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Colin Fay
Colin Fay

Posted on • Originally published at colinfay.me on

Can I host my R packages on npm? (Spoiler: yes)

#rstats #npm

I’m a big fan of how dependencies are managed in the NodeJS world, be internally when developing, or when it comes to where they are hosted(i.e via npm, the Node Package Manager). Of course, it has its downside(that I won’t be talking about here), but from a developer's point of view, the easiness of publication and installation is really nice.

While building hordes, a NodeJSmodule that interacts with R, I wanted to add a way to automatically install the companion R package when installing the Node module from npm. And when I found how to, I thought: hey, maybe we can generalize that for any R package!

First of all, why would you want to do that?

Well, because why not?

And also, because the easiness of publication offers a rapid way to publish online an R package that you need to send to production: for example, if you have an R package that needs to be installed in a Docker image that you want to send to prod NOW, CRAN is not a solution, passing a tar.gz works but means you have to share the tar.gz with the Dockerfile, and it can feel weird to install stuff from GitHub, even more, if you want to be sure to install a fixed version. Plus there is always the issue of GitHub API rate limit, that you can bypass by setting a personal token, but that means that your token is passed to the container.

Anyway, I wanted to see if I could use npm as a platform for publishing an R package, whatever the excuse/reason you want to find for doing that.

Setting the package.json

So I took my {dockerstats} package(github.com/ColinFay/dockerstats), as an example of a package I’ll push to npm.

The first thing you need to do when you build a Node module is to add a file called package.json. To do that, go to your package folder and run in your terminal npm init -y. That command will add the default file in your working directory.

This is what the default package.json file looks like:

{
  "name": "dockerstats",
  "version": "1.0.0",
  "description": "<!-- README.md is generated from README.Rmd. Please edit that file -->",
  "main": "index.js",
  "directories": {
    "man": "man",
    "test": "tests"
  },
  "scripts": {
    "test": "echo \"Error: no test specified\" && exit 1"
  },
  "repository": {
    "type": "git",
    "url": "git+https://github.com/ColinFay/dockerstats.git"
  },
  "keywords": [],
  "author": "",
  "license": "ISC",
  "bugs": {
    "url": "https://github.com/ColinFay/dockerstats/issues"
  },
  "homepage": "https://github.com/ColinFay/dockerstats#readme"
}
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Kind of nice of npm to have matched the git info (and apparently the first line of the Readme.md).

Next step, add this file to the .Rbuildignore, so it doesn’t return an error at check.

Rscript -e "usethis::use_build_ignore('package.json')"
✔ Setting active project to 'XXX/R/opensource/dockerstats'
✔ Adding '^package\\.json$' to '.Rbuildignore'
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Now, let’s complete the JSON file with what we will need: updating the description, adding an author, changing the license… and of course, the most important thing: adding a script to install the R package. This last part will be performed with the postinstall command available in the "scripts" entry: the command contained here will be run after the node module is “installed” (here, nothing related to Node will be installed, we’re just using the structure for this postinstall behavior).

{
    "name": "r-dockerstats",
    "version": "0.1.0",
    "description": "`{dockerstats}` is a small wrapper around `docker stats` that returns the output of this command as an R data.frame. ",
    "directories": {
        "man": "man",
        "test": "tests"
    },
    "scripts": {
        "test": "Rscript -e 'devtools::check()'",
        "compile-readme": "Rscript -e 'knitr::knit(\"Readme.Rmd\")'",
        "postinstall": "Rscript -e 'source(\"install.R\")'"
    },
    "repository": {
        "type": "git",
        "url": "git+https://github.com/ColinFay/dockerstats.git"
    },
    "keywords": [
        "RStats",
        "Docker"
    ],
    "author": "Colin Fay <contact@colinfay.me> (https://colinfay.me)",
    "license": "MIT",
    "bugs": {
        "url": "https://github.com/ColinFay/dockerstats/issues"
    },
    "homepage": "https://github.com/ColinFay/dockerstats#readme"
}
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What is R specific to this package.json:

  • test calls devtools::check(), so I can run this command by doingnpm test
  • compile-readme will knit the README.Rmd into its md counterpart, I can call it using npm run compile-readme
  • postinstall will launch R and source the script below, inserted in the project <!-- end list --> 
#!/usr/bin/env Rscript --vanilla

installr <- function(){
    # Creating a directory where to install {remotes} in case it's
    # not already on the machine, and remove this 
    # directory when the function exits
    dir.create("rtemplib")
    on.exit(unlink("rtemplib", TRUE, TRUE))

    if (!requireNamespace("remotes", quietly = TRUE)){
        # If {remotes} is not found, we install it inside the temp lib
        install.packages("remotes", lib = "rtemplib", repos = "https://cloud.r-project.org/")
        library(remotes, lib.loc = "rtemplib")
    } else {
        # {remotes} was found on the machine, load it
        library(remotes)
    }
    # Install the local directory on the machine
    install_local()

}

installr()
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And of course, don’t forget to add this script to the buildignore:

Rscript -e "usethis::use_build_ignore('install.R')"
✔ Adding '^install\.R$' to '.Rbuildignore'
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Let’s start by trying to install the package locally (i.e not from npmbut from our local machine)

# Removing {dockerstats}
$ Rscript -e "remove.packages('dockerstats')"
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
(as ‘lib’ is unspecified)

# Trying to load it fails
$ Rscript -e "library(dockerstats)"
Error in library(dockerstats) : there is no package called ‘dockerstats’
Execution halted

# Installing the local package (we are in the {dockerstats} root directory)
$ npm install
> r-dockerstats@1.0.0 postinstall XXX/R/opensource/dockerstats
> Rscript -e 'source("install.R")'

