parameters from one fig file to another.here i need to send the arguments and also obtain these parameters so as to do further processing.i havent been able to find a solution to this problem. i would be glad if someone helps me out with this problem. thanking you in advance
There are three ways I found to do this:
Method 1: Use setappdata and getappdata like so:
setappdata(0,'some_var',value)
some_other_var = getappdata(0,'some_var')
You would use setappdata() in the m-file for fig1 to store whatever data you wanted to pass around, and then call getappdata() in another m-file to retrieve it. The argument 0 to the two functions specifies the MATLAB root workspace, which is accessible by your program everywhere (i.e. it is global). As such, when you close your figures that data will still be available. You may want to use rmappdata to remove them.
Method 2: Use guidata:
Assuming you created your GUI with GUIDE, then you have access to a structure called handles which is passed around everywhere and which you can edit, and so you can do this in a GUI callback:
handles.some_var = some_value
guidata(hObject,handles)
Then you can access handles.some_var elsewhere in some other callback (because handles is automatically passed into it for you) in your other m-file:
some_other_var = get(handles.some_var)
Method 3: Use UserData:
Store the variable you want from your first figure:
set(name_of_fig, 'UserData', some_var)
Then to get it from your other one:
some_other_var = get(name_of_fig, 'UserData')
(Disclaimer: My actual knowledge of MATLAB is not all that great, but it helps to be able to find good resources like this and this, and even this from the official docs. What I've written here may be wrong, so you should definitely consult the docs for more help.)
I would do like this (assuming you're using the GUI builder GUIDE).
Let's say that your figures/m-files are named firstFigure.fig/m and secondFigure.fig/m. In the code of firstFigure, just call secondFigure and pass your parameters as arguments:
someNumber = 1;
someText = 'test';
aMatrix = rand(3);
secondFigure(someNumber, someText, aMatrix);
The arguments will be available to secondFigure as a variable varargin in the callback functions
function varargout = secondFigure(varargin)
and
function secondFigure_OpeningFcn(hObject, eventdata, handles, varargin)
varagin is a cell structure; use cell2mat and char to convert it back:
theNumber = cell2mat(varargin(1));
theText = char(varargin(2));
theTextAgain = cell2mat(varargin(2));
theMatrix = cell2mat(varargin(3));
This may help:
http://www.mathworks.ch/matlabcentral/newsreader/view_thread/171989
The easiest method is to wrap the parameters in a cell array and send them directly to the GUI constructor. A call with two parameters might look like:
figure2({param1, param2})
Then you can unpack the arguments in the opening function (figure2_OpeningFcn) with code like:
handles.par1 = varargin{1}{1};
handles.par2 = varargin{1}{2};
These lines must be placed somewhere before the line that says guidata(hObject, handles);. Then you can access handles.par1 and handles.par2 directly in all the other callbacks.
I assume you are using GUIDE to generate your GUI. You can find figure2_OpeningFcn in figure2.m which will be located in the same directory as figure2.fig.
Note: you can also return values from a figure, returnvalue = my_figure({my_input}). If you'd like instructions on that too, leave a comment and I'll extend my answer.
I get an error when using an R function that I wrote:
Warning messages:
1: glm.fit: algorithm did not converge
2: glm.fit: algorithm did not converge
What I have done:
Step through the function
Adding print to find out at what line the error occurs suggests two functions that should not use glm.fit. They are window() and save().
My general approaches include adding print and stop commands, and stepping through a function line by line until I can locate the exception.
However, it is not clear to me using those techniques where this error comes from in the code. I am not even certain which functions within the code depend on glm.fit. How do I go about diagnosing this problem?
I'd say that debugging is an art form, so there's no clear silver bullet. There are good strategies for debugging in any language, and they apply here too (e.g. read this nice article). For instance, the first thing is to reproduce the problem...if you can't do that, then you need to get more information (e.g. with logging). Once you can reproduce it, you need to reduce it down to the source.
Rather than a "trick", I would say that I have a favorite debugging routine:
When an error occurs, the first thing that I usually do is look at the stack trace by calling traceback(): that shows you where the error occurred, which is especially useful if you have several nested functions.
Next I will set options(error=recover); this immediately switches into browser mode where the error occurs, so you can browse the workspace from there.
If I still don't have enough information, I usually use the debug() function and step through the script line by line.
The best new trick in R 2.10 (when working with script files) is to use the findLineNum() and setBreakpoint() functions.
