[BioC] alternate /tmp for Bioconductor install

[Marcus Davy]

The following lookup in R may also be useful as an alternative to lookup from the http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/ url. 
You can obtain a list of dependancies (and more).

a <- CRAN.packages(CRAN=getOption("BIOC"))
 
a[,c("Package","Version","Depends")]
          Package     Version   Depends                                                            
aCGH      "aCGH"      "1.1.4"   "R (>= 1.8.0), cluster, repeated, rmutil, survival, multtest,\nsma"
affy      "affy"      "1.5.8-1" "R (>= 1.9.0), Biobase (>= 1.4.22), reposTools"                    
affycomp  "affycomp"  "1.4.3"   "R (>= 1.8.1), Biobase (>= 1.1.0)"                                 
affydata  "affydata"  "1.4.0"   "R (>= 1.6.2), affy (>= 1.2)"                                      
affylmGUI "affylmGUI" "1.2.5"   "limma, tcltk, affy"
...

> packageDescription("affy", field="Version")
[1] "1.5.8-1"

This list should be querying the current release packages of Biocondcutor 1.6. Can somebody verify that?


Marcus


>>> Kasper Daniel Hansen <k.hansen at biostat.ku.dk> 20/05/2005 10:21:18 p.m. >>>
It could in principle be scritable and might even be a little worthwhile 
to do it. But basically the BioC version number is corresponds to a 
whole list of individual package numbers. As sson as you move away from 
the getBioC script you can have a big mix of development and release 
level packages.

Kasper


On Fri, May 20, 2005 at 02:40:04PM -0500, Robert Citek wrote:
> 
> On May 20, 2005, at 11:52 AM, Seth Falcon wrote:
> >Well, there isn't a global Bioc version that you get query.  The best
> >thing to do is to compare the version numbers of a few packages
> >against what is on the Bioconductor website.
> >
> >For example,
> >
> >>library(Biobase)
> >>sessionInfo()
> >>
> >R version 2.1.0, 2005-04-29, x86_64-unknown-linux-gnu
> >
> >attached base packages:
> >[1] "tools"     "methods"   "stats"     "graphics"  "grDevices"  
> >"utils"
> >[7] "datasets"  "base"
> >
> >other attached packages:
> > Biobase
> >"1.5.12"
> >
> >And then verify the version here:
> >http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/ 
> 
> I'm not that familiar with R, but I imagine that the above is  
> scriptable.  That is, I should be able to traverse the package  
> dependency tree and query each package for its version.  Is that  
> possible within R?
> 
> Regards,
> - Robert
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch 
> https://stat.ethz.ch/mailman/listinfo/bioconductor 

-- 
Kasper Daniel Hansen, Research Assistant
Department of Biostatistics, University of Copenhagen

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch 
https://stat.ethz.ch/mailman/listinfo/bioconductor

______________________________________________________

The contents of this e-mail are privileged and/or confidenti...{{dropped}}