INSTALL.md

Installing MarkovHC:

Quick Installation

1. Install R and RStudio

MarkovHC is a package written in R and designed to be used in the RStudio interactive environment.

R can be obtained and installed from https://cran.rstudio.com.

MarkovHC has only been tested under R version 3.5.1 and 3.6.1, and may fail to install under R 3.4.x until some of its dependencies are updated.

Following installation of R, Rstudio can be obtained and installed from https://www.rstudio.com/products/rstudio/download/. The free version of RStudio Desktop is sufficient.

2. Install required R packages and MarkovHC

We wrote a script that will attempt to install all requirements for MarkovHC and then MarkovHC itself. Start RStudio and then run the installation script from the console:

source("https://github.com/ZhenyiWangTHU/MarkovHC/blob/master/MarkovHC-install.R")

Manual installation

If something went wrong previously, you may have try installing some of MarkovHC's dependencies manually:

A. Install and attach the devtools package

devtools is required to compile and install MarkovHC, since it's distributed through GitHub.

install.packages("devtools")

B. Install required packages

Because these packages must be installed before installing MarkovHC (otherwise its installation will fail.)

install.packages(setdiff(c("parallel", "doParallel", "dbscan", "igraph", "Matrix", "Rcpp", "plyr", "dplyr", "doBy", "ggraph"), .packages(all.available=T)))

C. Install MarkovHC

MarkovHC can be installed directly from the GitHub repository

library(devtools)
install_github(repo="ZhenyiWangTHU/MarkovHC",subdir = "/MarkovHC")

If you do not want to update the installed dependencies, you could run this command install_github(repo="ZhenyiWangTHU/MarkovHC",subdir = "/MarkovHC", dep = FALSE)

Or download MarkovHC_2.0.0.tar.gz and install in R

install.packages('MarkovHC_2.0.0.tar.gz')