Re: [R] [BioC] problem loading affycoretools - solved!

From: Jenny Drnevich <drnevich_at_uiuc.edu>
Date: Sat 12 Aug 2006 - 04:59:59 EST

Hi Martin,

The patched version works fine - thanks for pointing it out! As for problems installing RWinEdt, do you have WinEdt downloaded and installed? www.winedt.com I've found it to be a useful editor for R - well worth the nominal fee after the trial period has ended.

Cheers,
Jenny

At 01:01 PM 8/11/2006, Martin Morgan wrote:
>Hi Jenny --
>
>This sounds like a problem that is addressed in the 'patched' version
>of 2.3.1, from the CHANGES file:
>
>R 2.3.1 patched
>===============
>
>winMenuAdd() could crash when too many menus were added. (PR#8961)
>
>The patched version is at CRAN:
>
>R Binaries --> windows --> Base and then hunt fort the link 'r-patched
>snapshot build'.
>
>I haven't been able to test this explicitly with RWinEdt, which does
>not seem to want to install easily on my computer. If this is the
>solution, then perhaps you could forward a 'solved!' note to the list?
>
>Martin
>--
>Bioconductor
>
>Jenny Drnevich <drnevich@uiuc.edu> writes:
>
> > 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.
> >
> > Cheers,
> > Jenny
> >
> >
> > 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?
> >>
> >>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
> >>
> >>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 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@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/affyc
> oretools_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@uiuc.edu
> >>
> >>_______________________________________________
> >>Bioconductor mailing list
> >>Bioconductor@stat.math.ethz.ch
> >>https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>Search the archives:
> >>http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > 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@uiuc.edu
> >
> > ______________________________________________
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.



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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Sat Aug 12 05:05:13 2006

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