An R package for simple logging
This package takes a different approach compared to other R packages like the
log4r,
futile.logger and
logging packages. Whereas these are
inspired by Java’s log4j or Python’s
logging module, rlogging masks
R’s message(), warning() and stop() functions to provide the option to
write uniform log messages to the console and/or a text file.
This simple approach provides a number of benefits:
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.
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.
So you can use the message() command to output informative or debugging
messages. The warning() 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 to stderr 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.
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.
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)
Use the install_github() command from the devtools package.
Download and install manually:
git clone https://github.com/mjkallen/rlogging.git
R CMD INSTALL rlogging
MIT license. See the LICENSE file for details.