If I am running a long R script from the command line (R --slave script.R), then how can I get it to give line numbers at errors?
I don't want to add debug commands to the script if at all possible; I just want R to behave like most other scripting languages.
This won't give you the line number, but it will tell you where the failure happens in the call stack which is very helpful:
traceback()
[Edit:] When running a script from the command line you will have to skip one or two calls, see traceback() for interactive and non-interactive R sessions
I'm not aware of another way to do this without the usual debugging suspects:
debug()
browser()
options(error=recover) [followed by options(error = NULL) to revert it]
You might want to look at this related post.
[Edit:] Sorry...just saw that you're running this from the command line. In that case I would suggest working with the options(error) functionality. Here's a simple example:
options(error = quote({dump.frames(to.file=TRUE); q()}))
You can create as elaborate a script as you want on an error condition, so you should just decide what information you need for debugging.
Otherwise, if there are specific areas you're concerned about (e.g. connecting to a database), then wrap them in a tryCatch() function.
Doing options(error=traceback) provides a little more information about the content of the lines leading up to the error. It causes a traceback to appear if there is an error, and for some errors it has the line number, prefixed by #. But it's hit or miss, many errors won't get line numbers.
Support for this will be forthcoming in R 2.10 and later. Duncan Murdoch just posted to r-devel on Sep 10 2009 about findLineNum and setBreapoint:
I've just added a couple of functions to R-devel to help with
debugging. findLineNum() finds which line of which function
corresponds to a particular line of source code; setBreakpoint() takes
the output of findLineNum, and calls trace() to set a breakpoint
there.
These rely on having source reference debug information in the code.
This is the default for code read by source(), but not for packages.
To get the source references in package code, set the environment
variable R_KEEP_PKG_SOURCE=yes, or within R, set
options(keep.source.pkgs=TRUE), then install the package from source
code. Read ?findLineNum for details on how to tell it to search
within packages, rather than limiting the search to the global
environment.
For example,
x <- " f <- function(a, b) {
if (a > b) {
a
} else {
b
}
}"
eval(parse(text=x)) # Normally you'd use source() to read a file...
findLineNum("<text>#3") # <text> is a dummy filename used by
parse(text=)
This will print
f step 2,3,2 in <environment: R_GlobalEnv>
and you can use
setBreakpoint("<text>#3")
to set a breakpoint there.
There are still some limitations (and probably bugs) in the code; I'll
be fixing thos
You do it by setting
options(show.error.locations = TRUE)
I just wonder why this setting is not a default in R? It should be, as it is in every other language.
Specifying the global R option for handling non-catastrophic errors worked for me, along with a customized workflow for retaining info about the error and examining this info after the failure. I am currently running R version 3.4.1.
Below, I've included a description of the workflow that worked for me, as well as some code I used to set the global error handling option in R.
As I have it configured, the error handling also creates an RData file containing all objects in working memory at the time of the error. This dump can be read back into R using load() and then the various environments as they existed at the time of the error can be inspected interactively using debugger(errorDump).
I will note that I was able to get line numbers in the traceback() output from any custom functions within the stack, but only if I used the keep.source=TRUE option when calling source() for any custom functions used in my script. Without this option, setting the global error handling option as below sent the full output of the traceback() to an error log named error.log, but line numbers were not available.
Here's the general steps I took in my workflow and how I was able to access the memory dump and error log after a non-interactive R failure.
I put the following at the top of the main script I was calling from the command line. This sets the global error handling option for the R session. My main script was called myMainScript.R. The various lines in the code have comments after them describing what they do. Basically, with this option, when R encounters an error that triggers stop(), it will create an RData (*.rda) dump file of working memory across all active environments in the directory ~/myUsername/directoryForDump and will also write an error log named error.log with some useful information to the same directory. You can modify this snippet to add other handling on error (e.g., add a timestamp to the dump file and error log filenames, etc.).
options(error = quote({
setwd('~/myUsername/directoryForDump'); # Set working directory where you want the dump to go, since dump.frames() doesn't seem to accept absolute file paths.
dump.frames("errorDump", to.file=TRUE, include.GlobalEnv=TRUE); # First dump to file; this dump is not accessible by the R session.
sink(file="error.log"); # Specify sink file to redirect all output.
dump.frames(); # Dump again to be able to retrieve error message and write to error log; this dump is accessible by the R session since not dumped to file.
cat(attr(last.dump,"error.message")); # Print error message to file, along with simplified stack trace.
cat('\nTraceback:');
cat('\n');
traceback(2); # Print full traceback of function calls with all parameters. The 2 passed to traceback omits the outermost two function calls.
sink();
q()}))
Make sure that from the main script and any subsequent function calls, anytime a function is sourced, the option keep.source=TRUE is used. That is, to source a function, you would use source('~/path/to/myFunction.R', keep.source=TRUE). This is required for the traceback() output to contain line numbers. It looks like you may also be able to set this option globally using options( keep.source=TRUE ), but I have not tested this to see if it works. If you don't need line numbers, you can omit this option.