As a final comment: depending upon the error, it is also very helpful to set try() or tryCatch() statements around external function calls (especially when dealing with S4 classes). That will sometimes provide even more information, and it also gives you more control over how errors are handled at run time.
These related questions have a lot of suggestions:
Debugging tools for the R language
Debugging lapply/sapply calls
Getting the state of variables after an error occurs in R
R script line numbers at error?
The best walkthrough I've seen so far is:
http://www.biostat.jhsph.edu/%7Erpeng/docs/R-debug-tools.pdf
Anybody agree/disagree?
As was pointed out to me in another question, Rprof() and summaryRprof() are nice tools to find slow parts of your program that might benefit from speeding up or moving to a C/C++ implementation. This probably applies more if you're doing simulation work or other compute- or data-intensive activities. The profr package can help visualizing the results.
I'm on a bit of a learn-about-debugging kick, so another suggestion from another thread:
Set options(warn=2) to treat warnings like errors
You can also use options to drop you right into the heat of the action when an error or warning occurs, using your favorite debugging function of choice. For instance:
Set options(error=recover) to run recover() when an error occurs, as Shane noted (and as is documented in the R debugging guide. Or any other handy function you would find useful to have run.
And another two methods from one of #Shane's links:
Wrap an inner function call with try() to return more information on it.
For *apply functions, use .inform=TRUE (from the plyr package) as an option to the apply command
#JoshuaUlrich also pointed out a neat way of using the conditional abilities of the classic browser() command to turn on/off debugging:
Put inside the function you might want to debug browser(expr=isTRUE(getOption("myDebug")))
And set the global option by options(myDebug=TRUE)
You could even wrap the browser call: myBrowse <- browser(expr=isTRUE(getOption("myDebug"))) and then call with myBrowse() since it uses globals.
Then there are the new functions available in R 2.10:
findLineNum() takes a source file name and line number and returns the function and environment. This seems to be helpful when you source() a .R file and it returns an error at line #n, but you need to know what function is located at line #n.
setBreakpoint() takes a source file name and line number and sets a breakpoint there
The codetools package, and particularly its checkUsage function can be particularly helpful in quickly picking up syntax and stylistic errors that a compiler would typically report (unused locals, undefined global functions and variables, partial argument matching, and so forth).
setBreakpoint() is a more user-friendly front-end to trace(). Details on the internals of how this works are available in a recent R Journal article.
If you are trying to debug someone else's package, once you have located the problem you can over-write their functions with fixInNamespace and assignInNamespace, but do not use this in production code.
None of this should preclude the tried-and-true standard R debugging tools, some of which are above and others of which are not. In particular, the post-mortem debugging tools are handy when you have a time-consuming bunch of code that you'd rather not re-run.
Finally, for tricky problems which don't seem to throw an error message, you can use options(error=dump.frames) as detailed in this question:
Error without an error being thrown
At some point, glm.fit is being called. That means one of the functions you call or one of the functions called by those functions is using either glm, glm.fit.
Also, as I mention in my comment above, that is a warning not an error, which makes a big difference. You can't trigger any of R's debugging tools from a warning (with default options before someone tells me I am wrong ;-).
If we change the options to turn warnings into errors then we can start to use R's debugging tools. From ?options we have:
‘warn’: sets the handling of warning messages. If ‘warn’ is
negative all warnings are ignored. If ‘warn’ is zero (the
default) warnings are stored until the top-level function
returns. If fewer than 10 warnings were signalled they will
be printed otherwise a message saying how many (max 50) were
signalled. An object called ‘last.warning’ is created and
can be printed through the function ‘warnings’. If ‘warn’ is
one, warnings are printed as they occur. If ‘warn’ is two or
larger all warnings are turned into errors.
So if you run
options(warn = 2)
then run your code, R will throw an error. At which point, you could run
traceback()
to see the call stack. Here is an example.
> options(warn = 2)
> foo <- function(x) bar(x + 2)
> bar <- function(y) warning("don't want to use 'y'!")
> foo(1)
Error in bar(x + 2) : (converted from warning) don't want to use 'y'!
> traceback()
7: doWithOneRestart(return(expr), restart)
6: withOneRestart(expr, restarts[[1L]])
5: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg,
call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
4: .signalSimpleWarning("don't want to use 'y'!", quote(bar(x +
2)))
3: warning("don't want to use 'y'!")
