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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file! -->
```{r knitr_config, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# containerit <img src="man/figures/logo.png" align="right" alt="containerit logo" width="200" style="padding: 0 0 10px 10px;" />
<!-- badges: start -->
[](https://doi.org/10.21105/joss.01603)
[](https://www.repostatus.org/#wip)
[](https://travis-ci.org/o2r-project/containerit)
[](https://ci.appveyor.com/project/nuest/containerit-rrvpq)
[](https://github.com/o2r-project/containerit/issues/68)
[](https://gitter.im/o2r-project/containerit)
<span data-badge-popover="bottom" data-badge-type="2" data-doi="10.21105/joss.01603" data-condensed="true" data-hide-no-mentions="true" class="altmetric-embed"></span>
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<script type='text/javascript' src='https://d1bxh8uas1mnw7.cloudfront.net/assets/embed.js'></script>
`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://microbadger.com/images/o2rproject/containerit "Get your own version badge on microbadger.com") [](https://microbadger.com/images/o2rproject/containerit "Get your own image badge on microbadger.com") [](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://microbadger.com/images/o2rproject/containerit:geospatial "Get your own version badge on microbadger.com") [](https://microbadger.com/images/o2rproject/containerit:geospatial "Get your own image badge on microbadger.com") [](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.
## 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.