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README

ExampleRPackage package README.

What you will need for this lesson is:

  • A working R of version at least as new as 3.6, with 4.* preferred.
  • A network connection.
  • To install the R packages listed in the next subsection.
  • A text editor or IDE (integrated development environment) for editing R files.
  • For the source-control steps a git client (either command line or graphical).
  • Some ability to delete files/directories.
  • A command-line shell able to run R CMD steps.

Configuring your machine

Instructions on how to configure a machine are given here

These steps require some knowledge of working with your computer, network access, disk space, and admin rights. We strongly advise you take the steps in this section before class. We also strongly advise taking the trouble to run these steps. Having full control of a package-enabled R environment is very powerful. Please reach out for help if you are stuck on steps.

Once you have your machine configured start up R and install the packages we will be using.

A word of warning

There are many systems and tutorials that sit on top of higher order R tools. These can be useful, but, one must remember in R “Writing R Extensions” is the primary source for how to develop R packges.

Packages we assume you have installed

We assume your machine has a current working R, command-shell (bash / zsh), and text editor (emacs, vim, or other).

Start R and run the following.

install.packages(c(
   "tinytest",   # for running tests
   "roxygen2",   # to generate manuals from comments
   "knitr",      # to generate vignettes from markdown
   "rmarkdown",  # to convert markdown formats, may not need this
   "wrapr"       # example for argument list checking
   ))

The file structure of this project

DESCRIPTION    # the main project control file

R              # project source code directory
 /example_function.R  # our example function
 /package_help.R      # package documentation
 
README.Rmd     # package documentation source
README.md      # package documentation, produced from README.Rmd

inst           # installed items distributed with package
    /tinytest  # package test directory
    /tinytest/test_ExampleRPackage.R  # the one test we have now

vignettes      # where we place longer documents
         /Example_Vignette.Rmd  # Example markdown document

tests             # test trigger, do not edit
     /tinytest.R  # test trigger, do not edit

.Rbuildignore  # file that tells the builder what files to ignore

.gitignore     # file that tells version control what files to skip

NAMESPACE      # project imports/exports, produced by roxygen2

man            # roxygen2 generated documentation
   /ExampleRPackage.Rd   # generated package documentation
   /example_function.Rd  # generated function documentation

ExampleRPackage.Rproj   # (optional) config file for RStudio

How to copy this project

From GitHub

Point browser to https://github.com/WinVector/ExampleRPackage and press “Fork” in the upper right portion of the page.

Copying the project at the command line (base/zsh for Linux, MacOS, or Windows with Windows Subsystem for Linux)

From a bash/zsh command line:

# get a copy of the repository
git clone https://github.com/WinVector/ExampleRPackage.git

# remove the .git directory to sever it from the original repository
cd ExampleRPackage
rm -rf .git

# start up a new git repository
git init .
git add -A .
git commit -m"example package"

Then associate the package with your own repository by creating an new empty repository on GitHub and following their “preexisting project” instructions (adding a remote).

Procedures for working with packages.

For all of these steps we are assuming your current directory is the top-level of the package you are working with. This can be accomplished with the setwd() command. Alternately one can use an RStudio project, which largely keeps track of the working directory.

Build Package

We will run this with our working directory inside our package (please see getwd()/setwd() for how to navigate between directories in R). This will produce the file ExampleRPackage_0.1.0.tar.gz.

library(wrapr)

