containerit

containerit: Generating Dockerfiles for reproducible research with R - Published in JOSS (2019)

https://github.com/o2r-project/containerit

Science Score: 95.0%

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 5 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
✓
Committers with academic emails
5 of 16 committers (31.3%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

docker dockerfile r reproducible-research reproducible-science

Keywords from Contributors

reproducibility

Last synced: 4 months ago · JSON representation

Repository

Package an R workspace and all dependencies as a Docker container

Basic Info

Host: GitHub
Owner: o2r-project
License: gpl-3.0
Language: R
Default Branch: master
Homepage: https://o2r.info/containerit/
Size: 1.62 MB

Statistics

Stars: 291
Watchers: 11
Forks: 29
Open Issues: 86
Releases: 2

Topics

docker dockerfile r reproducible-research reproducible-science

Created over 9 years ago · Last pushed almost 4 years ago

Metadata Files

Readme Changelog Contributing License Codemeta

README.Rmd

---
output: github_document
---


```{r knitr_config, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

# containerit 


[![DOI](https://joss.theoj.org/papers/10.21105/joss.01603/status.svg)](https://doi.org/10.21105/joss.01603)
[![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
[![Travis CI build status](https://travis-ci.org/o2r-project/containerit.svg?branch=master)](https://travis-ci.org/o2r-project/containerit)
[![Appveyor build status](https://ci.appveyor.com/api/projects/status/2242hcwagoafxaxq?svg=true)](https://ci.appveyor.com/project/nuest/containerit-rrvpq)
[![](https://www.r-pkg.org/badges/version/containerit)](https://github.com/o2r-project/containerit/issues/68)
[![Join the chat at https://gitter.im/o2r-project/containerit](https://badges.gitter.im/o2r-project/containerit.svg)](https://gitter.im/o2r-project/containerit)




`containerit` packages R script/session/workspace and all dependencies as a [Docker](https://docker.com/) container by automagically generating a suitable `Dockerfile`.
The package's website is [https://o2r.info/containerit/](https://o2r.info/containerit/).

## Prerequisites

- `containerit` only fully works if you have [Docker](https://en.wikipedia.org/wiki/Docker_(software)) installed and is only tested with [Docker Engine - Community](https://docs.docker.com/install/overview/) (previously called Docker Community Edition or Docker CE).
- `R (>= 3.5.0)` is needed so that some dependencies (e.g. BiocManager) are available; older versions of R predate the development of the package and were never tested.

## Quick start

### Try out `containerit` in a container

You can spin up a Docker container with `containerit` pre-installed if you want to try out the package.
The default of the [`containerit` images on Docker Hub](#images) is to start plain R, but you can also start an with [RStudio](https://www.rstudio.com/products/rstudio/) session in a browser.

**Note**: The `geospatial` variant is used so that examples from `containerit` vignettes are likely to work.
For a minimal `Dockerfile` to run `containerit`, see `inst/docker/minimal/Dockerfile`.

```{bash, eval=FALSE}
docker run --rm -it -e PASSWORD=o2r -p 8787:8787 o2rproject/containerit:geospatial /init
```

Now go to http://localhost:8787 and log in with the user `rstudio` and password `o2r`.
Continue in section [Use](#use).

### Install

Installation is only possible from GitHub:

```{r, eval=FALSE}
# install.packages("remotes")
remotes::install_github("o2r-project/containerit")
```

### Use

`containerit` can create `Dockerfile` objects in R and render them as `Dockerfile` instructions based on session information objects or runnable R files (`.R`, `.Rmd`).

```{r use_session}
suppressPackageStartupMessages(library("containerit"))
my_dockerfile <- containerit::dockerfile(from = utils::sessionInfo())
```

```{r use_print}
print(my_dockerfile)
```

You can disable logging:

```{r disable_logger, results='hide'}
futile.logger::flog.threshold(futile.logger::ERROR)
```

Now we create a Dockerfile for a specific R version and a given R Markdown file.
The option `filter_baseimage_pkgs` is used to not add any packages already available in the base image, which can save a lot of build time.

