/usr/lib/R/site-library/phyloseq/scripts/installer.R is in r-bioc-phyloseq 1.22.3-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# An example function for installing phyloseq from various sources
##############################
install_phyloseq = function(branch = "release",
minRVersion = "3.3.0",
verbose = TRUE){
if(!compareVersion(as.character(getRversion()), minRVersion) >=0){
stop("phyloseq installation script failed.\n",
"R ", minRVersion, " or greater is required.")
}
branch <- as.character(branch)
if(branch == "release"){
if(verbose){
message("Installing the release version from BioC")
}
source("http://bioconductor.org/biocLite.R")
biocLite("phyloseq", suppressUpdates=TRUE)
return("phyloseq installed from BioC release branch (if no errors).")
}
if(branch == "devel"){
if(verbose){
message("\n\nInstalling phyloseq from the devel version from BioC...\n")
}
biocLite("phyloseq",
siteRepos="http://bioconductor.org/packages/devel/bioc",
suppressUpdates=TRUE,
type="source")
return("phyloseq installed from BioC devel branch (if no errors).")
}
if(branch == "github"){
if(verbose){
message("Installing the devel version from joey711/master from GitHub")
}
if(!require("devtools", quietly=TRUE)){
# Note: needs Curl for RCurl
install.packages("devtools")
}
library("devtools")
devtools::install_github("joey711/phyloseq")
return("phyloseq installed from GitHub `joey711/phyloseq` (if no errors).")
}
return("You probably selected an unsupported argument to `branch`.
Try again using 'release', 'devel', or 'github'.")
}
###############
# Execute the function w/ default params.
# You can select alternatives if you want :-)
###############
install_phyloseq()
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