Sean,

Thanks for your advice. I followed your suggestion and typed

source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("affycoretools")

and there is nothing abnormal. However, when I type
library(affycoretools), it pops up the following lines:

Loading required package: affy
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affyio
Loading required package: preprocessCore
Loading required package: limma
Loading required package: GOstats
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: annotate
Loading required package: xtable
Loading required package: RBGL
Loading required package: Category
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: biomaRt
Loading required package: RCurl
Error: package 'RCurl' could not be loaded
In addition: Warning message:
In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
  there is no package called 'RCurl'

Below is what I got from using sessionInfo() for diagnose

R version 2.6.1 (2007-11-26) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] GOstats_2.4.0        Category_2.4.0       genefilter_1.16.0   
 [4] survival_2.34        RBGL_1.14.0          annotate_1.16.1     
 [7] xtable_1.5-2         GO.db_2.0.2          AnnotationDbi_1.0.6 
[10] RSQLite_0.6-4        DBI_0.2-4            graph_1.16.1        
[13] limma_2.12.0         affy_1.16.0          preprocessCore_1.0.0
[16] affyio_1.6.1         Biobase_1.16.2      

loaded via a namespace (and not attached):
[1] cluster_1.11.9

Seems that it still can not find the package Rcurl. 

James

Sean Davis <sdavis2@mail.nih.gov> wrote: 

On Dec 19, 2007 3:36 PM, James Anderson <janderson_net@yahoo.com> wrote:
 Dear list,

Is there any specific requirement for installation of affycoretools? like the version of R, etc. I am trying to install affycoretools, but there is always some error msg like:

Error: package ' GO.db' required by 'GOstats' could not be found.
After I fix the above error, there is some new error:

Error: package 'DBI' required by 'AnnotationDbi' could not be found
I fix this one there is some new one and seems that it will never end. 

So what should I do in order to install affycoretools?
In addition, the function affystart in affycoretools can be used to plot the distribution of intensity, what is the corresponding function in package affy to perform the same task? I am trying to plot the intensity distribution from two batches of data. 

Hi, James.

You probably want to be using biocLite() to do installations of packages.  See here for details:

http://www.bioconductor.org/download 

If you have still have problems, perhaps showing us what you have tried, and the output from sessionInfo() will help to diagnose the problem.

Sean



 

       
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