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https://github.com/reconhub/deployer
Self-contained R environment on a thumb drive
https://github.com/reconhub/deployer
Last synced: 8 days ago
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Self-contained R environment on a thumb drive
- Host: GitHub
- URL: https://github.com/reconhub/deployer
- Owner: reconhub
- Created: 2017-05-31T07:54:34.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2020-10-20T10:15:10.000Z (about 4 years ago)
- Last Synced: 2024-11-30T20:54:19.437Z (12 days ago)
- Language: R
- Size: 19.6 MB
- Stars: 10
- Watchers: 6
- Forks: 3
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- jimsghstars - reconhub/deployer - Self-contained R environment on a thumb drive (R)
README
The *RECON deployer* project focusses on distributing an R environment for outbreak response on a thumb drive. This environment should provide:
* the latest stable version of R for Windows and MacOSX
* the corresponding version of Rtools
* the latest stable version of Rstudio for Windows and MacOSX
* a large selection of relevant R packages hosted on CRAN
* all RECON packages hosted on github (sources)
* some other packages hosted on github, required by the above
* scripts to permit seemless installation of the local CRAN and github packages
## Using a *deployer*
You can find versioned releases of deployers at
https://github.com/reconhub/deployer/releases that detail how the deployer was
built and how to download/decompress it. If you want to build one from scratch,
see Building a new deployer
The *RECON deployer* is meant to be copied on a USB stick, although strictly
speaking it is medium-agnostic. To use the *deployer*, go to the folder where it
is stored, open the file called `README.html`, and follow the instructions
provided there.
## Building a new *deployer*
To build/generate a new *deployer*, you can use the R script [`generate_deployer.R`](./generate_deployer.R):
```
cd ..
Rscript reconhub--deployer/generate_deployer.R
```
### Details
The RECON Deployer is an application of `nomad`, a R package for creating
portable R environments. This script will do the following:
1. attempt to upgrade [provisioner](https://github.com/mrc-ide/provisionr) and
[nomad](https://github.com/reconhub/nomad)
2. generate the deployer
3. split the deployer into 4 compressed files with md5sums that can be [uploaded
to github for release](https://github.com/reconhub/deployer/releases/new )
The files you end up with are:
| File name | Description |
|--------------------|------------------------------------------------|
|`/` | Source Directory for the deployer |
|`_md5sums.txt`| summary of the above files |
|`_release.md` | release page to be placed on github |
| | |
|`_base.tar` | source packages, cheat sheets, and instructions|
|`_extra.tar` | binaries for R, git, Rtools, and RStudio |
|`_macosx.tar` | binary packages built for macos |
|`_windows.tar`| binary packages built for windows |
> Note: These will likely be over 1GB each, so make sure you have a strong
> internet connection when uploading these to github.
Once downloaded from the github release page, the users can decompress the files
via R:
```r
untar('_base.tar')
untar('_extra.tar')
untar('_macosx.tar')
untar('_windows.tar')
```
### Generating the deployer manually
The RECON Deployer is an application of `nomad`, a R package for creating
portable R environments. You first need to install this package, which also depends on `provisionr`:
```r
remotes::install_github("mrc-ide/provisionr", upgrade = FALSE)
remotes::install_github("reconhub/nomad", upgrade = FALSE)
```
To create a deployer in a given directory named `deployer_[date]`, type:
```r
out_dir <- paste("deployer", gsub("-", "_", Sys.Date()), sep = "_")
nomad::build("reconhub/deployer", out_dir)
```
## Adding or updating packages
If you need to add or update an R package, you can use the [`add_packages.R`](./add_packages.R)
script with the names of the CRAN packages to use.
```
Rscript add_packages.R officer kableExtra
```
If you have non-cran packages, then be sure to add the github repositories to
[`package_sources.txt`](./package_sources.txt).