# assumes our current directory is our package
# see setwd()/getwd() for how to change directories
rebuild_current_package_and_attach <- function(
   ...,  # not used, force later arguments to bind by name
   package_dir = getwd(),  # default to package is current directory.
   lib = .libPaths()[[1]]  # where to attach package
   ) {
   wrapr::stop_if_dot_args(substitute(list(...)), "rebuild_current_package")
   start_time <- date()
   message(paste("rebuild_current_package working in directory", package_dir))
   message(paste("rebuild_current_package working in lib", lib))
   # get package name from current directory
   pkg_name <- tail(strsplit(package_dir, .Platform$file.sep)[[1]], n = 1)
   message(paste("rebuild_current_package working on package", pkg_name))
   # get into a clean state with no package installed/attached
   detach_str <- paste0('package:', pkg_name)
   res <- tryCatch(do.call(detach, list(detach_str)), error = function(e) e)
   if(pkg_name %in% rownames(installed.packages())) {
      remove.packages(pkg_name, lib = lib)
   }
   # regenerate man/.Rd files from roxygen comments
   res_text <- capture.output(suppressMessages(roxygen2::roxygenize(package.dir = package_dir)))
   # rebuild a source distribution of package
   res <- system(paste("R CMD build", package_dir), 
                 intern = TRUE)
   # find the tar name
   matches <- res[grepl(pkg_name, res)]
   pkg_pattern <- paste0(pkg_name, '[_.0-9]+', '.tar.gz')
   matches <- matches[grepl(pkg_pattern, matches)]
   if(length(matches) != 1) {
      stop("having trouble finding package tar name from R CMD build output")
   }
   str_span <- regexpr(pkg_pattern, matches)
   tar_name <- substr(matches, str_span, str_span + attr(str_span, 'match.length') - 1)
   # install the package from the source distribution
   res_text <- capture.output(install.packages(tar_name, repos = NULL, verbose = FALSE, quiet = TRUE))
   # attach package for use
   res_text <- capture.output(library(pkg_name, character.only = TRUE))
   end_time <- date()
   return(list(
      pkg_name = pkg_name,
      tar_name = tar_name,
      package_dir = package_dir,
      package_dir = package_dir,
      lib = lib,
      start_time = start_time,
      end_time = end_time
   ))
}
# re-document, re-build, re-install, and re-attach package
# write only name of package and tar file name into current work-space
(unpack[pkg_name, tar_name] := rebuild_current_package_and_attach())

# rebuild_current_package working in directory /Users/johnmount/Documents/work/ExampleRPackage
# rebuild_current_package working in lib /Users/johnmount/Library/R/4.0/library
# rebuild_current_package working on package ExampleRPackage
# 
# $pkg_name
# [1] "ExampleRPackage"
# 
# $tar_name
# [1] "ExampleRPackage_0.1.0.tar.gz"
# 
# $package_dir
# [1] "/Users/johnmount/Documents/work/ExampleRPackage"
# 
# $package_dir
# [1] "/Users/johnmount/Documents/work/ExampleRPackage"
# 
# $lib
# [1] "/Users/johnmount/Library/R/4.0/library"
# 
# $start_time
# [1] "Fri Nov 27 11:13:31 2020"
# 
# $end_time
# [1] "Fri Nov 27 11:13:35 2020"
ls()
## [1] "pkg_name"                           "rebuild_current_package_and_attach"
## [3] "tar_name"

print(pkg_name)
## [1] "ExampleRPackage"

print(tar_name)
## [1] "ExampleRPackage_0.1.0.tar.gz"

Probably want to restart R at this point and re-attach the package with library(ExampleRPackage).

Build README.md from README.Rmd

knitr::knit("README.Rmd")

Some time after rebuilding README.md you may want to rebuild the package again to make sure the new copy is included in the package tar.

Run tests

This package is already setup to use tinytest. Existing packages can be configured to work with tinytest by running tinytest::setup_tinytest('.').

# test directory of tests
dir <- system.file('tinytest', 
                   package = 'ExampleRPackage', 
                   mustWork = TRUE)
print(dir)
## [1] "/Users/johnmount/Library/R/4.0/library/ExampleRPackage/tinytest"

test_text <- capture.output(tinytest::run_test_dir(
   dir,
   verbose = TRUE,
   color = FALSE))
cat(paste(test_text, collapse = '\n'))
## Running test_ExampleRPackage.R........    1 tests OK 
## [1] "All ok, 1 results"