✔ checking for file ‘/private/var/folders/5z/rm2h62lj45d332kfpj28c8zm0000gn/T/RtmplcREug/fileb68433db245/dockerstats/DESCRIPTION’ ...
─ preparing ‘dockerstats’: (588ms)
✔ checking DESCRIPTION meta-information
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
   Removed empty directory ‘dockerstats/rtemplib’
─ building ‘dockerstats_0.1.0.tar.gz’

* installing *source* package ‘dockerstats’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dockerstats)
up to date in 5.717s
found 0 vulnerabilities

# Checking that the package now loads
$ Rscript -e "library(dockerstats);dockerstats()"
     Container Name ID CPUPerc MemUsage MemLimit
1 e9466ba17125 mongohexmake e9466ba17125 0.41 43.45MiB 7.78GiB
  MemPerc NetI NetO BlockI BlockO PIDs record_time extra
1 0.55 2.43kB 0B 0B 0B 28 2020-07-28 21:28:02
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🎉

That seems to work, let’s try to push it to npm.

# Publishing the package
$ npm publish
npm notice 
npm notice 📦 r-dockerstats@0.1.0
npm notice === Tarball Contents === 
npm notice 148B .Rbuildignore                            
npm notice 129B CRAN-RELEASE                             
npm notice 944B DESCRIPTION                              
npm notice 39B LICENSE                                  
npm notice 313B NAMESPACE                                
npm notice 892B package.json                             
npm notice 1.2kB cran-comments.md                         
npm notice 1.1kB LICENSE.md                               
npm notice 13.7kB README.md                                
npm notice 30.8kB man/figures/README-unnamed-chunk-12-1.png
npm notice 18.9kB man/figures/README-unnamed-chunk-13-1.png
npm notice 19.5kB man/figures/README-unnamed-chunk-14-1.png
npm notice 26.3kB man/figures/README-unnamed-chunk-15-1.png
npm notice 770B R/available.R                            
npm notice 2.2kB R/converters.R                           
npm notice 1.5kB R/csv.R                                  
npm notice 161B dev/dev.R                                
npm notice 231B R/dockerstats-package.R                  
npm notice 336B tests/testthat/helper-config.R           
npm notice 736B install.R                                
npm notice 817B R/stats_recurse.R                        
npm notice 3.8kB R/stats.R                                
npm notice 863B tests/testthat/test-converters.R         
npm notice 233B tests/testthat/test-stats.R              
npm notice 299B tests/testthat/test-utils.R              
npm notice 66B tests/testthat.R                         
npm notice 1.4kB man/byte-conversion.Rd                   
npm notice 2.2kB man/csv.Rd                               
npm notice 329B man/docker_stats_names.Rd                
npm notice 671B man/dockerstats_available.Rd             
npm notice 968B man/dockerstats_recurse.Rd               
npm notice 367B man/dockerstats-package.Rd               
npm notice 1.5kB man/dockerstats.Rd                       
npm notice 4.0kB README.Rmd                               
npm notice 386B dockerstats.Rproj                        
npm notice === Tarball Details === 
npm notice name: r-dockerstats                           
npm notice version: 0.1.0                                   
npm notice package size: 88.0 kB                                 
npm notice unpacked size: 137.7 kB                                
npm notice shasum: 7dddb83c54ea7b25be55cabae3ab030f2bfdec29
npm notice integrity: sha512-RsH+yhCrSnAe5[...]9zp+Il2uIuWIg==
npm notice total files: 35                                      
npm notice 
+ r-dockerstats@0.1.0
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Yeay! https://www.npmjs.com/package/r-dockerstats. That was alsoblazing fast (just a couple of seconds).

Can we really install it from npm now?

# Removing {dockerstats}
$ Rscript -e "remove.packages('dockerstats')"
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
(as ‘lib’ is unspecified)

# Trying to load it fails
$ Rscript -e "library(dockerstats)"
Error in library(dockerstats) : there is no package called ‘dockerstats’
Execution halted

# Installing from npm
$ npm install -g r-dockerstats

> r-dockerstats@0.1.0 postinstall /Users/colin/.npm-global/lib/node_modules/r-dockerstats
> Rscript -e 'source("install.R")'

✔ checking for file ‘/private/var/folders/5z/rm2h62lj45d332kfpj28c8zm0000gn/T/RtmpC6bEWW/filec6a6667653f/r-dockerstats/DESCRIPTION’ ...
─ preparing ‘dockerstats’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
   Removed empty directory ‘dockerstats/rtemplib’
─ building ‘dockerstats_0.1.0.tar.gz’

* installing *source* package ‘dockerstats’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dockerstats)
+ r-dockerstats@0.1.0
added 1 package from 1 contributor in 7.109s

$ Rscript -e "library(dockerstats);dockerstats()"
     Container Name ID CPUPerc MemUsage MemLimit
1 e9466ba17125 mongohexmake e9466ba17125 0.71 43.48MiB 7.78GiB
  MemPerc NetI NetO BlockI BlockO PIDs record_time extra
1 0.55 2.43kB 0B 0B 0B 28 2020-07-28 21:33:27
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Nice!

Some note on the install:

  • I used npm install -g because it will install via the “global” node module folder. If I hadn’t used this flag, I would have first needed to init an npm project in the current folder.

  • To meet production standards, I should also use npm install -g r-dockerstats@0.1.0, so that I have the fixed version.

Install Node on your machine

Of course, before trying it yourself, you’ll need to install NodeJS, which will bundle npm with it.

The Downloads page from NodeJS comes with a series of installers that you might find handy.

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