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https://github.com/jefferis/packagedevelopmenttaskview

[Task View]: R "PackageDevelopment" Task View
https://github.com/jefferis/packagedevelopmenttaskview
Last synced: 27 days ago
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[Task View]: R "PackageDevelopment" Task View
Host: GitHub
URL: https://github.com/jefferis/packagedevelopmenttaskview
Owner: jefferis
Created: 2014-07-26T20:18:22.000Z (over 10 years ago)
Default Branch: master
Last Pushed: 2014-09-04T18:19:29.000Z (about 10 years ago)
Last Synced: 2023-04-16T09:10:57.008Z (over 1 year ago)
Language: R
Size: 194 KB
Stars: 1
Watchers: 2
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
Awesome Lists containing this project

README

        CRAN Task View: Package Development

-----------------------------------

Maintainer:

Luca Braglia

Contact:

lbraglia at gmail.com

Packages provide a mechanism for loading optional code, data and documentation as needed. At the very minimum only a text editor and an R installation are needed for package creation. Nonetheless many useful tools and R packages themselves have been provided to ease or improve package development. This Task View focuses on these tools/R packages, grouped by topics.

Main reference for Packages Development is ["Writing R Extension"](http://cran.rstudio.com/doc/manuals/R-exts.html) manual. For further documentation and tutorial see the "Related links" section below.

If you think that some packages/tools are missing from the list, feel free to [e-mail](mailto:[email protected]) me or look [here](http://github.com/lbraglia/PackageDevelopmentTaskView/blob/master/CONTRIBUTING.md).

Many thanks to: Cristophe Dutang, Darren Norris, Dirk Eddelbuettel, Gabor Grothendieck, Gregory Jefferis, John Maindonald, Spencer Graves, Tobias Verbeke and the R-core team.

First steps

-----------

### Searching for already existing packages

Before starting a new package it's worth searching for already available packages, both from a developer's standpoint ("do not reinvent the wheel") and from a user's one (many packages implementing same/similar procedures can be confusing). If a package addressing the same functionality already exists, you may consider contributing at it instead of starting a new one.

-   `utils::RSiteSearch` allows to search for keywords/phrases in help pages (all the CRAN packages except those for Windows only and some from Bioconductor), vignettes or task views, using the search engine at . A convenient wrapper around `RSiteSearch` that adds hits ranking is `findFn` function, from the [sos](http://cran.rstudio.com/web/packages/sos/index.html) package.

-   [RSeek](http://rseek.org/) allows to search for keywords/phrases in books, task views, support lists, function/packages, blogs etc.

-   [Rdocumentation](http://rdocumentation.org/) allows to search for keywords/phrases in help pages for all CRAN and some Bioconductor/GitHub packages.

### Initializing an R package

-   `utils::package.skeleton` automates some of the setup for a new source package. It creates directories, saves functions, data, and R code files provided to appropriate places, and creates skeleton help files and a `Read-and-delete-me` file describing further steps in packaging

-   `kitten` from the [pkgKitten](http://cran.rstudio.com/web/packages/pkgKitten/index.html) package allows to specify the main `DESCRIPTION` entries and doesn't create source code and data files from global environment objects or sourced files. It's used to initialize a simple package that passes `R CMD check` cleanly.

-   `create` from the [devtools](http://cran.rstudio.com/web/packages/devtools/index.html) package is similar to `package.skeleton` except it allows to specify `DESCRIPTION` entries and doesn't create source code and data files from global environment objects or sourced files.

-   `Rcpp.package.skeleton` from the [Rcpp](http://cran.rstudio.com/web/packages/Rcpp/index.html) package adds to `package.skeleton` the C++ via `Rcpp` handling, by modifying eg. `DESCRIPTION` and `NAMESPACE` accordingly, creating examples if needed and allowing the user to specify (with a character vector of paths) which C++ files to include in `src` directory . Finally the user can decide main `DESCRIPTION` entries.

Source code

-----------

### Foreign Languages Interfaces

-   The [inline](http://cran.rstudio.com/web/packages/inline/index.html) package eases adding code in C, C++ or Fortran to R. It takes care of the compilation, linking and loading of embedded code segments that are stored as R strings.

-   The [Rcpp](http://cran.rstudio.com/web/packages/Rcpp/index.html) package offers a number of C++ classes that makes transferring R objects to C++ functions (and back) easier.

-   The [rJava](http://cran.rstudio.com/web/packages/rJava/index.html) package provides a low-level interface to Java similar to the `.Call` interface for C and C++.

