[BioC] The package gcrma downloaded from Bioconductor cannot run in my linux machine

Qian Li qli at jax.org
Wed Jul 6 17:41:48 CEST 2005

Hi, dear sir/madam in bioconductor:

I initially downloaded and installed Bioconductor 1.6 into our linux 
machine for the purpose of affymetrix array analysis. I used the script 
provided on the web

to finish download and installation in R session. Then I loaded packages 
"affy" and "gcrma" to start my data processing work. Everything looked fine 
until I tried to run function "gcrma" with my real data. The system gave me 
an error message said: no slot of name "Imports" for this object of class 
"localPkg". I tried many methods to figure out the problem, including all 
the tips and clues provided by bioconductor. Unfortunately, I didn't find 
the answer for my problem. So I decide to seek help from you. My co-worker 
ran the same data set in his PC with Bioconductor 1.6, it worked very well. 
I am not sure what caused the error, could you help me to find the best 
solution for the problem? I pasted all the information in R session under 
my linux system as following.  The linux system we are using now is Red Hat 
8.0,  R version is 2.1.1.  Bioconductor 1.6 was installed into my user 
directory rather than the system directory automatically by script. No any 
system upgrading  during the installation process.

Many thanks in advance!


Total information:

R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.

 > library(affy); library(maanova); library(gcrma)
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
          Vignettes contain introductory material.  To view,
          simply type: openVignette()
          For details on reading vignettes, see
          the openVignette help page.
Loading required package: reposTools

Attaching package: 'maanova'

         The following object(s) are masked from package:datasets :


Loading required package: matchprobes
 > BeforeProcessedData <- ReadAffy(celfile.path="../Cell_Data/")
 > GCRmaData=gcrma(BeforeProcessedData)
Computing affinities[1] "Checking to see if your internet connection works..."
Note: Using download type: Source
Error in FUN(X[[1]], ...) : no slot of name "Imports" for this object of 
class "localPkg"

Qian Li
Data Analyst
The Jackson Lab
600 Main Street
Bar Harbor, ME   04609
Telephone: 288-6715
Email: qli at jax.org

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