```{bash pull, include=FALSE}
docker pull rocker/verse:3.6.2
```

```{r use_file}
rmd_dockerfile <- containerit::dockerfile(from = "inst/demo.Rmd",
                                          image = "rocker/verse:3.5.2",
                                          maintainer = "o2r",
                                          filter_baseimage_pkgs = TRUE)
print(rmd_dockerfile)
```

For extended instructions, see the vignettes at in the directory `vignettes/`, which are readable online at https://o2r.info/containerit/articles/.

## Images

```{r image_names, echo=FALSE, results='hide'}
dockerfiles_path <- "inst/docker/Dockerfile"
suppressPackageStartupMessages(library("here"))
dockerfile_latest <- readLines(here(dockerfiles_path))
base_image = sub(".*? (.+)", "\\1", dockerfile_latest[[2]])
dockerfile_geospatial <- readLines(here("inst/docker/geospatial/Dockerfile"))
geospatial_base_image = sub(".*? (.+)", "\\1", dockerfile_geospatial[[2]])
```

Images are available starting from different base images.
All images are also available with version tags.

The `Dockerfile`s are available in the directory `` `r dockerfiles_path` ``.

### verse

```{bash, eval=FALSE}
docker inspect o2rproject/containerit
```

Base image: `` `r base_image` ``

[![](https://images.microbadger.com/badges/version/o2rproject/containerit.svg)](https://microbadger.com/images/o2rproject/containerit "Get your own version badge on microbadger.com") [![](https://images.microbadger.com/badges/image/o2rproject/containerit.svg)](https://microbadger.com/images/o2rproject/containerit "Get your own image badge on microbadger.com") [![](https://images.microbadger.com/badges/commit/o2rproject/containerit.svg)](https://microbadger.com/images/o2rproject/containerit "Get your own commit badge on microbadger.com")

### geospatial

```{bash eval=FALSE}
docker inspect o2rproject/containerit:geospatial
```

Base image: `` `r geospatial_base_image` ``

[![](https://images.microbadger.com/badges/version/o2rproject/containerit:geospatial.svg)](https://microbadger.com/images/o2rproject/containerit:geospatial "Get your own version badge on microbadger.com") [![](https://images.microbadger.com/badges/image/o2rproject/containerit:geospatial.svg)](https://microbadger.com/images/o2rproject/containerit:geospatial "Get your own image badge on microbadger.com") [![](https://images.microbadger.com/badges/commit/o2rproject/containerit:geospatial.svg)](https://microbadger.com/images/o2rproject/containerit:geospatial "Get your own commit badge on microbadger.com")

## RStudio Add-in

[RStudio Addins](https://rstudio.github.io/rstudioaddins/) allow to create interactive user interfaces for the RStudio development environment.
Courtesy of a great contribution by a [group of enthusiasts](https://github.com/o2r-project/containerit/issues/27#issuecomment-440869329) at the [ROpenSci OZ Unconference 2018](https://ozunconf18.ropensci.org/), there are several forms to quickly create `Dockefile`s from different use cases, e.g. the current session, a vector of expressions, or a script file.

![screenshots containerit RStudio Addin forms](https://user-images.githubusercontent.com/1325054/61534429-e1345980-aa2f-11e9-8f5d-e6f67e5d7dde.png)

## Contribute

All help is welcome: asking questions, providing documentation, testing, or even development.

Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md).
By participating in this project you agree to abide by its terms.

See [CONTRIBUTING.md](CONTRIBUTING.md) for details.

## Development

[r-hub builder](https://builder.r-hub.io/) is great for running checks, e.g. before submitting to CRAN and on other operating systems.

```{r checking, eval=FALSE}
library("rhub")
rhub::check_for_cran()
rhub::check_on_windows()
```

You can build the [`pkgdown`](https://pkgdown.r-lib.org/) site with

```{r pkgdown, eval=FALSE}
pkgdown::build_site()
```

You can build the Docker images locally with the current development version using the following commands.

