[BioC] problem loading affycoretools
James W. MacDonald
jmacdon at med.umich.edu
Thu Aug 10 20:02:52 CEST 2006
Hi Jenny,
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?
Hmmm. That's odd. I just checked the package build, and everything looks
OK for the windows build. I'm wondering if it is OK to just delete a
package like that - in the past there wasn't that much involved with the
installation/removal of packages, but these days there are more things
going on 'under the hood', so that might be a problem.
You might try remove.packages("affycoretools") and then biocLite()
again. No idea why the package might be crashing R. In my experience,
that almost always happens with a package that contains C code rather
than something simple like affycoretools, which is R code only.
Anyway, I would try removing and re-installing again. The error you are
getting shouldn't be a problem - it is just complaining because the
package is trying to add an entry to the vignettes menu item when it
doesn't think there is one (BTW, is there a vignette in
R_HOME/library/affycoretools/doc?).
>
> Thanks,
> Jenny
>
> P.S. It was great to finally meet many of you at the BioC2006 conference!
It was nice to meet you as well!
Best,
Jim
>
>
> 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
>
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
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