Signed executable

Convert the powershell script to an executable:

ps2exe .\FHAST_Shiny.ps1

Sign the executable:

signtool sign /tr http://CAtimestampserver.com /td SHA256 /fd SHA256 FHAST_Shiny.exe

Creating a Testing signing certificate

Using PowerShell

New-SelfSignedCertificate -DnsName [email protected] -Type CodeSigning -CertStoreLocation cert:\CurrentUser\My Export-Certificate -Cert (Get-ChildItem Cert:\CurrentUser\My -CodeSigningCert)[0] -FilePath code_signing.crt Import-Certificate -FilePath .\code_signing.crt -Cert Cert:\CurrentUser\TrustedPublisher

Using Trusted Certificates

Creating a Certificate Signing Request

https://help.sectigostore.com/support/solutions/articles/22000266869-java-keystore

Install certificates from authority to machine

Download from authority and install (can probably double click)

Extract private key

keytool -srckeystore keystore.jks -srcstorepass {password} -destkeystore private.p12 -deststoretype PKCS12 -deststorepass {password} -destkeypass {password} -importkeystore

Sign the executable

signtool sign /debug /tr http://timestamp.comodoca.com/rfc3161 /td SHA256 /fd SHA256 /f private.p12 /p {password} FHAST_Shiny.exe

DesktopDeployR

A framework for deploying self-contained R-based applications to the desktop

Overview

Allows developers to share R based applications to users as desktop applications by providing both a portable R executable environment and a private application package library.

For more information on how this framework was developed please read:

• http://oddhypothesis.blogspot.com/2014/04/deploying-self-contained-r-apps-to.html
• http://oddhypothesis.blogspot.com/2016/04/desktop-deployr.html

Target Audience

Software Developers and Research Scientists who need to share applications in an environment where installing system / OS level software can be challenging and where use of other isolation and portability techniques (e.g. Docker containers) is not feasible.

Usage

Develop an Application

This deployment strategy has been tested with R based applications developed with Shiny, RGTK, and Tcl/Tk UIs. The specifics of how to make applications with each of these frameworks are beyond the scope of these instructions.

Clone this repository

cd /path/to/deployment/staging
git clone https://github.com/wleepang/DesktopDeployR.git MyApplication

The git clone command above will clone the framework into a folder named MyApplication.

Alternatively, you can fork this repository into your own Github account and clone from there.

Create a branch for your app

It is highly recommended that you create a branch for your application:

cd /path/to/MyApplication
git checkout -b MyApplication

This will allow you to easily track your application code and any customizations you make to the framework.

"Install" R-Portable into the framework

The framework can be used with both a system installed version of R or R-Portable. The latter is recommended as it provides the most application isolation and allows for applications to be deployed to users unable to install R on their own (i.e. they lack sufficient system privileges).

Download R-portable from: https://sourceforge.net/projects/rportable/

Install it into:

/<appname/dist/

Customize the framework for your application

Install application scripts / assets

For example - a shiny app:

• create a folder called app/shiny

• put ui.R, server.R, and any other related files into app/shiny

• edit app/app.R:

   # assuming all shiny app code (ui.R and server.R are in ./app/shiny)
   shiny::runApp('./app/shiny')

Specify package dependencies

Edit app/packages.txt - adding your app's primary package dependencies, one package per line.

For a shiny app that depends on ggplot, app/packages.txt should look like:

jsonlite  # required by DesktopDeployR
shiny
ggplot

Packages listed here, along with their dependencies, are installed in a private application library (app/library) when the application is run for the first time.

Note, the above only works for packages available on CRAN. Custom packages need to be installed manually. The recommended method is to use devtools:

$ Rscript -e "devtools::install('path/to/package', lib = '<appname>/app/library')"

Configure application launch options

The file app/config.cfg is a JSON-ish formatted file that configures how the application is launched. Block (/* ... */) and line level (// ...) comments are allowed - they are removed to create valid JSON before the file is parsed.

Root level options:

Option	Description
appname	The name of the application. Displayed in the title of the progress bar shown during initialization, and used to name folders for logs based on logging settings (see below).
packages	(Optional: Default: "http://cran.rstudio.com") An object with a single element cran that specifies the CRAN mirror to use for installing packages. Alternatively, this can point to a private CRAN-like package repository for more control over package versions.
r_exec	(Optional; Default: "dist\\R-Portable\\App\\R-Portable\\bin\\") An object with elements specifying R execution options (see below).
logging	(Optional; Default: undefined) An object with elements specifying logging options (see below)

R Executable Options

Option	Description
home	(Optional; Default: "dist\\R-Portable\\App\\R-Portable\\bin\\") Path to <R_HOME>/bin - the R environment to use to run the app.
command	(Optional; Default: Rscript.exe) Name of the specific R interpreter executable to use.
options	(Optional; Default: --vanilla) Options to pass to the R interpreter executable.

Logging Options:

Option	Description
filename	(Optional; Default: "error.log") Name of the application log file. This file captures all text sent to stdout and stderr by the application.
use_userprofile	(Optional; Default: false) Boolean flag to set where application logs are kept. If true the application log file is written to %USERPROFILE%/.<appname>/.

Rename the application launching batch script file

Rename appname.bat as appropriate - e.g. to MyApplication.bat.

Deploy your application

Option 1

The entire application folder is copied to the deployed location. This is the easiest way to deploy. Note, it is possible to place / launch an application from a network share. If this is the case, be sure to set logging.use_userprofile: true in the application launch configuration.

Option 2

Create an installer using NSIS installer or InnoSetup. This is ideal for installing on isolated workstations. Both R-portable and package dependencies can be compiled with the installer. This means that a "first run" that ensures all package dependencies, must occur before compiling an installer.

TBD: an example InnoSetup installer compile script

Notes

Using a different (newer) version of R

Either replace ./dist/R-Portable/ with the version of R-Portable that is required or modify ./app/config.cfg to point to the desired R installation (e.g. a system install).

Version tracking

Due to their potentially large sizes, it is not recommended that the following folders be tracked by version control (i.e. Git):

• /app/library/
• /dist/R-Portable

Application Structure

/<appname>          # - application deployment root
./app/              # - application working directory

	./library/        # - application specific package library

	./shiny/          # - application framework folder (in this case, shiny)
		./global.R      # - global constants and functions for shiny-app
		./server.R      # - server processing function for shiny-app
		./ui.R          # - user interface definition function for shiny-app

	./app.R           # - application launch entry script
	./config.cfg      # - application configuration file
	./packages.txt    # - list of primary package dependencies
	./...             # - other application files

./dist/             # - application launch framework
	./R-Portable/     # - "vanilla" R interpreter (downloaded separately)
	./script/
		./R
			./run.R       # - R environment initialization and application launch
		./wsf
			./js
				./JSON.minify.js  # - JS to JSON minifier, allows comments in JSON files
				./json2.js  # - JSON parsing library
				./run.js    # - OS application launch script
			./run.wsf     # - merges javascript dependencies and launch script
	./USAGE.md        # - notes on how the dist folder is structured

/<appname>.bat      # - batch file to start application
/README.md          # - this file or brief description of application