2: bar(x + 2)
1: foo(1)
Here you can ignore the frames marked 4: and higher. We see that foo called bar and that bar generated the warning. That should show you which functions were calling glm.fit.
If you now want to debug this, we can turn to another option to tell R to enter the debugger when it encounters an error, and as we have made warnings errors we will get a debugger when the original warning is triggered. For that you should run:
options(error = recover)
Here is an example:
> options(error = recover)
> foo(1)
Error in bar(x + 2) : (converted from warning) don't want to use 'y'!
Enter a frame number, or 0 to exit
1: foo(1)
2: bar(x + 2)
3: warning("don't want to use 'y'!")
4: .signalSimpleWarning("don't want to use 'y'!", quote(bar(x + 2)))
5: withRestarts({
6: withOneRestart(expr, restarts[[1]])
7: doWithOneRestart(return(expr), restart)
Selection:
You can then step into any of those frames to see what was happening when the warning was thrown.
To reset the above options to their default, enter
options(error = NULL, warn = 0)
As for the specific warning you quote, it is highly likely that you need to allow more iterations in the code. Once you've found out what is calling glm.fit, work out how to pass it the control argument using glm.control - see ?glm.control.
So browser(), traceback() and debug() walk into a bar, but trace() waits outside and keeps the motor running.
By inserting browser somewhere in your function, the execution will halt and wait for your input. You can move forward using n (or Enter), run the entire chunk (iteration) with c, finish the current loop/function with f, or quit with Q; see ?browser.
With debug, you get the same effect as with browser, but this stops the execution of a function at its beginning. Same shortcuts apply. This function will be in a "debug" mode until you turn it off using undebug (that is, after debug(foo), running the function foo will enter "debug" mode every time until you run undebug(foo)).
A more transient alternative is debugonce, which will remove the "debug" mode from the function after the next time it's evaluated.
traceback will give you the flow of execution of functions all the way up to where something went wrong (an actual error).
You can insert code bits (i.e. custom functions) in functions using trace, for example browser. This is useful for functions from packages and you're too lazy to get the nicely folded source code.
My general strategy looks like:
Run traceback() to see look for obvious issues
Set options(warn=2) to treat warnings like errors
Set options(error=recover) to step into the call stack on error
After going through all the steps suggested here I just learned that setting .verbose = TRUE in foreach() also gives me tons of useful information. In particular foreach(.verbose=TRUE) shows exactly where an error occurs inside the foreach loop, while traceback() does not look inside the foreach loop.
Mark Bravington's debugger which is available as the package debug on CRAN is very good and pretty straight forward.
library(debug);
mtrace(myfunction);
myfunction(a,b);
#... debugging, can query objects, step, skip, run, breakpoints etc..
qqq(); # quit the debugger only
mtrace.off(); # turn off debugging
The code pops up in a highlighted Tk window so you can see what's going on and, of course you can call another mtrace() while in a different function.
HTH
I like Gavin's answer: I did not know about options(error = recover). I also like to use the 'debug' package that gives a visual way to step through your code.
require(debug)
mtrace(foo)
foo(1)
At this point it opens up a separate debug window showing your function, with a yellow line showing where you are in the code. In the main window the code enters debug mode, and you can keep hitting enter to step through the code (and there are other commands as well), and examine variable values, etc. The yellow line in the debug window keeps moving to show where you are in the code. When done with debugging, you can turn off tracing with:
mtrace.off()
Based on the answer I received here, you should definitely check out the options(error=recover) setting. When this is set, upon encountering an error, you'll see text on the console similar to the following (traceback output):
> source(<my filename>)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
Enter a frame number, or 0 to exit
1: source(<my filename>)
2: eval.with.vis(ei, envir)
3: eval.with.vis(expr, envir, enclos)
4: LinearParamSearch(data = dataset, y = data.frame(LGD = dataset$LGD10), data.names = data
5: LinearParamSearch.R#66: plot(x = x, y = y.data, xlab = names(y), ylab = data.names[i])
6: LinearParamSearch.R#66: plot.default(x = x, y = y.data, xlab = names(y), ylab = data.nam
7: LinearParamSearch.R#66: localWindow(xlim, ylim, log, asp, ...)
8: LinearParamSearch.R#66: plot.window(...)
Selection:
At which point you can choose which "frame" to enter. When you make a selection, you'll be placed into browser() mode:
Selection: 4
Called from: stop(gettextf("replacement has %d rows, data has %d", N, n),
domain = NA)
Browse[1]>
And you can examine the environment as it was at the time of the error. When you're done, type c to bring you back to the frame selection menu. When you're done, as it tells you, type 0 to exit.
