-----Original Message-----
From: Herve Pages [mailto:hpages at fhcrc.org]
Sent: Wed 11/8/2006 4:02 PM
To: Steven McKinney
Cc: Bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] stale link to reposTools in BioC FAQ?
Hi Steven,
Steven McKinney wrote:
Hi Herve,
[...]
It seems quite a few things in the documented
method for updating packages have changed, so
there are several stale/outdated links and
info items in the FAQ and elsewhere in the
BioC web site.
Can you please provide the URLs?
-------------------------------------------------------------
reposTools link is on this page:
http://www.bioconductor.org/docs/faq/
reposTools Tools for dealing with file repositories and allow users to easily install, update, and distribute packages, vignettes, and other files.
-------------------------------------------------------------
Another link is on this page:
http://www.bioconductor.org/whatisit
The vignettes are generated using the Sweave function from the R package tools. They are documents that intermix text, code, and output (textual and graphical) and can be regenerated automatically whenever the data or analyses change. Additional supporting software for vignettes will aid users in obtaining data and sample code, step through specific analyses, and apply these analyses to their own data (reposTools package).
-------------------------------------------------------------
This page still refers to reposTools:
http://www.bioconductor.org/docs/install-howto.html
In an R command window, type the following:
source("http://www.bioconductor.org/biocLite.R")
biocLite()
This will install the following subset of packages by default:
affy affydata affyPLM
annaffy annotate Biobase
Biostrings DynDoc gcrma
genefilter geneplotter hgu95av2
limma marray matchprobes
multtest reposTools ROC
vsn xtable
-------------------------------------------------------------
Although this page/node states that packages can be updated with bioClite and getBioC,
the sections describing bioClite and getBioC only discuss installing new
packages, not updating packages periodically to keep up with changes.
http://www.bioconductor.org/docs/faq/index.html#For%20Unix/Linux
Users are encouraged to use biocLite.R or getBioC to obtain, install and update their packages. Information on how to use these functions can be found in the biocLite and getBioC sections of this document.
-------------------------------------------------------------
I just ran an update using
update.packages(ask = FALSE) ## CRAN updates
update.packages(repos = getOption("BioC.Repos"), ask = FALSE) ## BioC updates
Where did you get this code from? Did it work for you?
I tried various combinations of calls to update.packages, looked in the
internals of getBioC, getOption, install.packages, etc. The
above calls seemed to work best. Your suggestion below looks better.
I have not yet determined which function set up list item BioC.Repos
in my options, information from anyone who knows this would be appreciated.