Merge pull request #214 from pharmaverse/parmsam-pfizer-patch-1

add name to DESCRIPTION as author

.github/workflows/check-standard.yaml

@@ -23,9 +23,8 @@ jobs:
  matrix:
  config:
  - {os: windows-latest, r: 'release'}
- - {os: macOS-latest, r: 'release'}
- - {os: ubuntu-20.04, r: '3.5', repos: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-20.04, r: '3.6', repos: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ - {os: ubuntu-20.04, r: '4.1', repos: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ - {os: ubuntu-20.04, r: '4.2', repos: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
  - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
  - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 

.github/workflows/spellcheck.yaml

@@ -0,0 +1,33 @@
+---
+name: Spellcheck
+
+on:
+ push:
+ branches:
+ - main
+ - dev
+ pull_request:
+ branches:
+ - main
+ - dev
+
+jobs:
+ spell:
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v3
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ needs: spelling
+
+ - name: Run Spelling Check test
+ uses: insightsengineering/r-spellcheck-action@v3
+ with:
+ exclude: data/*

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: logrx
 Title: A Logging Utility Focus on Clinical Trial Programming Workflows
-Version: 0.2.2
+Version: 0.3.0
 Authors@R: 
  c(
  person(given = "Nathan",
@@ -23,6 +23,10 @@ Authors@R:
  family = "Masel",
  email = "nmasel@its.jnj.com",
  role = "aut"),
+ person(given = "Sam",
+ family = "Parmar",
+ email = "samir.parmar@pfizer.com",
+ role = "aut"),
  person(given = "GSK/Atorus JPT",
  role = c("cph", "fnd"))
  )
@@ -50,7 +54,8 @@ Imports:
  waiter,
  tibble,
  digest,
- lintr
+ lifecycle,
+ methods
 Suggests: 
  testthat (>= 3.0.0),
  knitr,
@@ -60,8 +65,12 @@ Suggests:
  pkgdown,
  Tplyr,
  haven,
- here
+ lintr,
+ xml2,
+ here,
+ readr,
+ tidyselect
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 Depends: 
- R (>= 3.5.0)
+ R (>= 4.0.0)

NAMESPACE

@@ -6,6 +6,7 @@ export(log_config)
 export(log_init)
 export(log_remove)
 export(log_write)
+export(read_log_file)
 export(write_log_header)
 export(write_unapproved_functions)
 export(write_used_functions)
@@ -15,9 +16,9 @@ importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,mutate)
+importFrom(dplyr,rename_with)
 importFrom(dplyr,select)
 importFrom(dplyr,ungroup)
-importFrom(lintr,lint)
 importFrom(magrittr,"%>%")
 importFrom(miniUI,gadgetTitleBar)
 importFrom(miniUI,miniContentPanel)
@@ -51,14 +52,20 @@ importFrom(shiny,uiOutput)
 importFrom(stats,aggregate)
 importFrom(stringi,stri_wrap)
 importFrom(stringr,str_c)
+importFrom(stringr,str_count)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_extract)
+importFrom(stringr,str_remove)
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_starts)
+importFrom(stringr,str_trim)
 importFrom(tibble,tibble)
 importFrom(tidyr,all_of)
 importFrom(tidyr,complete)
 importFrom(tidyr,pivot_wider)
+importFrom(tidyr,separate)
 importFrom(utils,capture.output)
 importFrom(utils,getParseData)
 importFrom(utils,lsf.str)

NEWS.md

@@ -1,3 +1,16 @@
+
+# logrx 0.3.0
+
+- Moved website theme to bootstrap 5, enabled search (#179)
+- Add `show_repo_url` option in `axecute()` to capture repo URL(s) into log file (#167)
+- Moved website theme to Bootstrap 5, enabled search (#179)
+- Add `include_rds` argument to `axecute()` to export log as rds file
+- Add `read_log_file()` to read logrx log file as optional function
+- Add `library_call_linter()` to ensure all library calls are at the top of the script (#163)
+- Remove argument for remove_log_object from `axecute()` still accessible via `log_write()` (#182)
+- Added functionality so `axecute()` works with `.Rmd` files (#140)
+- R Version switched from `>3.5` to `>4.0` in `DESCRIPTION` file (#198)
+
 # logrx 0.2.2
 
  - Hotfix to remove unnecessary `across()` and update `.data$var` top new syntax to match updates in source packages (#172)

R/axecute.R

@@ -8,15 +8,18 @@
 #' @param file String. Path to file to execute
 #' @param log_name String. Name of log file
 #' @param log_path String. Path to log file
-#' @param remove_log_object Boolean. Should the log object be removed after
-#' writing the log file? Defaults to TRUE
+#' @param include_rds Boolean. Option to export log object as Rds file.
+#' Defaults to FALSE
 #' @param quit_on_error Boolean. Should the session quit with status 1 on error?
 #' Defaults to TRUE
 #' @param 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
+#' @param show_repo_url Boolean. Should the repository URLs be reported
+#' Defaults to FALSE
+#' @param ... Not used
 #'
 #' @importFrom purrr map_chr
 #'
@@ -31,13 +34,29 @@
 #' 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"))
 axecute <- function(file, log_name = NA,
  log_path = NA,
- remove_log_object = TRUE,
+ include_rds = FALSE,
  quit_on_error = TRUE,
- to_report = c("messages", "output", "result")){
+ to_report = c("messages", "output", "result"),
+ show_repo_url = FALSE,
+ ...){
+ # deprecations
+ if (methods::hasArg(remove_log_object)) {
+ lifecycle::deprecate_stop("0.3.0", "axecute(remove_log_object = )", "axecute(include_rds = )")
+ }
+
+ # remove log object
+ remove_log_object <- TRUE
 