I gave this answer to a more recent question, but am adding it here for completeness.
Personally I tend not to use functions to debug. I often find that this causes as much trouble as it solves. Also, coming from a Matlab background I like being able to do this in an integrated development environment (IDE) rather than doing this in the code. Using an IDE keeps your code clean and simple.
For R, I use an IDE called "RStudio" (http://www.rstudio.com), which is available for windows, mac, and linux and is pretty easy to use.
Versions of Rstudio since about October 2013 (0.98ish?) have the capability to add breakpoints in scripts and functions: to do this, just click on the left margin of the file to add a breakpoint. You can set a breakpoint and then step through from that point on. You also have access to all of the data in that environment, so you can try out commands.
See http://www.rstudio.com/ide/docs/debugging/overview for details. If you already have Rstudio installed, you may need to upgrade - this is a relatively new (late 2013) feature.
You may also find other IDEs that have similar functionality.
Admittedly, if it's a built-in function you may have to resort to some of the suggestions made by other people in this discussion. But, if it's your own code that needs fixing, an IDE-based solution might be just what you need.
To debug Reference Class methods without instance reference
ClassName$trace(methodName, browser)
I am beginning to think that not printing error line number - a most basic requirement - BY DEFAILT- is some kind of a joke in R/Rstudio. The only reliable method I have found to find where an error occurred is to make the additional effort of calloing traceback() and see the top line.
I get an error when using an R function that I wrote:
Warning messages:
1: glm.fit: algorithm did not converge
2: glm.fit: algorithm did not converge
What I have done:
Step through the function
Adding print to find out at what line the error occurs suggests two functions that should not use glm.fit. They are window() and save().
My general approaches include adding print and stop commands, and stepping through a function line by line until I can locate the exception.
However, it is not clear to me using those techniques where this error comes from in the code. I am not even certain which functions within the code depend on glm.fit. How do I go about diagnosing this problem?
I'd say that debugging is an art form, so there's no clear silver bullet. There are good strategies for debugging in any language, and they apply here too (e.g. read this nice article). For instance, the first thing is to reproduce the problem...if you can't do that, then you need to get more information (e.g. with logging). Once you can reproduce it, you need to reduce it down to the source.
Rather than a "trick", I would say that I have a favorite debugging routine:
When an error occurs, the first thing that I usually do is look at the stack trace by calling traceback(): that shows you where the error occurred, which is especially useful if you have several nested functions.
Next I will set options(error=recover); this immediately switches into browser mode where the error occurs, so you can browse the workspace from there.
If I still don't have enough information, I usually use the debug() function and step through the script line by line.
The best new trick in R 2.10 (when working with script files) is to use the findLineNum() and setBreakpoint() functions.
As a final comment: depending upon the error, it is also very helpful to set try() or tryCatch() statements around external function calls (especially when dealing with S4 classes). That will sometimes provide even more information, and it also gives you more control over how errors are handled at run time.
These related questions have a lot of suggestions:
Debugging tools for the R language
Debugging lapply/sapply calls
Getting the state of variables after an error occurs in R
R script line numbers at error?
The best walkthrough I've seen so far is:
http://www.biostat.jhsph.edu/%7Erpeng/docs/R-debug-tools.pdf
Anybody agree/disagree?
As was pointed out to me in another question, Rprof() and summaryRprof() are nice tools to find slow parts of your program that might benefit from speeding up or moving to a C/C++ implementation. This probably applies more if you're doing simulation work or other compute- or data-intensive activities. The profr package can help visualizing the results.
I'm on a bit of a learn-about-debugging kick, so another suggestion from another thread:
Set options(warn=2) to treat warnings like errors
You can also use options to drop you right into the heat of the action when an error or warning occurs, using your favorite debugging function of choice. For instance:
Set options(error=recover) to run recover() when an error occurs, as Shane noted (and as is documented in the R debugging guide. Or any other handy function you would find useful to have run.
And another two methods from one of #Shane's links:
Wrap an inner function call with try() to return more information on it.
For *apply functions, use .inform=TRUE (from the plyr package) as an option to the apply command
#JoshuaUlrich also pointed out a neat way of using the conditional abilities of the classic browser() command to turn on/off debugging:
Put inside the function you might want to debug browser(expr=isTRUE(getOption("myDebug")))
And set the global option by options(myDebug=TRUE)
You could even wrap the browser call: myBrowse <- browser(expr=isTRUE(getOption("myDebug"))) and then call with myBrowse() since it uses globals.