```{bash dev_containers, eval=FALSE}
docker build --tag containerit:dev --file inst/docker/Dockerfile.local .
docker build --tag containerit:geospatial-dev --file inst/docker/geospatial/Dockerfile.local .
```

You can use [`pre-commit` hooks](https://github.com/lorenzwalthert/pre-commit-hooks) to avoid some mistakes.

A [codemeta](https://codemeta.github.io/) file, `codemeta.json`, with metadata about the package and its dependencies is generated automatically when this document is compiled.

```{r codemeta, results='hide'}
codemetar::write_codemeta(".")
```

## Citation

```{r citation, echo=FALSE, comment=""}
citation("containerit")
```

## License

containerit is licensed under GNU General Public License, version 3, see file LICENSE.

Copyright (C) 2019 - o2r project.

Owner

Name: Opening Reproducible Research
Login: o2r-project
Kind: organization
Email: daniel.nuest@uni-muenster.de
Location: Münster

Website: http://o2r.info
Repositories: 52
Profile: https://github.com/o2r-project

JOSS Publication

containerit: Generating Dockerfiles for reproducible research with R

Published

August 21, 2019

DOI

10.21105/joss.01603

Volume 4, Issue 40, Page 1603

Authors

Daniel Nüst

Institute for Geoinformatics, University of Münster, Germany

Matthias Hinz

Professorship for Geoinformatics and Geodesy, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany

Editor

Yuan Tang

CodeMeta (codemeta.json)

{
  "@context": [
    "https://doi.org/10.5063/schema/codemeta-2.0",
    "http://schema.org"
  ],
  "@type": "SoftwareSourceCode",
  "identifier": "containerit",
  "description": "Package R sessions, scripts, workspace directories, and R\n    Markdown documents together with all dependencies to execute them in\n    Docker containers.  This package is supported by the project Opening\n    Reproducible Research (<https://o2r.info>).",
  "name": "containerit: Package R in Docker Containers",
  "codeRepository": "https://github.com/o2r-project/containerit/",
  "relatedLink": "https://o2r.info/containerit/",
  "issueTracker": "https://github.com/o2r-project/containerit/issues",
  "license": "https://spdx.org/licenses/GPL-3.0",
  "version": "0.6.0.9004",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.1.0 (2021-05-18)",
  "author": [
    {
      "@type": "Person",
      "givenName": "Daniel",
      "familyName": "Nuest",
      "email": "daniel.nuest@uni-muenster.de",
      "@id": "https://orcid.org/0000-0003-2392-6140"
    },
    {
      "@type": "Person",
      "givenName": "Matthias",
      "familyName": "Hinz",
      "email": "matthias.m.hinz@gmail.com",
      "@id": "https://orcid.org/0000-0001-6837-9406"
    }
  ],
  "contributor": [
    {
      "@type": "Person",
      "givenName": "Patrick",
      "familyName": "Schratz",
      "@id": "https://orcid.org/0000-0003-0748-6624"
    },
    {
      "@type": "Person",
      "givenName": "Mark",
      "familyName": "Edmondson"
    },
    {
      "@type": "Person",
      "givenName": "Ben",
      "familyName": "Marwick",
      "@id": "https://orcid.org/0000-0001-7879-4531"
    },
    {
      "@type": "Person",
      "givenName": "Claire",
      "familyName": "Miller",
      "@id": "https://orcid.org/0000-0003-0758-9447"
    },
    {
      "@type": "Person",
      "givenName": "Elise",
      "familyName": "Gould",
      "@id": "https://orcid.org/0000-0002-6585-538X"
    },
    {
      "@type": "Person",
      "givenName": "Marc",
      "familyName": "Greenaway"
    }
  ],
  "copyrightHolder": {},
  "funder": {},
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Daniel",
      "familyName": "Nuest",
      "email": "daniel.nuest@uni-muenster.de",
      "@id": "https://orcid.org/0000-0003-2392-6140"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "BiocGenerics",
      "name": "BiocGenerics",
      "provider": {
        "@id": "https://www.bioconductor.org",
        "@type": "Organization",
        "name": "BioConductor",
        "url": "https://www.bioconductor.org"
      },
      "sameAs": "https://bioconductor.org/packages/release/bioc/html/BiocGenerics.html"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "codetools",
      "name": "codetools",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=codetools"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "covr",
      "name": "covr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=covr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "coxrobust",
      "name": "coxrobust",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=coxrobust"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "docopt",
      "name": "docopt",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=docopt"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "dplyr",
      "name": "dplyr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=dplyr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "fortunes",
      "name": "fortunes",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=fortunes"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "ggplot2",
      "name": "ggplot2",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=ggplot2"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "gstat",
