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README.md


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:

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 and nomad
  2. generate the deployer
  3. split the deployer into 4 compressed files with md5sums that can be uploaded to github for release

The files you end up with are:

File name Description
<name>/ Source Directory for the deployer
<name>_md5sums.txt summary of the above files
<name>_release.md release page to be placed on github
<name>_base.tar source packages, cheat sheets, and instructions
<name>_extra.tar binaries for R, git, Rtools, and RStudio
<name>_macosx.tar binary packages built for macos
<name>_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:

untar('<name>_base.tar')
untar('<name>_extra.tar')
untar('<name>_macosx.tar')
untar('<name>_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:

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:

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 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.

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