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logrxpackage

Source: vignettes/logrx.Rmd
logrx.Rmd

Generating a log

The purpose of the logrx package is to generate a log upon execution of an R script which enables traceability and reproducibility of the executed code. Generating a log with logrx can be as simple as running one line of code as seen in the below example of how to use the axecute() function.. However, logrx has much more advanced capabilities to meet the demands of Clinical Reporting. To learn additional techniques about executing code with logrx please visit our Execution Vignette.

axecute()

axecute() enables the command line submission of a program. A log is set-up around the program, and its code is run safely and loudly (using safely() from the purrr package). The log will be generated in the same folder as the script unless you specify differently.

axecute("my_script.R")

logrx addin:

A log can be generated using the logrx addin, which is a simple point and click interface that allows you to run a single program. The Addin ships with the package and is available once you use install the package. The gif on the Get Started page gives a quick snapshot of its intended use.

Log attributes

We have compiled a brief overview of the information that we capture in the log file generated by logrx. We allow users to customize sections of the log based on their needs for a log, e.g. you can toggle on/off the messages, outputs, errors and messages. You can also build into your log approved and unapproved packages used in your R script - see Logging Unapproved Package and Function Use for additional guidance. To see an example of what is included in a log file for an adsl.R script see Logging for an ADSL dataset.

The following attributes are recorded in the log:

  • Metadata: logrx package information
    • Version of the package
    • Type of build
    • Link to the GitHub repository
  • User and File Information
    • User that generated the log
    • Name and path of the script for which the log was generated
    • hash_sum: A unique hashsum is created for the log file
  • Session Information: The R session information
    • R version
    • OS and system
    • GUI
    • Language and timezone
    • Packages - List of all available packages in the environment
    • External Software - List of all external software
  • Repo URLs (optional) - URLs of the repositories for use by install.packages() and updated.packages()
  • Masked Functions - List of all functions masked by packages
  • Program Run Time Information - Start, end, and run times
  • Used Package and Functions (optional) - List of all packages and functions used in the script for which the log was generated
  • Unapproved Package and Functions (optional) - List of all packages and functions used in the script for which the log was generated that are not part of the approved list of packages and functions.
  • Errors and Warnings - List of Errors and Warnings created during execution of the script. Since R does not return line numbers along with error or warning messages we do not include them in the log. The R programming language uses a call stack during execution making finding the exact location of an error without human interaction complicated.
  • Messages, Output and Results (optional) - List of Messages, Outputs and Results created during execution of the script. In certain situations the log will not capture these if they are redirected to a different location.
  • Extra Info (optional) - Extra info that use can manually add via a list object
  • Log Output File - Name and path of the log