Then there are the new functions available in R 2.10:
findLineNum() takes a source file name and line number and returns the function and environment. This seems to be helpful when you source() a .R file and it returns an error at line #n, but you need to know what function is located at line #n.
setBreakpoint() takes a source file name and line number and sets a breakpoint there
The codetools package, and particularly its checkUsage function can be particularly helpful in quickly picking up syntax and stylistic errors that a compiler would typically report (unused locals, undefined global functions and variables, partial argument matching, and so forth).
setBreakpoint() is a more user-friendly front-end to trace(). Details on the internals of how this works are available in a recent R Journal article.
If you are trying to debug someone else's package, once you have located the problem you can over-write their functions with fixInNamespace and assignInNamespace, but do not use this in production code.
None of this should preclude the tried-and-true standard R debugging tools, some of which are above and others of which are not. In particular, the post-mortem debugging tools are handy when you have a time-consuming bunch of code that you'd rather not re-run.
Finally, for tricky problems which don't seem to throw an error message, you can use options(error=dump.frames) as detailed in this question:
Error without an error being thrown
At some point, glm.fit is being called. That means one of the functions you call or one of the functions called by those functions is using either glm, glm.fit.
Also, as I mention in my comment above, that is a warning not an error, which makes a big difference. You can't trigger any of R's debugging tools from a warning (with default options before someone tells me I am wrong ;-).
If we change the options to turn warnings into errors then we can start to use R's debugging tools. From ?options we have:
‘warn’: sets the handling of warning messages. If ‘warn’ is
negative all warnings are ignored. If ‘warn’ is zero (the
default) warnings are stored until the top-level function
returns. If fewer than 10 warnings were signalled they will
be printed otherwise a message saying how many (max 50) were
signalled. An object called ‘last.warning’ is created and
can be printed through the function ‘warnings’. If ‘warn’ is
one, warnings are printed as they occur. If ‘warn’ is two or
larger all warnings are turned into errors.
So if you run
options(warn = 2)
then run your code, R will throw an error. At which point, you could run
traceback()
to see the call stack. Here is an example.
> options(warn = 2)
> foo <- function(x) bar(x + 2)
> bar <- function(y) warning("don't want to use 'y'!")
> foo(1)
Error in bar(x + 2) : (converted from warning) don't want to use 'y'!
> traceback()
7: doWithOneRestart(return(expr), restart)
6: withOneRestart(expr, restarts[[1L]])
5: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg,
call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
4: .signalSimpleWarning("don't want to use 'y'!", quote(bar(x +
2)))
3: warning("don't want to use 'y'!")
2: bar(x + 2)
1: foo(1)
Here you can ignore the frames marked 4: and higher. We see that foo called bar and that bar generated the warning. That should show you which functions were calling glm.fit.
If you now want to debug this, we can turn to another option to tell R to enter the debugger when it encounters an error, and as we have made warnings errors we will get a debugger when the original warning is triggered. For that you should run:
options(error = recover)
Here is an example:
> options(error = recover)
> foo(1)
Error in bar(x + 2) : (converted from warning) don't want to use 'y'!
Enter a frame number, or 0 to exit
1: foo(1)
2: bar(x + 2)
3: warning("don't want to use 'y'!")
4: .signalSimpleWarning("don't want to use 'y'!", quote(bar(x + 2)))
5: withRestarts({
6: withOneRestart(expr, restarts[[1]])
7: doWithOneRestart(return(expr), restart)
Selection:
You can then step into any of those frames to see what was happening when the warning was thrown.
To reset the above options to their default, enter
options(error = NULL, warn = 0)
As for the specific warning you quote, it is highly likely that you need to allow more iterations in the code. Once you've found out what is calling glm.fit, work out how to pass it the control argument using glm.control - see ?glm.control.
So browser(), traceback() and debug() walk into a bar, but trace() waits outside and keeps the motor running.
By inserting browser somewhere in your function, the execution will halt and wait for your input. You can move forward using n (or Enter), run the entire chunk (iteration) with c, finish the current loop/function with f, or quit with Q; see ?browser.
