outsider

outsider: Install and run programs, outside of R, inside of R - Published in JOSS (2020)

https://github.com/ropensci-archive/outsider

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 8 DOI reference(s) in README
✓
Academic publication links
Links to: joss.theoj.org, zenodo.org
○
Committers with academic emails
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (18.6%) to scientific vocabulary

Keywords

docker reproducibility rstats

Last synced: 4 months ago · JSON representation

Repository

:warning: ARCHIVED :warning: Install and run programs, outside of R, inside of R

Basic Info

Host: GitHub
Owner: ropensci-archive
License: other
Language: R
Default Branch: master
Homepage:
Size: 1.68 MB

Statistics

Stars: 45
Watchers: 5
Forks: 7
Open Issues: 0
Releases: 2

Archived

Topics

docker reproducibility rstats

Created over 7 years ago · Last pushed over 3 years ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

Install and run programs, outside of R, inside of R

The Outsider is always unhappy, but he is an agent that ensures the happiness for millions of ‘Insiders’.

The Outsider, Wilson, 1956.

Integrating external programs into a deployable, R workflow can be challenging. Although there are many useful functions and packages (e.g. base::system()) for calling code and software from alternative languages, these approaches require users to independently install dependant software and may not work across platforms. outsider aims to make this easier by allowing users to install, run and control programs outside of R across all operating systems.

It’s like whalebrew but exclusively for R.

For more detailed information, check out the outsider website

Installation

To install the development version of the package …

r remotes::install_github('ropensci/outsider')

Additionally, you will also need to install Docker desktop. To install Docker visit the Docker website and follow the instructions for your operating system: Install Docker.

Compatibility

Tested and functioning on Linux, Mac OS and Windows. (For some older versions of Windows, the legacy Docker Toolbox may be required instead of Docker Desktop.)

Quick example

``` r library(outsider)

> ----------------

> outsider v 0.1.1

> ----------------

> - Security notice: be sure of which modules you install

outsider modules are hosted on GitHub and other code-sharing sites

this repo is a demonstration outsider module

it contains a function for printing 'Hello World!' in Ubuntu 18.04

repo <- 'dombennett/om..hello.world' module_install(repo = repo, force = TRUE)

look up the help files for the module

module_help(repo = repo)

import the 'hello_world' function

helloworld <- moduleimport(fname = 'hello_world', repo = repo)

run the imported function

hello_world()

> Hello world!

> ------------

> DISTRIB_ID=Ubuntu

> DISTRIB_RELEASE=18.04

> DISTRIB_CODENAME=bionic

> DISTRIB_DESCRIPTION="Ubuntu 18.04.1 LTS"

```

Available external programs

Modules available on GitHub since 12:08 30 May 2020 (CEST)

● astral

● beast

● PyRate

● RAxML

● pasta

…. Plus, at least, 10 more!

For more details, see the available modules table

Real-World Example: Aligning biological sequences

Installing and running a multiple sequence alignment program (mafft).

(See “Evolutionary tree pipeline” for running this program yourself.)

Not finding a module you need?

Try raising an issue to request someone make a module, Raise an Issue.

Otherwise, why not make it yourself? Check out the outsider.devtools package.

Security notice :rotating_light:

There is a risk that outsider modules may be malicious. Modules make use of the program Docker which allows any program to be efficiently deployed by wrapping the program’s code, along with everything that program requires to run e.g. operating system, dependent libraries, into an executable container.

While this is useful for providing users with whichever programs they require, there is a potential security risk if, along with the desired program and dependencies, malicious software is also shipped.

A well-known malicious example of Docker container exploitation is in cryptocurrency mining. A container may ship with a cryptocurrency mining software that would make use of your computer’s resources while you ran you the module.

To minimise any security risks Be sure of which modules you install on your machine. Whenever installing a new module, outsider will alert you to the potential security risks. Before installing a new module, ask yourself:

Is this module from a well-known developer?
How many others are using this module?