Check package

check_text <- system(paste("R CMD check", tar_name),
       intern = TRUE)
cat(paste(check_text, collapse = '\n'))
## * using log directory ‘/Users/johnmount/Documents/work/ExampleRPackage/ExampleRPackage.Rcheck’
## * using R version 4.0.2 (2020-06-22)
## * using platform: x86_64-apple-darwin17.0 (64-bit)
## * using session charset: UTF-8
## * checking for file ‘ExampleRPackage/DESCRIPTION’ ... OK
## * checking extension type ... Package
## * this is package ‘ExampleRPackage’ version ‘0.1.0’
## * package encoding: UTF-8
## * checking package namespace information ... OK
## * checking package dependencies ... OK
## * checking if this is a source package ... OK
## * checking if there is a namespace ... OK
## * checking for executable files ... OK
## * checking for hidden files and directories ... OK
## * checking for portable file names ... OK
## * checking for sufficient/correct file permissions ... OK
## * checking whether package ‘ExampleRPackage’ can be installed ... OK
## * checking installed package size ... OK
## * checking package directory ... OK
## * checking ‘build’ directory ... OK
## * checking DESCRIPTION meta-information ... OK
## * checking top-level files ... OK
## * checking for left-over files ... OK
## * checking index information ... OK
## * checking package subdirectories ... OK
## * checking R files for non-ASCII characters ... OK
## * checking R files for syntax errors ... OK
## * checking whether the package can be loaded ... OK
## * checking whether the package can be loaded with stated dependencies ... OK
## * checking whether the package can be unloaded cleanly ... OK
## * checking whether the namespace can be loaded with stated dependencies ... OK
## * checking whether the namespace can be unloaded cleanly ... OK
## * checking loading without being on the library search path ... OK
## * checking dependencies in R code ... OK
## * checking S3 generic/method consistency ... OK
## * checking replacement functions ... OK
## * checking foreign function calls ... OK
## * checking R code for possible problems ... OK
## * checking Rd files ... OK
## * checking Rd metadata ... OK
## * checking Rd cross-references ... OK
## * checking for missing documentation entries ... OK
## * checking for code/documentation mismatches ... OK
## * checking Rd \usage sections ... OK
## * checking Rd contents ... OK
## * checking for unstated dependencies in examples ... OK
## * checking installed files from ‘inst/doc’ ... OK
## * checking files in ‘vignettes’ ... OK
## * checking examples ... OK
## * checking for unstated dependencies in ‘tests’ ... OK
## * checking tests ...
##  OK
## * checking for unstated dependencies in vignettes ... OK
## * checking package vignettes in ‘inst/doc’ ... OK
## * checking running R code from vignettes ...
##   ‘Example_Vignette.Rmd’ using ‘UTF-8’... OK
##  NONE
## * checking re-building of vignette outputs ... OK
## * checking PDF version of manual ... OK
## * DONE
## Status: OK

Example code

example_function(3)
## [1] 4

Sharing packages

Install from file

install.packages(tar_name, repos = NULL)

Install from tar on github

# get this path by copying Github's download link
url <- "https://github.com/WinVector/ExampleRPackage/raw/main/ExampleRPackage_0.1.0.tar.gz"
install.packages(url, repos = NULL)

Install package from github

remotes::install_github("https://github.com/WinVector/ExampleRPackage")

Submitting to CRAN

Submitting to CRAN is a specialized step. First your package must pass all checks and all CRAN rules (most of which are listed in “Writing R Extensions”). It is important to note the following:

  • The purpose of CRAN, as stated by some members, is a reliable experience for users electing to take packages from CRAN. CRAN considers unreliability in single extension packages as reputation risk for R/CRAN itself. Note this is different purpose than serving package authors.
  • CRAN is not a test system, the assumption is you are only submitting packages that should pass all requirements to CRAN- not using CRAN to confirm the package meets requirements.
  • All initial package submissions to CRAN are hand-checked with a emphasis on the package purpose and description.
  • Minimizing dependencies (and not having non-CRAN dependencies) is a must. I believe CRAN currently checks if packages import more than 20 non-default dependencies and raises on issue.
  • Do not get “lawyerly” with CRAN. CRAN feedback tends to have a purpose. It may appear to the non-cognoscenti that some packages have variances or are allowed around the rules. Either this is not the case, or it is a point of strong negative contention. In either case it is not a good idea to attempt to copy bad practices from other packages.
  • CRAN packages must be testable in isolation and free of file-system side-effects.

For now I am going to leave CRAN submissions as a “to be covered later” topic.

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