-  # lower everything for consistency and check values
+ # lower everything for consistency and check values
  to_report <- map_chr(to_report, tolower)
  match.arg(to_report, several.ok = TRUE)
 
@@ -51,7 +70,11 @@ axecute <- function(file, log_name = NA,
  any_errors <- get_log_element("errors")
 
  # write log
- log_write(file = file, remove_log_object = remove_log_object, to_report = to_report)
+ log_write(file = file,
+ remove_log_object = remove_log_object,
+ show_repo_url = show_repo_url,
+ include_rds = include_rds,
+ to_report = to_report)
 
  # if error, quit with status = 1 if not interactive
  if(!interactive() & !is.null(any_errors) & quit_on_error) {

R/get.R

@@ -96,7 +96,7 @@ get_file_path <- function(file = NA, normalize = TRUE){
 #' @noRd
 #'
 get_session_info <- function(){
- return(capture.output(session_info(info = "all")))
+ return(session_info(info = "all"))
 }
 
 
@@ -155,6 +155,16 @@ get_masked_functions <- function(){
 #'
 get_used_functions <- function(file){
 
+ # if markdown, write R code, including inline, to a script
+ # use this script to find functions used
+ if (grepl("*.Rmd$", file, ignore.case = TRUE)){
+ tmpfile <- tempfile(fileext = ".R")
+ on.exit(unlink(tmpfile))
+ withr::local_options(list(knitr.purl.inline = TRUE))
+ knitr::purl(file, tmpfile)
+ file <- tmpfile
+ }
+
  # catch error
  retfun <- safely(parse,
  quiet = FALSE,
@@ -191,14 +201,24 @@ get_used_functions <- function(file){
  names_from = "token") %>%
  ungroup()
 
- combine_tokens <- wide_tokens %>%
+ # if package is present, but symbol or special is not, a function did not follow the ::
+ # ex. knitr::opts_chunk$set()
+ # for this case, remove row that contains the package
+ # set will still be captured but we will be able to link it to a package in this current version
+ wide_tokens_wo_orphans <- wide_tokens[!(!is.na(wide_tokens$SYMBOL_PACKAGE) & is.na(wide_tokens$SYMBOL_FUNCTION_CALL) & is.na(wide_tokens$SPECIAL)),]
+
+ combine_tokens <- wide_tokens_wo_orphans %>%
  mutate(function_name = coalesce(.data[["SYMBOL_FUNCTION_CALL"]],
  .data[["SPECIAL"]]))
 
- get_library(combine_tokens) %>%
+ distinct_use <- get_library(combine_tokens) %>%
  select(all_of(c("function_name", "library"))) %>%
  distinct()
 
+ distinct_use[is.na(distinct_use)] <- "!!! NOT FOUND !!!"
+
+ distinct_use
+
 }
 
 
@@ -278,15 +298,33 @@ get_unapproved_use <- function(approved_packages, used_packages) {
 #'
 #' @param file File path of file being run
 #'
-#' @importFrom lintr lint
-#'
 #' @return results from `lintr::lint()`
 #'
 #' @noRd
 #'
 get_lint_results <- function(file) {
+
+ if (!requireNamespace("lintr", quietly = TRUE)) {
+ message(strwrap("Linting will not be included in the log. Install the
+ lintr package to use the log.rx.lint feature.",
+ prefix = " ", initial = ""))
+ return()
+ }
+
  # lint file if option is turned on
  if (!is.logical(getOption('log.rx.lint'))) {
- lint(file, getOption('log.rx.lint'))
+ lintr::lint(file, getOption('log.rx.lint'))
  }
 }
+
+#' Get repository URLs
+#'
+#' Obtain repository URLs possibly used to install packages in session
+#'
+#' @return results from `getOption("repos")` as list
+#'
+#' @noRd
+#'
+get_repo_urls <- function() {
+ as.list(getOption("repos"))
+}

R/interact.R

@@ -110,6 +110,13 @@ set_log_name_path <- function(log_name = NA, log_path = NA) {
 #' @noRd
 run_safely <- function(file) "dummy"
 
+#' Is this a R Markdown file
+#' @param file String. Path to file to execute
+#' @noRd
+is_rmarkdown <- function(file) {
+ grepl("*.Rmd$", file, ignore.case = TRUE)
+}
+
 #' Dummy function for running a file
 #' @noRd
 run_file <- function(file){
@@ -118,7 +125,13 @@ run_file <- function(file){
  } else{
  exec_env <- getOption("log.rx.exec.env")
  }
- source(file, local = exec_env)
+
+ if(is_rmarkdown(file)){
+ rmarkdown::render(file, envir = exec_env)
+ } else{
+ source(file, local = exec_env)
+ }
+
 }
 
 #' Safely run an R script and record results, outputs, messages, errors, warnings
@@ -139,7 +152,7 @@ run_safely_loudly <- function(file) {
  set_log_element("result", ret$result$result)
  set_log_element("warnings", ret$warnings)
  set_log_element("errors", ret$result$error)
- set_log_element("hash_sum", digest::sha1(readLines(file)))
+ set_log_element("hash_sum", digest::sha1(readLines(file, warn = FALSE)))
 
  # Session Info
  set_log_element("session_info", get_session_info())