      "name": "gstat",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=gstat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "knitr",
      "name": "knitr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=knitr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "lattice",
      "name": "lattice",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=lattice"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "lintr",
      "name": "lintr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=lintr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "magrittr",
      "name": "magrittr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=magrittr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "maptools",
      "name": "maptools",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=maptools"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "remotes",
      "name": "remotes",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=remotes"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rgdal",
      "name": "rgdal",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rgdal"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rmarkdown",
      "name": "rmarkdown",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rprojroot",
      "name": "rprojroot",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rprojroot"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "sessioninfo",
      "name": "sessioninfo",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=sessioninfo"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "sf",
      "name": "sf",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=sf"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "sp",
      "name": "sp",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=sp"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    }
  ],
  "softwareRequirements": [
    {
      "@type": "SoftwareApplication",
      "identifier": "R",
      "name": "R",
      "version": ">= 3.5.0"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "automagic",
      "name": "automagic",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=automagic"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "BiocManager",
      "name": "BiocManager",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=BiocManager"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "callr",
      "name": "callr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=callr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "desc",
      "name": "desc",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=desc"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "devtools",
      "name": "devtools",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=devtools"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "fs",
      "name": "fs",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=fs"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "futile.logger",
      "name": "futile.logger",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=futile.logger"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "jsonlite",
      "name": "jsonlite",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=jsonlite"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "methods",
      "name": "methods"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "miniUI",
      "name": "miniUI",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=miniUI"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rjson",
      "name": "rjson",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rjson"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rstudioapi",
      "name": "rstudioapi",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rstudioapi"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "semver",
      "name": "semver",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=semver"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "shiny",
      "name": "shiny",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=shiny"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "shinyFiles",
      "name": "shinyFiles",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=shinyFiles"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "stevedore",
      "name": "stevedore",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=stevedore"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "stringr",
      "name": "stringr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=stringr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "sysreqs",
      "name": "sysreqs",
      "sameAs": "https://github.com/r-hub/sysreqs"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "utils",
      "name": "utils"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "versions",
      "name": "versions",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=versions"
    }
  ],
  "keywords": [
    "docker",
    "reproducible-research",
    "reproducible-science",
    "r",
    "dockerfile"
  ],
  "citation": [
    {
      "@type": "ScholarlyArticle",
      "datePublished": "2019",