From the terminal (outside R), call the main script in batch mode using Rscript myMainScript.R. This starts a new non-interactive R session and runs the script myMainScript.R. The code snippet given in step 1 that has been placed at the top of myMainScript.R sets the error handling option for the non-interactive R session.
Encounter an error somewhere within the execution of myMainScript.R. This may be in the main script itself, or nested several functions deep. When the error is encountered, handling will be performed as specified in step 1, and the R session will terminate.
An RData dump file named errorDump.rda and and error log named error.log are created in the directory specified by '~/myUsername/directoryForDump' in the global error handling option setting.
At your leisure, inspect error.log to review information about the error, including the error message itself and the full stack trace leading to the error. Here's an example of the log that's generated on error; note the numbers after the # character are the line numbers of the error at various points in the call stack:
Error in callNonExistFunc() : could not find function "callNonExistFunc"
Calls: test_multi_commodity_flow_cmd -> getExtendedConfigDF -> extendConfigDF
Traceback:
3: extendConfigDF(info_df, data_dir = user_dir, dlevel = dlevel) at test_multi_commodity_flow.R#304
2: getExtendedConfigDF(config_file_path, out_dir, dlevel) at test_multi_commodity_flow.R#352
1: test_multi_commodity_flow_cmd(config_file_path = config_file_path,
spot_file_path = spot_file_path, forward_file_path = forward_file_path,
data_dir = "../", user_dir = "Output", sim_type = "spot",
sim_scheme = "shape", sim_gran = "hourly", sim_adjust = "raw",
nsim = 5, start_date = "2017-07-01", end_date = "2017-12-31",
compute_averages = opt$compute_averages, compute_shapes = opt$compute_shapes,
overwrite = opt$overwrite, nmonths = opt$nmonths, forward_regime = opt$fregime,
ltfv_ratio = opt$ltfv_ratio, method = opt$method, dlevel = 0)
At your leisure, you may load errorDump.rda into an interactive R session using load('~/path/to/errorDump.rda'). Once loaded, call debugger(errorDump) to browse all R objects in memory in any of the active environments. See the R help on debugger() for more info.
This workflow is enormously helpful when running R in some type of production environment where you have non-interactive R sessions being initiated at the command line and you want information retained about unexpected errors. The ability to dump memory to a file you can use to inspect working memory at the time of the error, along with having the line numbers of the error in the call stack, facilitate speedy post-mortem debugging of what caused the error.
First, options(show.error.locations = TRUE) and then traceback(). The error line number will be displayed after #
Related
I have encountered an error when running a batch file. It goes like this, I run test-setup.cmd which calls another batch file test-env.cmd
test-setup.cmd calls by using this line:
call %SCRIPT_HOME%\test-env.cmd
where SCRIPT_HOME is set up as SCRIPT_HOME=%~dp0
test-env.cmd has this line:
if [%TEST_HOME%] == [] set TEST_HOME=D:\Program Files\Test\test-02.2.3.Final
After running the test-setup.cmd a message appears like this:
Files\Test\test-02.2.3.Final was unexpected at this time
Note that I have setup the TEST_HOME in the system environment variables.
Please help, thank you.
The syntax of your if command is incorrect. It would work if %TEST_HOME% didn't contain any spaces, but since it does you must use double quotes:
if "%TEST_HOME%" == "" set TEST_HOME=D:\Program Files\Test\test-02.2.3.Final
Mind you, since you're just testing to see whether the variable exists, it would be a lot more efficient to do that directly:
if not defined TEST_HOME set TEST_HOME=D:\Program Files\Test\test-02.2.3.Final
TL;DR
How to find where exactly vim or nvim error started (which file?) when I'm interested in fixing the actual issue and not just removing the bad plugin? Anything better than strace and guesswork to find the error origin?
Issue
I often add a plugin to my vim or nvim config and end up getting errors on hooks (buffer open, close, write):
"test.py" [New] 0L, 0C written
Error detected while processing function 343[12]..272:
line 8:
E716: Key not present in Dictionary: _exec
E116: Invalid arguments for function get(a:args, 'exec', a:1['_exec'])
E15: Invalid expression: get(a:args, 'exec', a:1['_exec'])
The problem is, I have no idea where those come from, only get some line number of unknown file and I know it's not my vim/nvim config file.
Somewhere, you have a plugin that has defined a dictionary with anonymous-functions (check the help related to this tag).
For the curious ones, it's done this way:
let d = {}
function! d.whatever() abort
throw "blah"
endfunction
When you execute this function, you'll get the kind of error you're currently observing. That's why I stopped working this way to prefer:
let d = {}
function s:whatever() abort
throw "blah"
endfunction
let d.whatever = function('s:whatever') " a workaround is required for older versions of vim
" At least this way I'll get a `<SNR>42_whatever` in the exception throwpoint, and thus a scriptname.
That's the why. Now, back to your problem, AFAIK, the only things you'll be able to know are the two functions that have been called:
in line 12 of :function {343}, you've called
:function {272} which contains an error at line 8.
Thanks to these two commands (may be prefixed with :verbose, I don't remember exactly), you'll get the source code of the two functions, which you should be able to use in order to grep your plugins to know where it appears.
Following is the code I have used :-
require(realpath(dirname(__FILE__).'/../../../email/apps/common/framework/YiiBase.php'));
$config = require(realpath(dirname(__FILE__).'/../../../email/apps/customer/config/main.php'));
Yii::createWebApplication($config);
var_dump(Yii::app()->User->id);
i am getting following error:-
Message: include(): Failed opening 'Yii.php' for inclusion (include_path='.:/usr/share/php:/usr/share/pear')
Filename: framework/YiiBase.php
Line Number: 428
Be kind write full absolute path for the script that executes the code and location of the files YiiBase.php and main.php.
Solution from the creator of Yii says:
require_once('path/to/yii.php');
Yii::createWebApplication($config);
// you can access Yii::app() now as usual
$session = Yii::app()->session;
//....use session as you wish
My file that can help you start is:
// change the following paths if necessary
$yii=dirname(__FILE__).'/../yii/yii.php';
$config=dirname(__FILE__).'/protected/config/main.php';
// remove the following lines when in production mode
defined('YII_DEBUG') or define('YII_DEBUG',true);
// specify how many levels of call stack should be shown in each log message
defined('YII_TRACE_LEVEL') or define('YII_TRACE_LEVEL',3);
require_once($yii);
Yii::createWebApplication($config);
NOTE
Its is not recommended you use YiiBase. Use either yii or yiilite. YiiBase serves as base class and is not intended to be used directly (to the best of my kowledge). Also check paths if they real point to the file!
I have a file called backup.lua, which the program should write to every so often in order to backup its status, in case of a failure.
The problem is that the program writes the backup.lua file completely fine first-time round, but any other times it refuses to write to the file.
I tried removing the file while the program was still open but Windows told me that the file was in use by 'CrysisWarsDedicatedServer.exe', which is the program. I have told the host Lua function to close the backup.lua file, so why isn't it letting me modify the file at will after it has been closed?
I can't find anything on the internet (Google actually tried to correct my search) and the secondary programmer on the project doesn't know either.
So I'm wondering if any of you folks know what we are doing wrong here?
Host function code:
function ServerBackup(todo)
local write, read;
if todo=="write" then
write = true;
else
read = true;
end
if (write) then
local source = io.open(Root().."Mods/Infinity/System/Read/backup.lua", "w");
System.Log(TeamInstantAction:GetTeamScore(2).." for 2, and for 1: "..TeamInstantAction:GetTeamScore(1))
System.LogAlways("[System] Backing up serverdata to file 'backup.lua'");
source:write("--[[ The server is dependent on this file; editing it will lead to serious problems.If there is a problem with this file, please re-write it by accessing the backup system ingame.--]]");
source:write("Backup = {};Backup.Time = '"..os.date("%H:%M").."';Backup.Date = '"..os.date("%d/%m/%Y").."';");
source:write(XFormat("TeamInstantAction:SetTeamScore(2, %d);TeamInstantAction:SetTeamScore(1, %d);TeamInstantAction:UpdateScores();",TeamInstantAction:GetTeamScore(2), TeamInstantAction:GetTeamScore(1) ));
source:close();
for i,player in pairs(g_gameRules.game:GetPlayers() or {}) do
if (IsModerator(player)) then
CMPlayer(player, "[!backup] Completed server backup.");
end
end
end
--local source = io.open(Root().."Mods/Infinity/System/Read/backup.lua", "r"); Can the file be open here and by the Lua scriptloader too?
if (read) then
System.LogAlways("[System] Restoring serverdata from file 'backup.lua'");
--source:close();
Backup = {};
Script.LoadScript(Root().."Mods/Infinity/System/Read/backup.lua");
if not Backup or #Backup < 1 then
System.LogAlways("[System] Error restoring serverdata from file 'backup.lua'");
end
end
end
Thanks all :).
Edit:
Although the file is now written to the disk fine, the system fails to read the dumped file.
