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Installation
A recent major update to the igraph package, version 0.6+, is not backward compatible and causes certain versions of phyloseq to fail to install properly. Although this only actually effects a small minority of functions in phyloseq, it causes the vignettes to fail to build, which in-turn causes package installation to stop with an error.
THIS BUG IS FIXED in the latest release of phyloseq on GitHub (see the "Mildly Harder Way" below), but I am still working with Bioconductor on a targeted update to the release version of phyloseq there. I will be sure to update the devel version on Bioconductor as well to bring that up to date with the latest GitHub version.
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")The latest stable release of phyloseq on Bioconductor and the latest development release of phyloseq on Bioconductor can be found at these respective links, as well as some interesting phyloseq use data in the form of the number of downloads of the respective versions each month from Bioconductor.
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")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
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("igraph0")
install.packages("picante")
install.packages("vegan")
install.packages("RJSONIO")
install.packages("plyr")