Set Local Bioconductor Repository

Question

[anothergeek]

I have set up a local Bioconductor repository (and CRAN mirror), and would now like to be able to install Bioconductor on fresh machines using the

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

... method, but installing from the local site.

What are the steps to required to do this?

It is an Ubuntu machine, but I presume the steps apply to other platforms

Answer 1

[Nathan Harmston]

So I've never done this personally but reading through

1. http://www.bioconductor.org/biocLite.R
2. http://bioconductor.org/getBioC.R

would lead me to believe that you need to have a R script that calls a local version of getBioC.R ....

scriptUrl <- paste("http://bioconductor.org",
                       "installScripts",
                       choppedRVer,
                       "biocinstall.R", sep="/")

replacing the bioconductor.org with the local mirror?

I can't say this will work for definite but its probably a good place to start!

HTH a little.

Answer 2

[Jan Oosting]

source("http://bioconductor.org/biocLite.R")
# Bioconductor mirror
options("BioC_mirror"="http://local.bioconductor.mirror")
# CRAN mirror
r <- getOption("repos")
r["CRAN"] <- "http://local.cran.mirror/"
options(repos=r)
#
biocLite()

Answer 3

[Farshad]

Easier method is to go through regular install.packages as below:

• Download the appropriate file from the Bioconductor package home (in this case, I have used the windows binary)
• Make sure you copy the file in your working directory.
• install the package as below:

install.packages("package.zip", repos = NULL, type = "binary")

It should go through easily, if the parameters are set correctly.