So, now the problem is that the "LoadScript" function isn't doing what you expect:
Because I'm psychic, i have divined that you're writing a Crysis plugin, and are attempting to use it's LoadScript API call.
(Please don't assume everyone here would guess this, or be bothered to look for it. It's vital information that must form part of your questions)
The script you're writing attempts to set Backup - but your script, as written - does not separate lines with newline characters. As the first line is a comment, the entire script will be ignored.
Basicallty the script you've written looks like this, which is all treated as a comment.
--[[ comment ]]--Backup="Hello!"
You need to write a "\n" after the comment (and, I'd recommend in other places too) to make it like this. In fact, you don't really need block comments at all.
-- comment
Backup="Hello!"
This example routine generates two Throw::nocatch warning messages in the kernel window. Can they be handled somehow?
The example consists of this code in a file "test.m" created in C:\Temp:
Needs["JLink`"];
$FrontEndLaunchCommand = "Mathematica.exe";
UseFrontEnd[NotebookWrite[CreateDocument[], "Testing"]];
Then these commands pasted and run at the Windows Command Prompt:
PATH = C:\Program Files\Wolfram Research\Mathematica\8.0\;%PATH%
start MathKernel -noprompt -initfile "C:\Temp\test.m"
Addendum
The reason for using UseFrontEnd as opposed to UsingFrontEnd is that an interactive front end may be required to preserve output and messages from notebooks that are usually run interactively. For example, with C:\Temp\test.m modified like so:
Needs["JLink`"];
$FrontEndLaunchCommand="Mathematica.exe";
UseFrontEnd[
nb = NotebookOpen["C:\\Temp\\run.nb"];
SelectionMove[nb, Next, Cell];
SelectionEvaluate[nb];
];
Pause[10];
CloseFrontEnd[];
and a notebook C:\Temp\run.nb created with a single cell containing:
x1 = 0; While[x1 < 1000000,
If[Mod[x1, 100000] == 0,
Print["x1=" <> ToString[x1]]]; x1++];
NotebookSave[EvaluationNotebook[]];
NotebookClose[EvaluationNotebook[]];
this code, launched from a Windows Command Prompt, will run interactively and save its output. This is not possible to achieve using UsingFrontEnd or MathKernel -script "C:\Temp\test.m".
During the initialization, the kernel code is in a mode which prevents aborts.
Throw/Catch are implemented with Abort, therefore they do not work during initialization.
A simple example that shows the problem is to put this in your test.m file:
Catch[Throw[test]];
Similarly, functions like TimeConstrained, MemoryConstrained, Break, the Trace family, Abort and those that depend upon it (like certain data paclets) will have problems like this during initialization.
A possible solution to your problem might be to consider the -script option:
math.exe -script test.m
Also, note that in version 8 there is a documented function called UsingFrontEnd, which does what UseFrontEnd did, but is auto-configured, so this:
Needs["JLink`"];
UsingFrontEnd[NotebookWrite[CreateDocument[], "Testing"]];
should be all you need in your test.m file.
See also: Mathematica Scripts
Addendum
One possible solution to use the -script and UsingFrontEnd is to use the 'run.m script
included below. This does require setting up a 'Test' kernel in the kernel configuration options (basically a clone of the 'Local' kernel settings).
The script includes two utility functions, NotebookEvaluatingQ and NotebookPauseForEvaluation, which help the script to wait for the client notebook to finish evaluating before saving it. The upside of this approach is that all the evaluation control code is in the 'run.m' script, so the client notebook does not need to have a NotebookSave[EvaluationNotebook[]] statement at the end.
NotebookPauseForEvaluation[nb_] := Module[{},While[NotebookEvaluatingQ[nb],Pause[.25]]]
NotebookEvaluatingQ[nb_]:=Module[{},
SelectionMove[nb,All,Notebook];
Or##Map["Evaluating"/.#&,Developer`CellInformation[nb]]
]
UsingFrontEnd[
nb = NotebookOpen["c:\\users\\arnoudb\\run.nb"];
SetOptions[nb,Evaluator->"Test"];
SelectionMove[nb,All,Notebook];
SelectionEvaluate[nb];
NotebookPauseForEvaluation[nb];
NotebookSave[nb];
]
I hope this is useful in some way to you. It could use a few more improvements like resetting the notebook's kernel to its original and closing the notebook after saving it,
but this code should work for this particular purpose.
On a side note, I tried one other approach, using this:
UsingFrontEnd[ NotebookEvaluate[ "c:\\users\\arnoudb\\run.nb", InsertResults->True ] ]
But this is kicking the kernel terminal session into a dialog mode, which seems like a bug
to me (I'll check into this and get this reported if this is a valid issue).