[BioC] problem loading affycoretools

[Jenny Drnevich]

Hi Jim & all,

I'm having trouble getting affycoretools to work. I apparently had 
downloaded & installed affycoretools before, but had never used it. When I 
tried to load it today, I got an error message saying I was missing a 
dependent package, GOstats. So I used biocLite() to download & install 
GOstats & it's dependencies. Then when I tried to load affycoretools, I 
crashed my Rgui. I restarted the Rgui a few times in different ways, and 
each time I tried to load affycoretools, it crashed the Rgui. So then I 
went and deleted R_HOME/library/affycoretools and tried using biocLite() to 
get it again. This time it didn't crash, but it gave a warning message 
about it not containing a vignette (see below for output & sessionInfo). I 
checked on bioconductor.org, and there is a vignette for affycoretools. I 
haven't tried any of the functions yet, but I'm worried that something's 
amiss. Any suggestions on what to check or reload?

Thanks,
Jenny

P.S. It was great to finally meet many of you at the BioC2006 conference!


R : Copyright 2006, The R Foundation for Statistical Computing
Version 2.3.1 (2006-06-01)
ISBN 3-900051-07-0

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

Welcome to Bioconductor


     Vignettes contain introductory material.

     To view, simply type 'openVignette()' or start with 'help(Biobase)'.

     For details on reading vignettes, see the openVignette help page.


Loading required package: affyio
Loading required package: affydata
Loading required package: Biobase
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: reposTools
Loading required package: simpleaffy
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Welcome to 'affyQCReport' V 1.6-1
Further information available at: www.bifix.org
       mailto: craig.parman at bifix.org
Loading required package: ade4
Loading required package: scatterplot3d

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

Running getBioC version 0.1.6 with R version 2.3.1
Running biocinstall version 1.8.4 with R version 2.3.1
Your version of R requires version 1.8 of Bioconductor.
trying URL 
'http://bioconductor.org/packages/1.8/bioc/bin/windows/contrib/2.3/affycoretools_1.4.0.zip'
Content type 'application/zip' length 10626563 bytes
opened URL
downloaded 10377Kb

package 'affycoretools' successfully unpacked and MD5 sums checked

The downloaded packages are in
         C:\Documents and Settings\drnevich\Local 
Settings\Temp\RtmpfRnlqb\downloaded_packages
updating HTML package descriptions

 > library(affycoretools)

Loading required package: GOstats
Loading required package: graph
Loading required package: Ruuid
Loading required package: GO
Loading required package: annotate
Loading required package: RBGL
Loading required package: xtable

Attaching package: 'xtable'


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

          label

Loading required package: multtest
Loading required package: Category
Loading required package: KEGG
Loading required package: hgu95av2
Warning message:
affycoretools contains no vignette, nothing is added to the menu bar in: 
addVigs2WinMenu("affycoretools")

 > sessionInfo()
Version 2.3.1 (2006-06-01)
i386-pc-mingw32

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

other attached packages:
affycoretools       GOstats      Category      hgu95av2          KEGG
       "1.4.0"       "1.6.0"       "1.4.1"      "1.12.0"      "1.12.0"
      multtest        xtable          RBGL      annotate            GO
      "1.10.2"       "1.3-2"       "1.8.1"      "1.10.0"      "1.12.0"
         graph         Ruuid         made4 scatterplot3d          ade4
      "1.10.4"      "1.10.0"       "1.6.0"      "0.3-24"       "1.4-1"
  affyQCReport    simpleaffy    genefilter      survival    reposTools
      "1.10.0"       "2.6.0"      "1.10.1"        "2.26"      "1.10.0"
       affyPLM         gcrma   matchprobes      affydata          affy
       "1.8.0"       "2.4.1"       "1.4.0"       "1.8.0"      "1.10.0"
        affyio       Biobase         limma       RWinEdt
       "1.0.0"      "1.10.0"       "2.7.2"       "1.7-4"
 >


Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu