Installation

HEMDAG is available on CRAN, through Bioconda and from source code. You can use one of the following ways for installing HEMDAG.

Installation via Conda

This is the recommended way to install HEMDAG for normal users because it will enable you to switch software versions easily. In addition R with all needed dependencies will be installed.

First, you have to install the Miniconda Python3 distribution. See here for installation instructions. Make sure to:

  • install the Python3 version of Miniconda.
  • answer yes to the question whether conda shall be put into your PATH.

Then, you can install HEMDAG with

$ conda install -c bioconda -c conda-forge r-hemdag

from the Bioconda channel.

Global Installation

You can directly install the library via R by typing in your terminal:

$ R -e 'install.packages("HEMDAG", repos="http://cran.us.r-project.org")'

Alternatively, you can install the HEMDAG library by typing in the R environment:

install.packages("HEMDAG");

Another possibility to install the development version of HEMDAG is by using the devtools package (link):

library(devtools);
install_github("marconotaro/hemdag");

Dependencies

To install or build HEMDAG the following dependencies are required:

  • R (≥ 2.10)

  • R dependencies

    • graph (bioconductor)
    • rbgl (bioconductor)
    • precrec
    • preprocessCore (bioconductor)
    • plyr
    • foreach
    • doParallel

Note

CRAN does not automatically install Bioconductor packages. To install them:

if(!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")

BiocManager::install("graph")
BiocManager::install("rbgl")
BiocManager::install("preprocessCore")

Installing from Source

Here we describe how to build HEMDAG from scratch.

Package from CRAN

On a Linux environment, download the package source from the CRAN repo and save it (for instance) in the folder pippo. Then type:

R CMD INSTALL pippo/HEMDAG_<pkg-version-number>.tar.gz

Note

Replace <pkg-version-number> with the version number of the downloaded HEMDAG package.

Direct Git Checkout

Note

You only need to install from source if you want to develop HEMDAG yourself.

Below, we will download the HEMDAG sources and build them in ~/hemdag:

~ $ cd ~
~ $ git clone https://github.com/marconotaro/hemdag.git

Building

You can build HEMDAG by using:

R CMD build hemdag

This will generate the file HEMDAG_<package-version-number>.tar.gz and just install the package via:

R CMD INSTALL HEMDAG_<package-version-number>.tar.gz