version 0.1.6

DESCRIPTION

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+Package: PaRe
+Type: Package
+Title: A Way to Perform Code Review or QA on Other Packages
+Version: 0.1.6
+Language: en-US
+Authors@R: 
+    person("Maarten", "van Kessel", email = "m.l.vankessel@erasmusmc.nl",
+           role = c("aut", "cre"))
+Description: Reviews other packages during code review by looking at their
+    dependencies, code style, code complexity, and how internally defined
+    functions interact with one another.
+License: Apache License (>= 2)
+Encoding: UTF-8
+RoxygenNote: 7.2.3
+Imports: cli, cyclocomp, desc, DiagrammeR, DiagrammeRsvg, dplyr, glue,
+        lintr, magrittr, pak, rmarkdown, rsvg, stringr, igraph, utils,
+        R6, git2r, checkmate
+Suggests: ggplot2, plotly, ggraph, DT, magick, withr, cowplot, knitr
+VignetteBuilder: knitr
+NeedsCompilation: no
+Packaged: 2023-06-01 12:52:15 UTC; mvankessel
+Author: Maarten van Kessel [aut, cre]
+Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>
+Repository: CRAN
+Date/Publication: 2023-06-02 14:20:02 UTC

MD5

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+1519f8c68904fd60ab2bf7cb5d98ebe7 *DESCRIPTION
+1f8872827c5944a4083e3a67e01f02d0 *NAMESPACE
+aad2cad56d82c4b5e9ee1ec417d26814 *NEWS.md
+5c8bca3dc5926d17a2a309d1dbc4c7bf *R/PaRe-package.R
+690883c60013852f5e1e67c9e1e20c61 *R/R6-Code.R
+9f0aa369b24fc227f2ed394b6a74331e *R/R6-File.R
+d25793e59157161699a9e85b28d038c3 *R/R6-Function.R
+c3d6fd02375b2a402a2fa2278561d38f *R/R6-Repository.R
+759240826d491eb327652b7ad6de4c1e *R/callInvestigators.R
+fbc031d8397fe8efb4d64f6cdc05c7c3 *R/checkDependencies.R
+52ccf7d4a66821ba4cc94aa1db884cc7 *R/countPackageLines.R
+37cbb3dc068ad015a9c72a647c7ca331 *R/getDefaultPermittedPackages.R
+e95fbb0329c0e82edd8ffd93e3bc909e *R/getDefinedFunctions.R
+69852b6bfc046756a05a93a2e2d3a023 *R/getFunctionDiagram.R
+4d443a770d57ac467518f85be4908f08 *R/getFunctionUse.R
+c08fe9be2825ff23a9e8e6373c72dbf2 *R/getGraphData.R
+104933a17bab0332671d5df4c421eaaf *R/lint.R
+fed35bb6ac121b590457b12920738143 *R/makeReport.R
+22cf21bc6d779cfaf99249dfb069aefc *R/pkgDiagram.R
+cf794928715019cf81bd51d467156178 *R/utils-pipe.R
+b2680f14304ba0e862d85ce606ebffa2 *README.md
+743e77e9164f0eabaeade4b1262a0267 *build/vignette.rds
+b29edef0eaedf18b9a00f64e65c4647c *inst/WORDLIST
+9c8d99b624a6acc9e819124ef5d0fa37 *inst/doc/Documentation.R
+3e92daaaab2b0928ef8d0d4d75b2217f *inst/doc/Documentation.Rmd
+f5e2df68ae4391463d9649a9f12930a8 *inst/doc/Documentation.html
+d62b3c4c1af50d76ef77784a8cb26bd1 *inst/img/logo.png
+a48bb48401b7f3d9405b85111c0a6262 *inst/rmd/ReportInjectable.Rmd
+70fbd9c5231bc16201c45c9c271d8f2b *inst/rmd/report.Rmd
+40a1c71111751992f944d14f4c839718 *inst/testScript.R
+1c6f840fc50c6d11fd8c53b2cedbdb65 *inst/whiteList.csv
+4fe9810cdec58eda3bfd93e477573bf0 *man/Code.Rd
+fb1c213c6b9774076e61f655dbb9afc5 *man/File.Rd
+e05e6a2583a3a1d45895a14c200d8487 *man/Function.Rd
+0b662bfc2940703b4776f7eca130e4d9 *man/PaRe-package.Rd
+2a106d209f264abd4bb8eba10424d299 *man/Repository.Rd
+9efdbb8f255557ca0e1aed582a822e4a *man/checkDependencies.Rd
+191038bb66a3ca92eb08629a684471fa *man/checkInstalled.Rd
+5d24f00a3b1c79f76e517767facab5d9 *man/countPackageLines.Rd
+a750171ab37365cf4e08891f31dfdef7 *man/exportDiagram.Rd
+d62b3c4c1af50d76ef77784a8cb26bd1 *man/figures/logo.png
+62e4e2187dfa893177dee47f2fc7d064 *man/functionUseGraph.Rd
+d9d02cef6ba33a7b26f8af5d96a43d8d *man/funsUsedInFile.Rd
+6c54a9011ed177bbc0b223d0d15ff0e4 *man/funsUsedInLine.Rd
+f8ed967e0f6c6a5b2fa9b6cb484881d2 *man/getApplyCall.Rd
+9b56d8b89ccfab34cbbd51ff0ae46455 *man/getApplyFromLines.Rd
+9449067e6d546c8e59e6263344857a4e *man/getDefaultPermittedPackages.Rd
+0887d0268048f11b856276cd43dbf7fc *man/getDefinedFunctions.Rd
+bd79616a02aeb7b24252589b8e791e44 *man/getDlplyCall.Rd
+db99b8a1b7df318559684f9059d18afb *man/getDlplyCallFromLines.Rd
+90b311a7a4cf0ac0b8e02c9aee9c3c6b *man/getDoCall.Rd
+25c52bd7287adcf8e95cb75210714962 *man/getDoCallFromLines.Rd
+3c8631da7d854f8689114201685f074d *man/getExportedFunctions.Rd
+999d509f746457ee6992f6a206ebb253 *man/getFunCall.Rd
+ad9da8b01b43dd94c4f1b6530fb61698 *man/getFunctionDiagram.Rd
+81bb8a731d079ef3650b8c8ba3889530 *man/getFunctionUse.Rd
+1704f69ebd707789588385e0e18caf77 *man/getFunsPerDefFun.Rd
+d14143c9b0a631d6ee07e9da956d9867 *man/getGraphData.Rd
+6a06c7ec69c0448aebb99477a73c2448 *man/getMultiLineFun.Rd
+712130e4b2595aa06645060ecf99b684 *man/getVersionDf.Rd
+96a5525f819d289864457554355638ee *man/graphToDot.Rd
+3317219e33b132612ef58ffe716c6122 *man/lintRepo.Rd
+1661e131088af5b3b005be41f40886f5 *man/lintScore.Rd
+9d46ba40fef91083f85bad7ab179f083 *man/makeGraph.Rd
+7a9c2b84f2d796a47a21cd5f5ed6ae21 *man/makeReport.Rd
+29ee7383caa7fc8c14f52bd035509064 *man/pipe.Rd
+5ef87067fec0edf62a0670b70e14c467 *man/pkgDiagram.Rd
+e0db61bd097f0f30c129ec957562e993 *man/printMessage.Rd
+d33e53f5d0121239eb85c6150e326189 *man/whiteList.Rd
+3e92daaaab2b0928ef8d0d4d75b2217f *vignettes/Documentation.Rmd
+08d9d6b171b970059f24dabd6c576712 *vignettes/img/glueDiagram.svg
+78c2ea0c0cc50c7ba60892bc9e42e460 *vignettes/img/glueGraph.png

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export("%>%")
+export(File)
+export(Function)
+export(Repository)
+export(checkDependencies)
+export(countPackageLines)
+export(exportDiagram)
+export(getDefaultPermittedPackages)
+export(getDefinedFunctions)
+export(getFunctionDiagram)
+export(getFunctionUse)
+export(getGraphData)
+export(lintRepo)
+export(lintScore)
+export(makeReport)
+export(pkgDiagram)
+export(whiteList)
+import(DiagrammeR)
+import(DiagrammeRsvg)
+import(R6)
+import(checkmate)
+import(glue)
+import(lintr)
+import(pak)
+import(rmarkdown)
+import(rsvg)
+import(stringr)
+import(utils)
+importFrom(cli,cli_alert)
+importFrom(cli,cli_alert_danger)
+importFrom(cli,cli_alert_info)
+importFrom(cli,cli_alert_warning)
+importFrom(cli,col_blue)
+importFrom(cli,col_green)
+importFrom(cli,col_magenta)
+importFrom(cli,col_red)
+importFrom(cli,col_yellow)
+importFrom(cli,style_bold)
+importFrom(cyclocomp,cyclocomp)
+importFrom(desc,description)
+importFrom(dplyr,arrange)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,filter)
+importFrom(dplyr,group_by)
+importFrom(dplyr,mutate)
+importFrom(dplyr,relocate)
+importFrom(dplyr,rename)
+importFrom(dplyr,select)
+importFrom(dplyr,summarise)
+importFrom(dplyr,tally)
+importFrom(dplyr,tibble)
+importFrom(git2r,blame)
+importFrom(git2r,hash)
+importFrom(git2r,is_empty)
+importFrom(git2r,pull)
+importFrom(git2r,tree)
+importFrom(igraph,V)
+importFrom(igraph,all_simple_paths)
+importFrom(igraph,graph_from_data_frame)
+importFrom(igraph,induced_subgraph)
+importFrom(igraph,write_graph)
+importFrom(magrittr,"%>%")