      "author": [
        {
          "@type": "Person",
          "givenName": "Daniel",
          "familyName": "Nüst"
        },
        {
          "@type": "Person",
          "givenName": "Matthias",
          "familyName": "Hinz"
        }
      ],
      "name": "{containerit: Generating Dockerfiles for reproducible research with R}",
      "identifier": "10.21105/joss.01603",
      "url": "https://doi.org/10.21105/joss.01603",
      "pagination": "1603",
      "@id": "https://doi.org/10.21105/joss.01603",
      "sameAs": "https://doi.org/10.21105/joss.01603",
      "isPartOf": {
        "@type": "PublicationIssue",
        "issueNumber": "40",
        "datePublished": "2019",
        "isPartOf": {
          "@type": [
            "PublicationVolume",
            "Periodical"
          ],
          "volumeNumber": "4",
          "name": "{Journal of Open Source Software}"
        }
      }
    }
  ],
  "releaseNotes": "https://github.com/o2r-project/containerit/blob/master/NEWS.md",
  "readme": "https://github.com/o2r-project/containerit/blob/master/README.md",
  "fileSize": "3364.864KB",
  "contIntegration": [
    "https://travis-ci.org/o2r-project/containerit",
    "https://ci.appveyor.com/project/nuest/containerit-rrvpq"
  ],
  "developmentStatus": "https://www.repostatus.org/#wip"
}

GitHub Events

Total

Watch event: 3

Last Year

Watch event: 3

Committers

Last synced: 5 months ago

All Time

Total Commits: 347
Total Committers: 16
Avg Commits per committer: 21.688
Development Distribution Score (DDS): 0.225

Past Year

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

Top Committers

Name	Email	Commits
nuest	d**t@u**e	269
matthiashinz	m**z@g**m	39
Claire Miller	m**2@s**u	10
Kyle Niemeyer	k**r@g**m	4
Mark Greenaway	m**g@m**u	4
egouldo	e**d@u**u	4
Ben Marwick	b**k@h**m	3
Vanessa Sochat	v**t@s**u	3
Mark Edmondson	g**b@m**e	2
pat-s	p**z@g**m	2
Jimmy Briggs	j**1@o**m	2
7048730	7****0	1
Esther Lyon Delsordo	5****o	1
OmaymaS	1****S	1
MatthiasHinz	c**t@m**u	1
egouldo	e**d@g**m	1

Committer Domains (Top 20 + Academic)

matthiashinz.eu: 1 markedmondson.me: 1 stanford.edu: 1 unimelb.edu.au: 1 maths.usyd.edu.au: 1 student.unimelb.edu.au: 1 uni-muenster.de: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 70
Total pull requests: 30
Average time to close issues: 7 months
Average time to close pull requests: about 2 months
Total issue authors: 16
Total pull request authors: 11
Average comments per issue: 1.36
Average comments per pull request: 0.93
Merged pull requests: 23
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

nuest (48)
MarkEdmondson1234 (3)
vsoch (3)
pat-s (2)
muschellij2 (2)
Timmimim (2)
athammad (1)
natemiller (1)
cole-brokamp (1)
holgerbrandl (1)
mischa2002k2 (1)
stephlocke (1)
brnleehng (1)
leungi (1)
wtzhou74 (1)

Pull Request Authors

nuest (14)
kyleniemeyer (4)
pat-s (2)
benmarwick (2)
muschellij2 (2)
vsoch (1)
OmaymaS (1)
jimbrig (1)
esther-lyondelsordo (1)
certifiedwaif (1)
JosiahParry (1)

Top Labels

Issue Labels

enhancement (10) idea (7) help wanted (5) feature (3) demo/documentation (2) wontfix (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads: unknown

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 2

proxy.golang.org: github.com/o2r-project/containerit

Documentation: https://pkg.go.dev/github.com/o2r-project/containerit#section-documentation
License: gpl-3.0
Latest release: v0.6.0
published over 6 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.5%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 4 months ago

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
BiocManager * imports
automagic * imports
callr * imports
desc * imports
devtools * imports
fs * imports
futile.logger * imports
jsonlite * imports
methods * imports
miniUI * imports
rjson * imports
rstudioapi * imports
semver * imports
shiny * imports
shinyFiles * imports
stevedore * imports
stringr * imports
sysreqs * imports
utils * imports
versions * imports
BiocGenerics * suggests
codetools * suggests
covr * suggests
coxrobust * suggests
docopt * suggests
dplyr * suggests
fortunes * suggests
ggplot2 * suggests
gstat * suggests
knitr * suggests
lattice * suggests
lintr * suggests
magrittr * suggests
maptools * suggests
remotes * suggests
rgdal * suggests
rmarkdown * suggests
rprojroot * suggests
sessioninfo * suggests
sf * suggests
sp * suggests
testthat * suggests

tests/testthat/github/DESCRIPTION cran

R >= 3.5.0 depends
methods * depends
graphics * imports

tests/testthat/package_description/DESCRIPTION cran

R >= 3.4.0 depends
methods * depends
Rcpp >= 0.12.18 imports
grDevices * imports
graphics * imports
grid * imports
units >= 0.6 imports
utils * imports
covr * suggests
dplyr >= 0.8 suggests
ggplot2 * suggests
knitr * suggests
lwgeom >= 0.1 suggests
maps * suggests

containerit

Science Score: 95.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

JOSS Publication

containerit: Generating Dockerfiles for reproducible research with R

Authors

Editor

Tags

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

proxy.golang.org: github.com/o2r-project/containerit

Rankings

Dependencies