### Debugging

### Code Analysis

-   The [codetools](http://cran.rstudio.com/web/packages/codetools/index.html) package.

### Profiling

-   Profiling data is provided by `utils::Rprof` and can be summarized by `utils::summaryRprof`

-   The [profr](http://cran.rstudio.com/web/packages/profr/index.html) package can visualize output from the `Rprof` interface for profiling.

-   The [proftools](http://cran.rstudio.com/web/packages/proftools/index.html) package and the [aprof](http://cran.rstudio.com/web/packages/aprof/index.html) package can also be used to analyze profiling output.

### Benchmarking

-   `base::system.time` is a basic timing utility

-   [microbenchmark](http://cran.rstudio.com/web/packages/microbenchmark/index.html)

-   [rbenchmark](http://cran.rstudio.com/web/packages/rbenchmark/index.html)

### Unit Testing

[RUnit](http://cran.rstudio.com/web/packages/RUnit/index.html) [svUnit](http://cran.rstudio.com/web/packages/svUnit/index.html) [testthat](http://cran.rstudio.com/web/packages/testthat/index.html)

Documentation

-------------

### Writing Package Documentation

### Writing Vignettes

### Spell Checking

Tools and services

------------------

### Editors

### IDEs

### Makefiles

[GNU Make](http://www.gnu.org/software/make/) is a tool that tipically builds executable programs and libraries from source code by reading files called `Makefile`. It can be used to manage R package as well; [maker](http://github.com/ComputationalProteomicsUnit/maker) is a `Makefile` completely devoted to R package development.

### Hosting services

Many [hosting services](http://en.wikipedia.org/wiki/Comparison_of_open-source_software_hosting_facilities) are available. The most common in the R community are:

-   [R-Forge](http://r-forge.r-project.org/), based on [subversion](http://subversion.apache.org/).

-   [GitHub](http://github.com/), [mainly](http://help.github.com/articles/support-for-subversion-clients) based on [git](http://git-scm.com/). It can handle [continuous integration](http://en.wikipedia.org/wiki/Continuous_integration) for R packages with [Travis CI](http://travis-ci.org/): more info on that [here](http://github.com/craigcitro/r-travis).

### Building services

-   [WinBuilder](http://win-builder.r-project.org/) is a service intended for useRs who do not have Windows available for checking and building Windows binary packages. The package sources (after an `R CMD check`) can be uploaded via html form or passive ftp in binary mode; after checking/building a mail will be sent to the `Maintainer` with links to the package zip file and logs for download/inspection.

### CRAN packages:

-   [aprof](http://cran.rstudio.com/web/packages/aprof/index.html)

-   [codetools](http://cran.rstudio.com/web/packages/codetools/index.html)

-   [devtools](http://cran.rstudio.com/web/packages/devtools/index.html)

-   [inline](http://cran.rstudio.com/web/packages/inline/index.html)

-   [microbenchmark](http://cran.rstudio.com/web/packages/microbenchmark/index.html)

-   [pkgKitten](http://cran.rstudio.com/web/packages/pkgKitten/index.html)

-   [profr](http://cran.rstudio.com/web/packages/profr/index.html)

-   [proftools](http://cran.rstudio.com/web/packages/proftools/index.html)

-   [rbenchmark](http://cran.rstudio.com/web/packages/rbenchmark/index.html)

-   [Rcpp](http://cran.rstudio.com/web/packages/Rcpp/index.html)

-   [rJava](http://cran.rstudio.com/web/packages/rJava/index.html)

-   [RUnit](http://cran.rstudio.com/web/packages/RUnit/index.html)

-   [sos](http://cran.rstudio.com/web/packages/sos/index.html)

-   [svUnit](http://cran.rstudio.com/web/packages/svUnit/index.html)

-   [testthat](http://cran.rstudio.com/web/packages/testthat/index.html)

### Related links:

-   [[Manual] "Writing R Extension" by R-core team](http://cran.rstudio.com/doc/manuals/R-exts.html)

-   [[Tutorial] "Creating R Packages: A Tutorial" by Friedrich Leisch](http://cran.rstudio.com/doc/contrib/Leisch-CreatingPackages.pdf)

-   [[Book] "Software for Data Analysis" by John Chambers](http://www.springer.com/mathematics/computational+science+%26+engineering/book/978-0-387-75935-7)

-   [[Book] "Advanced R" by Hadley Wickham](http://adv-r.had.co.nz)

-   [[Book] "R packages" by Hadley Wickham](http://r-pkgs.had.co.nz/)