Repository Mirror for your Cloud Server and Webhosting

Title:

A Logging Utility Focus on Clinical Trial Programming Workflows

Version:

0.4.0

Description:

A utility to facilitate the logging and review of R programs in clinical trial programming workflows.

License:

MIT + file LICENSE

URL:

https://pharmaverse.github.io/logrx/, https://github.com/pharmaverse/logrx

BugReports:

https://github.com/pharmaverse/logrx/issues

Encoding:

UTF-8

LazyData:

true

RoxygenNote:

7.3.2

Imports:

dplyr (≥ 1.0.0), magrittr, purrr, rlang, stats, tidyr, stringr, sessioninfo (≥ 1.2), stringi, tibble, digest, lifecycle, methods

Suggests:

testthat (≥ 3.0.0), knitr, rmarkdown, withr, covr, pkgdown, Tplyr, haven, lintr (≥ 3.1.1), xml2, here, readr, rstudioapi, tidyselect, renv, yaml

VignetteBuilder:

knitr

Config/testthat/edition:

Depends:

R (≥ 4.0.0)

NeedsCompilation:

Packaged:

2025-05-05 12:17:38 UTC; kosib

Author:

Nathan Kosiba [aut, cre], Thomas Bermudez [aut], Ben Straub [aut], Michael Rimler [aut], Nicholas Masel [aut], Sam Parmar [aut], GSK/Atorus JPT [cph, fnd]

Maintainer:

Nathan Kosiba <nhkosiba@gmail.com>

Repository:

CRAN

Date/Publication:

2025-05-05 13:50:02 UTC

Approved packages and functions

Description

A dataset that stores approved packages and functions for use. Each row contains a library and function_name. This dataset is used to illustrate the data format to be stored in the log.rx.approved option.

Usage

approved

Format

A tibble with 6 rows and 2 variables:

function_name: Name of the function
library: Name of the package

Examples

logrx::approved

Creation of a log and axecution of a file

Description

axecute() creates a log, executes a file, and returns 0 if there are no errors or 1 if there are any errors

Usage

axecute(
  file,
  log_name = NA,
  log_path = NA,
  include_rds = FALSE,
  quit_on_error = TRUE,
  to_report = c("messages", "output", "result"),
  show_repo_url = FALSE,
  extra_info = NA,
  ...
)

Arguments

file

String. Path to file to execute

log_name

String. Name of log file

log_path

String. Path to log file

include_rds

Boolean. Option to export log object as Rds file. Defaults to FALSE

quit_on_error

Boolean. Should the session quit with status 1 on error? Defaults to TRUE

to_report

String vector. Objects to optionally report, may include as many as necessary:

messages: any messages generated by program execution
output: any output generated by program execution
result: any result generated by program execution

show_repo_url

Boolean. Should the repository URLs be reported Defaults to FALSE

extra_info

List. Objects to optionally add on to end of log in a special extra info section. List printed in YAML format. Optional

...

Not used

Value

0 if there are no errors or 1 if there are any errors

Examples

dir <- tempdir()
text <- 'print("Hello, logrx-person!")'
fileConn <- file(file.path(dir, "hello.R"))
writeLines(text, fileConn)
close(fileConn)

axecute(file.path(dir, "hello.R"))


fileConn <- file(file.path(dir, "hello.Rmd"))
writeLines(text, fileConn)
close(fileConn)

axecute(file.path(dir, "hello.Rmd"))

Build approved packages and functions tibble

Description

A utility function to help you build your approved packages and functions list. This can be used by logrx to log unapproved use of packages and functions.

