Installation

Installation

Easy Way (Bioconductor release)

The official stable version of phyloseq is available from Bioconductor. (Note: the Bioconductor release schedule mirrors the R release schedule, and so you may need to update your version of R to the latest version). See if the following works without an error. If not, skip to the "Mildly Harder Way" below.

source("http://bioconductor.org/biocLite.R")
biocLite("phyloseq")

Mildly Harder Way

If the above fails it is probably because of a mismatch with your current version of R and that required. One option is to update your version of R; not necessarily recommended if this means jumping out of the current stable version. Alternatively, install phyloseq from GitHub (this is the most frequently updated development version). Use the following command(s) from within R to perform the installation:

First, install the Bioconductor dependencies

Install the Bioconductor dependencies (genefilter is optional):

source("http://bioconductor.org/biocLite.R")
biocLite("multtest")
biocLite("genefilter")

Second, build/install package from GitHub repository

Install phyloseq using GitHub as an alternative repository with the install_github command in the devtools package.

# Make sure you have devtools installed
install.packages("devtools")
# Load the devtools package
library("devtools")
# Build and install phyloseq
install_github("phyloseq", "joey711")

Windows Users must first install Rtools:

Windows users will likely need the Rtools package installed in order to build anything from source. Rtools

Your own fork:

For installing your own fork of phyloseq from your own repository, just change the "joey711" argument to your GitHub username (and if you named the repository something other than "phyloseq", change that too.

CRAN dependencies

The install_github command should also install any missing dependencies automagically (assuming they are in the CRAN repository). However, if you want to install them ahead of time, or re-install them, the following section contains the code to install them directly:

Install the CRAN dependencies (doParallel is optional):

install.packages("ape")
install.packages("doParallel")
install.packages("foreach")
install.packages("ggplot2")
install.packages("igraph")
install.packages("picante")
install.packages("vegan")
install.packages("RJSONIO")
install.packages("plyr")