beach adventure 2
chitrakatha
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The art of logging
In essence, logging is the act of displaying diagnostic and informative messages during the execution of a software program. Log messages can be used to debug software, to inform the user of the progress of long calculations, to document scripts, or to support the auditing of software and the results of complicated calculations.
R has a number of functions which can be used for logging purposes. Most people will be familiar with the
cat() command, which concatenates its arguments and prints the result to the console or to a text file. In practice, you will want a little more control over the level of detail of logging messages. Also, you will need to put a cat() statement before each warning() and stop() command to ensure that these events will show up in the logs. Because these two commands and the message()command write to stderr, the messages may get lost when running R scripts in batch mode.The rlogging package
To provide a slightly more advanced logging facility compared to using only the
cat() command, I have created the rlogging package. The idea is to use three existing commands in R’s base package, namely message(), warning(), and stop() to provide three logging levels: ‘INFO’, ‘WARN’, and ‘STOP’ respectively. The package provides a wrapper around these commands (i.e. it ‘masks’ them) to output time-stamped log messages to the console and a text file. For example, the message()command prints a log message if the logging level is set to ‘INFO’:> message("Hello world!")
[2013-09-20 07:56:07] [INFO] Hello world!
>
Each message starts with the timestamp and the logging level so it’s easy to find (e.g. using grep) different types of log messages in the log file.
Warnings and errors
So you can use the
message() command to output informative or debugging messages. Thewarning() command also (immediately) writes a time-stamped message to the console and log file, but it also retains its original behaviour. This means that, by default, warning messages are collected and shown only after the program is finished. These can be recalled with the warnings() function and suppressed by setting options(warn=-1). Note that the latter does not suppress the log messages. See the next section on logging levels which allow you to control this behaviour. Here’s a session which demonstrates the use of warning():> GetLogLevel()
[1] "INFO"
> warning("Be careful!")
[2013-09-20 08:56:32] [WARN] Be careful!
Warning message:
In warning("Be careful!") : Be careful!
> warnings()
Warning message:
In warning("Be careful!") : Be careful!
> options(warn=-1)
> warning("Be careful!")
[2013-09-20 08:56:56] [WARN] Be careful!
>
As you can see, the first
warning() prints the same message twice: the first one is the time-stamped log message (which is also written to the log file) and the second one is the message written tostderr by the warning() command in R’s base package. The second warning() only prints the time-stamped log message because the printing of warnings has been suppressed.
Like the
warning() function, the stop() function also retains its original behaviour, i.e. it prints the error message and stops the execution of the program. The difference is that a log message is also created so there is no need to add an extra cat() statement right before the call to stop(). This is especially useful when running R scripts in batch mode and messages to stderr may be lost. Here again, the same message is printed to the console twice, but this can not be suppressed. Note that the behaviour of the stopifnot() command is not changed by the package, therefore this command does not write a log message.Logging levels
Each of the three functions is linked to one of three logging levels: ‘INFO’, ‘WARN’, and ‘STOP’. The following table summarizes when messages are printed:
Level message() warning() stop()
INFO yes yes yes
WARN no yes yes
STOP no no yes
Error messages are always printed, but information messages and warnings can be suppressed.
Log file
By default, log messages are appended to a file rlogging.log in the current working directory. You can change the name and location of this file with the
SetLogFile(file, folder) command provided by the package:SetLogFile("mylogfile.txt") # use 'mylogfile.txt' in the current working directory
SetLogFile(folder="~") # save 'mylogfile.txt' in my home directory
SetLogFile(file="mylogfile.txt", folder="~") # same as both commands above
If you do not want to write to a file, then you set the file to
NULL as in the following example:SetLogFile(NULL)Fork it!
Want additional features? Want to change the look of the log messages? You can find the package source code on Github at
https://github.com/mjkallen/rlogging and fork it to make the required changes.
Happy logging.
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