Usage

build_approved(pkg_list, file = NULL)

Arguments

pkg_list

Named list of character vectors:

Name is the package name
Value is a character vector of approved functions or 'All'

file

String. Name of file where the approved tibble will be written to. If not specified, the tibble is returned

Default: NULL

Permitted Files: .RDS

Details

For more details see the vignette: vignette("approved", package = "logrx")

Value

Tibble with two columns (library, function) and one row per function

Examples

approved_pkgs <- list(
  base = c("library", "mean"),
  dplyr = "All"
)

# build and return
build_approved(approved_pkgs)

# build and save
dir <- tempdir()
build_approved(approved_pkgs, file.path(dir, "approved.rds"))

Configuration of the log.rx environment

Description

log_config() initialises the log.rx environment, adds its attributes, and sets them

Usage

log_config(file = NA, log_name = NA, log_path = NA, extra_info = NA)

Arguments

file

String. Path to file executed. Optional

log_name

String. Name of log file. Optional

log_path

String. Path to log file. Optional

extra_info

List. Objects to add on to end of log in a special extra info section. Optional

Value

Nothing

Examples

dir <- tempdir()
text <- 'print("Hello, Timberperson!")'
fileConn <- file(file.path(dir, "hello.R"))
writeLines(text, fileConn)
close(fileConn)

file <- file.path(dir, "hello.R")

# Initialise and configure the log.rx environment
log_config(file)

# Run the script and record results, outputs, messages, errors, and warnings
logrx:::run_safely_loudly(file)

# Write the log
log_write(file)

Initialization of the log.rx environment

Description

log_init() initialises the log.rx environment

Usage

log_init()

Value

Nothing

Examples

# Initialise the log.rx environment
log_init()

# Remove the log.rx environment
log_remove()

log.rx object removal

Description

log_remove() removes the log.rx object by setting options("log.rx") to NULL

Usage

log_remove()

Value

Nothing

Examples

# Initialise the log.rx environment
log_init()

# Remove the log.rx environment
log_remove()

Formatting and writing of the log.rx object to a log file

Description

log_write() gets and formats the content of the log.rx before writing it to a log file

Usage

log_write(
  file = NA,
  remove_log_object = TRUE,
  show_repo_url = FALSE,
  include_rds = FALSE,
  extra_info = NA,
  to_report = c("messages", "output", "result")
)

Arguments

file

String. Path to file executed

remove_log_object

Boolean. Should the log object be removed after writing the log file? Defaults to TRUE

show_repo_url

Boolean. Should the repo URLs be reported Defaults to FALSE

include_rds

Boolean. Option to export log object as Rds file. Defaults to FALSE

extra_info

List. Objects to add on to end of log in a special extra info section. Optional

to_report

String vector. Objects to optionally report; additional information in axecute

Value

Nothing

Examples

dir <- tempdir()
text <- 'print("Hello, Timberperson!")'
fileConn <- file(file.path(dir, "hello.R"))
writeLines(text, fileConn)
close(fileConn)

file <- file.path(dir, "hello.R")

# Initialise and configure the log.rx environment
log_config(file)

# Run the script and record results, outputs, messages, errors, and warnings
logrx:::run_safely_loudly(file)

# Write the log
log_write(file)

Read and parse logrx file

Description

Read and parse logrx file

Usage

read_log_file(file)

Arguments

file

String. Path to a logrx log file

Value

Tibble. Object that includes nested and parsed content

Examples

## Not run: 
read_log_file(previous_log_filepath)

## End(Not run)

Formatting of log file section headers

Description

write_log_header formats a string and returns it as a formatted log file section header

Usage

write_log_header(title_string)

Arguments

title_string

String. Used as section title

Value

Vector of strings. Formatted log file section header

Examples

## Not run: 
write_log_header("Section Header")

## End(Not run)

Formats and returns a vector of unapproved functions

Description

write_unapproved_functions() gets log.rx unapproved_packages_functions attribute, formats and returns the list of unapproved functions

Usage

write_unapproved_functions()

Value

Formatted vector of unapproved functions

Examples

## Not run: 
write_unapproved_functions()

## End(Not run)

Formats and returns a vector of used package functions

Description

write_used_functions() gets log.rx used_packages_functions attribute, formats and returns the list of used package functions

Usage

write_used_functions()

Value

Formatted vector of used package functions

Examples

## Not run: 
write_used_functions()

## End(Not run)