Consider checking the stats on the module’s GitHub page (e.g. number of stars/watchers) or looking-up the details of the developer (e.g. email forums, twitter, academic profile).

Additionally, you may wish to check the Dockerfile of the module. Does it install programs from well-known code repositories (e.g. apt-get)? Or is it running lines of code from unknown/untrackable URL sources?

How does it work?

outsider makes use of the program docker which allows users to create small, deployable machines, called Docker images. The advantage of these images is that they can be run on any machine that has Docker installed, regardless of operating system. The outsider package makes external programs available in R by facilitating the interaction between Docker and the R console through outsider modules. These modules consist of two parts: a Dockerfile that describes the Docker image that contains the external program and an R package for interacting with the Docker image. Upon installing and running a module through outsider, a Docker image is launched and the R code of the module is used to interact with the external program. Anyone can create a module. They are hosted on GitHub as well as other code-sharing sites and can be searched for and downloaded through outsider.

$outsider\_outline$

Outsider CI statuses

Statuses of package building checks and tests, run monthly.

| Repo | Linux (Travis CI) | Windows 10 (Appveyor) | | ------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | outsider.base | | | | outsider | | | | outsider.devtools | | | | Outsider Test suites* | | |

*Mock pipelines to test the interaction of all the packages.

Version

Released version 0.1, see NEWS.

Citation

Bennett et al., (2020). outsider: Install and run programs, outside of R, inside of R. Journal of Open Source Software, 5(45), 2038, https://doi.org/10.21105/joss.02038

Maintainer

Dom Bennett

$ropensci\_footer$

Owner

Name: rOpenSci Archive
Login: ropensci-archive
Kind: organization
Email: info@ropensci.org

Website: ropensci.org
Repositories: 259
Profile: https://github.com/ropensci-archive

Abandoned rOpenSci projects -- email info@ropensci.org if you have questions!

CodeMeta (codemeta.json)

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GitHub Events

Total

Last Year

Committers

Last synced: 5 months ago

All Time

Total Commits: 221
Total Committers: 3
Avg Commits per committer: 73.667
Development Distribution Score (DDS): 0.014

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Dominic Bennett	d**t@g**m	218
Maëlle Salmon	m**n@y**e	2
Arfon Smith	a****n	1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 15
Total pull requests: 1
Average time to close issues: 11 months
Average time to close pull requests: about 12 hours
Total issue authors: 2
Total pull request authors: 1
Average comments per issue: 1.07
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

DomBennett (14)
maelle (1)

Pull Request Authors

arfon (1)

Top Labels

Issue Labels

enhancement (11) newmodule (2) bug (2) help wanted (1)

Pull Request Labels

Dependencies

DESCRIPTION cran

R >= 3.3.0 depends
crayon * imports
curl * imports
jsonlite * imports
outsider.base * imports
remotes >= 2.0 imports
tibble * imports
yaml * imports
ape * suggests
knitr >= 1.0 suggests
rlang * suggests
ssh * suggests
testthat >= 2.1 suggests

outsider

Science Score: 49.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README-not.md

Install and run programs, outside of R, inside of R

Installation

Compatibility

Quick example

> ----------------

> outsider v 0.1.1

> ----------------

> - Security notice: be sure of which modules you install

outsider modules are hosted on GitHub and other code-sharing sites

this repo is a demonstration outsider module

it contains a function for printing 'Hello World!' in Ubuntu 18.04

look up the help files for the module

import the 'hello_world' function

run the imported function

> Hello world!

> ------------

> DISTRIB_ID=Ubuntu

> DISTRIB_RELEASE=18.04

> DISTRIB_CODENAME=bionic

> DISTRIB_DESCRIPTION="Ubuntu 18.04.1 LTS"

Available external programs

Real-World Example: Aligning biological sequences

Not finding a module you need?

Security notice :rotating_light:

How does it work?

Outsider CI statuses

Version

Citation

Maintainer

Owner

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies