[BioC] Re: trouble installing "affy" package

[Jeffrey Chang]

I still don't know what the problem is, but I've hacked my way around 
it in a *really* ugly way.  The key seems to be in the error message:
> Error in getClass(Class, where = topenv(parent.frame())) :
>          "MIAME" is not a defined class

I downloaded the affy_1.3.27.tar.gz source and tried to install it 
manually (using R CMD INSTALL).  I continued to get the message, and I 
traced it down to code in AffyBatch.R.  That file begins with the 
declaration of a new class:

setClass("AffyBatch",
          representation(cdfName="character",
                         nrow="numeric",
                         ncol="numeric"),
          prototype=list(exprs=matrix(nr=0,nc=0),
          se.exprs = matrix(nr=0,nc=0),
          description=new("MIAME"),
          annotation="",
          notes="",
          cdfName="",
          nrow=0,
          ncol=0), contains="exprSet")


For some reason, R is not importing Biobase correctly (if anyone knows 
why, please tell me!) so it doesn't know about MIAME and complains.  
Similarly, it also doesn't know about "exprSet" so can't create the 
class.

Since I am not planning on using this file, I commented out the entire 
file and installed the package without this functionality.  The correct 
fix would be to figure out why R can't find Biobase, but I don't know 
enough about R to do that.

Jeff


On Jan 29, 2004, at 1:15 PM, Jeffrey Chang wrote:

> 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
>