[R] [BioC] problem loading affycoretools (more details)

Jenny Drnevich drnevich at uiuc.edu
Fri Aug 11 17:46:41 CEST 2006

Hi again,

I have been playing around with the order of loading packages, and as far 
as I can tell, there's nothing specific with affycoretools that's causing 
my Rgui to crash (i.e., shuts down and the Microsoft 'please send error 
report' box pops up). Instead, it has something to do with the order & type 
of packages that are loaded that add items to the menu bar by themselves, 
or adding more options under 'Vignettes'. Specific combinations of any 3 
of: affycoretools, RWinEdt, affyPLM or affylmGUI can cause the crash. So 
far, I haven't been able to get it to crash without affycoretools, even if 
I load all the dependencies by themselves, but that may just be because I 
don't know of another package that adds to the menu bar.  After playing 
around with this for a while, even combinations of two packages (that 
loaded fine before) started to crash the Rgui until I rebooted my PC. I 
remember having similar sorts of trouble a while back when manually 
downloading zipped packages and installing them via the menu - after doing 
a few, clicking on the menu again in the same R session would cause the 
Rgui to crash. As this may not be specific to Bioconductor (except that you 
may not put so many items in the menu unless you're using BioC packages), 
I'm cross posting to the R mailing list.


At 12:37 PM 8/10/2006, Jenny Drnevich wrote:
>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?
>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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>'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 an HTML browser interface to help.
>Type 'q()' to quit R.
>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
>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
>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:
>  > sessionInfo()
>Version 2.3.1 (2006-06-01)
>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
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at uiuc.edu
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

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

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

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