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Compact Package Representations

Source: vignettes/pkglite.Rmd
pkglite.Rmd

Introduction

pkglite offers a solution for converting R package source code to a compact, text-based representation and restore the source package structure from the representation. There are three specific aims:

  1. To provide a tool for packing and restoring R packages as plain text assets that are easy to store, transfer, and review.
  2. To provide a grammar for specifying the file packing scope that is functional, precise, and extendable.
  3. To provide a standard for exchanging the packed asset that is unambiguous, human-friendly, and machine-readable.

To achieve these goals, we developed a pipe-friendly workflow, the concept of file specifications and file collections, and a format specification for the output file pkglite.txt. These designs allow us to leave a clear and skimmable trace in the code when generating such compact representations, thus improves reproducibility.

Example workflow

To demonstrate the basic usage of pkglite, we will show how to pack and unpack one or multiple R packages.

Pack one package

First, locate the input package directory and the output file:

pkg <- system.file("examples/pkg1", package = "pkglite")
txt <- tempfile(fileext = ".txt")

Use the following chain of calls to pack a default set of files in the R package under directory pkg into the file txt:

pkg %>%
  collate(file_default()) %>%
  pack(output = txt, quiet = TRUE)

The collate() function evaluates one or more file specifications to generate a file collection. They fully determine the scope of the files to pack here. For details, check vignette("filespec", package = "pkglite").

Check the first lines of the output file:

txt %>%
  readLines() %>%
  head(11) %>%
  cat(sep = "\n")
#> # Generated by pkglite: do not edit by hand
#> # Use pkglite::unpack() to restore the packages
#> 
#> Package: pkg1
#> File: DESCRIPTION
#> Format: text
#> Content:
#>   Package: pkg1
#>   Type: Package
#>   Title: Example Package One
#>   Version: 0.1.0

Check the number of lines the output file:

txt %>%
  readLines() %>%
  length()
#> [1] 1081

Unpack one package

To unpack (restore) the file structures from the text file, use unpack():

out <- file.path(tempdir(), "onepkg")
txt %>% unpack(output = out, quiet = TRUE)

This will create a directory named after the R package under the output directory:

out %>%
  file.path("pkg1") %>%
  list.files()
#> [1] "data"        "DESCRIPTION" "man"         "NAMESPACE"   "NEWS.md"    
#> [6] "R"           "README.md"   "vignettes"

To install the packages after unpacking them, use unpack(..., install = TRUE).

Pack multiple packages

pack() accepts one or more input directories. Therefore, one can pack multiple R packages (file collections) into one file at once:

pkg1 <- system.file("examples/pkg1", package = "pkglite")
pkg2 <- system.file("examples/pkg2", package = "pkglite")

fc1 <- pkg1 %>% collate(file_default())
fc2 <- pkg2 %>% collate(file_default())

pack(fc1, fc2, output = txt, quiet = TRUE)

Since the two example packages have almost identical content, the number of lines in the text file is doubled here (three header lines excluded):

txt %>%
  readLines() %>%
  length()
#> [1] 2159

Unpack multiple packages

Use the same call to unpack (and install) multiple R packages from the text file:

out <- file.path(tempdir(), "twopkgs")
txt %>% unpack(output = out, quiet = TRUE)
out %>%
  file.path("pkg1") %>%
  list.files()
#> [1] "data"        "DESCRIPTION" "man"         "NAMESPACE"   "NEWS.md"    
#> [6] "R"           "README.md"   "vignettes"
out %>%
  file.path("pkg2") %>%
  list.files()
#> [1] "data"        "DESCRIPTION" "man"         "NAMESPACE"   "NEWS.md"    
#> [6] "R"           "README.md"   "vignettes"

The file format specification for pkglite.txt is described in vignette("format", package = "pkglite").

Helper functions

Verify if the text file contains only ASCII characters:

txt %>% verify_ascii()
#> [1] TRUE

Remove lines of file content from the text file:

txt %>% remove_content(c("## New Features", "## Improvements"), quiet = TRUE)
txt %>%
  readLines() %>%
  length()
#> [1] 2157