With debug, you get the same effect as with browser, but this stops the execution of a function at its beginning. Same shortcuts apply. This function will be in a "debug" mode until you turn it off using undebug (that is, after debug(foo), running the function foo will enter "debug" mode every time until you run undebug(foo)).
A more transient alternative is debugonce, which will remove the "debug" mode from the function after the next time it's evaluated.
traceback will give you the flow of execution of functions all the way up to where something went wrong (an actual error).
You can insert code bits (i.e. custom functions) in functions using trace, for example browser. This is useful for functions from packages and you're too lazy to get the nicely folded source code.
My general strategy looks like:
Run traceback() to see look for obvious issues
Set options(warn=2) to treat warnings like errors
Set options(error=recover) to step into the call stack on error
After going through all the steps suggested here I just learned that setting .verbose = TRUE in foreach() also gives me tons of useful information. In particular foreach(.verbose=TRUE) shows exactly where an error occurs inside the foreach loop, while traceback() does not look inside the foreach loop.
Mark Bravington's debugger which is available as the package debug on CRAN is very good and pretty straight forward.
library(debug);
mtrace(myfunction);
myfunction(a,b);
#... debugging, can query objects, step, skip, run, breakpoints etc..
qqq(); # quit the debugger only
mtrace.off(); # turn off debugging
The code pops up in a highlighted Tk window so you can see what's going on and, of course you can call another mtrace() while in a different function.
HTH
I like Gavin's answer: I did not know about options(error = recover). I also like to use the 'debug' package that gives a visual way to step through your code.
require(debug)
mtrace(foo)
foo(1)
At this point it opens up a separate debug window showing your function, with a yellow line showing where you are in the code. In the main window the code enters debug mode, and you can keep hitting enter to step through the code (and there are other commands as well), and examine variable values, etc. The yellow line in the debug window keeps moving to show where you are in the code. When done with debugging, you can turn off tracing with:
mtrace.off()
Based on the answer I received here, you should definitely check out the options(error=recover) setting. When this is set, upon encountering an error, you'll see text on the console similar to the following (traceback output):
> source(<my filename>)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
Enter a frame number, or 0 to exit
1: source(<my filename>)
2: eval.with.vis(ei, envir)
3: eval.with.vis(expr, envir, enclos)
4: LinearParamSearch(data = dataset, y = data.frame(LGD = dataset$LGD10), data.names = data
5: LinearParamSearch.R#66: plot(x = x, y = y.data, xlab = names(y), ylab = data.names[i])
6: LinearParamSearch.R#66: plot.default(x = x, y = y.data, xlab = names(y), ylab = data.nam
7: LinearParamSearch.R#66: localWindow(xlim, ylim, log, asp, ...)
8: LinearParamSearch.R#66: plot.window(...)
Selection:
At which point you can choose which "frame" to enter. When you make a selection, you'll be placed into browser() mode:
Selection: 4
Called from: stop(gettextf("replacement has %d rows, data has %d", N, n),
domain = NA)
Browse[1]>
And you can examine the environment as it was at the time of the error. When you're done, type c to bring you back to the frame selection menu. When you're done, as it tells you, type 0 to exit.
I gave this answer to a more recent question, but am adding it here for completeness.
Personally I tend not to use functions to debug. I often find that this causes as much trouble as it solves. Also, coming from a Matlab background I like being able to do this in an integrated development environment (IDE) rather than doing this in the code. Using an IDE keeps your code clean and simple.
For R, I use an IDE called "RStudio" (http://www.rstudio.com), which is available for windows, mac, and linux and is pretty easy to use.
Versions of Rstudio since about October 2013 (0.98ish?) have the capability to add breakpoints in scripts and functions: to do this, just click on the left margin of the file to add a breakpoint. You can set a breakpoint and then step through from that point on. You also have access to all of the data in that environment, so you can try out commands.
See http://www.rstudio.com/ide/docs/debugging/overview for details. If you already have Rstudio installed, you may need to upgrade - this is a relatively new (late 2013) feature.
You may also find other IDEs that have similar functionality.
Admittedly, if it's a built-in function you may have to resort to some of the suggestions made by other people in this discussion. But, if it's your own code that needs fixing, an IDE-based solution might be just what you need.
To debug Reference Class methods without instance reference
ClassName$trace(methodName, browser)
I am beginning to think that not printing error line number - a most basic requirement - BY DEFAILT- is some kind of a joke in R/Rstudio. The only reliable method I have found to find where an error occurred is to make the additional effort of calloing traceback() and see the top line.