[BioC] Re: trouble installing "affy" package

[Wolfgang Huber]

References: <1BF3BA9E-5287-11D8-90FC-000A956845CE at duke.edu> 
<FE8987DC-52AD-11D8-90FC-000A956845CE at duke.edu>

Hi Jeffrey,

loading Biobase, and the class definitions of AffyBatch.R are really
essential for the functioning of the affy package. I don't think you can
expect to get any kind of meaningful results without these. So the
proper thing to do is to find out why Biobase doesn't install.

When you downlonad Biobase_1.XX.tar.gz file manually and try to install,
do you get an error message, and which? What version are you using?

If you succeed to load Biobase, can you send us the output of

  > library(Biobase)
  > ls("package:Biobase")
  > showClass("exprSet")
  > showClass("MIAME")

Best wishes
   Wolfgang


Jeffrey Chang wrote:
> 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
>>
> 
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-- 
-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber
-------------------------------------


-- 
-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber