logrx
has been built
with both the flexibility of code execution and a number of different
use cases in mind. While the basic case has been outlined in our Get
Started vignette, here we will be discussing different methods of
execution and creation of log files. These examples are meant to guide
users who wish to explore different methods of execution or for those
using logrx
to create scripting.
Below you will find a number of examples for different methods of
execution, these go in an increasing level of complexity and increasing
level of technical knowledge. The below examples are meant to be
starting points for those interested in using logrx
in more
complex settings.
axecute()
The easiest of the execution methods to use is
axecute()
. This function can be used to execute code from
an R terminal or using command line scripts. A log is set-up around the
program, and its code is run safely and loudly (using
safely()
from {purrr}
).
log_*()
functionsThe log_*()
family of functions are the core of
logrx
and are used internally to configure, write, and
remove the log and other objects. While these are exported functions of
the package, they are intended to be used in special cases where
axecute()
will not work.
Use the log_*()
functions to do the following:
log_init()
to create the environment
log.rx
log_config()
to add the core elements of the log to
the environment, and basic elements that are available at the time of
configuration
run_safely_loudly()
to execute the program code, and
capture errors, warnings, messages, output, and result. This must be
passed an executable R file to run and create the log elements
from
log_write()
to generate and format the log
log_remove()
to remove the log.rx
environment created by code execution
While executing from an R terminal is nice if you have access to one,
you can also execute your code using system command line. This is done
using the Rscript -e
command which executes a file using
the registered Rscript executable. Below are a few examples of how to
use the command line to execute a file and create a log as well as how
to manipulate the outputs of the execution. These are likely to be
advanced examples for most users.
The below chunk will run the file my_script.R and output any standard output that is created by the execution of the file to the default location.
The below chunk will run the file my_script.R
and output
any standard output that is created by the execution of the file to a
file called temp.log
. This output can then later be
accessed should the user want to check the output of the file
execution.
Rscript -e "logrx::axecute('my_script.R', log_name = 'my_script.log', log_path = '.')" > temp.log 2>&1
The below chunk will run the file my_script.R
and output
any standard output that is created by the execution of the file to a
file called temp.log
. It will then take the contents of the
temp.log
file and add those to the end of the log file
generated by the file execution and remove the temporary output log.
logrx
While logrx
is built around creating a log for a program
it can just as easily be used when running an entire set of programs.
The axecute()
function has been built with both single file
execution and scripted file execution in mind. With the use of simple
functions such as lapply()
scripting is easy. Below is some
sample code of how lapply()
can be used with
axecute()
.
If your scripting needs to work on the contents of a directory
instead of a pre-defined list, functions such as list.files
can be used to obtain a list of files to use. Below is an example of how
this can be applied in practice by getting all files ending in
.R
in the current working directory using a regular
expression, and then using lapply()
to run the files using
axecute()
.
Additionally, if you need your code to run using a shell scripting
language such as bash these files can be created to run using the
previously outlined Command Line Execution examples. The above scripting
examples can be translated into a variety of different scripting
languages. Below is an example where the bash script is executed in a
directory of R files, this should execute all R files in the directory
using axecute()
and create a corresponding set of log
files.