[Bioc-devel] stale link to reposTools in BioC FAQ?

Steven McKinney smckinney at bccrc.ca
Thu Nov 9 03:22:05 CET 2006

Hi Herve,

> -----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 there are several stale/outdated links and 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:

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:

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:

In an R command window, type the following:


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.


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.

> getOption("BioC.Repos")
[1] "http://www.bioconductor.org/packages/1.9/bioc"            "http://www.bioconductor.org/packages/1.9/data/annotation"
[3] "http://www.bioconductor.org/packages/1.9/data/experiment" "http://www.bioconductor.org/packages/1.9/omegahat"       
> options()$BioC.Repos
[1] "http://www.bioconductor.org/packages/1.9/bioc"            "http://www.bioconductor.org/packages/1.9/data/annotation"
[3] "http://www.bioconductor.org/packages/1.9/data/experiment" "http://www.bioconductor.org/packages/1.9/omegahat"       

> On my system it doesn't:
> > getOption("BioC.Repos")
> If you are using R >= 2.3.0, you can try this instead:
> > library(Biobase)
> > update.packages(rep=biocReposList(), ask = FALSE)

Yes, I have close to the latest and greatest.
> sessionInfo()
R version 2.4.0 Patched (2006-10-31 r39758) 


attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"  "base"     

other attached packages:
polycor mvtnorm ellipse 
"0.7-2" "0.7-5" "0.3-2" 

> Cheers,
> H.

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