[BioC] trouble installing "affy" package

[Tom R. Fahland]

I got that error also. 
I installed Biobase by the usual "R CMD.." method, then affy and it
worked for me. (don't ask me why). 

PS. What package(s) do people find the most useful for general 
Gene expression data analysis once they have normalized data. 
I'm looking at supclust, pamr, etc from R Cran area. I plan to do a lot
of 
supervised clustering, etc.

Tom Fahland 

-----Original Message-----
From: Jeffrey Chang [mailto:jeffrey.chang at duke.edu] 
Sent: Thursday, January 29, 2004 10:15
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] trouble installing "affy" package


Hello everybody,

I'm trying to install Bioconductor into a freshly compiled R 1.8.1 on 
OS X 10.3.2.  I'm sourcing the getBioC.R from 
http://www.bioconductor.org and trying to install the "release" 
version:

 > getBioC(relLevel="release")

It looks like R is getting sources from
http://www.bioconductor.org/repository/release1.3/package/Source

However, when it tries to install "affy", it complains about a missing 
"Biobase" package and the installation fails.  However, Biobase seems 
to be installed properly.  Executing at R prompt
     > library("Biobase")
seems to complete without error.

However, executing
     > library("affy")
     Error in library("affy") : There is no package called 'affy' fails.

I have included a portion of the error messages at the bottom of this 
email.  Has anyone seen this before, or know how to fix it?

Thanks,
Jeff



[...]
** R
** data
** demo
** inst
** save image
[1] FALSE
Warning message:
There is no package called 'Biobase' in: library(package, 
character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts,
[1] TRUE [1] TRUE Error in getClass(Class, where =
topenv(parent.frame())) :
          "MIAME" is not a defined class
Execution halted
cat: stdout: Broken pipe
ERROR: execution of package source for 'affy' failed
** Removing '/opt/local/lib/R/library/affy'
Warning message:
Installation of package affy had non-zero exit status in: 
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)  From
URL:  
http://www.bioconductor.org/repository/release1.3/package/Source
        tkWidgets version 1.3.0
        affy version 1.3.27

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