if (!requireNamespace("BiocManager", quietly=TRUE))
BiocManager::install("systemPipeShiny", dependencies=TRUE)

This will install all required packages including suggested packages that are required by the core modules. Be aware, it will take quite some time if you are installing on Linux where only source installation is available. Windows and Mac binary installations will be much faster.


To install the package, please use the BiocManager::install command:

if (!requireNamespace("BiocManager", quietly=TRUE))

By the minimum installation, all the 3 core modules are not installed. You can still start the app, and When you start the app and click on these modules, it will tell to enable these modules, what packages and command you need to run. Just follow the instructions. So, install as you need.

Most recent

To obtain the most recent updates immediately, one can install it directly from GitHub{blk} as follow:

if (!requireNamespace("remotes", quietly=TRUE))
remotes::install("systemPipeR/systemPipeShiny", dependencies=TRUE)

Similarly, remotes::install("systemPipeR/systemPipeShiny") for the minimum develop version.


If you are on Linux, you may also need the following libraries before installing SPS. Different distributions may have different commands, but the following commands are examples for Ubuntu:

sudo apt-get install -y libicu-dev
sudo apt-get install -y pandoc
sudo apt-get install -y zlib1g-dev
sudo apt-get install -y libcurl4-openssl-dev
sudo apt-get install -y libssl-dev      
sudo apt-get install -y make

On other Linux distributions, the install commands may be slightly different.

Last modified 2021-08-09 : Update (b185b16d)