NEWS.md

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+PaRe 0.1.6
+==========
+
+1. Started tracking changes in NEWS.md
+2. Added significant changes to documentation.
+3. Optimizations using R6 representations.
+4. Added functionality to subset package diagram
+5. Added git blame functionality
+
+PaRe 0.1.5
+==========
+
+1. Added R6 code representations.
+
+PaRe 0.1.0
+==========
+
+1. Initial transfer from DependencyReviewer to Package Reviewer.
+

R/PaRe-package.R

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+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @import utils
+#' @import pak
+#' @import glue
+#' @import stringr
+#' @import lintr
+#' @import rmarkdown
+#' @import DiagrammeR
+#' @import DiagrammeRsvg
+#' @import rsvg
+#' @import R6
+#' @import checkmate
+#' @importFrom igraph graph_from_data_frame V write_graph all_simple_paths induced_subgraph graph_from_data_frame
+#' @importFrom cli style_bold col_yellow col_red col_magenta col_green col_blue cli_alert_warning cli_alert_info cli_alert_danger cli_alert
+#' @importFrom dplyr filter tibble arrange select bind_rows select tally summarise rename relocate mutate group_by
+#' @importFrom git2r pull tree hash is_empty blame
+#' @importFrom desc description
+#' @importFrom magrittr %>%
+#' @importFrom cyclocomp cyclocomp
+## usethis namespace: end
+NULL
+
+#' whiteList
+#'
+#' data.frame containing links to csv-files which should be used to fetch
+#' white-listed dependencies.
+#'
+#' By default three csv's are listed:
+#' 1. darwin
+#' 2. hades
+#' 3. tidyverse
+#'
+#' The data.frame is locally fetched under:
+#' `system.file(package = "PaRe", "whiteList.csv")`
+#'
+#' Manual insertions into this data.frame can be made, or the data.frame can
+#' be overwritten entirely.
+#'
+#' The data.frame itself has the following structure:
+#'
+#' |  column |              data type | description |
+#' | ------- | ---------------------- | ----------- |
+#' |  source | \link[base]{character} | name of the source |
+#' |    link | \link[base]{character} | link or path to the csv-file |
+#' | package | \link[base]{character} | columnname of the package name column in the csv-file being linked to |
+#' | version | \link[base]{character} | columnname of the version column in the csv-file being linked to |
+#'
+#' The csv-files that are being pointed to should have the following structure:
+#'
+#' @export
+#' @examples
+#' if (interactive()) {
+#'   # Dropping tidyverse
+#'   whiteList <- whiteList %>%
+#'     dplyr::filter(source != "tidyverse")
+#'
+#'   # getDefaultPermittedPackages will now only use darwin and hades
+#'   getDefaultPermittedPackages()
+#' }
+whiteList <- dplyr::tibble(read.csv(
+  system.file(package = "PaRe", "whiteList.csv")
+))
+
+utils::globalVariables(".data")

R/R6-Code.R

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+#' @title
+#' R6 Code class
+#'
+#' @description
+#' Class representing a piece of code.
+#'
+#' @family
+#' Representations
+Code <- R6::R6Class(
+  classname = "Code",
+  # Public ----
+  public = list(
+    #' @description
+    #' Initializer method
+    #'
+    #' @param name (\link[base]{character})\cr
+    #' Name of Code object.
+    #' @param lines (\link[base]{character})\cr
+    #' Vector of lines Code object.
+    #'
+    #' @return `invisible(self)`
+    initialize = function(name, lines) {
+      private$name <- name
+      private$lines <- lines
+      private$nLines <- length(lines)
+      return(invisible(self))
+    },
+
+    #' @description
+    #' Overload generic print, to print Code object.
+    #'
+    #' @param ...
+    #' further arguments passed to or from other methods. See \link[base]{print}.
+    #'
+    #' @return ([base]{character})
+    print = function(...) {
+      classTypes <- class(self)
+      classTypes <- paste0(glue::glue("<{classTypes}>"), collapse = " ")
+
+      cat(
+        glue::glue(
+          "{classTypes}
+        Name: {private$name}
+        # Lines: {private$nLines}
+        "
+        )
+      )
+    },
+
+    #' @description
+    #' Get method for lines.
+    #'
+    #' @return (\link[base]{character})\cr
+    #' Vector of lines in the Code object.
+    getLines = function() {
+      return(private$lines)
+    },
+
+    #' @description
+    #' Get method for number of lines.
+    #'
+    #' @return (\link[base]{numeric})
+    #' Number of lines in the Code object.
+    getNLines = function() {
+      return(private$nLines)
+    },
+
+    #' @description
+    #' Get method for Name.
+    #'
+    #' @return (\link[base]{character})\cr
+    #' Name of the Code object.
+    getName = function() {
+      return(private$name)
+    }
+  ),
+  # Private ----
+  private = list(
+    name = "",
+    lines = c(),
+    nLines = 0
+  )
+)